Author: "Christophe Fraser" / Database: OpenAIRE - Searchworks@Jio Institute Digital Library Search Results

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1. Uptake of medical male circumcision with household-based testing, and the association of traditional male circumcision and HIV infection

Author: Kidist Zewdie, Michael Pickles, Sian Floyd, Sarah Fidler, Helen Ayles, Peter Bock, Graeme Hoddinott, Nomtha Mandla, Kwame Shanaube, Musonda Simwinga, Christophe Fraser, Janet Seeley, Estelle Piwowar-Manning, Richard Hayes, and Deborah Donnell
Subjects: Infectious Diseases, Immunology, Immunology and Allergy
Abstract: OBJECTIVES: Voluntary medical male circumcision (VMMC) is an important component of combination HIV prevention. Inclusion of traditionally circumcised HIV negative men in VMMC uptake campaigns may be important if traditional male circumcision is less protective against HIV acquisition than VMMC. METHODS: We used data from the HIV Prevention Trials Network (HPTN) 071 (PopART) study. This cluster-randomized trial assessed the impact of a combination prevention package on population-level HIV incidence in 21 study communities in Zambia and South Africa. We evaluated uptake of VMMC, using a two-stage analysis approach and used discrete-time survival analysis to evaluate the association between the types of male circumcision and HIV incidence. RESULTS: A total of 10 803 HIV-negative men with self-reported circumcision status were included in this study. At baseline, 56% reported being uncircumcised, 26% traditionally circumcised and 18% were medically circumcised. During the PopART intervention, 11% of uncircumcised men reported uptake of medical male circumcision. We found no significant difference in the uptake of VMMC in communities receiving the PopART intervention package and standard of care {adj. rate ratio=1·10 [95% confidence interval (CI) 0.82, 1.50, P = 0.48]}. The rate of HIV acquisition for medically circumcised men was 70% lower than for those who were uncircumcised adjusted hazard ratio (adjHR) = 0.30 (95% CI 0.16-0.55; P
Published: 2023

2. Projected outcomes of universal testing and treatment in a generalised HIV epidemic in Zambia and South Africa (the HPTN 071 [PopART] trial): a modelling study

Author: William J M Probert, Rafael Sauter, Michael Pickles, Anne Cori, Nomtha F Bell-Mandla, Justin Bwalya, Lucie Abeler-Dörner, Peter Bock, Deborah J Donnell, Sian Floyd, David Macleod, Estelle Piwowar-Manning, Timothy Skalland, Kwame Shanaube, Ethan Wilson, Blia Yang, Helen Ayles, Sarah Fidler, Richard J Hayes, Christophe Fraser, Richard Hayes, Nulda Beyers, Wafaa El-Sadr, Myron Cohen, Susan Eshleman, Yaw Agyei, Virginia Bond, Graeme Hoddinott, Deborah Donnell, Lynda Emel, Heather Noble, David Burns, Nirupama Sista, Sam Griffith, Ayana Moore, Tanette Headen, Rhonda White, Eric Miller, James Hargreaves, Katharina Hauck, Ranjeeta Thomas, Mohammed Limbada, Kalpana Sabapathy, Ab Schaap, Rory Dunbar, Musonda Simwinga, Peter Smith, Sten Vermund, Nomtha Mandla, Nozizwe Makola, Anneen van Deventer, Anelet James, Karen Jennings, James Kruger, Mwelwa Phiri, Barry Kosloff, Lawrence Mwenge, Sarah Kanema, William Probert, Ramya Kumar, Ephraim Sakala, Andrew Silumesi, Tim Skalland, Krista Yuhas, Medical Research Council (MRC), National Institute for Health Research, Abdul Latif Jameel Foundation, and Bill & Melinda Gates Foundation
Subjects: South Africa, Infectious Diseases, Epidemiology, Virology, Immunology, Humans, Zambia, Bayes Theorem, HIV Infections, HPTN 071 (PopART) Study Team, Epidemics, 11 Medical and Health Sciences
Abstract: Background The long-term impact of universal home-based testing and treatment as part of universal testing and treatment (UTT) on HIV incidence is unknown. We made projections using a detailed individual-based model of the effect of the intervention delivered in the HPTN 071 (PopART) cluster-randomised trial. Methods In this modelling study, we fitted an individual-based model to the HIV epidemic and HIV care cascade in 21 high prevalence communities in Zambia and South Africa that were part of the PopART cluster-randomised trial (intervention period Nov 1, 2013, to Dec 31, 2017). The model represents coverage of home-based testing and counselling by age and sex, delivered as part of the trial, antiretroviral therapy (ART) uptake, and any changes in national guidelines on ART eligibility. In PopART, communities were randomly assigned to one of three arms: arm A received the full PopART intervention for all individuals who tested positive for HIV, arm B received the intervention with ART provided in accordance with national guidelines, and arm C received standard of care. We fitted the model to trial data twice using Approximate Bayesian Computation, once before data unblinding and then again after data unblinding. We compared projections of intervention impact with observed effects, and for four different scenarios of UTT up to Jan 1, 2030 in the study communities. Findings Compared with standard of care, a 51% (95% credible interval 40–60) reduction in HIV incidence is projected if the trial intervention (arms A and B combined) is continued from 2020 to 2030, over and above a declining trend in HIV incidence under standard of care. Interpretation A widespread and continued commitment to UTT via home-based testing and counselling can have a substantial effect on HIV incidence in high prevalence communities. Funding National Institute of Allergy and Infectious Diseases, US President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation, National Institute on Drug Abuse, and National Institute of Mental Health.
Published: 2022

3. Characteristics and outcomes of an international cohort of 600 000 hospitalized patients with COVID-19

Author: Kartsonaki, Christiana, Baillie, J Kenneth, Barrio, Noelia García, Baruch, Joaquín, Beane, Abigail, Blumberg, Lucille, Bozza, Fernando, Broadley, Tessa, Burrell, Aidan, Carson, Gail, Citarella, Barbara Wanjiru, Dagens, Andrew, Dankwa, Emmanuelle A, Donnelly, Christl A, Dunning, Jake, Elotmani, Loubna, Escher, Martina, Farshait, Nataly, Goffard, Jean-Christophe, Gonçalves, Bronner P, Hall, Matthew, Hashmi, Madiha, Sim Lim Heng, Benedict, Ho, Antonia, Jassat, Waasila, Pedrera Jiménez, Miguel, Laouenan, Cedric, Lissauer, Samantha, Martin-Loeches, Ignacio, Mentré, France, Merson, Laura, Morton, Ben, Munblit, Daniel, Nekliudov, Nikita A, Nichol, Alistair D, Singh Oinam, Budha Charan, Ong, David, Panda, Prasan Kumar, Petrovic, Michele, Pritchard, Mark G, Ramakrishnan, Nagarajan, Ramos, Grazielle Viana, Roger, Claire, Sandulescu, Oana, Semple, Malcolm G, Sharma, Pratima, Sigfrid, Louise, Somers, Emily C, Streinu-Cercel, Anca, Taccone, Fabio, Vecham, Pavan Kumar, Kumar Tirupakuzhi Vijayaraghavan, Bharath, Wei, Jia, Wils, Evert-Jan, Ci Wong, Xin, Horby, Peter, Rojek, Amanda, Olliaro, Piero L, ISARIC Clinical Characterisation Group: Ali Abbas, Sheryl Ann Abdukahil, Nurul Najmee Abdulkadir, Ryuzo Abe, Laurent Abel, Lara Absil, Subhash Acharya, Andrew Acker, Elisabeth Adam, Diana Adrião, Saleh Al Ageel, Shakeel Ahmed, Kate Ainscough, Eka Airlangga, Tharwat Aisa, Ali Ait Hssain, Younes Ait Tamlihat, Takako Akimoto, Ernita Akmal, Eman Al Qasim, Razi Alalqam, Angela Alberti, Tala Al-Dabbous, Senthilkumar Alegesan, Cynthia Alegre, Marta Alessi, Beatrice Alex, Kévin Alexandre, Abdulrahman Al-Fares, Huda Alfoudri, Imran Ali, Adam Ali, Naseem Ali Shah, Kazali Enagnon Alidjnou, Jeffrey Aliudin, Qabas Alkhafajee, Clotilde Allavena, Nathalie Allou, Aneela Altaf, João Alves, Rita Alves, João Melo Alves, Maria Amaral, Nur Amira, Phoebe Ampaw, Roberto Andini, Claire Andréjak, Andrea Angheben, François Angoulvant, Séverine Ansart, Sivanesen Anthonidass, Massimo Antonelli, Carlos Alexandre Antunes de Brito, Ardiyan Apriyana, Yaseen Arabi, Irene Aragao, Francisco Arancibia, Carolline Araujo, Antonio Arcadipane, Patrick Archambault, Lukas Arenz, Jean-Benoît Arlet, Christel Arnold-Day, Lovkesh Arora, Rakesh Arora, Elise Artaud-Macari, Diptesh Aryal, Angel Asensio, Muhammad Ashraf, Namra Asif, Mohammad Asim, Jean Baptiste Assie, Amirul Asyraf, Anika Atique, A M Udara Lakshan Attanyake, Johann Auchabie, Hugues Aumaitre, Adrien Auvet, Laurène Azemar, Cecile Azoulay, Benjamin Bach, Delphine Bachelet, Claudine Badr, Nadia Baig, J Kevin Baird, Erica Bak, Agamemnon Bakakos, Nazreen Abu Bakar, Andriy Bal, Mohanaprasanth Balakrishnan, Valeria Balan, Firouzé Bani-Sadr, Renata Barbalho, Nicholas Yuri Barbosa, Wendy S Barclay, Saef Umar Barnett, Michaela Barnikel, Helena Barrasa, Audrey Barrelet, Cleide Barrigoto, Marie Bartoli, Mustehan Bashir, Romain Basmaci, Muhammad Fadhli Hassin Basri, Denise Battaglini, Jules Bauer, Diego Fernando Bautista Rincon, Denisse Bazan Dow, Alexandra Bedossa, Ker Hong Bee, Husna Begum, Sylvie Behilill, Albertus Beishuizen, Aleksandr Beljantsev, David Bellemare, Anna Beltrame, Beatriz Amorim Beltrão, Marine Beluze, Nicolas Benech, Lionel Eric Benjiman, Dehbia Benkerrou, Suzanne Bennett, Luís Bento, Jan-Erik Berdal, Delphine Bergeaud, Hazel Bergin, José Luis Bernal Sobrino, Giulia Bertoli, Lorenzo Bertolino, Simon Bessis, Sybille Bevilcaqua, Karine Bezulier, Amar Bhatt, Krishna Bhavsar, Claudia Bianco, Farah Nadiah Bidin, Moirangthem Bikram Singh, Felwa Bin Humaid, Mohd Nazlin Bin Kamarudin, François Bissuel, Patrick Biston, Laurent Bitker, Jonathan Bitton, Pablo Blanco-Schweizer, Catherine Blier, Frank Bloos, Mathieu Blot, Filomena Boccia, Laetitia Bodenes, Alice Bogaarts, Debby Bogaert, Anne-Hélène Boivin, Pierre-Adrien Bolze, François Bompart, Aurelius Bonfasius, Diogo Borges, Raphaël Borie, Hans Martin Bosse, Elisabeth Botelho-Nevers, Lila Bouadma, Olivier Bouchaud, Sabelline Bouchez, Dounia Bouhmani, Damien Bouhour, Kévin Bouiller, Laurence Bouillet, Camile Bouisse, Anne-Sophie Boureau, John Bourke, Maude Bouscambert, Aurore Bousquet, Jason Bouziotis, Bianca Boxma, Marielle Boyer-Besseyre, Maria Boylan, Axelle Braconnier, Cynthia Braga, Timo Brandenburger, Filipa Brás Monteiro, Luca Brazzi, Patrick Breen, Dorothy Breen, Kathy Brickell, Shaunagh Browne, Alex Browne, Nicolas Brozzi, Marjolein Brusse-Keizer, Nina Buchtele, Christian Buesaquillo, Polina Bugaeva, Marielle Buisson, Danilo Buonsenso, Erlina Burhan, Ingrid G Bustos, Denis Butnaru, André Cabie, Susana Cabral, Eder Caceres, Cyril Cadoz, Mia Callahan, Kate Calligy, Jose Andres Calvache, João Camões, Valentine Campana, Paul Campbell, Josie Campisi, Cecilia Canepa, Mireia Cantero, Pauline Caraux-Paz, Sheila Cárcel, Chiara Simona Cardellino, Sofia Cardoso, Filipe Cardoso, Filipa Cardoso, Nelson Cardoso, Simone Carelli, Nicolas Carlier, Thierry Carmoi, Gayle Carney, Inês Carqueja, Marie-Christine Carret, François Martin Carrier, Ida Carroll, Maire-Laure Casanova, Mariana Cascão, Siobhan Casey, José Casimiro, Bailey Cassandra, Silvia Castañeda, Nidyanara Castanheira, Guylaine Castor-Alexandre, Henry Castrillón, Ivo Castro, Ana Catarino, François-Xavier Catherine, Paolo Cattaneo, Roberta Cavalin, Giulio Giovanni Cavalli, Alexandros Cavayas, Adrian Ceccato, Minerva Cervantes-Gonzalez, Anissa Chair, Catherine Chakveatze, Adrienne Chan, Meera Chand, Christelle Chantalat Auger, Jean-Marc Chapplain, Julie Chas, Allegra Chatterjee, Mobin Chaudry, Jonathan Samuel Chávez Iñiguez, Anjellica Chen, Yih-Sharng Chen, Matthew Pellan Cheng, Antoine Cheret, Thibault Chiarabini, Julian Chica, Suresh Kumar Chidambaram, Leong Chin Tho, Catherine Chirouze, Davide Chiumello, Sung-Min Cho, Bernard Cholley, Marie-Charlotte Chopin, Ting Soo Chow, Yock Ping Chow, Hiu Jian Chua, Jonathan Chua, Jose Pedro Cidade, José Miguel Cisneros Herreros, Anna Ciullo, Jennifer Clarke, Emma Clarke, Rolando Claure-Del Granado, Sara Clohisey, Perren J Cobb, Cassidy Codan, Caitriona Cody, Alexandra Coelho, Megan Coles, Gwenhaël Colin, Michael Collins, Sebastiano Maria Colombo, Pamela Combs, Marie Connor, Anne Conrad, Sofía Contreras, Elaine Conway, Graham S Cooke, Mary Copland, Hugues Cordel, Amanda Corley, Sabine Cornelis, Alexander Daniel Cornet, Arianne Joy Corpuz, Andrea Cortegiani, Grégory Corvaisier, Emma Costigan, Camille Couffignal, Sandrine Couffin-Cadiergues, Roxane Courtois, Stéphanie Cousse, Rachel Cregan, Charles Crepy D'Orleans, Cosimo Cristella, Sabine Croonen, Gloria Crowl, Jonathan Crump, Claudina Cruz, Juan Luis Cruz Berm, Jaime Cruz Rojo, Marc Csete, Ailbhe Cullen, Matthew Cummings, Gerard Curley, Elodie Curlier, Colleen Curran, Paula Custodio, Ana da Silva Filipe, Charlene Da Silveira, Al-Awwab Dabaliz, Darren Dahly, Heidi Dalton, Jo Dalton, Seamus Daly, Nick Daneman, Corinne Daniel, Jorge Dantas, Frédérick D'Aragon, Menno de Jong, Gillian de Loughry, Diego de Mendoza, Etienne De Montmollin, Rafael Freitas de Oliveira França, Ana Isabel de Pinho Oliveira, Rosanna De Rosa, Cristina De Rose, Thushan de Silva, Peter de Vries, Jillian Deacon, David Dean, Alexa Debard, Marie-Pierre Debray, Nathalie DeCastro, William Dechert, Lauren Deconninck, Romain Decours, Eve Defous, Isabelle Delacroix, Eric Delaveuve, Karen Delavigne, Nathalie M Delfos, Ionna Deligiannis, Andrea Dell'Amore, Christelle Delmas, Pierre Delobel, Corine Delsing, Elisa Demonchy, Emmanuelle Denis, Dominique Deplanque, Pieter Depuydt, Mehul Desai, Diane Descamps, Mathilde Desvallées, Santi Dewayanti, Pathik Dhanger, Alpha Diallo, Sylvain Diamantis, André Dias, Juan Jose Diaz, Priscila Diaz, Rodrigo Diaz, Kévin Didier, Jean-Luc Diehl, Wim Dieperink, Jérôme Dimet, Vincent Dinot, Fara Diop, Alphonsine Diouf, Yael Dishon, Félix Djossou, Annemarie B Docherty, Helen Doherty, Arjen M Dondorp, Andy Dong, Maria Donnelly, Sean Donohue, Yoann Donohue, Chloe Donohue, Peter Doran, Céline Dorival, Eric D'Ortenzio, James Joshua Douglas, Renee Douma, Nathalie Dournon, Triona Downer, Joanne Downey, Mark Downing, Tom Drake, Aoife Driscoll, Murray Dryden, Claudio Duarte Fonseca, Vincent Dubee, François Dubos, Alexandre Ducancelle, Toni Duculan, Susanne Dudman, Abhijit Duggal, Paul Dunand, Mathilde Duplaix, Emanuele Durante-Mangoni, Lucian Durham, Bertrand Dussol, Juliette Duthoit, Xavier Duval, Anne Margarita Dyrhol-Riise, Sim Choon Ean, Marco Echeverria-Villalobos, Siobhan Egan, Carla Eira, Mohammed El Sanharawi, Subbarao Elapavaluru, Brigitte Elharrar, Jacobien Ellerbroek, Philippine Eloy, Tarek Elshazly, Iqbal Elyazar, Isabelle Enderle, Tomoyuki Endo, Chan Chee Eng, Ilka Engelmann, Vincent Enouf, Olivier Epaulard, Mariano Esperatti, Hélène Esperou, Marina Esposito-Farese, João Estevão, Manuel Etienne, Nadia Ettalhaoui, Anna Greti Everding, Mirjam Evers, Marc Fabre, Isabelle Fabre, Amna Faheem, Arabella Fahy, Cameron J Fairfield, Zul Fakar, Komal Fareed, Pedro Faria, Ahmed Farooq, Hanan Fateena, Arie Zainul Fatoni, Karine Faure, Raphaël Favory, Mohamed Fayed, Niamh Feely, Laura Feeney, Jorge Fernandes, Marília Andreia Fernandes, Susana Fernandes, François-Xavier Ferrand, Eglantine Ferrand Devouge, Joana Ferrão, Mário Ferraz, Sílvia Ferreira, Isabel Ferreira, Benigno Ferreira, Ricard Ferrer-Roca, Nicolas Ferriere, Céline Ficko, Claudia Figueiredo-Mello, William Finlayson, Juan Fiorda, Thomas Flament, Clara Flateau, Tom Fletcher, Letizia Lucia Florio, Deirdre Flynn, Claire Foley, Jean Foley, Victor Fomin, Tatiana Fonseca, Patricia Fontela, Simon Forsyth, Denise Foster, Giuseppe Foti, Erwan Fourn, Robert A Fowler, Marianne Fraher, Diego Franch-Llasat, John F Fraser, Christophe Fraser, Marcela Vieira Freire, Ana Freitas Ribeiro, Caren Friedrich, Ricardo Fritz, Stéphanie Fry, Nora Fuentes, Masahiro Fukuda, G Argin, Valérie Gaborieau, Rostane Gaci, Massimo Gagliardi, Jean-Charles Gagnard, Amandine Gagneux-Brunon, Sérgio Gaião, Linda Gail Skeie, Phil Gallagher, Carrol Gamble, Yasmin Gani, Arthur Garan, Rebekha Garcia, Julia Garcia-Diaz, Esteban Garcia-Gallo, Navya Garimella, Denis Garot, Valérie Garrait, Basanta Gauli, Nathalie Gault, Aisling Gavin, Anatoliy Gavrylov, Alexandre Gaymard, Johannes Gebauer, Eva Geraud, Louis Gerbaud Morlaes, Nuno Germano, Praveen Kumar Ghisulal, Jade Ghosn, Marco Giani, Jess Gibson, Tristan Gigante, Morgane Gilg, Elaine Gilroy, Guillermo Giordano, Michelle Girvan, Valérie Gissot, Daniel Glikman, Petr Glybochko, Eric Gnall, Geraldine Goco, François Goehringer, Siri Goepel, Jin Yi Goh, Jonathan Golob, Rui Gomes, Kyle Gomez, Joan Gómez-Junyent, Marie Gominet, Alicia Gonzalez, Patricia Gordon, Isabelle Gorenne, Laure Goubert, Cécile Goujard, Tiphaine Goulenok, Margarite Grable, Jeronimo Graf, Edward Wilson Grandin, Pascal Granier, Giacomo Grasselli, Christopher A Green, Courtney Greene, William Greenhalf, Segolène Greffe, Domenico Luca Grieco, Matthew Griffee, Fiona Griffiths, Ioana Grigoras, Albert Groenendijk, Anja Grosse Lordemann, Heidi Gruner, Yusing Gu, Jérémie Guedj, Martin Guego, Dewi Guellec, Anne-Marie Guerguerian, Daniela Guerreiro, Romain Guery, Anne Guillaumot, Laurent Guilleminault, Maisa Guimarães de Castro, Thomas Guimard, Marieke Haalboom, Daniel Haber, Hannah Habraken, Ali Hachemi, Amy Hackmann, Nadir Hadri, Fakhir Haidri, Sheeba Hakak, Adam Hall, Sophie Halpin, Jawad Hameed, Ansley Hamer, Raph L Hamers, Rebecca Hamidfar, Terese Hammond, Lim Yuen Han, Rashan Haniffa, Kok Wei Hao, Hayley Hardwick, Ewen M Harrison, Janet Harrison, Samuel Bernard Ekow Harrison, Alan Hartman, Mohd Shahnaz Hasan, Junaid Hashmi, Muhammad Hayat, Ailbhe Hayes, Leanne Hays, Jan Heerman, Lars Heggelund, Ross Hendry, Martina Hennessy, Aquiles Henriquez-Trujillo, Maxime Hentzien, Jaime Hernandez-Montfort, Andrew Hershey, Liv Hesstvedt, Astarini Hidayah, Eibhilin Higgins, Dawn Higgins, Rupert Higgins, Rita Hinchion, Samuel Hinton, Hiroaki Hiraiwa, Haider Hirkani, Hikombo Hitoto, Yi Bin Ho, Alexandre Hoctin, Isabelle Hoffmann, Wei Han Hoh, Oscar Hoiting, Rebecca Holt, Jan Cato Holter, Juan Pablo Horcajada, Koji Hoshino, Ikram Houas, Catherine L Hough, Stuart Houltham, Jimmy Ming-Yang Hsu, Jean-Sébastien Hulot, Stella Huo, Abby Hurd, Iqbal Hussain, Samreen Ijaz, Hajnal-Gabriela Illes, Patrick Imbert, Mohammad Imran, Rana Imran Sikander, Aftab Imtiaz, Hugo Inácio, Carmen Infante Dominguez, Yun Sii Ing, Elias Iosifidis, Mariachiara Ippolito, Sarah Isgett, Tiago Isidoro, Nadiah Ismail, Margaux Isnard, Junji Itai, Daniel Ivulich, Danielle Jaafar, Salma Jaafoura, Julien Jabot, Clare Jackson, Nina Jamieson, Victoria Janes, Pierre Jaquet, Coline Jaud-Fischer, Stéphane Jaureguiberry, Jeffrey Javidfar, Denise Jaworsky, Florence Jego, Anilawati Mat Jelani, Synne Jenum, Ruth Jimbo-Sotomayor, Ong Yiaw Joe, Ruth N Jorge García, Cédric Joseph, Mark Joseph, Swosti Joshi, Mercé Jourdain, Philippe Jouvet, Hanna Jung, Anna Jung, Dafsah Juzar, Ouifiya Kafif, Florentia Kaguelidou, Neerusha Kaisbain, Thavamany Kaleesvran, Sabina Kali, Alina Kalicinska, Smaragdi Kalomoiri, Muhammad Aisar Ayadi Kamaluddin, Zul Amali Che Kamaruddin, Nadiah Kamarudin, Paul Kambiya, Kavita Kamineni, Darshana Hewa Kandamby, Chris Kandel, Kong Yeow Kang, Darakhshan Kanwal, Pratap Karpayah, Todd Karsies, Daisuke Kasugai, Anant Kataria, Kevin Katz, Aasmine Kaur, Christy Kay, Hannah Keane, Seán Keating, Pulak Kedia, Claire Kelly, Yvelynne Kelly, Andrea Kelly, Niamh Kelly, Aoife Kelly, Sadie Kelly, Maeve Kelsey, Ryan Kennedy, Kalynn Kennon, Maeve Kernan, Younes Kerroumi, Sharma Keshav, Imrana Khalid, Osama Khalid, Antoine Khalil, Coralie Khan, Irfan Khan, Quratul Ain Khan, Sushil Khanal, Abid Khatak, Amin Khawaja, Krish Kherajani, Michelle E Kho, Saye Khoo, Ryan Khoo, Denisa Khoo, Nasir Khoso, Khor How Kiat, Yuri Kida, Peter Kiiza, Beathe Kiland Granerud, Anders Benjamin Kildal, Jae Burm Kim, Antoine Kimmoun, Detlef Kindgen-Milles, Alexander King, Nobuya Kitamura, Paul Klenerman, Rob Klont, Gry Kloumann Bekken, Stephen R Knight, Robin Kobbe, Chamira Kodippily, Malte Kohns Vasconcelos, Sabin Koirala, Mamoru Komatsu, Caroline Kosgei, Arsène Kpangon, Karolina Krawczyk, Vinothini Krishnan, Sudhir Krishnan, Oksana Kruglova, Deepali Kumar, Ganesh Kumar, Mukesh Kumar, Dinesh Kuriakose, Ethan Kurtzman, Demetrios Kutsogiannis, Galyna Kutsyna, Konstantinos Kyriakoulis, Marie Lachatre, Marie Lacoste, John G Laffey, Marie Lagrange, Fabrice Laine, Olivier Lairez, Sanjay Lakhey, Antonio Lalueza, Marc Lambert, François Lamontagne, Marie Langelot-Richard, Vincent Langlois, Eka Yudha Lantang, Marina Lanza, Cédric Laouénan, Samira Laribi, Delphine Lariviere, Stéphane Lasry, Sakshi Lath, Naveed Latif, Odile Launay, Didier Laureillard, Yoan Lavie-Badie, Andy Law, Teresa Lawrence, Cassie Lawrence, Minh Le, Clément Le Bihan, Cyril Le Bris, Georges Le Falher, Lucie Le Fevre, Quentin Le Hingrat, Marion Le Maréchal, Soizic Le Mestre, Gwenaël Le Moal, Vincent Le Moing, Hervé Le Nagard, Paul Le Turnier, Ema Leal, Marta Leal Santos, Todd C Lee, James Lee, Jennifer Lee, Heng Gee Lee, Biing Horng Lee, Yi Lin Lee, Su Hwan Lee, Gary Leeming, Laurent Lefebvre, Bénédicte Lefebvre, Benjamin Lefevre, Sylvie LeGac, Jean-Daniel Lelievre, François Lellouche, Adrien Lemaignen, Véronique Lemee, Anthony Lemeur, Gretchen Lemmink, Ha Sha Lene, Jenny Lennon, Rafael León, Marc Leone, Michela Leone, Quentin Lepiller, François-Xavier Lescure, Olivier Lesens, Mathieu Lesouhaitier, Amy Lester-Grant, Bruno Levy, Yves Levy, Claire Levy-Marchal, Katarzyna Lewandowska, Erwan L'Her, Gianluigi Li Bassi, Janet Liang, Ali Liaquat, Geoffrey Liegeon, Wei Shen Lim, Kah Chuan Lim, Chantre Lima, Lim Lina, Bruno Lina, Andreas Lind, Maja Katherine Lingad, Guillaume Lingas, Sylvie Lion-Daolio, Keibun Liu, Marine Livrozet, Patricia Lizotte, Antonio Loforte, Navy Lolong, Leong Chee Loon, Diogo Lopes, Dalia Lopez-Colon, Jose W Lopez-Revilla, Anthony L Loschner, Paul Loubet, Bouchra Loufti, Guillame Louis, Silvia Lourenco, Lara Lovelace-Macon, Lee Lee Low, Marije Lowik, Jia Shyi Loy, Jean Christophe Lucet, Carlos Lumbreras Bermejo, Carlos M Luna, Olguta Lungu, Liem Luong, Nestor Luque, Dominique Luton, Nilar Lwin, Ruth Lyons, Olavi Maasikas, Oryane Mabiala, Moïse Machado, Gabriel Macheda, Hashmi Madiha, Guillermo Maestro de la Calle, Rafael Mahieu, Sophie Mahy, Ana Raquel Maia, Lars S Maier, Mylène Maillet, Thomas Maitre, Maximilian Malfertheiner, Nadia Malik, Paddy Mallon, Fernando Maltez, Denis Malvy, Victoria Manda, Laurent Mandelbrot, Frank Manetta, Julie Mankikian, Edmund Manning, Aldric Manuel, Ceila Maria Sant Ana Malaque, Flávio Marino, Daniel Marino, Samuel Markowicz, Charbel Maroun Eid, Ana Marques, Catherine Marquis, Brian Marsh, Laura Marsh, Megan Marshal, John Marshall, Celina Turchi Martelli, Dori-Ann Martin, Emily Martin, Guillaume Martin-Blondel, Martin Martinot, Alejandro Martin-Quiros, João Martins, Ana Martins, Nuno Martins, Caroline Martins Rego, Gennaro Martucci, Olga Martynenko, Eva Miranda Marwali, Marsilla Marzukie, David Maslove, Sabina Mason, Sobia Masood, Basri Mat Nor, Moshe Matan, Meghena Mathew, Daniel Mathieu, Mathieu Mattei, Romans Matulevics, Laurence Maulin, Michael Maxwell, Javier Maynar, Thierry Mazzoni, Natalie Mc Evoy, Lisa Mc Sweeney, Colin McArthur, Anne McCarthy, Aine McCarthy, Colin McCloskey, Rachael McConnochie, Sherry McDermott, Sarah E McDonald, Aine McElroy, Samuel McElwee, Victoria McEneany, Allison McGeer, Chris McKay, Johnny McKeown, Kenneth A McLean, Paul McNally, Bairbre McNicholas, Elaine McPartlan, Edel Meaney, Cécile Mear-Passard, Maggie Mechlin, Maqsood Meher, Omar Mehkri, Ferruccio Mele, Luis Melo, Kashif Memon, Joao Joao Mendes, Ogechukwu Menkiti, Kusum Menon, Alexander J Mentzer, Emmanuelle Mercier, Noémie Mercier, Antoine Merckx, Mayka Mergeay-Fabre, Blake Mergler, António Mesquita, Roberta Meta, Osama Metwally, Agnès Meybeck, Dan Meyer, Alison M Meynert, Vanina Meysonnier, Amina Meziane, Mehdi Mezidi, Céline Michelanglei, Isabelle Michelet, Efstathia Mihelis, Vladislav Mihnovit, Hugo Miranda-Maldonado, Nor Arisah Misnan, Tahira Jamal Mohamed, Nik Nur Eliza Mohamed, Asma Moin, David Molina, Elena Molinos, Brenda Molloy, Mary Mone, Agostinho Monteiro, Claudia Montes, Giorgia Montrucchio, Shona C Moore, Sarah Moore, Lina Morales Cely, Lucia Moro, Catherine Motherway, Ana Motos, Hugo Mouquet, Clara Mouton Perrot, Julien Moyet, Caroline Mudara, Aisha Kalsoom Mufti, Ng Yong Muh, Dzawani Muhamad, Jimmy Mullaert, Fredrik Müller, Karl Erik Müller, Syed Muneeb, Nadeem Munir, Laveena Munshi, Aisling Murphy, Lorna Murphy, Marlène Murris, Srinivas Murthy, Himed Musaab, Himasha Muvindi, Gugapriyaa Muyandy, Dimitra Melia Myrodia, Farah Nadia Mohd-Hanafiah, Dave Nagpal, Alex Nagrebetsky, Mangala Narasimhan, Nageswaran Narayanan, Rashid Nasim Khan, Alasdair Nazerali-Maitland, Nadège Neant, Holger Neb, Erni Nelwan, Raul Neto, Emily Neumann, Pauline Yeung Ng, Wing Yiu Ng, Anthony Nghi, Duc Nguyen, Orna Ni Choileain, Niamh Ni Leathlobhair, Prompak Nitayavardhana, Stephanie Nonas, Nurul Amani Mohd Noordin, Marion Noret, Nurul Faten Izzati Norharizam, Lisa Norman, Alessandra Notari, Mahdad Noursadeghi, Karolina Nowicka, Adam Nowinski, Saad Nseir, Jose I Nunez, Nurnaningsih Nurnaningsih, Dwi Utomo Nusantara, Elsa Nyamankolly, Fionnuala O Brien, Annmarie O Callaghan, Annmarie O'Callaghan, Giovanna Occhipinti, Derbrenn OConnor, Max O'Donnell, Tawnya Ogston, Takayuki Ogura, Tak-Hyuk Oh, Sophie O'Halloran, Katie O'Hearn, Shinichiro Ohshimo, Agnieszka Oldakowska, João Oliveira, Larissa Oliveira, Jee Yan Ong, Wilna Oosthuyzen, Anne Opavsky, Peter Openshaw, Saijad Orakzai, Claudia Milena Orozco-Chamorro, Jamel Ortoleva, Javier Osatnik, Linda O'Shea, Miriam O'Sullivan, Siti Zubaidah Othman, Nadia Ouamara, Rachida Ouissa, Eric Oziol, Maïder Pagadoy, Justine Pages, Mario Palacios, Amanda Palacios, Massimo Palmarini, Giovanna Panarello, Hem Paneru, Lai Hui Pang, Mauro Panigada, Nathalie Pansu, Aurélie Papadopoulos, Rachael Parke, Melissa Parker, Briseida Parra, Taha Pasha, Jérémie Pasquier, Bruno Pastene, Fabian Patauner, Drashti Patel, Mohan Dass Pathmanathan, Luís Patrão, Patricia Patricio, Juliette Patrier, Lisa Patterson, Rajyabardhan Pattnaik, Mical Paul, Christelle Paul, Jorge Paulos, William A Paxton, Jean-François Payen, Kalaiarasu Peariasamy, Giles J Peek, Florent Peelman, Nathan Peiffer-Smadja, Vincent Peigne, Mare Pejkovska, Paolo Pelosi, Ithan D Peltan, Rui Pereira, Daniel Perez, Luis Periel, Thomas Perpoint, Antonio Pesenti, Vincent Pestre, Lenka Petrou, Ventzislava Petrov-Sanchez, Frank Olav Pettersen, Gilles Peytavin, Scott Pharand, Michael Piagnerelli, Walter Picard, Olivier Picone, Maria de Piero, Carola Pierobon, Djura Piersma, Carlos Pimentel, Raquel Pinto, Catarina Pires, Isabelle Pironneau, Lionel Piroth, Ayodhia Pitaloka, Riinu Pius, Laurent Plantier, Hon Shen Png, Julien Poissy, Ryadh Pokeerbux, Maria Pokorska-Spiewak, Sergio Poli, Georgios Pollakis, Diane Ponscarme, Jolanta Popielska, Diego Bastos Porto, Andra-Maris Post, Douwe F Postma, Pedro Povoa, Diana Póvoas, Jeff Powis, Sofia Prapa, Sébastien Preau, Christian Prebensen, Jean-Charles Preiser, Anton Prinssen, Gamage Dona Dilanthi Priyadarshani, Lucia Proença, Sravya Pudota, Oriane Puéchal, Bambang Pujo Semedi, Mathew Pulicken, Gregory Purcell, Luisa Quesada, Vilmaris Quinones-Cardona, Víctor Quirós González, Else Quist-Paulsen, Mohammed Quraishi, Maia Rabaa, Christian Rabaud, Ebenezer Rabindrarajan, Aldo Rafael, Marie Rafiq, Gabrielle Ragazzo, Mutia Rahardjani, Rozanah Abd Rahman, Ahmad Kashfi Haji Ab Rahman, Arsalan Rahutullah, Fernando Rainieri, Giri Shan Rajahram, Pratheema Ramachandran, Ahmad Afiq Ramli, Blandine Rammaert, Asim Rana, Rajavardhan Rangappa, Ritika Ranjan, Christophe Rapp, Aasiyah Rashan, Thalha Rashan, Ghulam Rasheed, Menaldi Rasmin, Indrek Rätsep, Cornelius Rau, Tharmini Ravi, Ali Raza, Andre Real, Stanislas Rebaudet, Sarah Redl, Brenda Reeve, Attaur Rehman, Liadain Reid, Dag Henrik Reikvam, Renato Reis, Jordi Rello, Jonathan Remppis, Martine Remy, Hongru Ren, Hanna Renk, Anne-Sophie Resseguier, Matthieu Revest, Oleksa Rewa, Luis Felipe Reyes, Tiago Reyes, Maria Ines Ribeiro, Antonia Ricchiuto, David Richardson, Denise Richardson, Laurent Richier, Siti Nurul Atikah Ahmad Ridzuan, Jordi Riera, Ana L Rios, Asgar Rishu, Patrick Rispal, Karine Risso, Maria Angelica Rivera Nuñez, Nicholas Rizer, Chiara Robba, André Roberto, Stephanie Roberts, David L Robertson, Olivier Robineau, Ferran Roche-Campo, Paola Rodari, Simão Rodeia, Bernhard Roessler, Pierre-Marie Roger, Emmanuel Roilides, Juliette Romaru, Roberto Roncon-Albuquerque, Mélanie Roriz, Manuel Rosa-Calatrava, Michael Rose, Dorothea Rosenberger, Nurul Hidayah Mohammad Roslan, Andrea Rossanese, Matteo Rossetti, Bénédicte Rossignol, Patrick Rossignol, Stella Rousset, Carine Roy, Benoît Roze, Desy Rusmawatiningtyas, Clark D Russell, Maria Ryan, Maeve Ryan, Steffi Ryckaert, Aleksander Rygh Holten, Isabela Saba, Sairah Sadaf, Musharaf Sadat, Valla Sahraei, Maximilien Saint-Gilles, Pranya Sakiyalak, Nawal Salahuddin, Leonardo Salazar, Jodat Saleem, Gabriele Sales, Stéphane Sallaberry, Charlotte Salmon Gandonniere, Hélène Salvator, Olivier Sanchez, Angel Sanchez-Miralles, Vanessa Sancho-Shimizu, Gyan Sandhu, Zulfiqar Sandhu, Pierre-François Sandrine, Marlene Santos, Shirley Sarfo-Mensah, Bruno Sarmento Banheiro, Iam Claire E Sarmiento, Benjamine Sarton, Ankana Satya, Sree Satyapriya, Rumaisah Satyawati, Egle Saviciute, Parthena Savvidou, Yen Tsen Saw, Justin Schaffer, Tjard Schermer, Arnaud Scherpereel, Marion Schneider, Stephan Schroll, Michael Schwameis, Gary Schwartz, Brendan Scicluna, Janet T Scott, James Scott-Brown, Nicholas Sedillot, Tamara Seitz, Jaganathan Selvanayagam, Mageswari Selvarajoo, Caroline Semaille, Rasidah Bt Senian, Eric Senneville, Claudia Sepulveda, Filipa Sequeira, Tânia Sequeira, Ary Serpa Neto, Pablo Serrano Balazote, Ellen Shadowitz, Syamin Asyraf Shahidan, Mohammad Shamsah, Anuraj Shankar, Shaikh Sharjeel, Catherine A Shaw, Victoria Shaw, Ashraf Sheharyar, Rohan Shetty, Rajesh Mohan Shetty, Haixia Shi, Nisreen Shiban, Mohiuddin Shiekh, Nobuaki Shime, Hiroaki Shimizu, Keiki Shimizu, Sally Shrapnel, Pramesh Sundar Shrestha, Shubha Kalyan Shrestha, Hoi Ping Shum, Nassima Si Mohammed, Ng Yong Siang, Jeanne Sibiude, Atif Siddiqui, Piret Sillaots, Catarina Silva, Rogério Silva, Maria Joao Silva, Wai Ching Sin, Dario Sinatti, Punam Singh, Budha Charan Singh, Pompini Agustina Sitompul, Karisha Sivam, Vegard Skogen, Sue Smith, Benjamin Smood, Coilin Smyth, Michelle Smyth, Morgane Snacken, Dominic So, Tze Vee Soh, Joshua Solomon, Tom Solomon, Agnès Sommet, Rima Song, Tae Song, Jack Song Chia, Michael Sonntagbauer, Azlan Mat Soom, Alberto Sotto, Edouard Soum, Marta Sousa, Ana Chora Sousa, Maria Sousa Uva, Vicente Souza-Dantas, Alexandra Sperry, Elisabetta Spinuzza, B P Sanka Ruwan Sri Darshana, Shiranee Sriskandan, Sarah Stabler, Thomas Staudinger, Stephanie-Susanne Stecher, Trude Steinsvik, Ymkje Stienstra, Birgitte Stiksrud, Eva Stolz, Amy Stone, Adrian Streinu-Cercel, David Stuart, Ami Stuart, Decy Subekti, Gabriel Suen, Jacky Y Suen, Asfia Sultana, Charlotte Summers, Dubravka Supic, Deepashankari Suppiah, Magdalena Surovcová, Suwarti Suwarti, Andrey Svistunov, Sarah Syahrin, Konstantinos Syrigos, Jaques Sztajnbok, Konstanty Szuldrzynski, Shirin Tabrizi, Lysa Tagherset, Shahdattul Mawarni Taib, Ewa Talarek, Sara Taleb, Jelmer Talsma, Renaud Tamisier, Maria Lawrensia Tampubolon, Kim Keat Tan, Yan Chyi Tan, Taku Tanaka, Hiroyuki Tanaka, Hayato Taniguchi, Huda Taqdees, Arshad Taqi, Coralie Tardivon, Pierre Tattevin, M Azhari Taufik, Hassan Tawfik, Richard S Tedder, Tze Yuan Tee, João Teixeira, Sofia Tejada, Marie-Capucine Tellier, Sze Kye Teoh, Vanessa Teotonio, François Téoulé, Pleun Terpstra, Olivier Terrier, Nicolas Terzi, Hubert Tessier-Grenier, Adrian Tey, Alif Adlan Mohd Thabit, Anand Thakur, Zhang Duan Tham, Suvintheran Thangavelu, Vincent Thibault, Simon-Djamel Thiberville, Benoît Thill, Jananee Thirumanickam, Shaun Thompson, Emma C Thomson, David Thomson, Surain Raaj Thanga Thurai, Ryan S Thwaites, Paul Tierney, Vadim Tieroshyn, Peter S Timashev, Jean-François Timsit, Noémie Tissot, Jordan Zhien Yang Toh, Maria Toki, Kristian Tonby, Sia Loong Tonnii, Margarida Torres, Antoni Torres, Rosario Maria Torres Santos-Olmo, Hernando Torres-Zevallos, Michael Towers, Tony Trapani, Théo Treoux, Cécile Tromeur, Ioannis Trontzas, Tiffany Trouillon, Jeanne Truong, Christelle Tual, Sarah Tubiana, Helen Tuite, Jean-Marie Turmel, Lance C W Turtle, Anders Tveita, Pawel Twardowski, Makoto Uchiyama, P G Ishara Udayanga, Andrew Udy, Roman Ullrich, Alberto Uribe, Asad Usman, Timothy M Uyeki, Cristinava Vajdovics, Piero Valentini, Luís Val-Flores, Amélie Valran, Stijn Van de Velde, Marcel van den Berge, Machteld Van der Feltz, Job van der Palen, Paul van der Valk, Nicky Van Der Vekens, Peter Van der Voort, Sylvie Van Der Werf, Laura van Gulik, Jarne Van Hattem, Carolien van Netten, Frank van Someren Greve, Ilonka van Veen, Hugo Van Willigen, Noémie Vanel, Henk Vanoverschelde, Pooja Varghese, Michael Varrone, Shoban Raj Vasudayan, Charline Vauchy, Shaminee Veeran, Aurélie Veislinger, Sebastian Vencken, Sara Ventura, Annelies Verbon, James Vickers, José Ernesto Vidal, César Vieira, Deepak Vijayan, Joy Ann Villanueva, Judit Villar, Pierre-Marc Villeneuve, Andrea Villoldo, Gayatri Vishwanathan, Benoit Visseaux, Hannah Visser, Chiara Vitiello, Harald Vonkeman, Fanny Vuotto, Suhaila Abdul Wahab, Noor Hidayu Wahab, Nadirah Abdul Wahid, Marina Wainstein, Wan Fadzlina Wan Muhd Shukeri, Chih-Hsien Wang, Steve Webb, Katharina Weil, Tan Pei Wen, Sanne Wesselius, T Eoin West, Murray Wham, Bryan Whelan, Nicole White, Paul Henri Wicky, Aurélie Wiedemann, Surya Otto Wijaya, Keith Wille, Suzette Willems, Virginie Williams, Calvin Wong, Yew Sing Wong, Teck Fung Wong, Natalie Wright, Gan Ee Xian, Lim Saio Xian, Kuan Pei Xuan, Ioannis Xynogalas, Siti Rohani Binti Mohd Yakop, Masaki Yamazaki, Yazdan Yazdanpanah, Nicholas Yee Liang Hing, Cécile Yelnik, Chian Hui Yeoh, Stephanie Yerkovich, Toshiki Yokoyama, Hodane Yonis, Obada Yousif, Saptadi Yuliarto, Akram Zaaqoq, Marion Zabbe, Kai Zacharowski, Masliza Zahid, Maram Zahran, Nor Zaila Binti Zaidan, Maria Zambon, Miguel Zambrano, Alberto Zanella, Konrad Zawadka, Nurul Zaynah, Hiba Zayyad, Alexander Zoufaly, David Zucman, Kartsonaki, Christiana, Baillie, J Kenneth, Barrio, Noelia García, Baruch, Joaquín, Beane, Abigail, Blumberg, Lucille, Bozza, Fernando, Broadley, Tessa, Burrell, Aidan, Carson, Gail, Citarella, Barbara Wanjiru, Dagens, Andrew, Dankwa, Emmanuelle A, Donnelly, Christl A, Dunning, Jake, Elotmani, Loubna, Escher, Martina, Farshait, Nataly, Goffard, Jean-Christophe, Gonçalves, Bronner P, Hall, Matthew, Hashmi, Madiha, Sim Lim Heng, Benedict, Ho, Antonia, Jassat, Waasila, Pedrera Jiménez, Miguel, Laouenan, Cedric, Lissauer, Samantha, Martin-Loeches, Ignacio, Mentré, France, Merson, Laura, Morton, Ben, Munblit, Daniel, Nekliudov, Nikita A, Nichol, Alistair D, Singh Oinam, Budha Charan, Ong, David, Panda, Prasan Kumar, Petrovic, Michele, Pritchard, Mark G, Ramakrishnan, Nagarajan, Ramos, Grazielle Viana, Roger, Claire, Sandulescu, Oana, Semple, Malcolm G, Sharma, Pratima, Sigfrid, Louise, Somers, Emily C, Streinu-Cercel, Anca, Taccone, Fabio, Vecham, Pavan Kumar, Kumar Tirupakuzhi Vijayaraghavan, Bharath, Wei, Jia, Wils, Evert-Jan, Ci Wong, Xin, Horby, Peter, Rojek, Amanda, Olliaro, Piero L, ISARIC Clinical Characterisation Group: Ali Abbas, Sheryl Ann Abdukahil, Nurul Najmee Abdulkadir, Ryuzo Abe, Laurent Abel, Lara Absil, Subhash Acharya, Andrew Acker, Elisabeth Adam, Diana Adrião, Saleh Al Ageel, Shakeel Ahmed, Kate Ainscough, Eka Airlangga, Tharwat Aisa, Ali Ait Hssain, Younes Ait Tamlihat, Takako Akimoto, Ernita Akmal, Eman Al Qasim, Razi Alalqam, Angela Alberti, Tala Al-Dabbous, Senthilkumar Alegesan, Cynthia Alegre, Marta Alessi, Beatrice Alex, Kévin Alexandre, Abdulrahman Al-Fares, Huda Alfoudri, Imran Ali, Adam Ali, Naseem Ali Shah, Kazali Enagnon Alidjnou, Jeffrey Aliudin, Qabas Alkhafajee, Clotilde Allavena, Nathalie Allou, Aneela Altaf, João Alves, Rita Alves, João Melo Alves, Maria Amaral, Nur Amira, Phoebe Ampaw, Roberto Andini, Claire Andréjak, Andrea Angheben, François Angoulvant, Séverine Ansart, Sivanesen Anthonidass, Massimo Antonelli, Carlos Alexandre Antunes de Brito, Ardiyan Apriyana, Yaseen Arabi, Irene Aragao, Francisco Arancibia, Carolline Araujo, Antonio Arcadipane, Patrick Archambault, Lukas Arenz, Jean-Benoît Arlet, Christel Arnold-Day, Lovkesh Arora, Rakesh Arora, Elise Artaud-Macari, Diptesh Aryal, Angel Asensio, Muhammad Ashraf, Namra Asif, Mohammad Asim, Jean Baptiste Assie, Amirul Asyraf, Anika Atique, A M Udara Lakshan Attanyake, Johann Auchabie, Hugues Aumaitre, Adrien Auvet, Laurène Azemar, Cecile Azoulay, Benjamin Bach, Delphine Bachelet, Claudine Badr, Nadia Baig, J Kevin Baird, Erica Bak, Agamemnon Bakakos, Nazreen Abu Bakar, Andriy Bal, Mohanaprasanth Balakrishnan, Valeria Balan, Firouzé Bani-Sadr, Renata Barbalho, Nicholas Yuri Barbosa, Wendy S Barclay, Saef Umar Barnett, Michaela Barnikel, Helena Barrasa, Audrey Barrelet, Cleide Barrigoto, Marie Bartoli, Mustehan Bashir, Romain Basmaci, Muhammad Fadhli Hassin Basri, Denise Battaglini, Jules Bauer, Diego Fernando Bautista Rincon, Denisse Bazan Dow, Alexandra Bedossa, Ker Hong Bee, Husna Begum, Sylvie Behilill, Albertus Beishuizen, Aleksandr Beljantsev, David Bellemare, Anna Beltrame, Beatriz Amorim Beltrão, Marine Beluze, Nicolas Benech, Lionel Eric Benjiman, Dehbia Benkerrou, Suzanne Bennett, Luís Bento, Jan-Erik Berdal, Delphine Bergeaud, Hazel Bergin, José Luis Bernal Sobrino, Giulia Bertoli, Lorenzo Bertolino, Simon Bessis, Sybille Bevilcaqua, Karine Bezulier, Amar Bhatt, Krishna Bhavsar, Claudia Bianco, Farah Nadiah Bidin, Moirangthem Bikram Singh, Felwa Bin Humaid, Mohd Nazlin Bin Kamarudin, François Bissuel, Patrick Biston, Laurent Bitker, Jonathan Bitton, Pablo Blanco-Schweizer, Catherine Blier, Frank Bloos, Mathieu Blot, Filomena Boccia, Laetitia Bodenes, Alice Bogaarts, Debby Bogaert, Anne-Hélène Boivin, Pierre-Adrien Bolze, François Bompart, Aurelius Bonfasius, Diogo Borges, Raphaël Borie, Hans Martin Bosse, Elisabeth Botelho-Nevers, Lila Bouadma, Olivier Bouchaud, Sabelline Bouchez, Dounia Bouhmani, Damien Bouhour, Kévin Bouiller, Laurence Bouillet, Camile Bouisse, Anne-Sophie Boureau, John Bourke, Maude Bouscambert, Aurore Bousquet, Jason Bouziotis, Bianca Boxma, Marielle Boyer-Besseyre, Maria Boylan, Axelle Braconnier, Cynthia Braga, Timo Brandenburger, Filipa Brás Monteiro, Luca Brazzi, Patrick Breen, Dorothy Breen, Patrick Breen, Kathy Brickell, Shaunagh Browne, Alex Browne, Nicolas Brozzi, Marjolein Brusse-Keizer, Nina Buchtele, Christian Buesaquillo, Polina Bugaeva, Marielle Buisson, Danilo Buonsenso, Erlina Burhan, Ingrid G Bustos, Denis Butnaru, André Cabie, Susana Cabral, Eder Caceres, Cyril Cadoz, Mia Callahan, Kate Calligy, Jose Andres Calvache, João Camões, Valentine Campana, Paul Campbell, Josie Campisi, Cecilia Canepa, Mireia Cantero, Pauline Caraux-Paz, Sheila Cárcel, Chiara Simona Cardellino, Sofia Cardoso, Filipe Cardoso, Filipa Cardoso, Nelson Cardoso, Simone Carelli, Nicolas Carlier, Thierry Carmoi, Gayle Carney, Inês Carqueja, Marie-Christine Carret, François Martin Carrier, Ida Carroll, Maire-Laure Casanova, Mariana Cascão, Siobhan Casey, José Casimiro, Bailey Cassandra, Silvia Castañeda, Nidyanara Castanheira, Guylaine Castor-Alexandre, Henry Castrillón, Ivo Castro, Ana Catarino, François-Xavier Catherine, Paolo Cattaneo, Roberta Cavalin, Giulio Giovanni Cavalli, Alexandros Cavayas, Adrian Ceccato, Minerva Cervantes-Gonzalez, Anissa Chair, Catherine Chakveatze, Adrienne Chan, Meera Chand, Christelle Chantalat Auger, Jean-Marc Chapplain, Julie Chas, Allegra Chatterjee, Mobin Chaudry, Jonathan Samuel Chávez Iñiguez, Anjellica Chen, Yih-Sharng Chen, Matthew Pellan Cheng, Antoine Cheret, Thibault Chiarabini, Julian Chica, Suresh Kumar Chidambaram, Leong Chin Tho, Catherine Chirouze, Davide Chiumello, Sung-Min Cho, Bernard Cholley, Marie-Charlotte Chopin, Ting Soo Chow, Yock Ping Chow, Hiu Jian Chua, Jonathan Chua, Jose Pedro Cidade, José Miguel Cisneros Herreros, Anna Ciullo, Jennifer Clarke, Emma Clarke, Rolando Claure-Del Granado, Sara Clohisey, Perren J Cobb, Cassidy Codan, Caitriona Cody, Alexandra Coelho, Megan Coles, Gwenhaël Colin, Michael Collins, Sebastiano Maria Colombo, Pamela Combs, Marie Connor, Anne Conrad, Sofía Contreras, Elaine Conway, Graham S Cooke, Mary Copland, Hugues Cordel, Amanda Corley, Sabine Cornelis, Alexander Daniel Cornet, Arianne Joy Corpuz, Andrea Cortegiani, Grégory Corvaisier, Emma Costigan, Camille Couffignal, Sandrine Couffin-Cadiergues, Roxane Courtois, Stéphanie Cousse, Rachel Cregan, Charles Crepy D'Orleans, Cosimo Cristella, Sabine Croonen, Gloria Crowl, Jonathan Crump, Claudina Cruz, Juan Luis Cruz Berm, Jaime Cruz Rojo, Marc Csete, Ailbhe Cullen, Matthew Cummings, Gerard Curley, Elodie Curlier, Colleen Curran, Paula Custodio, Ana da Silva Filipe, Charlene Da Silveira, Al-Awwab Dabaliz, Darren Dahly, Heidi Dalton, Jo Dalton, Seamus Daly, Nick Daneman, Corinne Daniel, Jorge Dantas, Frédérick D'Aragon, Menno de Jong, Gillian de Loughry, Diego de Mendoza, Etienne De Montmollin, Rafael Freitas de Oliveira França, Ana Isabel de Pinho Oliveira, Rosanna De Rosa, Cristina De Rose, Thushan de Silva, Peter de Vries, Jillian Deacon, David Dean, Alexa Debard, Marie-Pierre Debray, Nathalie DeCastro, William Dechert, Lauren Deconninck, Romain Decours, Eve Defous, Isabelle Delacroix, Eric Delaveuve, Karen Delavigne, Nathalie M Delfos, Ionna Deligiannis, Andrea Dell'Amore, Christelle Delmas, Pierre Delobel, Corine Delsing, Elisa Demonchy, Emmanuelle Denis, Dominique Deplanque, Pieter Depuydt, Mehul Desai, Diane Descamps, Mathilde Desvallées, Santi Dewayanti, Pathik Dhanger, Alpha Diallo, Sylvain Diamantis, André Dias, Juan Jose Diaz, Priscila Diaz, Rodrigo Diaz, Kévin Didier, Jean-Luc Diehl, Wim Dieperink, Jérôme Dimet, Vincent Dinot, Fara Diop, Alphonsine Diouf, Yael Dishon, Félix Djossou, Annemarie B Docherty, Helen Doherty, Arjen M Dondorp, Andy Dong, Maria Donnelly, Sean Donohue, Yoann Donohue, Chloe Donohue, Peter Doran, Céline Dorival, Eric D'Ortenzio, James Joshua Douglas, Renee Douma, Nathalie Dournon, Triona Downer, Joanne Downey, Mark Downing, Tom Drake, Aoife Driscoll, Murray Dryden, Murray Dryden, Claudio Duarte Fonseca, Vincent Dubee, François Dubos, Alexandre Ducancelle, Toni Duculan, Susanne Dudman, Abhijit Duggal, Paul Dunand, Mathilde Duplaix, Emanuele Durante-Mangoni, Lucian Durham, Bertrand Dussol, Juliette Duthoit, Xavier Duval, Anne Margarita Dyrhol-Riise, Sim Choon Ean, Marco Echeverria-Villalobos, Siobhan Egan, Carla Eira, Mohammed El Sanharawi, Subbarao Elapavaluru, Brigitte Elharrar, Jacobien Ellerbroek, Philippine Eloy, Tarek Elshazly, Iqbal Elyazar, Isabelle Enderle, Tomoyuki Endo, Chan Chee Eng, Ilka Engelmann, Vincent Enouf, Olivier Epaulard, Mariano Esperatti, Hélène Esperou, Marina Esposito-Farese, João Estevão, Manuel Etienne, Nadia Ettalhaoui, Anna Greti Everding, Mirjam Evers, Marc Fabre, Isabelle Fabre, Amna Faheem, Arabella Fahy, Cameron J Fairfield, Zul Fakar, Komal Fareed, Pedro Faria, Ahmed Farooq, Hanan Fateena, Arie Zainul Fatoni, Karine Faure, Raphaël Favory, Mohamed Fayed, Niamh Feely, Laura Feeney, Jorge Fernandes, Marília Andreia Fernandes, Susana Fernandes, François-Xavier Ferrand, Eglantine Ferrand Devouge, Joana Ferrão, Mário Ferraz, Sílvia Ferreira, Isabel Ferreira, Benigno Ferreira, Ricard Ferrer-Roca, Nicolas Ferriere, Céline Ficko, Claudia Figueiredo-Mello, William Finlayson, Juan Fiorda, Thomas Flament, Clara Flateau, Tom Fletcher, Letizia Lucia Florio, Deirdre Flynn, Claire Foley, Jean Foley, Victor Fomin, Tatiana Fonseca, Patricia Fontela, Simon Forsyth, Denise Foster, Giuseppe Foti, Erwan Fourn, Robert A Fowler, Marianne Fraher, Diego Franch-Llasat, John F Fraser, Christophe Fraser, Marcela Vieira Freire, Ana Freitas Ribeiro, Caren Friedrich, Ricardo Fritz, Stéphanie Fry, Nora Fuentes, Masahiro Fukuda, G Argin, Valérie Gaborieau, Rostane Gaci, Massimo Gagliardi, Jean-Charles Gagnard, Amandine Gagneux-Brunon, Sérgio Gaião, Linda Gail Skeie, Phil Gallagher, Carrol Gamble, Yasmin Gani, Arthur Garan, Rebekha Garcia, Julia Garcia-Diaz, Esteban Garcia-Gallo, Navya Garimella, Denis Garot, Valérie Garrait, Basanta Gauli, Nathalie Gault, Aisling Gavin, Anatoliy Gavrylov, Alexandre Gaymard, Johannes Gebauer, Eva Geraud, Louis Gerbaud Morlaes, Nuno Germano, Praveen Kumar Ghisulal, Jade Ghosn, Marco Giani, Jess Gibson, Tristan Gigante, Morgane Gilg, Elaine Gilroy, Guillermo Giordano, Michelle Girvan, Valérie Gissot, Daniel Glikman, Petr Glybochko, Eric Gnall, Geraldine Goco, François Goehringer, Siri Goepel, Jin Yi Goh, Jonathan Golob, Rui Gomes, Kyle Gomez, Joan Gómez-Junyent, Marie Gominet, Alicia Gonzalez, Patricia Gordon, Isabelle Gorenne, Laure Goubert, Cécile Goujard, Tiphaine Goulenok, Margarite Grable, Jeronimo Graf, Edward Wilson Grandin, Pascal Granier, Giacomo Grasselli, Christopher A Green, Courtney Greene, William Greenhalf, Segolène Greffe, Domenico Luca Grieco, Matthew Griffee, Fiona Griffiths, Ioana Grigoras, Albert Groenendijk, Anja Grosse Lordemann, Heidi Gruner, Yusing Gu, Jérémie Guedj, Martin Guego, Dewi Guellec, Anne-Marie Guerguerian, Daniela Guerreiro, Romain Guery, Anne Guillaumot, Laurent Guilleminault, Maisa Guimarães de Castro, Thomas Guimard, Marieke Haalboom, Daniel Haber, Hannah Habraken, Ali Hachemi, Amy Hackmann, Nadir Hadri, Fakhir Haidri, Sheeba Hakak, Adam Hall, Sophie Halpin, Jawad Hameed, Ansley Hamer, Raph L Hamers, Rebecca Hamidfar, Terese Hammond, Lim Yuen Han, Rashan Haniffa, Kok Wei Hao, Hayley Hardwick, Ewen M Harrison, Janet Harrison, Samuel Bernard Ekow Harrison, Alan Hartman, Mohd Shahnaz Hasan, Junaid Hashmi, Muhammad Hayat, Ailbhe Hayes, Leanne Hays, Jan Heerman, Lars Heggelund, Ross Hendry, Martina Hennessy, Aquiles Henriquez-Trujillo, Maxime Hentzien, Jaime Hernandez-Montfort, Andrew Hershey, Liv Hesstvedt, Astarini Hidayah, Eibhilin Higgins, Dawn Higgins, Rupert Higgins, Rita Hinchion, Samuel Hinton, Hiroaki Hiraiwa, Haider Hirkani, Hikombo Hitoto, Yi Bin Ho, Alexandre Hoctin, Isabelle Hoffmann, Wei Han Hoh, Oscar Hoiting, Rebecca Holt, Jan Cato Holter, Juan Pablo Horcajada, Koji Hoshino, Ikram Houas, Catherine L Hough, Stuart Houltham, Jimmy Ming-Yang Hsu, Jean-Sébastien Hulot, Stella Huo, Abby Hurd, Iqbal Hussain, Samreen Ijaz, Hajnal-Gabriela Illes, Patrick Imbert, Mohammad Imran, Rana Imran Sikander, Aftab Imtiaz, Hugo Inácio, Carmen Infante Dominguez, Yun Sii Ing, Elias Iosifidis, Mariachiara Ippolito, Sarah Isgett, Tiago Isidoro, Nadiah Ismail, Margaux Isnard, Junji Itai, Daniel Ivulich, Danielle Jaafar, Salma Jaafoura, Julien Jabot, Clare Jackson, Nina Jamieson, Victoria Janes, Pierre Jaquet, Coline Jaud-Fischer, Stéphane Jaureguiberry, Jeffrey Javidfar, Denise Jaworsky, Florence Jego, Anilawati Mat Jelani, Synne Jenum, Ruth Jimbo-Sotomayor, Ong Yiaw Joe, Ruth N Jorge García, Cédric Joseph, Mark Joseph, Swosti Joshi, Mercé Jourdain, Philippe Jouvet, Hanna Jung, Anna Jung, Dafsah Juzar, Ouifiya Kafif, Florentia Kaguelidou, Neerusha Kaisbain, Thavamany Kaleesvran, Sabina Kali, Alina Kalicinska, Smaragdi Kalomoiri, Muhammad Aisar Ayadi Kamaluddin, Zul Amali Che Kamaruddin, Nadiah Kamarudin, Paul Kambiya, Kavita Kamineni, Darshana Hewa Kandamby, Chris Kandel, Kong Yeow Kang, Darakhshan Kanwal, Pratap Karpayah, Todd Karsies, Daisuke Kasugai, Anant Kataria, Kevin Katz, Aasmine Kaur, Christy Kay, Hannah Keane, Seán Keating, Pulak Kedia, Claire Kelly, Yvelynne Kelly, Andrea Kelly, Niamh Kelly, Aoife Kelly, Sadie Kelly, Maeve Kelsey, Ryan Kennedy, Kalynn Kennon, Maeve Kernan, Younes Kerroumi, Sharma Keshav, Imrana Khalid, Osama Khalid, Antoine Khalil, Coralie Khan, Irfan Khan, Quratul Ain Khan, Sushil Khanal, Abid Khatak, Amin Khawaja, Krish Kherajani, Michelle E Kho, Saye Khoo, Ryan Khoo, Denisa Khoo, Nasir Khoso, Khor How Kiat, Yuri Kida, Peter Kiiza, Beathe Kiland Granerud, Anders Benjamin Kildal, Jae Burm Kim, Antoine Kimmoun, Detlef Kindgen-Milles, Alexander King, Nobuya Kitamura, Paul Klenerman, Rob Klont, Gry Kloumann Bekken, Stephen R Knight, Robin Kobbe, Chamira Kodippily, Malte Kohns Vasconcelos, Sabin Koirala, Mamoru Komatsu, Caroline Kosgei, Arsène Kpangon, Karolina Krawczyk, Vinothini Krishnan, Sudhir Krishnan, Oksana Kruglova, Deepali Kumar, Ganesh Kumar, Mukesh Kumar, Dinesh Kuriakose, Ethan Kurtzman, Demetrios Kutsogiannis, Galyna Kutsyna, Konstantinos Kyriakoulis, Marie Lachatre, Marie Lacoste, John G Laffey, Marie Lagrange, Fabrice Laine, Olivier Lairez, Sanjay Lakhey, Antonio Lalueza, Marc Lambert, François Lamontagne, Marie Langelot-Richard, Vincent Langlois, Eka Yudha Lantang, Marina Lanza, Cédric Laouénan, Samira Laribi, Delphine 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Chuan Lim, Chantre Lima, Lim Lina, Bruno Lina, Andreas Lind, Maja Katherine Lingad, Guillaume Lingas, Sylvie Lion-Daolio, Keibun Liu, Marine Livrozet, Patricia Lizotte, Antonio Loforte, Navy Lolong, Leong Chee Loon, Diogo Lopes, Dalia Lopez-Colon, Jose W Lopez-Revilla, Anthony L Loschner, Paul Loubet, Bouchra Loufti, Guillame Louis, Silvia Lourenco, Lara Lovelace-Macon, Lee Lee Low, Marije Lowik, Jia Shyi Loy, Jean Christophe Lucet, Carlos Lumbreras Bermejo, Carlos M Luna, Olguta Lungu, Liem Luong, Nestor Luque, Dominique Luton, Nilar Lwin, Ruth Lyons, Olavi Maasikas, Oryane Mabiala, Moïse Machado, Gabriel Macheda, Hashmi Madiha, Guillermo Maestro de la Calle, Rafael Mahieu, Sophie Mahy, Ana Raquel Maia, Lars S Maier, Mylène Maillet, Thomas Maitre, Maximilian Malfertheiner, Nadia Malik, Paddy Mallon, Fernando Maltez, Denis Malvy, Victoria Manda, Laurent Mandelbrot, Frank Manetta, Julie Mankikian, Edmund Manning, Aldric Manuel, Ceila Maria Sant Ana Malaque, Flávio Marino, Daniel Marino, Samuel Markowicz, Charbel Maroun Eid, Ana Marques, Catherine Marquis, Brian Marsh, Laura Marsh, Megan Marshal, John Marshall, Celina Turchi Martelli, Dori-Ann Martin, Emily Martin, Guillaume Martin-Blondel, Martin Martinot, Alejandro Martin-Quiros, João Martins, Ana Martins, Nuno Martins, Caroline Martins Rego, Gennaro Martucci, Olga Martynenko, Eva Miranda Marwali, Marsilla Marzukie, David Maslove, Sabina Mason, Sobia Masood, Basri Mat Nor, Moshe Matan, Meghena Mathew, Daniel Mathieu, Mathieu Mattei, Romans Matulevics, Laurence Maulin, Michael Maxwell, Javier Maynar, Thierry Mazzoni, Natalie Mc Evoy, Lisa Mc Sweeney, Colin McArthur, Colin McArthur, Anne McCarthy, Aine McCarthy, Colin McCloskey, Rachael McConnochie, Sherry McDermott, Sarah E McDonald, Aine McElroy, Samuel McElwee, Victoria McEneany, Allison McGeer, Chris McKay, Johnny McKeown, Kenneth A McLean, Paul McNally, Bairbre McNicholas, Elaine McPartlan, Edel Meaney, Cécile Mear-Passard, Maggie Mechlin, Maqsood Meher, Omar Mehkri, Ferruccio Mele, Luis Melo, Kashif Memon, Joao Joao Mendes, Ogechukwu Menkiti, Kusum Menon, Alexander J Mentzer, Emmanuelle Mercier, Noémie Mercier, Antoine Merckx, Mayka Mergeay-Fabre, Blake Mergler, António Mesquita, Roberta Meta, Osama Metwally, Agnès Meybeck, Dan Meyer, Alison M Meynert, Vanina Meysonnier, Amina Meziane, Mehdi Mezidi, Céline Michelanglei, Isabelle Michelet, Efstathia Mihelis, Vladislav Mihnovit, Hugo Miranda-Maldonado, Nor Arisah Misnan, Tahira Jamal Mohamed, Nik Nur Eliza Mohamed, Asma Moin, David Molina, Elena Molinos, Brenda Molloy, Mary Mone, Agostinho Monteiro, Claudia Montes, Giorgia Montrucchio, Shona C Moore, Sarah Moore, Lina Morales Cely, Lucia Moro, Catherine Motherway, Ana Motos, Hugo Mouquet, Clara Mouton Perrot, Julien Moyet, Caroline Mudara, Aisha Kalsoom Mufti, Ng Yong Muh, Dzawani Muhamad, Jimmy Mullaert, Fredrik Müller, Karl Erik Müller, Syed Muneeb, Nadeem Munir, Laveena Munshi, Aisling Murphy, Lorna Murphy, Aisling Murphy, Marlène Murris, Srinivas Murthy, Himed Musaab, Himasha Muvindi, Gugapriyaa Muyandy, Dimitra Melia Myrodia, Farah Nadia Mohd-Hanafiah, Dave Nagpal, Alex Nagrebetsky, Mangala Narasimhan, Nageswaran Narayanan, Rashid Nasim Khan, Alasdair Nazerali-Maitland, Nadège Neant, Holger Neb, Erni Nelwan, Raul Neto, Emily Neumann, Pauline Yeung Ng, Wing Yiu Ng, Anthony Nghi, Duc Nguyen, Orna Ni Choileain, Niamh Ni Leathlobhair, Prompak Nitayavardhana, Stephanie Nonas, Nurul Amani Mohd Noordin, Marion Noret, Nurul Faten Izzati Norharizam, Lisa Norman, Alessandra Notari, Mahdad Noursadeghi, Karolina Nowicka, Adam Nowinski, Saad Nseir, Jose I Nunez, Nurnaningsih Nurnaningsih, Dwi Utomo Nusantara, Elsa Nyamankolly, Fionnuala O Brien, Annmarie O Callaghan, Annmarie O'Callaghan, Giovanna Occhipinti, Derbrenn OConnor, Max O'Donnell, Tawnya Ogston, Takayuki Ogura, Tak-Hyuk Oh, Sophie O'Halloran, Katie O'Hearn, Shinichiro Ohshimo, Agnieszka Oldakowska, João Oliveira, Larissa Oliveira, Jee Yan Ong, Wilna Oosthuyzen, Anne Opavsky, Peter Openshaw, Saijad Orakzai, Claudia Milena Orozco-Chamorro, Jamel Ortoleva, Javier Osatnik, Linda O'Shea, Miriam O'Sullivan, Siti Zubaidah Othman, Nadia Ouamara, Rachida Ouissa, Eric Oziol, Maïder Pagadoy, Justine Pages, Mario Palacios, Amanda Palacios, Massimo Palmarini, Giovanna Panarello, Hem Paneru, Lai Hui Pang, Mauro Panigada, Nathalie Pansu, Aurélie Papadopoulos, Rachael Parke, Melissa Parker, Briseida Parra, Taha Pasha, Jérémie Pasquier, Bruno Pastene, Fabian Patauner, Drashti Patel, Mohan Dass Pathmanathan, Luís Patrão, Patricia Patricio, Juliette Patrier, Lisa Patterson, Rajyabardhan Pattnaik, Mical Paul, Christelle Paul, Jorge Paulos, William A Paxton, Jean-François Payen, Kalaiarasu Peariasamy, Giles J Peek, Florent Peelman, Nathan Peiffer-Smadja, Vincent Peigne, Mare Pejkovska, Paolo Pelosi, Ithan D Peltan, Rui Pereira, Daniel Perez, Luis Periel, Thomas Perpoint, Antonio Pesenti, Vincent Pestre, Lenka Petrou, Ventzislava Petrov-Sanchez, Frank Olav Pettersen, Gilles Peytavin, Scott Pharand, Michael Piagnerelli, Walter Picard, Olivier Picone, Maria de Piero, Carola Pierobon, Djura Piersma, Carlos Pimentel, Raquel Pinto, Catarina Pires, Isabelle Pironneau, Lionel Piroth, Ayodhia Pitaloka, Riinu Pius, Laurent Plantier, Hon Shen Png, Julien Poissy, Ryadh Pokeerbux, Maria Pokorska-Spiewak, Sergio Poli, Georgios Pollakis, Diane Ponscarme, Jolanta Popielska, Diego Bastos Porto, Andra-Maris Post, Douwe F Postma, Pedro Povoa, Diana Póvoas, Jeff Powis, Sofia Prapa, Sébastien Preau, Christian Prebensen, Jean-Charles Preiser, Anton Prinssen, Gamage Dona Dilanthi Priyadarshani, Lucia Proença, Sravya Pudota, Oriane Puéchal, Bambang Pujo Semedi, Mathew Pulicken, Gregory Purcell, Luisa Quesada, Vilmaris Quinones-Cardona, Víctor Quirós González, Else Quist-Paulsen, Mohammed Quraishi, Maia Rabaa, Christian Rabaud, Ebenezer Rabindrarajan, Aldo Rafael, Marie Rafiq, Gabrielle Ragazzo, Mutia Rahardjani, Rozanah Abd Rahman, Ahmad Kashfi Haji Ab Rahman, Arsalan Rahutullah, Fernando Rainieri, Giri Shan Rajahram, Pratheema Ramachandran, Ahmad Afiq Ramli, Blandine Rammaert, Asim Rana, Rajavardhan Rangappa, Ritika Ranjan, Christophe Rapp, Aasiyah Rashan, Thalha Rashan, Ghulam Rasheed, Menaldi Rasmin, Indrek Rätsep, Cornelius Rau, Tharmini Ravi, Ali Raza, Andre Real, Stanislas Rebaudet, Sarah Redl, Brenda Reeve, Attaur Rehman, Liadain Reid, Liadain Reid, Dag Henrik Reikvam, Renato Reis, Jordi Rello, Jonathan Remppis, Martine Remy, Hongru Ren, Hanna Renk, Anne-Sophie Resseguier, Matthieu Revest, Oleksa Rewa, Luis Felipe Reyes, Tiago Reyes, Maria Ines Ribeiro, Antonia Ricchiuto, David Richardson, Denise Richardson, Laurent Richier, Siti Nurul Atikah Ahmad Ridzuan, Jordi Riera, Ana L Rios, Asgar Rishu, Patrick Rispal, Karine Risso, Maria Angelica Rivera Nuñez, Nicholas Rizer, Chiara Robba, André Roberto, Stephanie Roberts, David L Robertson, Olivier Robineau, Ferran Roche-Campo, Paola Rodari, Simão Rodeia, Bernhard Roessler, Pierre-Marie Roger, Emmanuel Roilides, Juliette Romaru, Roberto Roncon-Albuquerque, Mélanie Roriz, Manuel Rosa-Calatrava, Michael Rose, Dorothea Rosenberger, Nurul Hidayah Mohammad Roslan, Andrea Rossanese, Matteo Rossetti, Bénédicte Rossignol, Patrick Rossignol, Stella Rousset, Carine Roy, Benoît Roze, Desy Rusmawatiningtyas, Clark D Russell, Maria Ryan, Maeve Ryan, Steffi Ryckaert, Aleksander Rygh Holten, Isabela Saba, Sairah Sadaf, Musharaf Sadat, Valla Sahraei, Maximilien Saint-Gilles, Pranya Sakiyalak, Nawal Salahuddin, Leonardo Salazar, Jodat Saleem, Gabriele Sales, Stéphane Sallaberry, Charlotte Salmon Gandonniere, Hélène Salvator, Olivier Sanchez, Angel Sanchez-Miralles, Vanessa Sancho-Shimizu, Gyan Sandhu, Zulfiqar Sandhu, Pierre-François Sandrine, Marlene Santos, Shirley Sarfo-Mensah, Bruno Sarmento Banheiro, Iam Claire E Sarmiento, Benjamine Sarton, Ankana Satya, Sree Satyapriya, Rumaisah Satyawati, Egle Saviciute, Parthena Savvidou, Yen Tsen Saw, Justin Schaffer, Tjard Schermer, Arnaud Scherpereel, Marion Schneider, Stephan Schroll, Michael Schwameis, Gary Schwartz, Brendan Scicluna, Janet T Scott, James Scott-Brown, Nicholas Sedillot, Tamara Seitz, Jaganathan Selvanayagam, Mageswari Selvarajoo, Caroline Semaille, Rasidah Bt Senian, Eric Senneville, Claudia Sepulveda, Filipa Sequeira, Tânia Sequeira, Ary Serpa Neto, Pablo Serrano Balazote, Ellen Shadowitz, Syamin Asyraf Shahidan, Mohammad Shamsah, Anuraj Shankar, Shaikh Sharjeel, Catherine A Shaw, Victoria Shaw, Ashraf Sheharyar, Rohan Shetty, Rajesh Mohan Shetty, Haixia Shi, Nisreen Shiban, Mohiuddin Shiekh, Nobuaki Shime, Hiroaki Shimizu, Keiki Shimizu, Sally Shrapnel, Pramesh Sundar Shrestha, Shubha Kalyan Shrestha, Hoi Ping Shum, Nassima Si Mohammed, Ng Yong Siang, Jeanne Sibiude, Atif Siddiqui, Piret Sillaots, Catarina Silva, Rogério Silva, Maria Joao Silva, Wai Ching Sin, Dario Sinatti, Punam Singh, Budha Charan Singh, Pompini Agustina Sitompul, Karisha Sivam, Vegard Skogen, Sue Smith, Benjamin Smood, Coilin Smyth, Michelle Smyth, Michelle Smyth, Morgane Snacken, Dominic So, Tze Vee Soh, Joshua Solomon, Tom Solomon, Agnès Sommet, Rima Song, Tae Song, Jack Song Chia, Michael Sonntagbauer, Azlan Mat Soom, Alberto Sotto, Edouard Soum, Marta Sousa, Ana Chora Sousa, Maria Sousa Uva, Vicente Souza-Dantas, Alexandra Sperry, Elisabetta Spinuzza, B P Sanka Ruwan Sri Darshana, Shiranee Sriskandan, Sarah Stabler, Thomas Staudinger, Stephanie-Susanne Stecher, Trude Steinsvik, Ymkje Stienstra, Birgitte Stiksrud, Eva Stolz, Amy Stone, Adrian Streinu-Cercel, David Stuart, Ami Stuart, Decy Subekti, Gabriel Suen, Jacky Y Suen, Asfia Sultana, Charlotte Summers, Dubravka Supic, Deepashankari Suppiah, Magdalena Surovcová, Suwarti Suwarti, Andrey Svistunov, Sarah Syahrin, Konstantinos Syrigos, Jaques Sztajnbok, Konstanty Szuldrzynski, Shirin Tabrizi, Lysa Tagherset, Shahdattul Mawarni Taib, Ewa Talarek, Sara Taleb, Jelmer Talsma, Renaud Tamisier, Maria Lawrensia Tampubolon, Kim Keat Tan, Yan Chyi Tan, Taku Tanaka, Hiroyuki Tanaka, Hayato Taniguchi, Huda Taqdees, Arshad Taqi, Coralie Tardivon, Pierre Tattevin, M Azhari Taufik, Hassan Tawfik, Richard S Tedder, Tze Yuan Tee, João Teixeira, Sofia Tejada, Marie-Capucine Tellier, Sze Kye Teoh, Vanessa Teotonio, François Téoulé, Pleun Terpstra, Olivier Terrier, Nicolas Terzi, Hubert Tessier-Grenier, Adrian Tey, Alif Adlan Mohd Thabit, Anand Thakur, Zhang Duan Tham, Suvintheran Thangavelu, Vincent Thibault, Simon-Djamel Thiberville, Benoît Thill, Jananee Thirumanickam, Shaun Thompson, Emma C Thomson, David Thomson, Surain Raaj Thanga Thurai, Ryan S Thwaites, Paul Tierney, Vadim Tieroshyn, Peter S Timashev, Jean-François Timsit, Noémie Tissot, Jordan Zhien Yang Toh, Maria Toki, Kristian Tonby, Sia Loong Tonnii, Margarida Torres, Antoni Torres, Rosario Maria Torres Santos-Olmo, Hernando Torres-Zevallos, Michael Towers, Tony Trapani, Théo Treoux, Cécile Tromeur, Ioannis Trontzas, Tiffany Trouillon, Jeanne Truong, Christelle Tual, Sarah Tubiana, Helen Tuite, Jean-Marie Turmel, Lance C W Turtle, Anders Tveita, Pawel Twardowski, Makoto Uchiyama, P G Ishara Udayanga, Andrew Udy, Roman Ullrich, Alberto Uribe, Asad Usman, Timothy M Uyeki, Cristinava Vajdovics, Piero Valentini, Luís Val-Flores, Amélie Valran, Stijn Van de Velde, Marcel van den Berge, Machteld Van der Feltz, Job van der Palen, Paul van der Valk, Nicky Van Der Vekens, Peter Van der Voort, Sylvie Van Der Werf, Laura van Gulik, Jarne Van Hattem, Carolien van Netten, Frank van Someren Greve, Ilonka van Veen, Hugo Van Willigen, Noémie Vanel, Henk Vanoverschelde, Pooja Varghese, Michael Varrone, Shoban Raj Vasudayan, Charline Vauchy, Shaminee Veeran, Aurélie Veislinger, Sebastian Vencken, Sara Ventura, Annelies Verbon, James Vickers, José Ernesto Vidal, César Vieira, Deepak Vijayan, Joy Ann Villanueva, Judit Villar, Pierre-Marc Villeneuve, Andrea Villoldo, Gayatri Vishwanathan, Benoit Visseaux, Hannah Visser, Chiara Vitiello, Harald Vonkeman, Fanny Vuotto, Suhaila Abdul Wahab, Noor Hidayu Wahab, Nadirah Abdul Wahid, Marina Wainstein, Wan Fadzlina Wan Muhd Shukeri, Chih-Hsien Wang, Steve Webb, Katharina Weil, Tan Pei Wen, Sanne Wesselius, T Eoin West, Murray Wham, Bryan Whelan, Nicole White, Paul Henri Wicky, Aurélie Wiedemann, Surya Otto Wijaya, Keith Wille, Suzette Willems, Virginie Williams, Calvin Wong, Yew Sing Wong, Teck Fung Wong, Natalie Wright, Gan Ee Xian, Lim Saio Xian, Kuan Pei Xuan, Ioannis Xynogalas, Siti Rohani Binti Mohd Yakop, Masaki Yamazaki, Yazdan Yazdanpanah, Nicholas Yee Liang Hing, Cécile Yelnik, Chian Hui Yeoh, Stephanie Yerkovich, Toshiki Yokoyama, Hodane Yonis, Obada Yousif, Saptadi Yuliarto, Akram Zaaqoq, Marion Zabbe, Kai Zacharowski, Masliza Zahid, Maram Zahran, Nor Zaila Binti Zaidan, Maria Zambon, Miguel Zambrano, Alberto Zanella, Konrad Zawadka, Nurul Zaynah, Hiba Zayyad, Alexander Zoufaly, David Zucman, University of Oxford, Infection, Anti-microbiens, Modélisation, Evolution (IAME (UMR_S_1137 / U1137)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Université Sorbonne Paris Nord, CHU Pontchaillou [Rennes], ARN régulateurs bactériens et médecine (BRM), Université de Rennes (UR)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), This work was made possible by the UK Foreign, Commonwealth and Development Office, Wellcome (215091/Z/18/Z, 205228/Z/16/Z, 220757/Z/20/Z), Bill & Melinda Gates Foundation (OPP1209135), UK Medical Research Council Clinical Research Training Fellowship (MR/V001671/1), the philanthropic support of the donors to the University of Oxford’s COVID-19 Research Response Fund, CIHR Coronavirus Rapid Research Funding Opportunity (OV2170359) and the co-ordination in Canada by Sunnybrook Research Institute, endorsement of the Irish Critical Care—Clinical Trials Group, co-ordination in Ireland by the Irish Critical Care—Clinical Trials Network at University College Dublin and funding by the Health Research Board of Ireland (CTN-2014–12), the Rapid European COVID-19 Emergency Response research (RECOVER) (H2020 project 101003589) and European Clinical Research Alliance on Infectious Diseases (ECRAID) (965313), the COVID clinical management team, AIIMS, Rishikesh, India, the COVID-19 Clinical Management team, Manipal Hospital Whitefield, Bengaluru, India, Cambridge NIHR Biomedical Research Centre, the dedication and hard work of the Groote Schuur Hospital Covid ICU Team, support by the Groote Schuur nursing and University of Cape Town registrar bodies co-ordinated by the Division of Critical Care at the University of Cape Town, the Liverpool School of Tropical Medicine and the University of Oxford, the dedication and hard work of the Norwegian SARS-CoV-2 study team, the Research Council of Norway (grant no. 312780) and a philanthropic donation from Vivaldi Invest A/S owned by Jon Stephenson von Tetzchner, Imperial NIHR Biomedical Research Centre, the Comprehensive Local Research Networks of which PJMO is an NIHR Senior Investigator (NIHR201385), Innovative Medicines Initiative Joint Undertaking under Grant Agreement No. 115523 COMBACTE, resources of which are composed of financial contribution from the European Union’s Seventh Framework Programme (FP7/2007– 2013) and EFPIA companies, in-kind contribution, the French COVID cohort (NCT04262921) is sponsored by INSERM and is funded by the REACTing (REsearch & ACtion emergING infectious diseases) consortium and by a grant of the French Ministry of Health (PHRC n 20–0424), Stiftungsfonds zur Förderung der Bekämpfung der Tuberkulose und anderer Lungenkrankheiten of the City of Vienna (project no. APCOV22BGM), Italian Ministry of Health ‘Fondi Ricerca corrente–L1P6’ to IRCCS Ospedale Sacro Cuore–Don Calabria, Australian Department of Health grant (3273191), Gender Equity Strategic Fund at University of Queensland, Artificial Intelligence for Pandemics (A14PAN) at University of Queensland, the Australian Research Council Centre of Excellence for Engineered Quantum Systems (EQUS, CE170100009), the Prince Charles Hospital Foundation, Australia, grants from Instituto de Salud Carlos III, Ministerio de Ciencia, Spain, Brazil, National Council for Scientific and Technological Development (scholarship no. 303953/2018–7), the Firland Foundation, Shoreline, Washington, USA, a grant from foundation Bevordering Onderzoek Franciscus, the South Eastern Norway Health Authority and the Research Council of Norway, and preparedness work conducted by the Short PeRiod IncideNce sTudy of Severe Acute Respiratory Infection. Data and Material provision was supported by grants from the National Institute for Health Research (NIHR, award CO-CIN-01), the Medical Research Council (MRC, and grant MC_PC_19059) and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with PHE (award no. 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award no. 200927), Liverpool Experimental Cancer Medicine Centre (grant no. C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award no. IS-BRC-1215–20013) and NIHR Clinical Research Network providing infrastructure support.
Subjects: Male, Epidemiology, MESH: Hospitalization, MESH: Proportional Hazards Models, MESH: Risk Factors, Risk Factors, MESH: Child, cohort study, MESH: COVID-19, Humans, MESH: SARS-CoV-2, Child, Proportional Hazards Models, MESH: Humans, MESH: Middle Aged, SARS-CoV-2, COVID-19, risk of death, General Medicine, Middle Aged, co-morbidities, symptoms, treatments, MESH: Male, Hospitalization, Intensive Care Units, MESH: Intensive Care Units, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, COVID-19/therapy
Abstract: Background We describe demographic features, treatments and clinical outcomes in the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) COVID-19 cohort, one of the world's largest international, standardized data sets concerning hospitalized patients. Methods The data set analysed includes COVID-19 patients hospitalized between January 2020 and January 2022 in 52 countries. We investigated how symptoms on admission, co-morbidities, risk factors and treatments varied by age, sex and other characteristics. We used Cox regression models to investigate associations between demographics, symptoms, co-morbidities and other factors with risk of death, admission to an intensive care unit (ICU) and invasive mechanical ventilation (IMV). Results Data were available for 689 572 patients with laboratory-confirmed (91.1%) or clinically diagnosed (8.9%) SARS-CoV-2 infection from 52 countries. Age [adjusted hazard ratio per 10 years 1.49 (95% CI 1.48, 1.49)] and male sex [1.23 (1.21, 1.24)] were associated with a higher risk of death. Rates of admission to an ICU and use of IMV increased with age up to age 60 years then dropped. Symptoms, co-morbidities and treatments varied by age and had varied associations with clinical outcomes. The case-fatality ratio varied by country partly due to differences in the clinical characteristics of recruited patients and was on average 21.5%. Conclusions Age was the strongest determinant of risk of death, with a ∼30-fold difference between the oldest and youngest groups; each of the co-morbidities included was associated with up to an almost 2-fold increase in risk. Smoking and obesity were also associated with a higher risk of death. The size of our international database and the standardized data collection method make this study a comprehensive international description of COVID-19 clinical features. Our findings may inform strategies that involve prioritization of patients hospitalized with COVID-19 who have a higher risk of death.
Published: 2023

4. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Author: S. Cotton, M.P. McHugh, R. Dewar, J.G. Haas, K. Templeton, Samuel C. Robson, Thomas R. Connor, Nicholas J. Loman, Tanya Golubchik, Rocio T. Martinez Nunez, David Bonsall, Andrew Rambaut, Luke B. Snell, Rich Livett, Catherine Ludden, Sally Corden, Eleni Nastouli, Gaia Nebbia, Ian Johnston, Jacqui A. Prieto, Kordo Saeed, David K. Jackson, Catherine Houlihan, Dan Frampton, William L. Hamilton, Adam A. Witney, Giselda Bucca, Cassie F. Pope, Catherine Moore, Emma C. Thomson, Teresa Cutino-Moguel, Ewan M. Harrison, Colin P. Smith, Fiona Rogan, Shaun M. Beckwith, Abigail Murray, Dawn Singleton, Kirstine Eastick, Liz A. Sheridan, Paul Randell, Leigh M. Jackson, Cristina V. Ariani, Sónia Gonçalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Samuel Moses, Sam Nicholls, Matthew Bull, Roberto Amato, Darren L. Smith, David M. Aanensen, Jeffrey C. Barrett, Beatrix Kele, Dinesh Aggarwal, James G. Shepherd, Martin D. Curran, Surendra Parmar, Matthew D. Parker, Catryn Williams, Sharon Glaysher, Anthony P. Underwood, Matthew Bashton, Nicole Pacchiarini, Katie F. Loveson, Matthew Byott, Alessandro M. Carabelli, Kate E. Templeton, Sharon J. Peacock, Thushan I. de Silva, Dennis Wang, Cordelia F. Langford, John Sillitoe, Rory N. Gunson, Simon Cottrell, Justin O’Grady, Dominic Kwiatkowski, Patrick J. Lillie, Nicholas Cortes, Nathan Moore, Claire Thomas, Phillipa J. Burns, Tabitha W. Mahungu, Steven Liggett, Angela H. Beckett, Matthew TG. Holden, Lisa J. Levett, Husam Osman, Mohammed O. Hassan-Ibrahim, David A. Simpson, Meera Chand, Ravi K. Gupta, Alistair C. Darby, Steve Paterson, Oliver G. Pybus, Erik M. Volz, Daniela de Angelis, David L. Robertson, Andrew J. Page, Inigo Martincorena, Louise Aigrain, Andrew R. Bassett, Nick Wong, Yusri Taha, Michelle J. Erkiert, Michael H. Spencer Chapman, Rebecca Dewar, Martin P. McHugh, Siddharth Mookerjee, Stephen Aplin, Matthew Harvey, Thea Sass, Helen Umpleby, Helen Wheeler, James P. McKenna, Ben Warne, Joshua F. Taylor, Yasmin Chaudhry, Rhys Izuagbe, Aminu S. Jahun, Gregory R. Young, Claire McMurray, Clare M. McCann, Andrew Nelson, Scott Elliott, Hannah Lowe, Anna Price, Matthew R. Crown, Sara Rey, Sunando Roy, Ben Temperton, Sharif Shaaban, Andrew R. Hesketh, Kenneth G. Laing, Irene M. Monahan, Judith Heaney, Emanuela Pelosi, Siona Silviera, Eleri Wilson-Davies, Helen Fryer, Helen Adams, Louis du Plessis, Rob Johnson, William T. Harvey, Joseph Hughes, Richard J. Orton, Lewis G. Spurgin, Yann Bourgeois, Chris Ruis, Áine O'Toole, Marina Gourtovaia, Theo Sanderson, Christophe Fraser, Jonathan Edgeworth, Judith Breuer, Stephen L. Michell, John A. Todd, Michaela John, David Buck, Kavitha Gajee, Gemma L. Kay, David Heyburn, Themoula Charalampous, Adela Alcolea-Medina, Katie Kitchman, Alan McNal, David T. Pritch, Samir Dervisevic, Peter Muir, Esther Robinson, Barry B. Vipond, Newara A. Ramadan, Christopher Jeanes, Danni Weldon, Jana Catalan, Neil Jones, Ana da Silva Filipe, Chris Williams, Marc Fuchs, Julia Miskelly, Aaron R. Jeffries, Karen Oliver, Naomi R. Park, Amy Ash, Cherian Koshy, Magdalena Barrow, Sarah L. Buchan, Anna Mantzouratou, Gemma Clark, Christopher W. Holmes, Sharon Campbell, Thomas Davis, Ngee Keong Tan, Julianne R. Brown, Kathryn A. Harris, Stephen P. Kidd, Paul R. Grant, Li Xu-McCrae, Alison Cox, Pinglawathee Madona, Marcus Pond, Paul A. Randell, Karen T. Withell, Cheryl Williams, Clive Graham, Rebecca Denton-Smith, Emma Swindells, Robyn Turnbull, Tim J. Sloan, Andrew Bosworth, Stephanie Hutchings, Hannah M. Pymont, Anna Casey, Liz Ratcliffe, Christopher R. Jones, Bridget A. Knight, Tanzina Haque, Jennifer Hart, Dianne Irish-Tavares, Eric Witele, Craig Mower, Louisa K. Watson DipHE, Jennifer Collins, Gary Eltringham, Dorian Crudgington, Ben Macklin, Miren Iturriza-Gomara, Anita O. Lucaci, Patrick C. McClure, Matthew Carlile, Nadine Holmes, Christopher Moore, Nathaniel Storey, Stefan Rooke, Gonzalo Yebra, Noel Craine, Malorie Perry, Nabil-Fareed Alikhan, Stephen Bridgett, Kate F. Cook, Christopher Fearn, Salman Goudarzi, Ronan A. Lyons, Thomas Williams, Sam T. Haldenby, Jillian Durham, Steven Leonard, Robert M. Davies, Rahul Batra, Beth Blane, Moira J. Spyer, Perminder Smith, Mehmet Yavus, Rachel J. Williams, Adhyana IK. Mahanama, Buddhini Samaraweera, Sophia T. Girgis, Samantha E. Hansford, Angie Green, Charlotte Beaver, Katherine L. Bellis, Matthew J. Dorman, Sally Kay, Liam Prestwood, Shavanthi Rajatileka, Joshua Quick, Radoslaw Poplawski, Nicola Reynolds, Andrew Mack, Arthur Morriss, Thomas Whalley, Bindi Patel, Iliana Georgana, Myra Hosmillo, Malte L. Pinckert, Joanne Stockton, John H. Henderson, Amy Hollis, William Stanley, Wen C. Yew, Richard Myers, Alicia Thornton, Alexander Adams, Tara Annett, Hibo Asad, Alec Birchley, Jason Coombes, Johnathan M. Evans, Laia Fina, Bree Gatica-Wilcox, Lauren Gilbert, Lee Graham, Jessica Hey, Ember Hilvers, Sophie Jones, Hannah Jones, Sara Kumziene-Summerhayes, Caoimhe McKerr, Jessica Powell, Georgia Pugh, Sarah Taylor, Alexander J. Trotter, Charlotte A. Williams, Leanne M. Kermack, Benjamin H. Foulkes, Marta Gallis, Hailey R. Hornsby, Stavroula F. Louka, Manoj Pohare, Paige Wolverson, Peijun Zhang, George MacIntyre-Cockett, Amy Trebes, Robin J. Moll, Lynne Ferguson, Emily J. Goldstein, Alasdair Maclean, Rachael Tomb, Igor Starinskij, Laura Thomson, Joel Southgate, Moritz UG. Kraemer, Jayna Raghwani, Alex E. Zarebski, Olivia Boyd, Lily Geidelberg, Chris J. Illingworth, Chris Jackson, David Pascall, Sreenu Vattipally, Timothy M. Freeman, Sharon N. Hsu, Benjamin B. Lindsey, Keith James, Kevin Lewis, Gerry Tonkin-Hill, Jaime M. Tovar-Corona, MacGregor Cox, Khalil Abudahab, Mirko Menegazzo, Ben EW. Taylor, Corin A. Yeats, Afrida Mukaddas, Derek W. Wright, Leonardo de Oliveira Martins, Rachel Colquhoun, Verity Hill, Ben Jackson, J.T. McCrone, Nathan Medd, Emily Scher, Jon-Paul Keatley, Tanya Curran, Sian Morgan, Patrick Maxwell, Ken Smith, Sahar Eldirdiri, Anita Kenyon, Alison H. Holmes, James R. Price, Tim Wyatt, Alison E. Mather, Timofey Skvortsov, John A. Hartley, Martyn Guest, Christine Kitchen, Ian Merrick, Robert Munn, Beatrice Bertolusso, Jessica Lynch, Gabrielle Vernet, Stuart Kirk, Elizabeth Wastnedge, Rachael Stanley, Giles Idle, Declan T. Bradley, Nicholas F. Killough, Jennifer Poyner, Matilde Mori, Owen Jones, Victoria Wright, Ellena Brooks, Carol M. Churcher, Laia Delgado Callico, Mireille Fragakis, Katerina Galai, Andrew Jermy, Sarah Judges, Anna Markov, Georgina M. McManus, Kim S. Smith, Peter MD. Thomas-McEwen, Elaine Westwick, Stephen W. Attwood, Frances Bolt, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Lizzie Meadows, Sarah Jeremiah, Nikki Smith, Luke Foulser, Amita Patel, Louise Berry, Tim Boswell, Vicki M. Fleming, Hannah C. Howson-Wells, Amelia Joseph, Manjinder Khakh, Michelle M. Lister, Paul W. Bird, Karlie Fallon, Thomas Helmer, Claire L. McMurray, Mina Odedra, Jessica Shaw, Julian W. Tang, Nicholas J. Willford, Victoria Blakey, Veena Raviprakash, Nicola Sheriff, Lesley-Anne Williams, Theresa Feltwell, Luke Bedford, James S. Cargill, Warwick Hughes, Jonathan Moore, Susanne Stonehouse, Laura Atkinson, Jack CD. Lee, Divya Shah, Natasha Ohemeng-Kumi, John Ramble, Jasveen Sehmi, Rebecca Williams, Wendy Chatterton, Monika Pusok, William Everson, Anibolina Castigador, Emily Macnaughton, Kate El Bouzidi, Temi Lampejo, Malur Sudhanva, Cassie Breen, Graciela Sluga, Shazaad SY. Ahmad, Ryan P. George, Nicholas W. Machin, Debbie Binns, Victoria James, Rachel Blacow, Lindsay Coupland, Louise Smith, Edward Barton, Debra Padgett, Garren Scott, Aidan Cross, Mariyam Mirfenderesky, Jane Greenaway, Kevin Cole, Phillip Clarke, Nichola Duckworth, Sarah Walsh, Kelly Bicknell, Robert Impey, Sarah Wyllie, Richard Hopes, Chloe Bishop, Vicki Chalker, Ian Harrison, Laura Gifford, Zoltan Molnar, Cressida Auckland, Cariad Evans, Kate Johnson, David G. Partridge, Mohammad Raza, Paul Baker, Stephen Bonner, Sarah Essex, Leanne J. Murray, Andrew I. Lawton, Shirelle Burton-Fanning, Brendan AI. Payne, Sheila Waugh, Andrea N. Gomes, Maimuna Kimuli, Darren R. Murray, Paula Ashfield, Donald Dobie, Fiona Ashford, Angus Best, Liam Crawford, Nicola Cumley, Megan Mayhew, Oliver Megram, Jeremy Mirza, Emma Moles-Garcia, Benita Percival, Megan Driscoll, Leah Ensell, Helen L. Lowe, Laurentiu Maftei, Matteo Mondani, Nicola J. Chaloner, Benjamin J. Cogger, Lisa J. Easton, Hannah Huckson, Jonathan Lewis, Sarah Lowdon, Cassandra S. Malone, Florence Munemo, Manasa Mutingwende, Roberto Nicodemi, Olga Podplomyk FD, Thomas Somassa, Andrew Beggs, Alex Richter, Claire Cormie, Joana Dias, Sally Forrest, Ellen E. Higginson, Mailis Maes, Jamie Young, Rose K. Davidson, Kathryn A. Jackson, Alexander J. Keeley, Jonathan Ball, Timothy Byaruhanga, Joseph G. Chappell, Jayasree Dey, Jack D. Hill, Emily J. Park, Arezou Fanaie, Rachel A. Hilson, Geraldine Yaze, Stephanie Lo, Safiah Afifi, Robert Beer, Joshua Maksimovic, Kathryn McCluggage, Karla Spellman, Catherine Bresner, William Fuller, Angela Marchbank, Trudy Workma, Ekaterina Shelest, Johnny Debebe, Fei Sang, Sarah Francois, Bernardo Gutierrez, Tetyana I. Vasylyeva, Flavia Flaviani, Manon Ragonnet-Cronin, Katherine L. Smollett, Alice Broos, Daniel Mair, Jenna Nichols, Kyriaki Nomikou, Lily Tong, Ioulia Tsatsani, Sarah O'Brien, Steven Rushton, Roy Sanderson, Jon Perkins, Seb Cotton, Abbie Gallagher, Elias Allara, Clare Pearson, David Bibby, Gavin Dabrer, Nicholas Ellaby, Eileen Gallagher, Jonathan Hubb, Angie Lackenby, David Lee, Nikos Manesis, Tamyo Mbisa, Steven Platt, Katherine A. Twohig, Mari Morgan, Alp Aydin, David J. Baker, Ebenezer Foster-Nyarko, Sophie J. Prosolek, Steven Rudder, Chris Baxter, Sílvia F. Carvalho, Deborah Lavin, Arun Mariappan, Clara Radulescu, Aditi Singh, Miao Tang, Helen Morcrette, Nadua Bayzid, Marius Cotic, Carlos E. Balcazar, Michael D. Gallagher, Daniel Maloney, Thomas D. Stanton, Kathleen A. Williamson, Robin Manley, Michelle L. Michelsen, Christine M. Sambles, David J. Studholme, Joanna Warwick-Dugdale, Richard Eccles, Matthew Gemmell, Richard Gregory, Margaret Hughes, Charlotte Nelson, Lucille Rainbow, Edith E. Vamos, Hermione J. Webster, Mark Whitehead, Claudia Wierzbicki, Adrienn Angyal, Luke R. Green, Max Whiteley, Emma Betteridge, Iraad F. Bronner, Ben W. Farr, Scott Goodwin, Stefanie V. Lensing, Shane A. McCarthy, Michael A. Quail, Diana Rajan, Nicholas M. Redshaw, Carol Scott, Lesley Shirley, Scott AJ. Thurston, Will Rowe, Amy Gaskin, Thanh Le-Viet, James Bonfield, Jennifier Liddle, Andrew Whitwham, University of St Andrews. School of Medicine, University of St Andrews. Infection and Global Health Division, and Apollo - University of Cambridge Repository
Subjects: Microbiology (medical), MCC, Introduction, SARS-CoV-2, NDAS, COVID-19, Care homes, General Medicine, NIS, Patient Discharge, Hospitals, Hospitalization, Infectious Diseases, SDG 3 - Good Health and Well-being, RA0421, RA0421 Public health. Hygiene. Preventive Medicine, Humans, Hospital discharge
Abstract: COG-UK is supported by funding from the MRC part of UK Research & Innovation, the National Institute of Health Research (Grant code MC_PC_19027), and Genome Research Limited, operating as the Welcome Sanger Institute. Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine. Publisher PDF
Published: 2023

5. How to avoid a local epidemic becoming a global pandemic

Author: Nils Chr. Stenseth, Rudolf Schlatte, Xiaoli Liu, Roger Pielke, Ruiyun Li, Bin Chen, Ottar N. Bjørnstad, Dimitri Kusnezov, George F. Gao, Christophe Fraser, Jason D. Whittington, Yuqi Bai, Ke Deng, Peng Gong, Dabo Guan, Yixiong Xiao, Bing Xu, and Einar Broch Johnsen
Subjects: Multidisciplinary
Abstract: Here, we combine international air travel passenger data with a standard epidemiological model of the initial 3 mo of the COVID-19 pandemic (January through March 2020; toward the end of which the entire world locked down). Using the information available during this initial phase of the pandemic, our model accurately describes the main features of the actual global development of the pandemic demonstrated by the high degree of coherence between the model and global data. The validated model allows for an exploration of alternative policy efficacies (reducing air travel and/or introducing different degrees of compulsory immigration quarantine upon arrival to a country) in delaying the global spread of SARS-CoV-2 and thus is suggestive of similar efficacy in anticipating the spread of future global disease outbreaks. We show that a lesson from the recent pandemic is that reducing air travel globally is more effective in reducing the global spread than adopting immigration quarantine. Reducing air travel out of a source country has the most important effect regarding the spreading of the disease to the rest of the world. Based upon our results, we propose a digital twin as a further developed tool to inform future pandemic decision-making to inform measures intended to control the spread of disease agents of potential future pandemics. We discuss the design criteria for such a digital twin model as well as the feasibility of obtaining access to the necessary online data on international air travel.
Published: 2023

6. Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year

Author: Michelle Kendall, Daphne Tsallis, Chris Wymant, Andrea Di Francia, Yakubu Balogun, Xavier Didelot, Luca Ferretti, and Christophe Fraser
Subjects: Multidisciplinary, General Physics and Astronomy, General Chemistry, General Biochemistry, Genetics and Molecular Biology
Abstract: The NHS COVID-19 app was launched in England and Wales in September 2020, with a Bluetooth-based contact tracing functionality designed to reduce transmission of SARS-CoV-2. We show that user engagement and the app’s epidemiological impacts varied according to changing social and epidemic characteristics throughout the app’s first year. We describe the interaction and complementarity of manual and digital contact tracing approaches. Results of our statistical analyses of anonymised, aggregated app data include that app users who were recently notified were more likely to test positive than app users who were not recently notified, by a factor that varied considerably over time. We estimate that the app’s contact tracing function alone averted about 1 million cases (sensitivity analysis 450,000–1,400,000) during its first year, corresponding to 44,000 hospital cases (SA 20,000–60,000) and 9,600 deaths (SA 4600–13,000).
Published: 2023

7. Demographics of People Who Transmit HIV-1 in Zambia: A Molecular Epidemiology Analysis in the HPTN-071 PopART Study

Author: Matthew Hall, Tanya Golubchik, David Bonsall, Lucie Abeler- Dörner, Mohammed Limbada, Barry Kosloff, Albertus Schaap, Mariateresa de Cesare, George MacIntyre-Cockett, Newton Otecko, William Probert, Oliver Ratmann, Ana Bulas Cruz, Estelle Piwowar-Manning, David Burns, Myron Cohen, Deborah Donnell, Susan Eshleman, Musonda Simwinga, Sarah Fidler, Richard J. Hayes, and Christophe Fraser
Published: 2023

8. Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias

Author: Rui André Nunes dos Santos, Matthew Hall, Christophe Fraser, Tanya Golubchik, and Matthew Bashton
Abstract: In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1.177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.
Published: 2022

9. Slowly declining growth rates and dynamic reporting delays characterise the Monkeypox epidemic in the UK over May-August 2022

Author: Jasmina Panovska-Griffiths, Robert Hinch, Josie Park, Thomas Ward, Andre Charlett, Fergus Cumming, Nicholas Watkins, and Christophe Fraser
Abstract: The monkeypox epidemic in the UK began in May 2022, and subsequently and rather quickly, rates of new cases have declined during August 2022. Identifying the causes of this decline requires accurate estimates of the time-varying epidemic growth rate r(t), which in turn depend upon the reporting delays (defined as the time from onset of symptoms to presenting to healthcare). Using a custom nowcasting method which allows for time-varying delays (EpiLine), we show that the reporting delay for Monkeypox in the UK decreased from an average of 22 days in early May 2022 to 10 days by early June and 7 days in August 2022. Accounting for these dynamic delays shows that the time-varying r(t) declined gradually in the UK over this period. Not accounting for varying time delays would have incorrectly characterised r(t) by a sharp increase followed by a rapid drop. We discuss the importance of this gradual decline, which helps identify the potential mechanisms responsible for the decline in the rate of spread of Monkeypox, which was gradual and started well before vaccines were widely used.
Published: 2022

10. The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

Author: Katrina Lythgoe, Matthew Hall, Gregory Young, Andrew Nelson, Lele Zhao, Christophe Fraser, Tanya Golubchik, Luca Ferretti, Darren Smith, Matthew Bashton, Mariateresa De Cesare, and Consortium, COVID-19 Genomics UK (COG-UK)
Subjects: General Immunology and Microbiology, SARS-CoV-2, Mutation, Humans, RNA, Viral, COVID-19, Genome, Viral, Genomics, General Medicine, General Agricultural and Biological Sciences, General Biochemistry, Genetics and Molecular Biology, General Environmental Science
Abstract: The raw material for viral evolution is provided by intra-host mutations occurring during replication, transcription or post-transcription. Replication and transcription of Coronaviridae proceed through the synthesis of negative-sense ‘antigenomes’ acting as templates for positive-sense genomic and subgenomic RNA. Hence, mutations in the genomes of SARS-CoV-2 and other coronaviruses can occur during (and after) the synthesis of either negative-sense or positive-sense RNA, with potentially distinct patterns and consequences. We explored for the first time the mutational spectrum of SARS-CoV-2 (sub)genomic and anti(sub)genomic RNA. We use a high-quality deep sequencing dataset produced using a quantitative strand-aware sequencing method, controlled for artefacts and sequencing errors, and scrutinized for accurate detection of within-host diversity. The nucleotide differences between negative- and positive-sense strand consensus vary between patients and do not show dependence on age or sex. Similarities and differences in mutational patterns between within-host minor variants on the two RNA strands suggested strand-specific mutations or editing by host deaminases and oxidative damage. We observe generally neutral and slight negative selection on the negative strand, contrasting with purifying selection in ORF1a, ORF1b and S genes of the positive strand of the genome.
Published: 2022

11. Limited emergence of resistance to Integrase strand transfer inhibitors (INSTIs) in HIV-experienced patients failing dolutegravir-based antiretroviral therapy: Cross-sectional analysis from a Northeast Nigerian cohort

Author: Adam Abdullahi, Ibrahim Musa Kida, Umar Abdullahi Maina, Amina Husaini Ibrahim, James Mshelia, Haruna Wisso, Abdullahi Adamu, James Ezenwa Onyemata, Haruna Yusuph, Sani H. Aliyu, Man Charurat, Alash’le Abimiku, Lucie Abeler-Dorner, Christophe Fraser, David Bonsall, Steven A. Kemp, and Ravindra K. Gupta
Abstract: BackgroundOwing to high levels of resistance to previous first-line non-nucleoside reverse transcriptase inhibitors (NNRTI)-based antiretroviral therapy (ART), consolidated recommendations since 2019, from the WHO and others, have indicated that dolutegravir (DTG) is the preferred drug of choice for HIV treatment, globally. There is a paucity of resistance outcome data from non-B HIV subtypes circulating across West Africa.AimWe aimed to characterise the mutational profiles of HIV-positive patients from a small North-East Nigeria cohort, failing a DTG-based ART regimen.MethodsPlasma samples were collected and stored from 61 HIV-1 infected participants. Following failure of DTG-based ART, all samples were sequenced by Illumina whole-genome, ultra-deep sequencing. Sequencing was successful in (n=33) participants with median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. Haplotype reconstruction and transmission were inferred using standard phylogenetic methods.ResultMost patients had mutational profiles that were reflective of prior exposure to first- and second-line ART including exposure to thymidine analogues, efavirenz and nevirapine. One patient had evidence of major INSTI DRMs (T66A, G118R, E138K and R263K), reducing efficacy of DTG. The participant was aged 18, infected with a subtype G virus and likely vertically infected.ConclusionThis study found low level resistance to DTG in the cohort, with one patient having high-level resistance to DTG and other INSTIs. Critical population level and long-term data on DTG outcomes are required to guide implementation and policy action across the region.
Published: 2022

12. EpiBeds: Data informed modelling of the COVID-19 hospital burden in England

Author: Christopher E. Overton, Lorenzo Pellis, Helena B. Stage, Francesca Scarabel, Joshua Burton, Christophe Fraser, Ian Hall, Thomas A. House, Chris Jewell, Anel Nurtay, Filippo Pagani, Katrina A. Lythgoe, Overton, Christopher E [0000-0002-8433-4010], Stage, Helena B [0000-0001-9938-8452], Scarabel, Francesca [0000-0003-0250-4555], Burton, Joshua [0000-0001-8530-0464], Nurtay, Anel [0000-0001-7107-1656], and Apollo - University of Cambridge Repository
Subjects: FOS: Computer and information sciences, FOS: Physical sciences, Statistics - Applications, Cellular and Molecular Neuroscience, Genetics, Humans, Applications (stat.AP), Quantitative Biology - Populations and Evolution, Molecular Biology, Pandemics, Ecology, Evolution, Behavior and Systematics, Medicine and health sciences, Ecology, Biology and life sciences, Populations and Evolution (q-bio.PE), COVID-19, Hospitals, Research and analysis methods, Physical sciences, Hospitalization, Computational Theory and Mathematics, England, FOS: Biological sciences, Modeling and Simulation, People and places, Research Article
Abstract: Acknowledgements: The authors would like to thank colleagues in SPI-M-O and JUNIPER consortium for various discussions around hospital modelling and forecasting., Funder: National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Emergency Preparedness and Response, Funder: Li Ka Shing Foundation; funder-id: http://dx.doi.org/10.13039/100007421, Funder: National Institute for Health Research Policy Research Programme in Operational Research (OPERA), The first year of the COVID-19 pandemic put considerable strain on healthcare systems worldwide. In order to predict the effect of the local epidemic on hospital capacity in England, we used a variety of data streams to inform the construction and parameterisation of a hospital progression model, EpiBeds, which was coupled to a model of the generalised epidemic. In this model, individuals progress through different pathways (e.g. may recover, die, or progress to intensive care and recover or die) and data from a partially complete patient-pathway line-list was used to provide initial estimates of the mean duration that individuals spend in the different hospital compartments. We then fitted EpiBeds using complete data on hospital occupancy and hospital deaths, enabling estimation of the proportion of individuals that follow the different clinical pathways, the reproduction number of the generalised epidemic, and to make short-term predictions of hospital bed demand. The construction of EpiBeds makes it straightforward to adapt to different patient pathways and settings beyond England. As part of the UK response to the pandemic, EpiBeds provided weekly forecasts to the NHS for hospital bed occupancy and admissions in England, Wales, Scotland, and Northern Ireland at national and regional scales.
Published: 2022

13. Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models

Author: Robert, Hinch, Jasmina, Panovska-Griffiths, William J M, Probert, Luca, Ferretti, Chris, Wymant, Francesco, Di Lauro, Nikolas, Baya, Mahan, Ghafari, Lucie, Abeler-Dörner, and Christophe, Fraser
Subjects: SARS-CoV-2, General Mathematics, Communicable Disease Control, General Engineering, COVID-19, Humans, General Physics and Astronomy, Seasons
Abstract: The SARS-CoV-2 epidemic has been extended by the evolution of more transmissible viral variants. In autumn 2020, the B.1.177 lineage became the dominant variant in England, before being replaced by the B.1.1.7 (Alpha) lineage in late 2020, with the sweep occurring at different times in each region. This period coincided with a large number of non-pharmaceutical interventions (e.g. lockdowns) to control the epidemic, making it difficult to estimate the relative transmissibility of variants. In this paper, we model the spatial spread of these variants in England using a meta-population agent-based model which correctly characterizes the regional variation in cases and distribution of variants. As a test of robustness, we additionally estimated the relative transmissibility of multiple variants using a statistical model based on the renewal equation, which simultaneously estimates the effective reproduction number R . Relative to earlier variants, the transmissibility of B.1.177 is estimated to have increased by 1.14 (1.12–1.16) and that of Alpha by 1.71 (1.65–1.77). The vaccination programme starting in December 2020 is also modelled. Counterfactual simulations demonstrate that the vaccination programme was essential for reopening in March 2021, and that if the January lockdown had started one month earlier, up to 30 k (24 k–38 k) deaths could have been prevented. This article is part of the theme issue ‘Technical challenges of modelling real-life epidemics and examples of overcoming these’.
Published: 2022

14. Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam

Author: Alexandra, Blenkinsop, Mélodie, Monod, Ard, van Sighem, Nikos, Pantazis, Daniela, Bezemer, Eline, Op de Coul, Thijs, van de Laar, Christophe, Fraser, Maria, Prins, Peter, Reiss, Godelieve J, de Bree, Oliver, Ratmann, On Behalf Of Hiv Transmission Elimination AMsterdam H-Team Collaboration, Infectious diseases, AII - Infectious diseases, APH - Global Health, Global Health, APH - Aging & Later Life, and Stichting Aidsfonds
Subjects: Male, FOS: Computer and information sciences, Acquired Immunodeficiency Syndrome, General Immunology and Microbiology, General Neuroscience, evolutionary biology, Populations and Evolution (q-bio.PE), global health, Bayes Theorem, HIV Infections, General Medicine, 0601 Biochemistry and Cell Biology, Statistics - Applications, General Biochemistry, Genetics and Molecular Biology, FOS: Biological sciences, Humans, epidemiology, viruses, Applications (stat.AP), Cities, Homosexuality, Male, Quantitative Biology - Populations and Evolution, Phylogeny
Abstract: Background:More than 300 cities including the city of Amsterdam in the Netherlands have joined the UNAIDS Fast-Track Cities initiative, committing to accelerate their HIV response and end the AIDS epidemic in cities by 2030. To support this commitment, we aimed to estimate the number and proportion of Amsterdam HIV infections that originated within the city, from Amsterdam residents. We also aimed to estimate the proportion of recent HIV infections during the 5-year period 2014–2018 in Amsterdam that remained undiagnosed.Methods:We located diagnosed HIV infections in Amsterdam using postcode data (PC4) at time of registration in the ATHENA observational HIV cohort, and used HIV sequence data to reconstruct phylogeographically distinct, partially observed Amsterdam transmission chains. Individual-level infection times were estimated from biomarker data, and used to date the phylogenetically observed transmission chains as well as to estimate undiagnosed proportions among recent infections. A Bayesian Negative Binomial branching process model was used to estimate the number, size, and growth of the unobserved Amsterdam transmission chains from the partially observed phylogenetic data.Results:Between 1 January 2014 and 1 May 2019, there were 846 HIV diagnoses in Amsterdam residents, of whom 516 (61%) were estimated to have been infected in 2014–2018. The rate of new Amsterdam diagnoses since 2014 (104 per 100,000) remained higher than the national rates excluding Amsterdam (24 per 100,000), and in this sense Amsterdam remained a HIV hotspot in the Netherlands. An estimated 14% [12–16%] of infections in Amsterdan MSM in 2014–2018 remained undiagnosed by 1 May 2019, and 41% [35–48%] in Amsterdam heterosexuals, with variation by region of birth. An estimated 67% [60–74%] of Amsterdam MSM infections in 2014–2018 had an Amsterdam resident as source, and 56% [41–70%] in Amsterdam heterosexuals, with heterogeneity by region of birth. Of the locally acquired infections, an estimated 43% [37–49%] were in foreign-born MSM, 41% [35–47%] in Dutch-born MSM, 10% [6–18%] in foreign-born heterosexuals, and 5% [2–9%] in Dutch-born heterosexuals. We estimate the majority of Amsterdam MSM infections in 2014–2018 originated in transmission chains that pre-existed by 2014.Conclusions:This combined phylogenetic, epidemiologic, and modelling analysis in the UNAIDS Fast-Track City Amsterdam indicates that there remains considerable potential to prevent HIV infections among Amsterdam residents through city-level interventions. The burden of locally acquired infection remains concentrated in MSM, and both Dutch-born and foreign-born MSM would likely benefit most from intensified city-level interventions.Funding:This study received funding as part of the H-TEAM initiative from Aidsfonds (project number P29701). The H-TEAM initiative is being supported by Aidsfonds (grant number: 2013169, P29701, P60803), Stichting Amsterdam Dinner Foundation, Bristol-Myers Squibb International Corp. (study number: AI424-541), Gilead Sciences Europe Ltd (grant number: PA-HIV-PREP-16-0024), Gilead Sciences (protocol numbers: CO-NL-276-4222, CO-US-276-1712, CO-NL-985-6195), and M.A.C AIDS Fund.
Published: 2022

15. Cost and cost-effectiveness of a universal HIV testing and treatment intervention in Zambia and South Africa: evidence and projections from the HPTN 071 (PopART) trial

Author: Abigail Harper, Lawrence Mwenge, Katharina Hauck, Blia Yang, Ranjeeta Thomas, Michael Pickles, Rafael Sauter, Helen Ayles, Sian Floyd, Surya Singh, Ronelle Burger, William J. M. Probert, Sarah Kanema, Sarah Fidler, Nosivuyile Vanqa, Anne Cori, Kwame Shanaube, Mwelwa Phiri, Christophe Fraser, Richard J. Hayes, Deborah Donnell, Justin Bwalya, Peter Bock, Nomtha Bell-Mandla, Pepfar, NIAID, NIMH, NIDA, BMGF, Medical Research Council (MRC), National Institute for Health Research, Abdul Latif Jameel Foundation, and National Institutes of Health
Subjects: Anti-HIV Agents, Cost effectiveness, Cost-Benefit Analysis, Impact evaluation, 030231 tropical medicine, Population, Zambia, HPTN 071 (PopART) study team, Hiv testing, 1117 Public Health and Health Services, HIV Testing, South Africa, 03 medical and health sciences, 0302 clinical medicine, Acquired immunodeficiency syndrome (AIDS), Humans, Medicine, 030212 general & internal medicine, education, Cost database, education.field_of_study, business.industry, Incidence (epidemiology), Articles, General Medicine, medicine.disease, Treatment intervention, RA Public aspects of medicine, business, 0605 Microbiology, Demography
Abstract: Summary Background The HPTN 071 (PopART) trial showed that a combination HIV prevention package including universal HIV testing and treatment (UTT) reduced population-level incidence of HIV compared with standard care. However, evidence is scarce on the costs and cost-effectiveness of such an intervention. Methods Using an individual-based model, we simulated the PopART intervention and standard care with antiretroviral therapy (ART) provided according to national guidelines for the 21 trial communities in Zambia and South Africa (for all individuals aged >14 years), with model parameters and primary cost data collected during the PopART trial and from published sources. Two intervention scenarios were modelled: annual rounds of PopART from 2014 to 2030 (PopART 2014–30; as the UNAIDS Fast-Track target year) and three rounds of PopART throughout the trial intervention period (PopART 2014–17). For each country, we calculated incremental cost-effectiveness ratios (ICERs) as the cost per disability-adjusted life-year (DALY) and cost per HIV infection averted. Cost-effectiveness acceptability curves were used to indicate the probability of PopART being cost-effective compared with standard care at different thresholds of cost per DALY averted. We also assessed budget impact by projecting undiscounted costs of the intervention compared with standard care up to 2030. Findings During 2014–17, the mean cost per person per year of delivering home-based HIV counselling and testing, linkage to care, promotion of ART adherence, and voluntary medical male circumcision via community HIV care providers for the simulated population was US$6·53 (SD 0·29) in Zambia and US$7·93 (0·16) in South Africa. In the PopART 2014–30 scenario, median ICERs for PopART delivered annually until 2030 were $2111 (95% credible interval [CrI] 1827–2462) per HIV infection averted in Zambia and $3248 (2472–3963) per HIV infection averted in South Africa; and $593 (95% CrI 526–674) per DALY averted in Zambia and $645 (538–757) per DALY averted in South Africa. In the PopART 2014–17 scenario, PopART averted one infection at a cost of $1318 (1098–1591) in Zambia and $2236 (1601–2916) in South Africa, and averted one DALY at $258 (225–298) in Zambia and $326 (266–391) in South Africa, when outcomes were projected until 2030. The intervention had almost 100% probability of being cost-effective at thresholds greater than $700 per DALY averted in Zambia, and greater than $800 per DALY averted in South Africa, in the PopART 2014–30 scenario. Incremental programme costs for annual rounds until 2030 were $46·12 million (for a mean of 341 323 people) in Zambia and $30·24 million (for a mean of 165 852 people) in South Africa. Interpretation Combination prevention with universal home-based testing can be delivered at low annual cost per person but accumulates to a considerable amount when scaled for a growing population. Combination prevention including UTT is cost-effective at thresholds greater than $800 per DALY averted and can be an efficient strategy to reduce HIV incidence in high-prevalence settings. Funding US National Institutes of Health, President's Emergency Plan for AIDS Relief, International Initiative for Impact Evaluation, Bill & Melinda Gates Foundation.
Published: 2021

16. Author response for 'Symptom‐based case definitions for COVID‐19: Time and geographical variations for detection at hospital admission among 260,000 patients'

Author: null Joaquin Baruch, null Amanda Rojek, null Christiana Kartsonaki, null Bharath K. T. Vijayaraghavan, null Bronner P. Gonçalves, null Mark G. Pritchard, null Laura Merson, null Jake Dunning, null Matthew Hall, null Louise Sigfrid, null Barbara W. Citarella, null Srinivas Murthy, null Trokon O. Yeabah, null Piero Olliaro, null Ali Abbas, null Sheryl Ann Abdukahil, null Nurul Najmee Abdulkadir, null Ryuzo Abe, null Laurent Abel, null Lara Absil, null Subhash Acharya, null Andrew Acker, null Elisabeth Adam, null Diana Adrião, null Saleh Al Ageel, null Shakeel Ahmed, null Kate Ainscough, null Eka Airlangga, null Tharwat Aisa, null Ali Ait Hssain, null Younes Ait Tamlihat, null Takako Akimoto, null Ernita Akmal, null Eman Al Qasim, null Razi Alalqam, null Angela Alberti, null Tala Al‐dabbous, null Senthilkumar Alegesan, null Cynthia Alegre, null Marta Alessi, null Beatrice Alex, null Kévin Alexandre, null Abdulrahman Al‐Fares, null Huda Alfoudri, null Imran Ali, null Adam Ali, null Naseem Ali Shah, null Kazali Enagnon Alidjnou, null Jeffrey Aliudin, null Qabas Alkhafajee, null Clotilde Allavena, null Nathalie Allou, null Aneela Altaf, null João Alves, null Rita Alves, null João Melo Alves, null Maria Amaral, null Nur Amira, null Phoebe Ampaw, null Roberto Andini, null Claire Andréjak, null Andrea Angheben, null François Angoulvant, null Séverine Ansart, null Sivanesen Anthonidass, null Massimo Antonelli, null Carlos Alexandre Antunes de Brito, null Ardiyan Apriyana, null Yaseen Arabi, null Irene Aragao, null Carolline Araujo, null Antonio Arcadipane, null Patrick Archambault, null Lukas Arenz, null Jean‐Benoît Arlet, null Lovkesh Arora, null Rakesh Arora, null Elise Artaud‐Macari, null Diptesh Aryal, null Angel Asensio, null Muhammad Ashraf, null Namra Asif, null Mohammad Asim, null Jean Baptiste Assie, null Amirul Asyraf, null Anika Atique, null A. M. Udara Lakshan Attanyake, null Johann Auchabie, null Hugues Aumaitre, null Adrien Auvet, null Eyvind W. Axelsen, null Laurène Azemar, null Cecile Azoulay, null Benjamin Bach, null Delphine Bachelet, null Claudine Badr, null Roar Bævre‐Jensen, null Nadia Baig, null J. Kenneth Baillie, null J. Kevin Baird, null Erica Bak, null Agamemnon Bakakos, null Nazreen Abu Bakar, null Andriy Bal, null Mohanaprasanth Balakrishnan, null Valeria Balan, null Firouzé Bani‐Sadr, null Renata Barbalho, null Nicholas Yuri Barbosa, null Wendy S. Barclay, null Saef Umar Barnett, null Michaela Barnikel, null Helena Barrasa, null Audrey Barrelet, null Cleide Barrigoto, null Marie Bartoli, null Joaquín Baruch, null Mustehan Bashir, null Romain Basmaci, null Muhammad Fadhli Hassin Basri, null Denise Battaglini, null Jules Bauer, null Diego Fernando Bautista Rincon, null Denisse Bazan Dow, null Abigail Beane, null Alexandra Bedossa, null Ker Hong Bee, null Husna Begum, null Sylvie Behilill, null Albertus Beishuizen, null Aleksandr Beljantsev, null David Bellemare, null Anna Beltrame, null Beatriz Amorim Beltrão, null Marine Beluze, null Nicolas Benech, null Lionel Eric Benjiman, null Dehbia Benkerrou, null Suzanne Bennett, null Luís Bento, null Jan‐Erik Berdal, null Delphine Bergeaud, null Hazel Bergin, null José Luis Bernal Sobrino, null Giulia Bertoli, null Lorenzo Bertolino, null Simon Bessis, null Sybille Bevilcaqua, null Karine Bezulier, null Amar Bhatt, null Krishna Bhavsar, null Claudia Bianco, null Farah Nadiah Bidin, null Moirangthem Bikram Singh, null Felwa Bin Humaid, null Mohd Nazlin Bin Kamarudin, null François Bissuel, null Laurent Bitker, null Jonathan Bitton, null Pablo Blanco‐Schweizer, null Catherine Blier, null Frank Bloos, null Mathieu Blot, null Filomena Boccia, null Laetitia Bodenes, null Alice Bogaarts, null Debby Bogaert, null Anne‐Hélène Boivin, null Pierre‐Adrien Bolze, null François Bompart, null Aurelius Bonfasius, null Diogo Borges, null Raphaël Borie, null Hans Martin Bosse, null Elisabeth Botelho‐Nevers, null Lila Bouadma, null Olivier Bouchaud, null Sabelline Bouchez, null Dounia Bouhmani, null Damien Bouhour, null Kévin Bouiller, null Laurence Bouillet, null Camile Bouisse, null Anne‐Sophie Boureau, null John Bourke, null Maude Bouscambert, null Aurore Bousquet, null Jason Bouziotis, null Bianca Boxma, null Marielle Boyer‐Besseyre, null Maria Boylan, null Fernando Augusto Bozza, null Axelle Braconnier, null Cynthia Braga, null Timo Brandenburger, null Filipa Brás Monteiro, null Luca Brazzi, null Patrick Breen, null Dorothy Breen, null Kathy Brickell, null Shaunagh Browne, null Alex Browne, null Nicolas Brozzi, null Sonja Hjellegjerde Brunvoll, null Marjolein Brusse‐Keizer, null Nina Buchtele, null Christian Buesaquillo, null Polina Bugaeva, null Marielle Buisson, null Danilo Buonsenso, null Erlina Burhan, null Aidan Burrell, null Ingrid G. Bustos, null Denis Butnaru, null André Cabie, null Susana Cabral, null Eder Caceres, null Cyril Cadoz, null Kate Calligy, null Jose Andres Calvache, null João Camões, null Valentine Campana, null Paul Campbell, null Josie Campisi, null Cecilia Canepa, null Mireia Cantero, null Pauline Caraux‐Paz, null Sheila Cárcel, null Chiara Simona Cardellino, null Sofia Cardoso, null Filipe Cardoso, null Filipa Cardoso, null Nelson Cardoso, null Simone Carelli, null Nicolas Carlier, null Thierry Carmoi, null Gayle Carney, null Inês Carqueja, null Marie‐Christine Carret, null François Martin Carrier, null Ida Carroll, null Gail Carson, null Maire‐Laure Casanova, null Mariana Cascão, null Siobhan Casey, null José Casimiro, null Bailey Cassandra, null Silvia Castañeda, null Nidyanara Castanheira, null Guylaine Castor‐Alexandre, null Henry Castrillón, null Ivo Castro, null Ana Catarino, null François‐Xavier Catherine, null Paolo Cattaneo, null Roberta Cavalin, null Giulio Giovanni Cavalli, null Alexandros Cavayas, null Adrian Ceccato, null Minerva Cervantes‐Gonzalez, null Anissa Chair, null Catherine Chakveatze, null Adrienne Chan, null Meera Chand, null Christelle Chantalat Auger, null Jean‐Marc Chapplain, null Julie Chas, null Allegra Chatterjee, null Mobin Chaudry, null Jonathan Samuel Chávez Iñiguez, null Anjellica Chen, null Yih‐Sharng Chen, null Matthew Pellan Cheng, null Antoine Cheret, null Thibault Chiarabini, null Julian Chica, null Suresh Kumar Chidambaram, null Leong Chin Tho, null Catherine Chirouze, null Davide Chiumello, null Sung‐Min Cho, null Bernard Cholley, null Marie‐Charlotte Chopin, null Ting Soo Chow, null Yock Ping Chow, null Jonathan Chua, null Hiu Jian Chua, null Jose Pedro Cidade, null José Miguel Cisneros Herreros, null Barbara Wanjiru Citarella, null Anna Ciullo, null Jennifer Clarke, null Emma Clarke, null Rolando Claure‐Del Granado, null Sara Clohisey, null Perren J. Cobb, null Cassidy Codan, null Caitriona Cody, null Alexandra Coelho, null Megan Coles, null Gwenhaël Colin, null Michael Collins, null Sebastiano Maria Colombo, null Pamela Combs, null Marie Connor, null Anne Conrad, null Sofía Contreras, null Elaine Conway, null Graham S. Cooke, null Mary Copland, null Hugues Cordel, null Amanda Corley, null Sabine Cornelis, null Alexander Daniel Cornet, null Arianne Joy Corpuz, null Andrea Cortegiani, null Grégory Corvaisier, null Emma Costigan, null Camille Couffignal, null Sandrine Couffin‐Cadiergues, null Roxane Courtois, null Stéphanie Cousse, null Rachel Cregan, null Sabine Croonen, null Gloria Crowl, null Jonathan Crump, null Claudina Cruz, null Juan Luis Cruz Bermúdez, null Jaime Cruz Rojo, null Marc Csete, null Ailbhe Cullen, null Matthew Cummings, null Gerard Curley, null Elodie Curlier, null Colleen Curran, null Paula Custodio, null Ana da Silva Filipe, null Charlene Da Silveira, null Al‐Awwab Dabaliz, null Andrew Dagens, null John Arne Dahl, null Darren Dahly, null Heidi Dalton, null Jo Dalton, null Seamus Daly, null Nick Daneman, null Corinne Daniel, null Emmanuelle A. Dankwa, null Jorge Dantas, null Frédérick D'Aragon, null Gillian de Loughry, null Diego de Mendoza, null Etienne De Montmollin, null Rafael Freitas de Oliveira França, null Ana Isabel de Pinho Oliveira, null Rosanna De Rosa, null Cristina De Rose, null Thushan de Silva, null Peter de Vries, null Jillian Deacon, null David Dean, null Alexa Debard, null Marie‐Pierre Debray, null Nathalie DeCastro, null William Dechert, null Lauren Deconninck, null Romain Decours, null Eve Defous, null Isabelle Delacroix, null Eric Delaveuve, null Karen Delavigne, null Nathalie M. Delfos, null Ionna Deligiannis, null Andrea Dell'Amore, null Christelle Delmas, null Pierre Delobel, null Corine Delsing, null Elisa Demonchy, null Emmanuelle Denis, null Dominique Deplanque, null Pieter Depuydt, null Mehul Desai, null Diane Descamps, null Mathilde Desvallées, null Santi Dewayanti, null Pathik Dhanger, null Alpha Diallo, null Sylvain Diamantis, null André Dias, null Juan Jose Diaz, null Priscila Diaz, null Rodrigo Diaz, null Kévin Didier, null Jean‐Luc Diehl, null Wim Dieperink, null Jérôme Dimet, null Vincent Dinot, null Fara Diop, null Alphonsine Diouf, null Yael Dishon, null Félix Djossou, null Annemarie B. Docherty, null Helen Doherty, null Arjen M. Dondorp, null Maria Donnelly, null Christl A. Donnelly, null Sean Donohue, null Yoann Donohue, null Chloe Donohue, null Peter Doran, null Céline Dorival, null Eric D'Ortenzio, null James Joshua Douglas, null Renee Douma, null Nathalie Dournon, null Triona Downer, null Joanne Downey, null Mark Downing, null Tom Drake, null Aoife Driscoll, null Murray Dryden, null Claudio Duarte Fonseca, null Vincent Dubee, null François Dubos, null Alexandre Ducancelle, null Toni Duculan, null Susanne Dudman, null Abhijit Duggal, null Paul Dunand, null Mathilde Duplaix, null Emanuele Durante‐Mangoni, null Lucian Durham, null Bertrand Dussol, null Juliette Duthoit, null Xavier Duval, null Anne Margarita Dyrhol‐Riise, null Sim Choon Ean, null Marco Echeverria‐Villalobos, null Siobhan Egan, null Linn Margrete Eggesbø, null Carla Eira, null Mohammed El Sanharawi, null Subbarao Elapavaluru, null Brigitte Elharrar, null Jacobien Ellerbroek, null Merete Ellingjord‐Dale, null Philippine Eloy, null Tarek Elshazly, null Iqbal Elyazar, null Isabelle Enderle, null Tomoyuki Endo, null Chan Chee Eng, null Ilka Engelmann, null Vincent Enouf, null Olivier Epaulard, null Martina Escher, null Mariano Esperatti, null Hélène Esperou, null Marina Esposito‐Farese, null João Estevão, null Manuel Etienne, null Nadia Ettalhaoui, null Anna Greti Everding, null Mirjam Evers, null Marc Fabre, null Isabelle Fabre, null Amna Faheem, null Arabella Fahy, null Cameron J. Fairfield, null Zul Fakar, null Komal Fareed, null Pedro Faria, null Ahmed Farooq, null Hanan Fateena, null Arie Zainul Fatoni, null Karine Faure, null Raphaël Favory, null Mohamed Fayed, null Niamh Feely, null Laura Feeney, null Jorge Fernandes, null Marília Andreia Fernandes, null Susana Fernandes, null François‐Xavier Ferrand, null Eglantine Ferrand Devouge, null Joana Ferrão, null Mário Ferraz, null Sílvia Ferreira, null Isabel Ferreira, null Benigno Ferreira, null Ricard Ferrer‐Roca, null Nicolas Ferriere, null Céline Ficko, null Claudia Figueiredo‐Mello, null William Finlayson, null Juan Fiorda, null Thomas Flament, null Clara Flateau, null Tom Fletcher, null Letizia Lucia Florio, null Deirdre Flynn, null Claire Foley, null Jean Foley, null Victor Fomin, null Tatiana Fonseca, null Patricia Fontela, null Simon Forsyth, null Denise Foster, null Giuseppe Foti, null Erwan Fourn, null Robert A. Fowler, null Marianne Fraher, null Diego Franch‐Llasat, null John F. Fraser, null Christophe Fraser, null Marcela Vieira Freire, null Ana Freitas Ribeiro, null Caren Friedrich, null Stéphanie Fry, null Nora Fuentes, null Masahiro Fukuda, null G. Argin, null Valérie Gaborieau, null Rostane Gaci, null Massimo Gagliardi, null Jean‐Charles Gagnard, null Amandine Gagneux‐Brunon, null Sérgio Gaião, null Linda Gail Skeie, null Phil Gallagher, null Carrol Gamble, null Yasmin Gani, null Arthur Garan, null Rebekha Garcia, null Noelia García Barrio, null Julia Garcia‐Diaz, null Esteban Garcia‐Gallo, null Navya Garimella, null Denis Garot, null Valérie Garrait, null Basanta Gauli, null Nathalie Gault, null Aisling Gavin, null Anatoliy Gavrylov, null Alexandre Gaymard, null Johannes Gebauer, null Eva Geraud, null Louis Gerbaud Morlaes, null Nuno Germano, null Praveen Kumar Ghisulal, null Jade Ghosn, null Marco Giani, null Jess Gibson, null Tristan Gigante, null Morgane Gilg, null Elaine Gilroy, null Guillermo Giordano, null Michelle Girvan, null Valérie Gissot, null Daniel Glikman, null Petr Glybochko, null Eric Gnall, null Geraldine Goco, null François Goehringer, null Siri Goepel, null Jean‐Christophe Goffard, null Jin Yi Goh, null Jonathan Golob, null Kyle Gomez, null Joan Gómez‐Junyent, null Marie Gominet, null Alicia Gonzalez, null Patricia Gordon, null Isabelle Gorenne, null Laure Goubert, null Cécile Goujard, null Tiphaine Goulenok, null Margarite Grable, null Jeronimo Graf, null Edward Wilson Grandin, null Pascal Granier, null Giacomo Grasselli, null Christopher A. Green, null Courtney Greene, null William Greenhalf, null Segolène Greffe, null Domenico Luca Grieco, null Matthew Griffee, null Fiona Griffiths, null Ioana Grigoras, null Albert Groenendijk, null Anja Grosse Lordemann, null Heidi Gruner, null Yusing Gu, null Jérémie Guedj, null Martin Guego, null Dewi Guellec, null Anne‐Marie Guerguerian, null Daniela Guerreiro, null Romain Guery, null Anne Guillaumot, null Laurent Guilleminault, null Maisa Guimarães de Castro, null Thomas Guimard, null Marieke Haalboom, null Daniel Haber, null Hannah Habraken, null Ali Hachemi, null Amy Hackmann, null Nadir Hadri, null Fakhir Haidri, null Sheeba Hakak, null Adam Hall, null Sophie Halpin, null Jawad Hameed, null Ansley Hamer, null Raph L. Hamers, null Rebecca Hamidfar, null Bato Hammarström, null Terese Hammond, null Lim Yuen Han, null Rashan Haniffa, null Kok Wei Hao, null Hayley Hardwick, null Ewen M. Harrison, null Janet Harrison, null Samuel Bernard Ekow Harrison, null Alan Hartman, null Mohd Shahnaz Hasan, null Junaid Hashmi, null Muhammad Hayat, null Ailbhe Hayes, null Leanne Hays, null Jan Heerman, null Lars Heggelund, null Ross Hendry, null Martina Hennessy, null Aquiles Henriquez‐Trujillo, null Maxime Hentzien, null Jaime Hernandez‐Montfort, null Andrew Hershey, null Liv Hesstvedt, null Astarini Hidayah, null Eibhilin Higgins, null Dawn Higgins, null Rupert Higgins, null Rita Hinchion, null Samuel Hinton, null Hiroaki Hiraiwa, null Haider Hirkani, null Hikombo Hitoto, null Yi Bin Ho, null Antonia Ho, null Alexandre Hoctin, null Isabelle Hoffmann, null Wei Han Hoh, null Oscar Hoiting, null Rebecca Holt, null Jan Cato Holter, null Peter Horby, null Juan Pablo Horcajada, null Koji Hoshino, null Ikram Houas, null Catherine L. Hough, null Stuart Houltham, null Jimmy Ming‐Yang Hsu, null Jean‐Sébastien Hulot, null Stella Huo, null Abby Hurd, null Iqbal Hussain, null Samreen Ijaz, null Hajnal‐Gabriela Illes, null Patrick Imbert, null Mohammad Imran, null Rana Imran Sikander, null Aftab Imtiaz, null Hugo Inácio, null Carmen Infante Dominguez, null Yun Sii Ing, null Elias Iosifidis, null Mariachiara Ippolito, null Sarah Isgett, null Tiago Isidoro, null Nadiah Ismail, null Margaux Isnard, null Mette Stausland Istre, null Junji Itai, null Daniel Ivulich, null Danielle Jaafar, null Salma Jaafoura, null Julien Jabot, null Clare Jackson, null Nina Jamieson, null Pierre Jaquet, null Coline Jaud‐Fischer, null Stéphane Jaureguiberry, null Denise Jaworsky, null Florence Jego, null Anilawati Mat Jelani, null Synne Jenum, null Ruth Jimbo‐Sotomayor, null Ong Yiaw Joe, null Ruth N. Jorge García, null Silje Bakken Jørgensen, null Cédric Joseph, null Mark Joseph, null Swosti Joshi, null Mercé Jourdain, null Philippe Jouvet, null Hanna Jung, null Anna Jung, null Dafsah Juzar, null Ouifiya Kafif, null Florentia Kaguelidou, null Neerusha Kaisbain, null Thavamany Kaleesvran, null Sabina Kali, null Alina Kalicinska, null Karl Trygve Kalleberg, null Smaragdi Kalomoiri, null Muhammad Aisar Ayadi Kamaluddin, null Zul Amali Che Kamaruddin, null Nadiah Kamarudin, null Kavita Kamineni, null Darshana Hewa Kandamby, null Chris Kandel, null Kong Yeow Kang, null Darakhshan Kanwal, null Pratap Karpayah, null Daisuke Kasugai, null Anant Kataria, null Kevin Katz, null Aasmine Kaur, null Christy Kay, null Hannah Keane, null Seán Keating, null Pulak Kedia, null Claire Kelly, null Yvelynne Kelly, null Andrea Kelly, null Niamh Kelly, null Aoife Kelly, null Sadie Kelly, null Maeve Kelsey, null Ryan Kennedy, null Kalynn Kennon, null Maeve Kernan, null Younes Kerroumi, null Sharma Keshav, null Imrana Khalid, null Osama Khalid, null Antoine Khalil, null Coralie Khan, null Irfan Khan, null Quratul Ain Khan, null Sushil Khanal, null Abid Khatak, null Amin Khawaja, null Krish Kherajani, null Michelle E. Kho, null Ryan Khoo, null Denisa Khoo, null Saye Khoo, null Nasir Khoso, null Khor How Kiat, null Yuri Kida, null Peter Kiiza, null Beathe Kiland Granerud, null Anders Benjamin Kildal, null Jae Burm Kim, null Antoine Kimmoun, null Detlef Kindgen‐Milles, null Alexander King, null Nobuya Kitamura, null Eyrun Floerecke Kjetland Kjetland, null Paul Klenerman, null Rob Klont, null Gry Kloumann Bekken, null Stephen R. Knight, null Robin Kobbe, null Chamira Kodippily, null Malte Kohns Vasconcelos, null Sabin Koirala, null Mamoru Komatsu, null Caroline Kosgei, null Arsène Kpangon, null Karolina Krawczyk, null Vinothini Krishnan, null Sudhir Krishnan, null Oksana Kruglova, null Ganesh Kumar, null Deepali Kumar, null Mukesh Kumar, null Pavan Kumar Vecham, null Dinesh Kuriakose, null Ethan Kurtzman, null Demetrios Kutsogiannis, null Galyna Kutsyna, null Konstantinos Kyriakoulis, null Marie Lachatre, null Marie Lacoste, null John G. Laffey, null Marie Lagrange, null Fabrice Laine, null Olivier Lairez, null Sanjay Lakhey, null Antonio Lalueza, null Marc Lambert, null François Lamontagne, null Marie Langelot‐Richard, null Vincent Langlois, null Eka Yudha Lantang, null Marina Lanza, null Cédric Laouénan, null Samira Laribi, null Delphine Lariviere, null Stéphane Lasry, null Sakshi Lath, null Naveed Latif, null Odile Launay, null Didier Laureillard, null Yoan Lavie‐Badie, null Andy Law, null Teresa Lawrence, null Cassie Lawrence, null Minh Le, null Clément Le Bihan, null Cyril Le Bris, null Georges Le Falher, null Lucie Le Fevre, null Quentin Le Hingrat, null Marion Le Maréchal, null Soizic Le Mestre, null Gwenaël Le Moal, null Vincent Le Moing, null Hervé Le Nagard, null Paul Le Turnier, null Ema Leal, null Marta Leal Santos, null Heng Gee Lee, null Biing Horng Lee, null Yi Lin Lee, null Todd C. Lee, null James Lee, null Jennifer Lee, null Su Hwan Lee, null Gary Leeming, null Laurent Lefebvre, null Bénédicte Lefebvre, null Benjamin Lefèvre, null Sylvie LeGac, null Jean‐Daniel Lelievre, null François Lellouche, null Adrien Lemaignen, null Véronique Lemee, null Anthony Lemeur, null Gretchen Lemmink, null Ha Sha Lene, null Jenny Lennon, null Rafael León, null Marc Leone, null Michela Leone, null Quentin Lepiller, null François‐Xavier Lescure, null Olivier Lesens, null Mathieu Lesouhaitier, null Amy Lester‐Grant, null Yves Levy, null Bruno Levy, null Claire Levy‐Marchal, null Katarzyna Lewandowska, null Erwan L'Her, null Gianluigi Li Bassi, null Janet Liang, null Ali Liaquat, null Geoffrey Liegeon, null Kah Chuan Lim, null Wei Shen Lim, null Chantre Lima, null Lim Lina, null Bruno Lina, null Andreas Lind, null Maja Katherine Lingad, null Guillaume Lingas, null Sylvie Lion‐Daolio, null Samantha Lissauer, null Keibun Liu, null Marine Livrozet, null Patricia Lizotte, null Antonio Loforte, null Navy Lolong, null Leong Chee Loon, null Diogo Lopes, null Dalia Lopez‐Colon, null Jose W. Lopez‐Revilla, null Anthony L. Loschner, null Paul Loubet, null Bouchra Loufti, null Guillame Louis, null Silvia Lourenco, null Lara Lovelace‐Macon, null Lee Lee Low, null Marije Lowik, null Jia Shyi Loy, null Jean Christophe Lucet, null Carlos Lumbreras Bermejo, null Carlos M. Luna, null Olguta Lungu, null Liem Luong, null Nestor Luque, null Dominique Luton, null Nilar Lwin, null Ruth Lyons, null Olavi Maasikas, null Oryane Mabiala, null Moïse Machado, null Gabriel Macheda, null Hashmi Madiha, null Guillermo Maestro de la Calle, null Rafael Mahieu, null Sophie Mahy, null Ana Raquel Maia, null Lars S. Maier, null Mylène Maillet, null Thomas Maitre, null Maximilian Malfertheiner, null Nadia Malik, null Paddy Mallon, null Fernando Maltez, null Denis Malvy, null Victoria Manda, null Laurent Mandelbrot, null Frank Manetta, null Julie Mankikian, null Edmund Manning, null Aldric Manuel, null Ceila Maria Sant'Ana Malaque, null Flávio Marino, null Daniel Marino, null Samuel Markowicz, null Charbel Maroun Eid, null Ana Marques, null Catherine Marquis, null Brian Marsh, null Laura Marsh, null Megan Marshal, null John Marshall, null Celina Turchi Martelli, null Dori‐Ann Martin, null Emily Martin, null Guillaume Martin‐Blondel, null Ignacio Martin‐Loeches, null Martin Martinot, null Alejandro Martin‐Quiros, null João Martins, null Ana Martins, null Nuno Martins, null Caroline Martins Rego, null Gennaro Martucci, null Olga Martynenko, null Eva Miranda Marwali, null Marsilla Marzukie, null David Maslove, null Sabina Mason, null Sobia Masood, null Basri Mat Nor, null Moshe Matan, null Meghena Mathew, null Daniel Mathieu, null Mathieu Mattei, null Romans Matulevics, null Laurence Maulin, null Michael Maxwell, null Javier Maynar, null Thierry Mazzoni, null Natalie Mc Evoy, null Lisa Mc Sweeney, null Colin McArthur, null Anne McCarthy, null Aine McCarthy, null Colin McCloskey, null Rachael McConnochie, null Sherry McDermott, null Sarah E. McDonald, null Aine McElroy, null Samuel McElwee, null Victoria McEneany, null Allison McGeer, null Chris McKay, null Johnny McKeown, null Kenneth A. McLean, null Paul McNally, null Bairbre McNicholas, null Elaine McPartlan, null Edel Meaney, null Cécile Mear‐Passard, null Maggie Mechlin, null Maqsood Meher, null Omar Mehkri, null Ferruccio Mele, null Luis Melo, null Kashif Memon, null Joao Joao Mendes, null Ogechukwu Menkiti, null Kusum Menon, null France Mentré, null Alexander J. Mentzer, null Noémie Mercier, null Emmanuelle Mercier, null Antoine Merckx, null Mayka Mergeay‐Fabre, null Blake Mergler, null António Mesquita, null Roberta Meta, null Osama Metwally, null Agnès Meybeck, null Dan Meyer, null Alison M. Meynert, null Vanina Meysonnier, null Amina Meziane, null Mehdi Mezidi, null Céline Michelanglei, null Isabelle Michelet, null Efstathia Mihelis, null Vladislav Mihnovit, null Hugo Miranda‐Maldonado, null Nor Arisah Misnan, null Tahira Jamal Mohamed, null Nik Nur Eliza Mohamed, null Asma Moin, null David Molina, null Elena Molinos, null Brenda Molloy, null Mary Mone, null Agostinho Monteiro, null Claudia Montes, null Giorgia Montrucchio, null Shona C. Moore, null Sarah Moore, null Lina Morales Cely, null Lucia Moro, null Ben Morton, null Catherine Motherway, null Ana Motos, null Hugo Mouquet, null Clara Mouton Perrot, null Julien Moyet, null Caroline Mudara, null Aisha Kalsoom Mufti, null Ng Yong Muh, null Dzawani Muhamad, null Jimmy Mullaert, null Fredrik Müller, null Karl Erik Müller, null Daniel Munblit, null Syed Muneeb, null Nadeem Munir, null Laveena Munshi, null Aisling Murphy, null Lorna Murphy, null Marlène Murris, null Himed Musaab, null Himasha Muvindi, null Gugapriyaa Muyandy, null Dimitra Melia Myrodia, null Farah Nadia Mohd‐Hanafiah, null Dave Nagpal, null Alex Nagrebetsky, null Mangala Narasimhan, null Nageswaran Narayanan, null Rashid Nasim Khan, null Alasdair Nazerali‐Maitland, null Nadège Neant, null Holger Neb, null Nikita Nekliudov, null Erni Nelwan, null Raul Neto, null Emily Neumann, null Pauline Yeung Ng, null Wing Yiu Ng, null Anthony Nghi, null Duc Nguyen, null Orna Ni Choileain, null Niamh Ni Leathlobhair, null Alistair Nichol, null Prompak Nitayavardhana, null Stephanie Nonas, null Nurul Amani Mohd Noordin, null Marion Noret, null Nurul Faten Izzati Norharizam, null Lisa Norman, null Alessandra Notari, null Mahdad Noursadeghi, null Karolina Nowicka, null Adam Nowinski, null Saad Nseir, null Jose I. Nunez, null Nurnaningsih Nurnaningsih, null Dwi Utomo Nusantara, null Elsa Nyamankolly, null Anders Benteson Nygaard, null Fionnuala O. Brien, null Annmarie O. Callaghan, null Annmarie O'Callaghan, null Giovanna Occhipinti, null Derbrenn OConnor, null Max O'Donnell, null Tawnya Ogston, null Takayuki Ogura, null Tak‐Hyuk Oh, null Sophie O'Halloran, null Katie O'Hearn, null Shinichiro Ohshimo, null Agnieszka Oldakowska, null João Oliveira, null Larissa Oliveira, null Piero L. Olliaro, null Jee Yan Ong, null David S. Y. Ong, null Wilna Oosthuyzen, null Anne Opavsky, null Peter Openshaw, null Saijad Orakzai, null Claudia Milena Orozco‐Chamorro, null Jamel Ortoleva, null Javier Osatnik, null Linda O'Shea, null Miriam O'Sullivan, null Siti Zubaidah Othman, null Nadia Ouamara, null Rachida Ouissa, null Eric Oziol, null Maïder Pagadoy, null Justine Pages, null Mario Palacios, null Amanda Palacios, null Massimo Palmarini, null Giovanna Panarello, null Prasan Kumar Panda, null Hem Paneru, null Lai Hui Pang, null Mauro Panigada, null Nathalie Pansu, null Aurélie Papadopoulos, null Rachael Parke, null Melissa Parker, null Briseida Parra, null Taha Pasha, null Jérémie Pasquier, null Bruno Pastene, null Fabian Patauner, null Drashti Patel, null Mohan Dass Pathmanathan, null Luís Patrão, null Patricia Patricio, null Juliette Patrier, null Lisa Patterson, null Rajyabardhan Pattnaik, null Mical Paul, null Christelle Paul, null Jorge Paulos, null William A. Paxton, null Jean‐François Payen, null Kalaiarasu Peariasamy, null Miguel Pedrera Jiménez, null Giles J. Peek, null Florent Peelman, null Nathan Peiffer‐Smadja, null Vincent Peigne, null Mare Pejkovska, null Paolo Pelosi, null Ithan D. Peltan, null Rui Pereira, null Daniel Perez, null Luis Periel, null Thomas Perpoint, null Antonio Pesenti, null Vincent Pestre, null Lenka Petrou, null Michele Petrovic, null Ventzislava Petrov‐Sanchez, null Frank Olav Pettersen, null Gilles Peytavin, null Scott Pharand, null Walter Picard, null Olivier Picone, null Maria de Piero, null Carola Pierobon, null Djura Piersma, null Carlos Pimentel, null Raquel Pinto, null Catarina Pires, null Isabelle Pironneau, null Lionel Piroth, null Ayodhia Pitaloka, null Riinu Pius, null Laurent Plantier, null Hon Shen Png, null Julien Poissy, null Ryadh Pokeerbux, null Maria Pokorska‐Spiewak, null Sergio Poli, null Georgios Pollakis, null Diane Ponscarme, null Jolanta Popielska, null Diego Bastos Porto, null Andra‐Maris Post, null Douwe F. Postma, null Pedro Povoa, null Diana Póvoas, null Jeff Powis, null Sofia Prapa, null Sébastien Preau, null Christian Prebensen, null Jean‐Charles Preiser, null Anton Prinssen, null Gamage Dona Dilanthi Priyadarshani, null Lucia Proença, null Sravya Pudota, null Oriane Puéchal, null Bambang Pujo Semedi, null Mathew Pulicken, null Gregory Purcell, null Luisa Quesada, null Vilmaris Quinones‐Cardona, null Víctor Quirós González, null Else Quist‐Paulsen, null Mohammed Quraishi, null Maia Rabaa, null Christian Rabaud, null Ebenezer Rabindrarajan, null Aldo Rafael, null Marie Rafiq, null Mutia Rahardjani, null Rozanah Abd Rahman, null Ahmad Kashfi Haji Ab Rahman, null Arsalan Rahutullah, null Fernando Rainieri, null Giri Shan Rajahram, null Pratheema Ramachandran, null Nagarajan Ramakrishnan, null Ahmad Afiq Ramli, null Blandine Rammaert, null Grazielle Viana Ramos, null Asim Rana, null Rajavardhan Rangappa, null Ritika Ranjan, null Christophe Rapp, null Aasiyah Rashan, null Thalha Rashan, null Ghulam Rasheed, null Menaldi Rasmin, null Indrek Rätsep, null Cornelius Rau, null Tharmini Ravi, null Ali Raza, null Andre Real, null Stanislas Rebaudet, null Sarah Redl, null Brenda Reeve, null Attaur Rehman, null Liadain Reid, null Dag Henrik Reikvam, null Renato Reis, null Jordi Rello, null Jonathan Remppis, null Martine Remy, null Hongru Ren, null Hanna Renk, null Anne‐Sophie Resseguier, null Matthieu Revest, null Oleksa Rewa, null Luis Felipe Reyes, null Tiago Reyes, null Maria Ines Ribeiro, null Antonia Ricchiuto, null David Richardson, null Denise Richardson, null Laurent Richier, null Siti Nurul Atikah Ahmad Ridzuan, null Jordi Riera, null Ana L. Rios, null Asgar Rishu, null Patrick Rispal, null Karine Risso, null Maria Angelica Rivera Nuñez, null Nicholas Rizer, null Chiara Robba, null André Roberto, null Stephanie Roberts, null David L. Robertson, null Olivier Robineau, null Ferran Roche‐Campo, null Paola Rodari, null Simão Rodeia, null Julia Rodriguez Abreu, null Bernhard Roessler, null Pierre‐Marie Roger, null Claire Roger, null Emmanuel Roilides, null Juliette Romaru, null Roberto Roncon‐Albuquerque, null Mélanie Roriz, null Manuel Rosa‐Calatrava, null Michael Rose, null Dorothea Rosenberger, null Nurul Hidayah Mohammad Roslan, null Andrea Rossanese, null Matteo Rossetti, null Bénédicte Rossignol, null Patrick Rossignol, null Stella Rousset, null Carine Roy, null Benoît Roze, null Desy Rusmawatiningtyas, null Clark D. Russell, null Maria Ryan, null Maeve Ryan, null Steffi Ryckaert, null Aleksander Rygh Holten, null Isabela Saba, null Sairah Sadaf, null Musharaf Sadat, null Valla Sahraei, null Maximilien Saint‐Gilles, null Pranya Sakiyalak, null Nawal Salahuddin, null Leonardo Salazar, null Jodat Saleem, null Gabriele Sales, null Stéphane Sallaberry, null Charlotte Salmon Gandonniere, null Hélène Salvator, null Olivier Sanchez, null Angel Sanchez‐Miralles, null Vanessa Sancho‐Shimizu, null Gyan Sandhu, null Zulfiqar Sandhu, null Pierre‐François Sandrine, null Oana Sandulescu, null Marlene Santos, null Shirley Sarfo‐Mensah, null Bruno Sarmento Banheiro, null Iam Claire E. Sarmiento, null Benjamine Sarton, null Ankana Satya, null Sree Satyapriya, null Rumaisah Satyawati, null Egle Saviciute, null Parthena Savvidou, null Yen Tsen Saw, null Justin Schaffer, null Tjard Schermer, null Arnaud Scherpereel, null Marion Schneider, null Stephan Schroll, null Michael Schwameis, null Gary Schwartz, null Janet T. Scott, null James Scott‐Brown, null Nicholas Sedillot, null Tamara Seitz, null Jaganathan Selvanayagam, null Mageswari Selvarajoo, null Caroline Semaille, null Malcolm G. Semple, null Rasidah Bt Senian, null Eric Senneville, null Filipa Sequeira, null Tânia Sequeira, null Ary Serpa Neto, null Pablo Serrano Balazote, null Ellen Shadowitz, null Syamin Asyraf Shahidan, null Mohammad Shamsah, null Anuraj Shankar, null Shaikh Sharjeel, null Pratima Sharma, null Catherine A. Shaw, null Victoria Shaw, null Ashraf Sheharyar, null Rohan Shetty, null Rajesh Mohan Shetty, null Haixia Shi, null Mohiuddin Shiekh, null Nobuaki Shime, null Keiki Shimizu, null Sally Shrapnel, null Pramesh Sundar Shrestha, null Shubha Kalyan Shrestha, null Hoi Ping Shum, null Nassima Si Mohammed, null Ng Yong Siang, null Jeanne Sibiude, null Atif Siddiqui, null Piret Sillaots, null Catarina Silva, null Rogério Silva, null Maria Joao Silva, null Benedict Sim Lim Heng, null Wai Ching Sin, null Dario Sinatti, null Punam Singh, null Budha Charan Singh, null Pompini Agustina Sitompul, null Karisha Sivam, null Vegard Skogen, null Sue Smith, null Benjamin Smood, null Coilin Smyth, null Michelle Smyth, null Morgane Snacken, null Dominic So, null Tze Vee Soh, null Lene Bergendal Solberg, null Joshua Solomon, null Tom Solomon, null Emily Somers, null Agnès Sommet, null Rima Song, null Myung Jin Song, null Tae Song, null Jack Song Chia, null Michael Sonntagbauer, null Azlan Mat Soom, null Arne Søraas, null Camilla Lund Søraas, null Alberto Sotto, null Edouard Soum, null Marta Sousa, null Ana Chora Sousa, null Maria Sousa Uva, null Vicente Souza‐Dantas, null Alexandra Sperry, null Elisabetta Spinuzza, null B. P. Sanka Ruwan Sri Darshana, null Shiranee Sriskandan, null Sarah Stabler, null Thomas Staudinger, null Stephanie‐Susanne Stecher, null Trude Steinsvik, null Ymkje Stienstra, null Birgitte Stiksrud, null Eva Stolz, null Amy Stone, null Adrian Streinu‐Cercel, null Anca Streinu‐Cercel, null David Stuart, null Ami Stuart, null Decy Subekti, null Gabriel Suen, null Jacky Y. Suen, null Asfia Sultana, null Charlotte Summers, null Dubravka Supic, null Deepashankari Suppiah, null Magdalena Surovcová, null Suwarti Suwarti, null Andrey Svistunov, null Sarah Syahrin, null Konstantinos Syrigos, null Jaques Sztajnbok, null Konstanty Szuldrzynski, null Shirin Tabrizi, null Fabio S. Taccone, null Lysa Tagherset, null Shahdattul Mawarni Taib, null Ewa Talarek, null Sara Taleb, null Jelmer Talsma, null Renaud Tamisier, null Maria Lawrensia Tampubolon, null Kim Keat Tan, null Yan Chyi Tan, null Taku Tanaka, null Hiroyuki Tanaka, null Hayato Taniguchi, null Huda Taqdees, null Arshad Taqi, null Coralie Tardivon, null Pierre Tattevin, null M. Azhari Taufik, null Hassan Tawfik, null Richard S. Tedder, null Tze Yuan Tee, null João Teixeira, null Sofia Tejada, null Marie‐Capucine Tellier, null Sze Kye Teoh, null Vanessa Teotonio, null François Téoulé, null Pleun Terpstra, null Olivier Terrier, null Nicolas Terzi, null Hubert Tessier‐Grenier, null Adrian Tey, null Alif Adlan Mohd Thabit, null Anand Thakur, null Zhang Duan Tham, null Suvintheran Thangavelu, null Vincent Thibault, null Simon‐Djamel Thiberville, null Benoît Thill, null Jananee Thirumanickam, null Shaun Thompson, null Emma C. Thomson, null Surain Raaj Thanga Thurai, null Ryan S. Thwaites, null Paul Tierney, null Vadim Tieroshyn, null Peter S. Timashev, null Jean‐François Timsit, null Bharath Kumar Tirupakuzhi Vijayaraghavan, null Noémie Tissot, null Jordan Zhien Yang Toh, null Maria Toki, null Kristian Tonby, null Sia Loong Tonnii, null Margarida Torres, null Antoni Torres, null Rosario Maria Torres Santos‐Olmo, null Hernando Torres‐Zevallos, null Michael Towers, null Tony Trapani, null Théo Treoux, null Cécile Tromeur, null Ioannis Trontzas, null Tiffany Trouillon, null Jeanne Truong, null Christelle Tual, null Sarah Tubiana, null Helen Tuite, null Jean‐Marie Turmel, null Lance C. W. Turtle, null Anders Tveita, null Pawel Twardowski, null Makoto Uchiyama, null P. G. Ishara Udayanga, null Andrew Udy, null Roman Ullrich, null Alberto Uribe, null Asad Usman, null Timothy M. Uyeki, null Cristinava Vajdovics, null Piero Valentini, null Luís Val‐Flores, null Amélie Valran, null Stijn Van de Velde, null Marcel van den Berge, null Machteld Van der Feltz, null Job van der Palen, null Paul van der Valk, null Nicky Van Der Vekens, null Peter Van der Voort, null Sylvie Van Der Werf, null Laura van Gulik, null Jarne Van Hattem, null Carolien van Netten, null Ilonka van Veen, null Noémie Vanel, null Henk Vanoverschelde, null Pooja Varghese, null Michael Varrone, null Shoban Raj Vasudayan, null Charline Vauchy, null Shaminee Veeran, null Aurélie Veislinger, null Sebastian Vencken, null Sara Ventura, null Annelies Verbon, null James Vickers, null José Ernesto Vidal, null César Vieira, null Deepak Vijayan, null Joy Ann Villanueva, null Judit Villar, null Pierre‐Marc Villeneuve, null Andrea Villoldo, null Gayatri Vishwanathan, null Benoit Visseaux, null Hannah Visser, null Chiara Vitiello, null Harald Vonkeman, null Fanny Vuotto, null Noor Hidayu Wahab, null Suhaila Abdul Wahab, null Nadirah Abdul Wahid, null Marina Wainstein, null Wan Fadzlina Wan Muhd Shukeri, null Chih‐Hsien Wang, null Steve Webb, null Jia Wei, null Katharina Weil, null Tan Pei Wen, null Sanne Wesselius, null T. Eoin West, null Murray Wham, null Bryan Whelan, null Nicole White, null Paul Henri Wicky, null Aurélie Wiedemann, null Surya Otto Wijaya, null Keith Wille, null Suzette Willems, null Virginie Williams, null Evert‐Jan Wils, null Xin Ci Wong, null Calvin Wong, null Yew Sing Wong, null Teck Fung Wong, null Natalie Wright, null Gan Ee Xian, null Lim Saio Xian, null Kuan Pei Xuan, null Ioannis Xynogalas, null Siti Rohani Binti Mohd Yakop, null Masaki Yamazaki, null Yazdan Yazdanpanah, null Nicholas Yee Liang Hing, null Cécile Yelnik, null Chian Hui Yeoh, null Stephanie Yerkovich, null Toshiki Yokoyama, null Hodane Yonis, null Obada Yousif, null Saptadi Yuliarto, null Akram Zaaqoq, null Marion Zabbe, null Kai Zacharowski, null Masliza Zahid, null Maram Zahran, null Nor Zaila Binti Zaidan, null Maria Zambon, null Alberto Zanella, null Konrad Zawadka, null Nurul Zaynah, null Hiba Zayyad, null Alexander Zoufaly, null David Zucman, and null ISARIC Clinical Characterisation Group
Published: 2022

17. Author response: Estimating the potential to prevent locally acquired HIV infections in a UNAIDS Fast-Track City, Amsterdam

Author: Alexandra Blenkinsop, Mélodie Monod, Ard van Sighem, Nikos Pantazis, Daniela Bezemer, Eline Op de Coul, Thijs van de Laar, Christophe Fraser, Maria Prins, Peter Reiss, Godelieve J de Bree, and Oliver Ratmann
Published: 2022

18. Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

Author: Daniel Mair, Adrian Signell, Daniel Laydon, Nadua Bayzid, Clare M McCann, Flavia Flaviani, Thomas Connor, Samir Bhatt, Catherine Moore, Dr Benjamin Lindsey, Malte Pinckert, Jane Masoli, Rachel Blacow, Jacqui Prieto, Ian Harrison, Scott Thurston, Lance Turtle, Thushan De Silva, Gregory Young, Natalie Groves, Andrew Nelson, Angie Lackenby, Lily Geidelberg, Mili Estee Torok, Brendan Payne, Katy Gaythorpe, Sonia Goncalves, Ewan Harrison, Andrew Rambaut, Angela Beckett, David Partridge, Swapnil Mishra, Dimitris Grammatopoulos, Judith Breuer, Jenna Nichols, Erik Volz, Sharon Glaysher, Harry David Wilson, Jack Lee, Marta Gallis, Christophe Fraser, Susan Hopkins, Patrick McClure, Derrick Crook, Juan Ledesma, Theocharis Tsoleridis, Natasha Palmalux, Matthew Dorman, Helen Lowe, Kordo Saeed, Oliver Ratmann, Darren Smith, Gilberto Betancor Quintana, Alan McNally, Matthew Bashton, Steven Rudder, Dennis Wang, Joseph Chappell, Elias Allara, Volz, Erik [0000-0001-6268-8937], Mishra, Swapnil [0000-0002-8759-5902], Geidelberg, Lily [0000-0002-8057-1844], Laydon, Daniel J [0000-0003-4270-3321], Jackson, Ben [0000-0002-9981-0649], Gaythorpe, Katy [0000-0003-3734-9081], Kwiatkowski, Dominic P [0000-0002-5023-0176], Flaxman, Seth [0000-0002-2477-4217], Gandy, Axel [0000-0002-6777-0451], Rambaut, Andrew [0000-0003-4337-3707], Ferguson, Neil M [0000-0002-1154-8093], Apollo - University of Cambridge Repository, Medical Research Council, Bill & Melinda Gates Foundation, and Medical Research Council (MRC)
Subjects: The COVID-19 Genomics UK (COG-UK) consortium, Adult, 0301 basic medicine, Time Factors, Adolescent, General Science & Technology, Lineage (evolution), Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Basic Reproduction Number, Population genetics, Genome, Viral, Biology, law.invention, Evolution, Molecular, Young Adult, 03 medical and health sciences, Age Distribution, 0302 clinical medicine, law, Phylogenetics, Humans, 030212 general & internal medicine, Child, Phylogeny, Aged, Aged, 80 and over, COVID-19 Genomics UK (COG-UK) consortium, Science & Technology, Multidisciplinary, Generation time, SARS-CoV-2, Infant, Newborn, COVID-19, Infant, Middle Aged, Transmissibility (vibration), 3. Good health, Multidisciplinary Sciences, 030104 developmental biology, Transmission (mechanics), England, Evolutionary biology, Child, Preschool, Spike Glycoprotein, Coronavirus, Science & Technology - Other Topics, Basic reproduction number
Abstract: The SARS-CoV-2 lineage B.1.1.7, designated variant of concern (VOC) 202012/01 by Public Health England1, was first identified in the UK in late summer to early autumn 20202. Whole-genome SARS-CoV-2 sequence data collected from community-based diagnostic testing for COVID-19 show an extremely rapid expansion of the B.1.1.7 lineage during autumn 2020, suggesting that it has a selective advantage. Here we show that changes in VOC frequency inferred from genetic data correspond closely to changes inferred by S gene target failures (SGTF) in community-based diagnostic PCR testing. Analysis of trends in SGTF and non-SGTF case numbers in local areas across England shows that B.1.1.7 has higher transmissibility than non-VOC lineages, even if it has a different latent period or generation time. The SGTF data indicate a transient shift in the age composition of reported cases, with cases of B.1.1.7 including a larger share of under 20-year-olds than non-VOC cases. We estimated time-varying reproduction numbers for B.1.1.7 and co-circulating lineages using SGTF and genomic data. The best-supported models did not indicate a substantial difference in VOC transmissibility among different age groups, but all analyses agreed that B.1.1.7 has a substantial transmission advantage over other lineages, with a 50% to 100% higher reproduction number.
Published: 2021

19. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial

Author: Lerato E, Magosi, Yinfeng, Zhang, Tanya, Golubchik, Victor, DeGruttola, Eric, Tchetgen Tchetgen, Vladimir, Novitsky, Janet, Moore, Pam, Bachanas, Tebogo, Segolodi, Refeletswe, Lebelonyane, Molly, Pretorius Holme, Sikhulile, Moyo, Joseph, Makhema, Shahin, Lockman, Christophe, Fraser, Myron Max, Essex, Marc, Lipsitch, and On Behalf Of The Botswana Combination Prevention Project And Pangea Consortium
Subjects: Male, General Immunology and Microbiology, Incidence, General Neuroscience, Prevalence, Humans, Female, HIV Infections, General Medicine, Epidemics, Phylogeny, General Biochemistry, Genetics and Molecular Biology
Abstract: Background:Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence.Methods:To elucidate patterns of HIV spread in universal test-and-treat trials, we quantified the contribution of geographic-location, gender, age, and randomized-HIV-intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana. We sequenced HIV viral whole genomes from 5114 trial participants among the 30 trial communities.Results:Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] vs. 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] vs. 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention.Conclusions:Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies.Funding:This study was supported by the National Institute of General Medical Sciences (U54GM088558), the Fogarty International Center (FIC) of the U.S. National Institutes of Health (D43 TW009610), and the President’s Emergency Plan for AIDS Relief through the Centers for Disease Control and Prevention (CDC) (Cooperative agreements U01 GH000447 and U2G GH001911).
Published: 2022

20. Large-scale calibration and simulation of COVID-19 epidemiologic scenarios to support healthcare planning

Author: Nick Groves-Kirkby, Ewan Wakeman, Seema Patel, Robert Hinch, Tineke Poot, Jonathan Pearson, Lily Tang, Edward Kendall, Ming Tang, Kim Moore, Scott Stevenson, Bryn Mathias, Ilya Feige, Simon Nakach, Laura Stevenson, Paul O'Dwyer, William Probert, Jasmina Panovska-Griffiths, and Christophe Fraser
Subjects: Infectious Diseases, Epidemiology, Virology, Public Health, Environmental and Occupational Health, Parasitology, Microbiology
Abstract: The COVID-19 pandemic has provided stiff challenges for planning and resourcing in health services in the UK and worldwide. Epidemiological models can provide simulations of how infectious disease might progress in a population given certain parameters. We adapted an agent-based model of COVID-19 to inform planning and decision-making within a healthcare setting, and created a software framework that automates processes for calibrating the model parameters to health data and allows the model to be run at national population scale on National Health Service (NHS) infrastructure. We developed a method for calibrating the model to three daily data streams (hospital admissions, intensive care occupancy, and deaths), and demonstrate that on cross-validation the model fits acceptably to unseen data streams including official estimates of COVID-19 incidence. Once calibrated, we use the model to simulate future scenarios of the spread of COVID-19 in England and show that the simulations provide useful projections of future COVID-19 clinical demand. These simulations were used to support operational planning in the NHS in England, and we present the example of the use of these simulations in projecting future clinical demand during the rollout of the national COVID-19 vaccination programme. Being able to investigate uncertainty and test sensitivities was particularly important to the operational planning team. This epidemiological model operates within an ecosystem of data technologies, drawing on a range of NHS, government and academic data sources, and provides results to strategists, planners and downstream data systems. We discuss the data resources that enabled this work and the data challenges that were faced.
Published: 2022

21. Ethics of instantaneous contact tracing using mobile phone apps in the control of the COVID-19 pandemic

Author: David Bonsall, Michael Parker, Christophe Fraser, and Lucie Abeler-Dörner
Subjects: Freedom, medicine.medical_specialty, Health (social science), 020205 medical informatics, Distancing, Computer science, Pneumonia, Viral, Population, Internet privacy, 02 engineering and technology, Trust, Health(social science), Betacoronavirus, 03 medical and health sciences, 0302 clinical medicine, Arts and Humanities (miscellaneous), Pandemic, 0202 electrical engineering, electronic engineering, information engineering, medicine, Humans, Current Controversy, Bioethical Issues, 030212 general & internal medicine, education, Pandemics, education.field_of_study, SARS-CoV-2, business.industry, Health Policy, Public health, COVID-19, ethics, Mobile Applications, 3. Good health, Issues, ethics and legal aspects, Privacy, Mobile phone, Software deployment, Infectious disease (medical specialty), Communicable Disease Control, Contact Tracing, Coronavirus Infections, business, Cell Phone, Contact tracing
Abstract: In this paper we discuss ethical implications of the use of mobile phone apps in the control of the COVID-19 pandemic. Contact tracing is a well-established feature of public health practice during infectious disease outbreaks and epidemics. However, the high proportion of pre-symptomatic transmission in COVID-19 means that standard contact tracing methods are too slow to stop the progression of infection through the population. To address this problem, many countries around the world have deployed or are developing mobile phone apps capable of supporting instantaneous contact tracing. Informed by the on-going mapping of ‘proximity events’ these apps are intended both to inform public health policy and to provide alerts to individuals who have been in contact with a person with the infection. The proposed use of mobile phone data for ‘intelligent physical distancing’ in such contexts raises a number of important ethical questions. In our paper, we outline some ethical considerations that need to be addressed in any deployment of this kind of approach as part of a multidimensional public health response. We also, briefly, explore the implications for its use in future infectious disease outbreaks.
Published: 2020

22. Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey

Author: Rui André Nunes dos Santos, Lance Turtle, Thushan De Silva, Angie Lackenby, Angela Beckett, Christophe Fraser, Patrick McClure, Zack Richards, Tanya Golubchik, and Matthew Bashton
Abstract: The Office for National Statistics COVID-19 Infection Survey is a large household-based surveillance study based in the United Kingdom. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing sequenced samples collected up until 13th November 2021. We observed four distinct sweeps or partial-sweeps, by lineages B.1.177, B.1.1.7/Alpha, B.1.617.2/Delta, and finally AY.4.2, a sublineage of B.1.617.2, with each sweeping lineage having a distinct growth advantage compared to their predecessors. Evolution was characterised by steady rates of evolution and increasing diversity within lineages, but with step increases in divergence associated with each sweeping major lineage, leading to a faster overall rate of evolution and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly as routine PCR testing is phased out or in settings where large-scale sequencing is not feasible.
Published: 2022

23. The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism

Author: Elen Vink, Lance Turtle, Thushan De Silva, Chris Davis, David Pascall, S Ray, Christophe Fraser, Patrick McClure, and Matthew Bashton
Abstract: Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron, the fifth VOC to be described, harbours 30 amino acid mutations in spike including 15 in the receptor-binding domain. Here, we demonstrate substantial evasion of neutralisation by Omicronin vitrousing sera from vaccinated individuals. Importantly, these data are mirrored by a substantial reduction in real-world vaccine effectiveness that is partially restored by booster vaccination. We also demonstrate that Omicron does not induce cell syncytia and favours a TMPRSS2-independent endosomal entry pathway. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant.
Published: 2022

24. Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study

Author: Harry D Wilson, Elaine O'Toole, Andrew Bassett, Moritz U. G. Kraemer, Beth Blane, Scott Goodwin, Giri Shankar, Joseph Hughes, Lucy R. Frost, Alicia Thornton, Scott Elliott, Tammy V Merrill, Sheila Waugh, Alexander Adams, Peter Muir, Graciela Sluga, Rebecca Williams, Hannah Dent, Christophe Fraser, Shavanthi Rajatileka, John C. Hartley, Luke B Snell, Benjamin J Cogger, Lance Turtle, Alex Makunin, John A. Todd, Victoria Wright, Daniela De Angelis, James McKenna, Dinesh Aggarwal, Jonathan K. Ball, Jillian Durham, Garren Scott, Thushan I de Silva, Veena Raviprakash, Hannah M Pymont, Jason Coombes, Anita Lucaci, Luke R. Green, Leigh M Jackson, Hermione J. Webster, Louis du Plessis, David A. Jackson, Minal Patel, Áine O'Toole, Ravi Gupta, Marc Niebel, Garry Scarlett, Rajiv Shah, Guy Mollett, Kathy Li, Rory Gunson, Matthew Bashton, Carl Jones, Sara Kumziene-Summerhayes, Zoltan Molnar, Siona Silveira, Malte L Pinckert, Catherine Ludden, Angeliki Karamani, Leanne Kane, Brendan A I Payne, Alan McNally, Clare M. McCann, Holli Carden, Mohammad Raza, Alison E. Mather, Kate B. Cook, Amy Gaskin, David J. Williams, Shaun R. Seaman, Christopher I. Jones, Gilberto Betancor, Matthew T. G. Holden, Jennifier Liddle, Meera Unnikrishnan, Angie Green, Ben Taylor, Kelly Bicknell, Alexander J. Trotter, Emma Meader, Leanne M Kermack, Nathaniel Storey, Michelle Cronin, Sally Forrest, Sarah Jeremiah, Asad Zaidi, M Morgan, Alasdair MacLean, Thomas R. Connor, Johnathan M Evans, Rachael Stanley, Ryan P George, Nadine Holmes, Richard H. Myers, Christine Sambles, Bernardo Gutierrez, Jeffrey K. J. Cheng, Tim Wyatt, Natasha Jesudason, Lindsay Coupland, Monika Pusok, Manon Ragonnet-Cronin, Jenifer Mason, Joshua Maksimovic, Russell Hope, Alison Holmes, David Simpson, Radoslaw Poplawski, Amelia Joseph, Erwan Acheson, James Bonfield, Mara K. N. Lawniczak, Sascha Ott, Lesley-Anne Williams, Jessica Lynch, Graham P. Taylor, Anita Kenyon, Elizabeth Wastenge, Megan Mayhew, Adhyana I K Mahanama, Stavroula F Louka, Chloe Bishop, Esther Robinson, Darren Smith, Anne M. Presanis, Matthew Carlile, Thomas D Stanton, Dennis Wang, Katerina Galai, Adam P Westhorpe, Flavia Flaviani, Michelle Wantoch, Max Whiteley, Yann Bourgeois, Matthew Gemmell, Mary Ramsay, A Lloyd, Simon Thelwall, Hannah C. Howson-Wells, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Robert Impey, Siddharth Mookerjee, Steven Platt, Emma Swindells, Laura Letchford, Alex Alderton, Lee Graham, Safiah Afifi, David C. Lee, Cassie Breen, Melisa Louise Fenton, Benita Percival, Adrian W Signell, Tanya Golubchik, Ian B Vipond, Eleri Wilson-Davies, Angie Lackenby, Laura Atkinson, Sarojini Pandey, Nazreen F. Hadjirin, Michael A Chapman, Huw Gulliver, Joana Dias, Grant Hall, Antony D Hale, Hassan Hartman, Alp Aydin, Louise Smith, Ashok Dadrah, Johnny Debebe, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Bridget Knight, Hannah E Bridgewater, Nadua Bayzid, Gemma L. Kay, Richard Gregory, Sally Kay, Ellena Brooks, Andre Charlett, Georgina M McManus, Riaz Jannoo, Victoria Blakey, Carol Scott, Rachel Nelson, Liz Ratcliffe, Gerry Tonkin-Hill, Verity Hill, Joanne D. Stockton, Danielle Leek, Steven Leonard, Stephanie Hutchings, Jonathan D. Moore, Kathryn Ann Harris, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Tanzina Haque, Katherine L. Bellis, Khalil Abudahab, Dianne Irish-Tavares, Gaia Nebbia, Kathryn A Jackson, Stephen W Attwood, Daniel Mair, Sreenu Vattipally, Susanne Stonehouse, Ian Merrick, Lucille Rainbow, Mathew A. Beale, Angela Helen Beckett, Ember Hilvers, Thomas Helmer, Jenna Nichols, Giselda Bucca, Salman Goudarzi, Christopher Ruis, Surendra Parmar, Angela Cowell, Alberto C Cerda, Divya K. Shah, Judith Heaney, E. Thomson, Kyriaki Nomikou, Nicole Pacchiarini, Katherine L Harper, Fatima Downing, M. Estée Török, Michelle L Michelsen, Aaron R. Jeffries, Jennifer Collins, Christopher Williams, Katie F. Loveson, Steven Rudder, Theocharis Tsoleridis, Robert Davies, David Robertson, Katherine Smollett, Kathryn McCluggage, Liam Crawford, Inigo Martincorena, Charlotte Beaver, Oliver Megram, Karla Spellman, Sam Haldenby, Emma Betteridge, William D. Fuller, Will P. M. Rowe, Cherian Koshy, Tim E. A. Peto, Alison Cox, Natasha Johnson, Tanya Curran, Sharif Shaaban, Tamyo Mbisa, Cordelia Langford, Eric Witele, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Paul W Bird, Louise Aigrain, Ronan Lyons, Amy Trebes, Sally Corden, Steven Rushton, Jack Cd Lee, Jane Greenaway, Hibo Asad, Amanda Bradley, Mohammed O Hassan-Ibrahim, Shane McCarthy, Fei Sang, Matthew Loose, Hannah Jones, Keith D. James, Chloe L Fisher, Chrystala Constantinidou, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Anna Price, Amy Ash, Michaela John, Alex Zarebski, Fenella D. Halstead, John Danesh, Christine Kitchen, Aminu S Jahun, Mark Whitehead, Julianne R Brown, Catherine Bresner, Marius Cotic, Stefanie V Lensing, Nick Levene, Louissa R Macfarlane-Smith, Wendy Hogsden, Cressida Auckland, Eleanor Drury, Richard Eccles, Jennifer Hart, Seema Nickbakhsh, Alisha Davies, David M. Aanensen, Shirelle Burton-Fanning, Ben Farr, Buddhini Samaraweera, Sarah Wyllie, Hannah Lowe, Richard J. Orton, Martin D. Curran, Carol Churcher, Karen Oliver, Elihu Aranday-Cortes, Wen Yew, Thanh Le-Viet, Matthew Parker, Katherine A Twohig, Shahjahan Miah, Samuel M. Nicholls, G MacIntyre-Cockett, Tranprit Saluja, Charlotte Nelson, Vicki Chalker, Roberto Amato, Ellen Higginson, Timothy M. Freeman, Christopher W Holmes, Yasmin Chaudhry, Elias Allara, Alec Birchley, Iraad Bronner, Emma Moles-Garcia, Angus I. Best, Anna L. Casey, Audrey Farbos, Nicholas W Machin, David W Eyre, Tim Boswell, Charlotte A Williams, Elen De Lacy, Matthew J. Bull, Matilde Mori, Carmen F. Manso, Peijun Zhang, Sahar Eldirdiri, Dimitris Grammatopoulos, Corin Yeats, Claudia Wierzbicki, David G Partridge, Kordo Saeed, Nichola Duckworth, David J. Studholme, Harmeet K Gill, Juan Ledesma, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Husam Osman, Julian A. Hiscox, Helen Adams, Christopher Fearn, Fabrícia F. Nascimento, Ulf Schaefer, James W. Harrison, Andrew J. Nelson, Joshua Quick, Mohammad Tauqeer Alam, Liam Prestwood, Nikos Manesis, Julian Tang, Justin O'Grady, Sophia T Girgis, Louise Berry, Gemma Clark, Marina Escalera Zamudio, Karlie Fallon, Tim J Sloan, Joanne Watkins, Clare Pearson, Andrew D Beggs, Rachel Williams, Luke Bedford, Trevor Robinson, Nicholas M Redshaw, Richard Hopes, Mirko Menegazzo, Katherine Twohig, Gabrielle Vernet, Steven Liggett, Mariateresa de Cesare, Derrick W. Crook, Dominic P. Kwiatkowski, Mark Kristiansen, Miren Iturriza-Gomara, Christopher I. Moore, Claire Cormie, Olivia Boyd, Nikki Smith, Noel Craine, Kathleen A. Williamson, John Boyes, Sian Ellard, Cristina V. Ariani, Wendy Chatterton, David Bonsall, Kevin Lewis, David Jorgensen, Ian Harrison, Christopher Jackson, Martin P McHugh, Danni Weldon, Michael A. Quail, Amita Patel, Lily Geidelberg, Myra Hosmillo, Judith Breuer, Cariad Evans, Edward Barton, Trudy Workman, Derek Fairley, Vineet Patel, Daniel Bradshaw, Robin Manley, Scott Aj Thurston, John Sillitoe, Monique Andersson, Sharon J. Peacock, Jamie Lopez-Bernal, Thomas Thompson, Nabil-Fareed Alikhan, Ben Temperton, Paul Baker, Robin J Moll, Laura Gifford, Nicholas J. Loman, Jayna Raghwani, Jacqui Prieto, Andrew Hesketh, Oliver G. Pybus, Adela Alcolea-Medina, David Buck, Gregory R Young, Alistair C. Darby, Sónia Gonçalves, Aileen G. Rowan, Tabitha Mahungu, Nicholas Ellaby, Jon-Paul Keatley, Lily Tong, Robert Beer, Martyn Guest, Lisa J Levett, Ali R Awan, Iliana Georgana, Paul E Brown, Li Xu-McCrae, Stephen P. Kidd, Sara Rey, Shazaad Ahmad, Danielle C. Groves, Tetyana I. Vasylyeva, David F. Bibby, Nathan Moore, Fiona Ashcroft, Igor Starinskij, Hannah Paul, Claire McMurray, Michael Spencer Chapman, Carlos Balcazar, Joanna Warwick-Dugdale, Pinglawathee Madona, Edith Vamos, Lesley Shirley, Kate Templeton, Luke Foulser, Igor Siveroni, Ewan M. Harrison, Sian Morgan, Diana Rajan, S Taylor, Laia Fina, Naomi Park, Sarah J. O'Brien, Alessandro M Carabelli, Angela Marchbank, Sunando Roy, Leonardo de Oliveira Martins, Steve Palmer, Jonathan Hubb, Alexander J Keeley, Francesc Coll, Malorie Perry, Paul J. Parsons, Anthony Underwood, Patawee Asamaphan, William L Hamilton, Tommy Nyberg, Sophie Palmer, Amanda Symmonds, Anoop Chauhan, Robert Johnson, Christopher J. R. Illingworth, James Shepherd, Wendy Smith, Rich Livett, Rachel Blacow, Margaret Hughes, Jeremy Mirza, Joanne Watts, Jonathan D. Edgeworth, Sarah François, Sue Edwards, Adrienn Angyal, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Paul Randell, Kate Johnson, Eileen Gallagher, Nick Cortes, Yusri Taha, Leah Ensell, Emanuela Pelosi, Stefan Rooke, Michelle Lister, Ana da Silva Filipe, Cassandra S Malone, Themoula Charalampous, Benjamin B Lindsey, Natalie Groves, Colin Smith, Ross J Harris, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Nicola Sheriff, Helen L Lowe, Rachel Jones, Ben Warne, Rose K Davidson, Declan Bradley, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Shirin Aliabadi, Andrew Whitwham, Patrick McClure, Samuel Robson, Sharon Glaysher, Robert J. Munn, Emma L. Wise, Laura Baxter, Kim S Smith, Catherine Moore, Bree Gatica-Wilcox, Alice Broos, Sarah Essex, David Baker, Manjinder Khakh, Dorota Jamrozy, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Robin Howe, Meera Chand, James I. Price, Marina Gourtovaia, Debra Padgett, Jaime Tovar-Corona, Stephen L. Michell, Matthew J. Dorman, Lizzie Meadows, David Heyburn, Iona Willingham, Rocio Martinez Nunez, Grace Taylor-Joyce, Claire M Bewshea, Anita Justice, Simon Cottrell, Rebecca C H Brown, Jamie Young, Gavin Dabrera, Matthew Wyles, Stephen Carmichael, Lisa Berry, Frances Bolt, Andrew Rambaut, Samir Dervisevic, Erik M. Volz, Rahul Batra, Caoimhe McKerr, Samantha McGuigan, Katie Jones, Mailis Maes, Rebecca Dewar, Mary Sinnathamby, Joel Southgate, and Lynn Monaghan
Subjects: medicine.medical_specialty, business.industry, Proportional hazards model, Public health, Hazard ratio, Attendance, C500, Vaccination, Infectious Diseases, Relative risk, Internal medicine, Cohort, medicine, business, Cohort study
Abstract: Background: \ud The SARS-CoV-2 delta (B.1.617.2) variant was first detected in England in March, 2021. It has since rapidly become the predominant lineage, owing to high transmissibility. It is suspected that the delta variant is associated with more severe disease than the previously dominant alpha (B.1.1.7) variant. We aimed to characterise the severity of the delta variant compared with the alpha variant by determining the relative risk of hospital attendance outcomes.\ud \ud Methods: \ud This cohort study was done among all patients with COVID-19 in England between March 29 and May 23, 2021, who were identified as being infected with either the alpha or delta SARS-CoV-2 variant through whole-genome sequencing. Individual-level data on these patients were linked to routine health-care datasets on vaccination, emergency care attendance, hospital admission, and mortality (data from Public Health England's Second Generation Surveillance System and COVID-19-associated deaths dataset; the National Immunisation Management System; and NHS Digital Secondary Uses Services and Emergency Care Data Set). The risk for hospital admission and emergency care attendance were compared between patients with sequencing-confirmed delta and alpha variants for the whole cohort and by vaccination status subgroups. Stratified Cox regression was used to adjust for age, sex, ethnicity, deprivation, recent international travel, area of residence, calendar week, and vaccination status.\ud \ud Findings: \ud Individual-level data on 43 338 COVID-19-positive patients (8682 with the delta variant, 34 656 with the alpha variant; median age 31 years [IQR 17–43]) were included in our analysis. 196 (2·3%) patients with the delta variant versus 764 (2·2%) patients with the alpha variant were admitted to hospital within 14 days after the specimen was taken (adjusted hazard ratio [HR] 2·26 [95% CI 1·32–3·89]). 498 (5·7%) patients with the delta variant versus 1448 (4·2%) patients with the alpha variant were admitted to hospital or attended emergency care within 14 days (adjusted HR 1·45 [1·08–1·95]). Most patients were unvaccinated (32 078 [74·0%] across both groups). The HRs for vaccinated patients with the delta variant versus the alpha variant (adjusted HR for hospital admission 1·94 [95% CI 0·47–8·05] and for hospital admission or emergency care attendance 1·58 [0·69–3·61]) were similar to the HRs for unvaccinated patients (2·32 [1·29–4·16] and 1·43 [1·04–1·97]; p=0·82 for both) but the precision for the vaccinated subgroup was low.\ud \ud Interpretation: \ud This large national study found a higher hospital admission or emergency care attendance risk for patients with COVID-19 infected with the delta variant compared with the alpha variant. Results suggest that outbreaks of the delta variant in unvaccinated populations might lead to a greater burden on health-care services than the alpha variant.\ud \ud Funding: \ud Medical Research Council; UK Research and Innovation; Department of Health and Social Care; and National Institute for Health Research.
Published: 2022

25. Many but small HIV-1 non-B transmission chains in the Netherlands

Author: Ard van Sighem, Christophe Fraser, Alexandra Blenkinsop, Jeroen van Kampen, Daniela Bezemer, Els Wessels, Oliver Ratmann, Thijs J W van de Laar, Peter Reiss, Marion Cornelissen, Matthew Hall, Medical Microbiology and Infection Prevention, AII - Infectious diseases, Global Health, Infectious diseases, APH - Aging & Later Life, Virology, and Stichting Aidsfonds
Subjects: Male, Epidemiology and Social, risk-group, Immunology, Human immunodeficiency virus (HIV), spread, HIV Infections, Context (language use), migrants, Biology, medicine.disease_cause, phylogeny, law.invention, phylogeographic origin, SDG 3 - Good Health and Well-being, law, Virology, unobserved size distribution, medicine, Humans, Immunology and Allergy, MSM, Homosexuality, Male, Heterosexuality, 11 Medical and Health Sciences, Netherlands, transmission chains, Phylogenetic tree, subtypes, virus diseases, 06 Biological Sciences, sub-epidemics, Confidence interval, 17 Psychology and Cognitive Sciences, Infectious Diseases, Transmission (mechanics), introduction, Cohort, HIV-1, Demography
Abstract: Objective The aim of this study was to investigate introductions and spread of different HIV-1 subtypes in the Netherlands. Design We identified distinct HIV-1 transmission chains in the Netherlands within the global epidemic context through viral phylogenetic analysis of partial HIV-1 polymerase sequences from individuals enrolled in the ATHENA national HIV cohort of all persons in care since 1996, and publicly available international background sequences. Methods Viral lineages circulating in the Netherlands were identified through maximum parsimony phylogeographic analysis. The proportion of HIV-1 infections acquired in-country among heterosexuals and MSM was estimated from phylogenetically observed, national transmission chains using a branching process model that accounts for incomplete sampling. Results As of 1 January 2019, 2589 (24%) of 10 971 (41%) HIV-1 sequenced individuals in ATHENA had non-B subtypes (A1, C, D, F, G) or circulating recombinant forms (CRF01AE, CRF02AG, CRF06-cpx). The 1588 heterosexuals were in 1224, and 536 MSM in 270 phylogenetically observed transmission chains. After adjustments for incomplete sampling, most heterosexual (75%) and MSM (76%) transmission chains were estimated to include only the individual introducing the virus (size = 1). Onward transmission occurred mostly in chains size 2-5 amongst heterosexuals (62%) and in chains size at least 10 amongst MSM (64%). Considering some chains originated in-country from other risk-groups, 40% (95% confidence interval: 36-44) of non-B-infected heterosexuals and 62% (95% confidence interval: 49-73) of MSM-acquired infection in-country. Conclusion Although most HIV-1 non-B introductions showed no or very little onward transmission, a considerable proportion of non-B infections amongst both heterosexuals and MSM in the Netherlands have been acquired in-country.
Published: 2022

26. Author response: Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/Ya Tsie trial

Author: Lerato E Magosi, Yinfeng Zhang, Tanya Golubchik, Victor DeGruttola, Eric Tchetgen Tchetgen, Vladimir Novitsky, Janet Moore, Pam Bachanas, Tebogo Segolodi, Refeletswe Lebelonyane, Molly Pretorius Holme, Sikhulile Moyo, Joseph Makhema, Shahin Lockman, Christophe Fraser, Myron Max Essex, and Marc Lipsitch
Published: 2021

27. Genomics-informed outbreak investigations of SARS-CoV-2 using civet

Author: Thomas Connor, Lance Turtle, Thushan De Silva, Angie Lackenby, Angela Beckett, Christophe Fraser, Patrick McClure, Tanya Golubchik, and Matthew Bashton
Abstract: The scale of data produced during the SARS-CoV-2 pandemic has been unprecedented, with more than 5 million sequences shared publicly at the time of writing. This wealth of sequence data provides important context for interpreting local outbreaks. However, placing sequences of interest into national and international context is difficult given the size of the global dataset. Often outbreak investigations and genomic surveillance efforts require running similar analyses again and again on the latest dataset and producing reports. We developed civet (cluster investigation and virus epidemiology tool) to aid these routine analyses and facilitate virus outbreak investigation and surveillance. Civet can place sequences of interest in the local context of background diversity, resolving the query into different ’catchments’ and presenting the phylogenetic results alongside metadata in an interactive, distributable report. Civet can be used on a fine scale for clinical outbreak investigation, for local surveillance and cluster discovery, and to routinely summarise the virus diversity circulating on a national level. Civet reports have helped researchers and public health bodies feedback genomic information in the appropriate context within a timeframe that is useful for public health.
Published: 2021

28. Monitoring key epidemiological parameters of SARS-CoV-2 transmission

Author: Moritz U G, Kraemer, Oliver G, Pybus, Christophe, Fraser, Simon, Cauchemez, Andrew, Rambaut, and Benjamin J, Cowling
Subjects: Infection Control, Time Factors, Virulence, SARS-CoV-2, COVID-19, Virus Replication, Publisher Correction, Databases, Databases as Topic, Risk Factors, Viral infection, Population Surveillance, Humans, Contact Tracing, Pandemics
Published: 2021

29. Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

Author: Mohammad Raza, Alison E. Mather, Gilberto Betancor, Ian Merrick, Ben Taylor, Mathew A. Beale, Helen Ward, Samir Dervisevic, Michelle Cronin, Aaron R. Jeffries, Louise Smith, Steven Rudder, Mara K. N. Lawniczak, Sascha Ott, Ashok Dadrah, Luke Bedford, Gabrielle Vernet, Erik M. Volz, Rahul Batra, Johnny Debebe, Caoimhe McKerr, Samantha McGuigan, Oliver Megram, Katie Jones, Mailis Maes, Rebecca Dewar, Emma Swindells, Robert E. Johnson, Myra Hosmillo, Wen C Yew, Vineet Patel, Scott Aj Thurston, Matthew Bashton, Luke B Snell, Lynn Monaghan, David Buck, Gregory R Young, Garren Scott, Louis du Plessis, Sara Kumziene-Summerhayes, David M. Aanensen, Carl Jones, Nadine Holmes, Bernardo Gutierrez, Elizabeth Wastenge, Stavroula F Louka, Dennis Wang, Richard I. Gregory, M. Estée Török, Alistair C. Darby, Ulf Schaefer, Marc Niebel, David Robertson, E. Thomson, Carol Churcher, Patrick C McClure, Scott Elliott, Sarah Jeremiah, Katerina Galai, Matthew W. Loose, Megan Mayhew, Adhyana I K Mahanama, Angeliki Karamani, Naomi R Park, David J. Williams, Lance Turtle, Lucy R. Frost, Alicia Thornton, Jennifier Liddle, M Morgan, Tim Wyatt, Paul W Bird, Chloe Bishop, Esther Robinson, Alasdair MacLean, Inigo Martincorena, Bridget A. Knight, Emma Meader, Thomas R. Connor, Hermione J. Webster, Peter Muir, Sarah Walsh, Stephanie W. Lo, Andrew Bosworth, Hannah E Bridgewater, David Simpson, Radoslaw Poplawski, Angus I. Best, David Baker, Laura Letchford, Cassie Breen, Yann Bourgeois, Matthew Gemmell, Nikki Smith, Alison Holmes, Iliana Georgana, Christophe Fraser, Natasha Jesudason, Johnathan M Evans, Rachael Stanley, Lesley-Anne Williams, Jessica Lynch, Hannah Lowe, Eleri Wilson-Davies, Paul A. Baker, Alex Makunin, James Bonfield, Helen Adams, Christopher Fearn, Peter J. Diggle, Harry D Wilson, Carmen F. Manso, Nichola Duckworth, D Haw, Anna L. Casey, Audrey Farbos, Sam Haldenby, Vicki Chalker, Roberto Amato, Elen De Lacy, Ben Farr, Eric Witele, Buddhini Samaraweera, G MacIntyre-Cockett, Husam Osman, Jane Greenaway, Justin O'Grady, Sally Forrest, Andrew Nelson, Monika Pusok, A Lloyd, Edward Barton, James W. Harrison, Sophie Palmer, Amanda Symmonds, James Shepherd, Nazreen F. Hadjirin, Stephen L. Michell, Mohammed O Hassan-Ibrahim, Fiona Ashcroft, Daniel Mair, Richard H. Myers, Dianne Irish-Tavares, Hannah C. Howson-Wells, Jacqui Prieto, Christine Sambles, Andrew Hesketh, Alp Aydin, Sónia Gonçalves, Tabitha Mahungu, Tanzina Haque, Nicholas Ellaby, Karen Oliver, Hannah Paul, Joanne Watts, Claire McMurray, Lisa J Levett, Darren Smith, Simon Cottrell, Joanna Warwick-Dugdale, Pinglawathee Madona, Matthew J. Dorman, Lizzie Meadows, Ali R Awan, Leanne M Kermack, Jennifer Hart, Angie Lackenby, Carol Scott, Michael Spencer Chapman, Lucille Rainbow, Kyriaki Nomikou, Julianne R Brown, Juan Ledesma, Adam P Westhorpe, Giri Shankar, Karlie Fallon, Tim J Sloan, Joanne Watkins, Robert Impey, Sue Edwards, Rebecca C H Brown, Robin J Moll, Karla Spellman, Laura Gifford, Jamie Young, Adrienn Angyal, Graham Phillip Taylor, Robin Manley, Gavin Dabrera, Michelle Wantoch, Rachel Williams, David Heyburn, Mirko Menegazzo, Derrick W. Crook, Gaia Nebbia, Rachel Nelson, Elaine O'Toole, Luke Foulser, Katherine L Harper, Fatima Downing, Hassan Hartman, Nathan Moore, Gemma L. Kay, Matthew Wyles, Thanh Le-Viet, Edith Vamos, John Sillitoe, Lesley Shirley, Nicholas J. Loman, Iona Willingham, Elihu Aranday-Cortes, Ian B Vipond, Jeremy Mirza, Alberto C Cerda, Michelle L Michelsen, Steven Riley, Alison Cox, Igor Siveroni, Nadua Bayzid, Shavanthi Rajatileka, Giselda Bucca, Benjamin J Cogger, Tim Boswell, Matthew J. Bull, Stephen Carmichael, Lisa Berry, Frances Bolt, Kylie E. C. Ainslie, Martyn Guest, Sarojini Pandey, Katherine L. Bellis, Shane A. McCarthy, Christopher Ruis, Fei Sang, David Bonsall, Danni Weldon, Alex Alderton, Lee Graham, Amy Trebes, Sally Corden, Adrian W Signell, Tanya Golubchik, Huw Gulliver, Rocio Martinez Nunez, Dinesh Aggarwal, Tanya Curran, Jonathan K. Ball, Sharif Shaaban, Paul Randell, Jillian Durham, Alec Birchley, Matilde Mori, Joana Dias, Katherine A Twohig, Grant Hall, Antony D Hale, Alan McNally, Jonathan D. Edgeworth, Safiah Afifi, Andrew Rambaut, Katherine Smollett, David N. Lee, Tamyo Mbisa, Shahjahan Miah, Steven Rushton, Grace Taylor-Joyce, Hannah M Pymont, Chloe L Fisher, Cordelia Langford, Alex G. Richter, Jane A. H. Masoli, Michael Gallagher, Vicki M. Fleming, Kathleen A. Williamson, Anna Price, Holli Carden, Khalil Abudahab, Joanne D. Stockton, Meera Unnikrishnan, Jennifer Collins, Emma Moles-Garcia, Michaela John, Christine Kitchen, Tranprit Saluja, Ian Harrison, Lily Tong, Thomas G. Thompson, Thomas Helmer, Amita Patel, Siona Silveira, Deborah Ashby, Claire M Bewshea, Anita Justice, Brendan A I Payne, Alexander J. Trotter, Nikos Manesis, Katie F. Loveson, Cristina V. Ariani, Wendy Chatterton, Robert J. Munn, Julian A. Hiscox, Robert Beer, Judith Breuer, Caroline E. Walters, Liam Crawford, Ara Darzi, Will P. M. Rowe, Cariad Evans, Matthew Parker, Tammy V Merrill, Louise Aigrain, Joshua Quick, Leigh M Jackson, Samuel M. Nicholls, Jonathan W. Moore, John A Hartley, Graham P. Taylor, Cherian Koshy, Shirelle Burton-Fanning, Sheila Waugh, Catherine Moore, Danielle C. Groves, Peijun Zhang, Sahar Eldirdiri, Derek Fairley, Tim E. A. Peto, Jack Cd Lee, Sharon Glaysher, Liam Prestwood, Hannah Dent, Anita Kenyon, Stephen P. Kidd, Nick Levene, Igor Starinskij, Joseph G. Chappell, Steve Paterson, Gary Eltringham, Laia Fina, Angela Marchbank, Daniel Bradshaw, Marina Escalera Zamudio, Scott Goodwin, Andrew D Beggs, Seema Nickbakhsh, Trevor Robinson, Christina Atchison, David K. Jackson, Kathy Li, Rory Gunson, Sunando Roy, Graham S Cooke, Steven Liggett, Yasmin Chaudhry, Anoop Chauhan, Ben Temperton, Mariateresa de Cesare, Paul E Brown, Li Xu-McCrae, Martin P McHugh, Catherine Ludden, Wendy Smith, Danielle Leek, Divya K. Shah, Judith Heaney, Dominic P. Kwiatkowski, Kate M. Johnson, Robin Howe, Malorie Perry, Tetyana I. Vasylyeva, David F. Bibby, Haowei Wang, Steve Palmer, Nicholas W Machin, Charlotte A Williams, Bree Gatica-Wilcox, Angie Green, John A. Todd, Paul Elliott, Noel Craine, Jeffrey K. J. Cheng, Kate Templeton, Jonathan Hubb, Joshua Maksimovic, Christl A. Donnelly, Monique Andersson, Christopher Holmes, Dimitris Grammatopoulos, Christopher B. Williams, David G Partridge, Aminu S Jahun, Alexander Adams, Marius Cotic, Sarah Essex, Christopher J. Moore, Trudy Workman, Nicola Sheriff, Helen L Lowe, Ewan M. Harrison, Dorota Jamrozy, Rachel Jones, Ellen Higginson, Erwan Acheson, Christopher R. Jones, Oliver G. Pybus, Francesc Coll, Sian Morgan, Paul J. Parsons, Patawee Asamaphan, Veena Raviprakash, Andrew R. Bassett, Declan Bradley, Laura Atkinson, Anthony Underwood, Graciela Sluga, Sally Kay, Ellena Brooks, Oliver Eales, Andrew Whitwham, Surendra Parmar, Angela Cowell, Nicole Pacchiarini, Theocharis Tsoleridis, Jason Coombes, Robert Davies, Flavia Flaviani, Benita Percival, Jenna Nichols, Natasha M. Johnson, Salman Goudarzi, Hibo Asad, Amanda Bradley, Hannah Jones, Chrystala Constantinidou, Georgina M McManus, Minal Patel, Steven Leonard, Rebecca Williams Bmbs, Andrew J. Page, Christoph Puethe, Nicola Reynolds, Amy Ash, John Danesh, Corin Yeats, Claudia Wierzbicki, Kordo Saeed, John Boyes, Michael A. Quail, Sharon J. Peacock, Nabil-Fareed Alikhan, Jon-Paul Keatley, Claudio Fronterre, Garry Scarlett, James McKenna, Thushan I de Silva, Malte L Pinckert, Kate B. Cook, Amy Gaskin, Rajiv Shah, Matthew T. G. Holden, Sophie J Prosolek, Nathaniel Storey, Ryan P George, Lindsay Coupland, Jenifer Mason, Matthew Carlile, Thomas D Stanton, Guy Mollett, Siddharth Mookerjee, Mary Ramsay, Steven Platt, Stephen W Attwood, Susanne Stonehouse, Sophie Jones, Venkat Sivaprakasam, Amy Plimmer, Mark Whitehead, Catherine Bresner, Stefanie V Lensing, Louissa R Macfarlane-Smith, Colin P. Smith, Wendy Hogsden, Charlotte Nelson, Ian Johnston, Jeffrey C. Barrett, Joshua B Singer, Samuel Robson, Zoltán Molnár, Emma L. Wise, Sian Ellard, Kim S Smith, Alice Broos, Manjinder Khakh, Kathryn A Jackson, Claire Cormie, Rachel Tucker, Ian Goodfellow, S.E. Moses, Nicola Cumley, Meera Chand, Debra Padgett, Cassandra S Malone, James V. Price, Themoula Charalampous, Ronan A Lyons, Natalie Groves, Stefan Rooke, Rebekah E Wilson, Stephen Bonner, Richard Stark, Sharon Campbell, Michelle Lister, Carlos Balcazar, Ana da Silva Filipe, Ben Warne, Thomas N. Williams, Marta Gallis, Lauren Gilbert, Rose K Davidson, Angela Helen Beckett, Ember Hilvers, Kathryn McCluggage, Eileen Gallagher, Charlotte Beaver, Nick Cortes, Alisha Davies, Yusri Taha, Leah Ensell, Emanuela Pelosi, Elias Allara, Cressida Auckland, Eleanor Drury, Richard Eccles, Adela Alcolea-Medina, William L Hamilton, Rich Livett, Rachel Blacow, Margaret Hughes, Sarah François, Melisa Louise Fenton, Liz Ratcliffe, Verity Hill, Stephanie Hutchings, Kathryn Ann Harris, Emma Betteridge, William D. Fuller, Sophia T Girgis, Louise Berry, Gemma Clark, Nicholas M Redshaw, Richard Hopes, Leonardo de Oliveira Martins, Alexander J Keeley, Beth Blane, Wendy S. Barclay, Victoria Wright, Anita Lucaci, Luke R. Green, Fenella D. Halstead, Sarah Wyllie, Iraad F. Bronner, Áine O'Toole, Ravi Gupta, Leanne Kane, Clare M. McCann, Michael R Chapman, David W Eyre, Kelly Bicknell, Aileen G. Rowan, Sara Rey, Shazaad Ahmad, Diana Rajan, S Taylor, Sarah J. O'Brien, Alessandro M Carabelli, Amelia Joseph, Max Whiteley, Riaz Jannoo, Victoria Blakey, Martin D. Curran, David J. Studholme, Harmeet K Gill, Thomas R. A. Davis, Sushmita Sridhar, Clive Graham, Julian Tang, Clare Pearson, Mark Kristiansen, Miren Iturriza-Gomara, National Institute for Health Research, and UK Research and Innovation
Subjects: Delta, Adult, Male, 2019-20 coronavirus outbreak, COVID-19 Vaccines, Vaccination Coverage, Coronavirus disease 2019 (COVID-19), Adolescent, General Science & Technology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Vaccine Efficacy, Biology, Young Adult, Exponential growth, Ethnicity, Prevalence, Humans, Child, Aged, Family Characteristics, Multidisciplinary, High prevalence, COVID-19 Genomics UK (COG-UK) Consortium11‡, SARS-CoV-2, Age Factors, COVID-19, Middle Aged, Virology, Hospitalization, England, Socioeconomic Factors, COVID-19 Nucleic Acid Testing, Child, Preschool, Female, Self Report
Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections were rising during early summer 2021 in many countries as a result of the Delta variant. We assessed reverse transcription polymerase chain reaction swab positivity in the Real-time Assessment of Community Transmission–1 (REACT-1) study in England. During June and July 2021, we observed sustained exponential growth with an average doubling time of 25 days, driven by complete replacement of the Alpha variant by Delta and by high prevalence at younger, less-vaccinated ages. Prevalence among unvaccinated people [1.21% (95% credible interval 1.03%, 1.41%)] was three times that among double-vaccinated people [0.40% (95% credible interval 0.34%, 0.48%)]. However, after adjusting for age and other variables, vaccine effectiveness for double-vaccinated people was estimated at between ~50% and ~60% during this period in England. Increased social mixing in the presence of Delta had the potential to generate sustained growth in infections, even at high levels of vaccination.
Published: 2021

30. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

Author: Thushan I. de Silva, Guihai Liu, Benjamin B. Lindsey, Danning Dong, Shona C. Moore, Nienyun Sharon Hsu, Dhruv Shah, Dannielle Wellington, Alexander J. Mentzer, Adrienn Angyal, Rebecca Brown, Matthew D. Parker, Zixi Ying, Xuan Yao, Lance Turtle, Susanna Dunachie, Mala K. Maini, Graham Ogg, Julian C. Knight, Yanchun Peng, Sarah L. Rowland-Jones, Tao Dong, David M. Aanensen, Khalil Abudahab, Helen Adams, Alexander Adams, Safiah Afifi, Dinesh Aggarwal, Shazaad S.Y. Ahmad, Louise Aigrain, Adela Alcolea-Medina, Nabil-Fareed Alikhan, Elias Allara, Roberto Amato, Tara Annett, Stephen Aplin, Cristina V. Ariani, Hibo Asad, Amy Ash, Paula Ashfield, Fiona Ashford, Laura Atkinson, Stephen W. Attwood, Cressida Auckland, Alp Aydin, David J. Baker, Paul Baker, Carlos E. Balcazar, Jonathan Ball, Jeffrey C. Barrett, Magdalena Barrow, Edward Barton, Matthew Bashton, Andrew R. Bassett, Rahul Batra, Chris Baxter, Nadua Bayzid, Charlotte Beaver, Angela H. Beckett, Shaun M. Beckwith, Luke Bedford, Robert Beer, Andrew Beggs, Katherine L. Bellis, Louise Berry, Beatrice Bertolusso, Angus Best, Emma Betteridge, David Bibby, Kelly Bicknell, Debbie Binns, Alec Birchley, Paul W. Bird, Chloe Bishop, Rachel Blacow, Victoria Blakey, Beth Blane, Frances Bolt, James Bonfield, Stephen Bonner, David Bonsall, Tim Boswell, Andrew Bosworth, Yann Bourgeois, Olivia Boyd, Declan T. Bradley, Cassie Breen, Catherine Bresner, Judith Breuer, Stephen Bridgett, Iraad F. Bronner, Ellena Brooks, Alice Broos, Julianne R. Brown, Giselda Bucca, Sarah L. Buchan, David Buck, Matthew Bull, Phillipa J. Burns, Shirelle Burton-Fanning, Timothy Byaruhanga, Matthew Byott, Sharon Campbell, Alessandro M. Carabelli, James S. Cargill, Matthew Carlile, Silvia F. Carvalho, Anna Casey, Anibolina Castigador, Jana Catalan, Vicki Chalker, Nicola J. Chaloner, Meera Chand, Joseph G. Chappell, Themoula Charalampous, Wendy Chatterton, Yasmin Chaudhry, Carol M. Churcher, Gemma Clark, Phillip Clarke, Benjamin J. Cogger, Kevin Cole, Jennifer Collins, Rachel Colquhoun, Thomas R. Connor, Kate F. Cook, Jason Coombes, Sally Corden, Claire Cormie, Nicholas Cortes, Marius Cotic, Seb Cotton, Simon Cottrell, Lindsay Coupland, MacGregor Cox, Alison Cox, Noel Craine, Liam Crawford, Aidan Cross, Matthew R. Crown, Dorian Crudgington, Nicola Cumley, Tanya Curran, Martin D. Curran, Ana da Silva Filipe, Gavin Dabrera, Alistair C. Darby, Rose K. Davidson, Alisha Davies, Robert M. Davies, Thomas Davis, Daniela de Angelis, Elen De Lacy, Leonardo de Oliveira Martins, Johnny Debebe, Rebecca Denton-Smith, Samir Dervisevic, Rebecca Dewar, Jayasree Dey, Joana Dias, Donald Dobie, Matthew J. Dorman, Fatima Downing, Megan Driscoll, Louis du Plessis, Nichola Duckworth, Jillian Durham, Kirstine Eastick, Lisa J. Easton, Richard Eccles, Jonathan Edgeworth, Sue Edwards, Kate El Bouzidi, Sahar Eldirdiri, Nicholas Ellaby, Scott Elliott, Gary Eltringham, Leah Ensell, Michelle J. Erkiert, Marina Escalera Zamudio, Sarah Essex, Johnathan M. Evans, Cariad Evans, William Everson, Derek J. Fairley, Karlie Fallon, Arezou Fanaie, Ben W. Farr, Christopher Fearn, Theresa Feltwell, Lynne Ferguson, Laia Fina, Flavia Flaviani, Vicki M. Fleming, Sally Forrest, Ebenezer Foster-Nyarko, Benjamin H. Foulkes, Luke Foulser, Mireille Fragakis, Dan Frampton, Sarah Francois, Christophe Fraser, Timothy M. Freeman, Helen Fryer, Marc Fuchs, William Fuller, Kavitha Gajee, Katerina Galai, Abbie Gallagher, Eileen Gallagher, Michael D. Gallagher, Marta Gallis, Amy Gaskin, Bree Gatica-Wilcox, Lily Geidelberg, Matthew Gemmell, Iliana Georgana, Ryan P. George, Laura Gifford, Lauren Gilbert, Sophia T. Girgis, Sharon Glaysher, Emily J. Goldstein, Tanya Golubchik, Andrea N. Gomes, Sónia Gonçalves, Ian G. Goodfellow, Scott Goodwin, Salman Goudarzi, Marina Gourtovaia, Clive Graham, Lee Graham, Paul R. Grant, Luke R. Green, Angie Green, Jane Greenaway, Richard Gregory, Martyn Guest, Rory N. Gunson, Ravi K. Gupta, Bernardo Gutierrez, Sam T. Haldenby, William L. Hamilton, Samantha E. Hansford, Tanzina Haque, Kathryn A. Harris, Ian Harrison, Ewan M. Harrison, Jennifer Hart, John A. Hartley, William T. Harvey, Matthew Harvey, Mohammed O. Hassan-Ibrahim, Judith Heaney, Thomas Helmer, John H. Henderson, Andrew R. Hesketh, Jessica Hey, David Heyburn, Ellen E. Higginson, Verity Hill, Jack D. Hill, Rachel A. Hilson, Ember Hilvers, Matthew T.G. Holden, Amy Hollis, Christopher W. Holmes, Nadine Holmes, Alison H. Holmes, Richard Hopes, Hailey R. Hornsby, Myra Hosmillo, Catherine Houlihan, Hannah C. Howson-Wells, Jonathan Hubb, Hannah Huckson, Warwick Hughes, Joseph Hughes, Margaret Hughes, Stephanie Hutchings, Giles Idle, Chris J. Illingworth, Robert Impey, Dianne Irish-Tavares, Miren Iturriza-Gomara, Rhys Izuagbe, Chris Jackson, Ben Jackson, Leigh M. Jackson, Kathryn A. Jackson, David K. Jackson, Aminu S. Jahun, Victoria James, Keith James, Christopher Jeanes, Aaron R. Jeffries, Sarah Jeremiah, Andrew Jermy, Michaela John, Rob Johnson, Kate Johnson, Ian Johnston, Owen Jones, Sophie Jones, Hannah Jones, Christopher R. Jones, Neil Jones, Amelia Joseph, Sarah Judges, Gemma L. Kay, Sally Kay, Jon-Paul Keatley, Alexander J. Keeley, Anita Kenyon, Leanne M. Kermack, Manjinder Khakh, Stephen P. Kidd, Maimuna Kimuli, Stuart Kirk, Christine Kitchen, Katie Kitchman, Bridget A. Knight, Cherian Koshy, Moritz U.G. Kraemer, Sara Kumziene-Summerhayes, Dominic Kwiatkowski, Angie Lackenby, Kenneth G. Laing, Temi Lampejo, Cordelia F. Langford, Deborah Lavin, Andrew I. Lawton, Jack Lee, David Lee, Stefanie V. Lensing, Steven Leonard, Lisa J. Levett, Thanh Le-Viet, Jonathan Lewis, Kevin Lewis, Jennifier Liddle, Steven Liggett, Patrick J. Lillie, Michelle M. Lister, Rich Livett, Stephanie Lo, Nicholas J. Loman, Matthew W. Loose, Stavroula F. Louka, Katie F. Loveson, Sarah Lowdon, Hannah Lowe, Helen L. Lowe, Anita O. Lucaci, Catherine Ludden, Jessica Lynch, Ronan A. Lyons, Katrina Lythgoe, Nicholas W. Machin, George MacIntyre-Cockett, Andrew Mack, Ben Macklin, Alasdair Maclean, Emily Macnaughton, Pinglawathee Madona, Mailis Maes, Laurentiu Maftei, Adhyana I.K. Mahanama, Tabitha W. Mahungu, Daniel Mair, Joshua Maksimovic, Cassandra S. Malone, Daniel Maloney, Nikos Manesis, Robin Manley, Anna Mantzouratou, Angela Marchbank, Arun Mariappan, Inigo Martincorena, Rocio T. Martinez Nunez, Alison E. Mather, Patrick Maxwell, Megan Mayhew, Tamyo Mbisa, Clare M. McCann, Shane A. McCarthy, Kathryn McCluggage, Patrick C. McClure, J.T. McCrone, Martin P. McHugh, James P. McKenna, Caoimhe McKerr, Georgina M. McManus, Claire L. McMurray, Claire McMurray, Alan McNally, Lizzie Meadows, Nathan Medd, Oliver Megram, Mirko Menegazzo, Ian Merrick, Stephen L. Michell, Michelle L. Michelsen, Mariyam Mirfenderesky, Jeremy Mirza, Julia Miskelly, Emma Moles-Garcia, Robin J. Moll, Zoltan Molnar, Irene M. Monahan, Matteo Mondani, Siddharth Mookerjee, Christopher Moore, Jonathan Moore, Nathan Moore, Catherine Moore, Helen Morcrette, Sian Morgan, Mari Morgan, Matilde Mori, Arthur Morriss, Samuel Moses, Craig Mower, Peter Muir, Afrida Mukaddas, Florence Munemo, Robert Munn, Abigail Murray, Leanne J. Murray, Darren R. Murray, Manasa Mutingwende, Richard Myers, Eleni Nastouli, Gaia Nebbia, Andrew Nelson, Charlotte Nelson, Sam Nicholls, Jenna Nichols, Roberto Nicodemi, Kyriaki Nomikou, Justin O’Grady, Sarah O'Brien, Mina Odedra, Natasha Ohemeng-Kumi, Karen Oliver, Richard J. Orton, Husam Osman, null xeine O'Toole, Nicole Pacchiarini, Debra Padgett, Andrew J. Page, Emily J. Park, Naomi R. Park, Surendra Parmar, David G. Partridge, David Pascall, Amita Patel, Bindi Patel, Steve Paterson, Brendan A.I. Payne, Sharon J. Peacock, Clare Pearson, Emanuela Pelosi, Benita Percival, Jon Perkins, Malorie Perry, Malte L. Pinckert, Steven Platt, Olga Podplomyk, Manoj Pohare, Marcus Pond, Cassie F. Pope, Radoslaw Poplawski, Jessica Powell, Jennifer Poyner, Liam Prestwood, Anna Price, James R. Price, Jacqui A. Prieto, David T. Pritchard, Sophie J. Prosolek, Georgia Pugh, Monika Pusok, Oliver G. Pybus, Hannah M. Pymont, Michael A. Quail, Joshua Quick, Clara Radulescu, Jayna Raghwani, Manon Ragonnet-Cronin, Lucille Rainbow, Diana Rajan, Shavanthi Rajatileka, Newara A. Ramadan, Andrew Rambaut, John Ramble, Paul A. Randell, Paul Randell, Liz Ratcliffe, Veena Raviprakash, Mohammad Raza, Nicholas M. Redshaw, Sara Rey, Nicola Reynolds, Alex Richter, David L. Robertson, Esther Robinson, Samuel C. Robson, Fiona Rogan, Stefan Rooke, Will Rowe, Sunando Roy, Steven Rudder, Chris Ruis, Steven Rushton, Felicity Ryan, Kordo Saeed, Buddhini Samaraweera, Christine M. Sambles, Roy Sanderson, Theo Sanderson, Fei Sang, Thea Sass, Emily Scher, Garren Scott, Carol Scott, Jasveen Sehmi, Sharif Shaaban, Divya Shah, Jessica Shaw, Ekaterina Shelest, James G. Shepherd, Liz A. Sheridan, Nicola Sheriff, Lesley Shirley, John Sillitoe, Siona Silviera, David A. Simpson, Aditi Singh, Dawn Singleton, Timofey Skvortsov, Tim J. Sloan, Graciela Sluga, Ken Smith, Kim S. Smith, Perminder Smith, Darren L. Smith, Louise Smith, Colin P. Smith, Nikki Smith, Katherine L. Smollett, Luke B. Snell, Thomas Somassa, Joel Southgate, Karla Spellman, Michael H. Spencer Chapman, Lewis G. Spurgin, Moira J. Spyer, Rachael Stanley, William Stanley, Thomas D. Stanton, Igor Starinskij, Joanne Stockton, Susanne Stonehouse, Nathaniel Storey, David J. Studholme, Malur Sudhanva, Emma Swindells, Yusri Taha, Ngee Keong Tan, Julian W. Tang, Miao Tang, Ben E.W. Taylor, Joshua F. Taylor, Sarah Taylor, Ben Temperton, Kate E. Templeton, Claire Thomas, Laura Thomson, Emma C. Thomson, Alicia Thornton, Scott A.J. Thurston, John A. Todd, Rachael Tomb, Lily Tong, Gerry Tonkin-Hill, M. Estee Torok, Jaime M. Tovar-Corona, Amy Trebes, Alexander J. Trotter, Ioulia Tsatsani, Robyn Turnbull, Katherine A. Twohig, Helen Umpleby, Anthony P. Underwood, Edith E. Vamos, Tetyana I. Vasylyeva, Sreenu Vattipally, Gabrielle Vernet, Barry B. Vipond, Erik M. Volz, Sarah Walsh, Dennis Wang, Ben Warne, Joanna Warwick-Dugdale, Elizabeth Wastnedge, Joanne Watkins, Louisa K. Watson, Sheila Waugh, Hermione J. Webster, Danni Weldon, Elaine Westwick, Thomas Whalley, Helen Wheeler, Mark Whitehead, Max Whiteley, Andrew Whitwham, Claudia Wierzbicki, Nicholas J. Willford, Lesley-Anne Williams, Rebecca Williams, Cheryl Williams, Chris Williams, Charlotte A. Williams, Rachel J. Williams, Thomas Williams, Catryn Williams, Kathleen A. Williamson, Eleri Wilson-Davies, Eric Witele, Karen T. Withell, Adam A. Witney, Paige Wolverson, Nick Wong, Trudy Workman, Victoria Wright, Derek W. Wright, Tim Wyatt, Sarah Wyllie, Li Xu-McCrae, Mehmet Yavus, Geraldine Yaze, Corin A. Yeats, Gonzalo Yebra, Wen C. Yew, Gregory R. Young, Jamie Young, Alex E. Zarebski, Peijun Zhang, J. Kenneth Baillie, Malcolm G. Semple, Peter J.M. Openshaw, Gail Carson, Beatrice Alex, Petros Andrikopoulos, Benjamin Bach, Wendy S. Barclay, Debby Bogaert, Kanta Chechi, Graham S. Cooke, Annemarie B. Docherty, Gonçalo dos Santos Correia, Marc-Emmanuel Dumas, Jake Dunning, Tom Fletcher, Christopher A. Green, William Greenhalf, Julian L. Griffin, Rishi K. Gupta, Ewen M. Harrison, Julian A. Hiscox, Antonia Ying Wai Ho, Peter W. Horby, Samreen Ijaz, Saye Khoo, Paul Klenerman, Andrew Law, Matthew R. Lewis, Sonia Liggi, Wei Shen Lim, Lynn Maslen, Laura Merson, Alison M. Meynert, Mahdad Noursadeghi, Michael Olanipekun, Anthonia Osagie, Massimo Palmarini, Carlo Palmieri, William A. Paxton, Georgios Pollakis, Nicholas Price, Clark D. Russell, Vanessa Sancho-Shimizu, Caroline J. Sands, Janet T. Scott, Louise Sigfrid, Tom Solomon, Shiranee Sriskandan, David Stuart, Charlotte Summers, Olivia V. Swann, Zoltan Takats, Panteleimon Takis, Richard S. Tedder, A.A. Roger Thompson, Ryan S. Thwaites, Maria Zambon, Hayley Hardwick, Chloe Donohue, Fiona Griffiths, Wilna Oosthuyzen, Cara Donegan, Rebecca G. Spencer, Jo Dalton, Michelle Girvan, Egle Saviciute, Stephanie Roberts, Janet Harrison, Laura Marsh, Marie Connor, Sophie Halpin, Clare Jackson, Carrol Gamble, Daniel Plotkin, James Lee, Gary Leeming, Murray Wham, Sara Clohisey, Ross Hendry, James Scott-Brown, Victoria Shaw, Sarah E. McDonald, Seán Keating, Katie A. Ahmed, Jane A. Armstrong, Milton Ashworth, Innocent G. Asiimwe, Siddharth Bakshi, Samantha L. Barlow, Laura Booth, Benjamin Brennan, Katie Bullock, Benjamin W.A. Catterall, Jordan J. Clark, Emily A. Clarke, Sarah Cole, Louise Cooper, Helen Cox, Christopher Davis, Oslem Dincarslan, Chris Dunn, Philip Dyer, Angela Elliott, Anthony Evans, Lorna Finch, Lewis W.S. Fisher, Terry Foster, Isabel Garcia-Dorival, Philip Gunning, Catherine Hartley, Rebecca L. Jensen, Christopher B. Jones, Trevor R. Jones, Shadia Khandaker, Katharine King, Robyn T. Kiy, Chrysa Koukorava, Annette Lake, Suzannah Lant, Diane Latawiec, Lara Lavelle-Langham, Daniella Lefteri, Lauren Lett, Lucia A. Livoti, Maria Mancini, Sarah McDonald, Laurence McEvoy, John McLauchlan, Soeren Metelmann, Nahida S. Miah, Joanna Middleton, Joyce Mitchell, Ellen G. Murphy, Rebekah Penrice-Randal, Jack Pilgrim, Tessa Prince, Will Reynolds, P. Matthew Ridley, Debby Sales, Victoria E. Shaw, Rebecca K. Shears, Benjamin Small, Krishanthi S. Subramaniam, Agnieska Szemiel, Aislynn Taggart, Jolanta Tanianis-Hughes, Jordan Thomas, Erwan Trochu, Libby van Tonder, Eve Wilcock, J. Eunice Zhang, Lisa Flaherty, Nicole Maziere, Emily Cass, Alejandra Doce Carracedo, Nicola Carlucci, Anthony Holmes, Hannah Massey, Lee Murphy, Nicola Wrobel, Sarah McCafferty, Kirstie Morrice, Alan MacLean, Kayode Adeniji, Daniel Agranoff, Ken Agwuh, Dhiraj Ail, Erin L. Aldera, Ana Alegria, Sam Allen, Brian Angus, Abdul Ashish, Dougal Atkinson, Shahedal Bari, Gavin Barlow, Stella Barnass, Nicholas Barrett, Christopher Bassford, Sneha Basude, David Baxter, Michael Beadsworth, Jolanta Bernatoniene, John Berridge, Colin Berry, Nicola Best, Pieter Bothma, David Chadwick, Robin Brittain-Long, Naomi Bulteel, Tom Burden, Andrew Burtenshaw, Vikki Caruth, Duncan Chambler, Nigel Chee, Jenny Child, Srikanth Chukkambotla, Tom Clark, Paul Collini, Catherine Cosgrove, Jason Cupitt, Maria-Teresa Cutino-Moguel, Paul Dark, Chris Dawson, Phil Donnison, Sam Douthwaite, Andrew Drummond, Ingrid DuRand, Ahilanadan Dushianthan, Tristan Dyer, Chi Eziefula, Chrisopher Fegan, Adam Finn, Duncan Fullerton, Sanjeev Garg, Atul Garg, Effrossyni Gkrania-Klotsas, Jo Godden, Arthur Goldsmith, Elaine Hardy, Stuart Hartshorn, Daniel Harvey, Peter Havalda, Daniel B. Hawcutt, Maria Hobrok, Luke Hodgson, Anil Hormis, Michael Jacobs, Susan Jain, Paul Jennings, Agilan Kaliappan, Vidya Kasipandian, Stephen Kegg, Michael Kelsey, Jason Kendall, Caroline Kerrison, Ian Kerslake, Oliver Koch, Gouri Koduri, George Koshy, Shondipon Laha, Steven Laird, Susan Larkin, Tamas Leiner, Patrick Lillie, James Limb, Vanessa Linnett, Jeff Little, Mark Lyttle, Michael MacMahon, Emily MacNaughton, Ravish Mankregod, Huw Masson, Elijah Matovu, Katherine McCullough, Ruth McEwen, Manjula Meda, Gary Mills, Jane Minton, Kavya Mohandas, Quen Mok, James Moon, Elinoor Moore, Patrick Morgan, Craig Morris, Katherine Mortimore, Mbiye Mpenge, Rohinton Mulla, Michael Murphy, Megan Nagel, Thapas Nagarajan, Mark Nelson, Lillian Norris, Matthew K. O'Shea, Igor Otahal, Marlies Ostermann, Mark Pais, Selva Panchatsharam, Danai Papakonstantinou, Hassan Paraiso, Brij Patel, Natalie Pattison, Justin Pepperell, Mark Peters, Mandeep Phull, Stefania Pintus, Jagtur Singh Pooni, Tim Planche, Frank Post, David Price, Rachel Prout, Nikolas Rae, Henrik Reschreiter, Tim Reynolds, Neil Richardson, Mark Roberts, Devender Roberts, Alistair Rose, Guy Rousseau, Bobby Ruge, Brendan Ryan, Taranprit Saluja, Matthias L. Schmid, Aarti Shah, Prad Shanmuga, Anil Sharma, Anna Shawcross, Jeremy Sizer, Manu Shankar-Hari, Richard Smith, Catherine Snelson, Nick Spittle, Nikki Staines, Tom Stambach, Richard Stewart, Pradeep Subudhi, Tamas Szakmany, Kate Tatham, Jo Thomas, Chris Thompson, Robert Thompson, Ascanio Tridente, Darell Tupper-Carey, Mary Twagira, Nick Vallotton, Rama Vancheeswaran, Lisa Vincent-Smith, Shico Visuvanathan, Alan Vuylsteke, Sam Waddy, Rachel Wake, Andrew Walden, Ingeborg Welters, Tony Whitehouse, Paul Whittaker, Ashley Whittington, Padmasayee Papineni, Meme Wijesinghe, Martin Williams, Lawrence Wilson, Stephen Winchester, Martin Wiselka, Adam Wolverson, Daniel G. Wootton, Andrew Workman, Bryan Yates, Peter Young, UK Research and Innovation, Division of Computational and Systems Medicine, Imperial College London, London, SW7 2AZ, UK, Imperial College London - National Heart and Lung Institute, Centre National de la Recherche Scientifique (CNRS), and Apollo - University of Cambridge Repository
Subjects: Molecular biology, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Science, Immunology, Biology, Epitope, Article, A900, 03 medical and health sciences, 0302 clinical medicine, Data sequences, Immune system, COVID-19 Genomics UK (COG-UK) Consortium, Virology, Cytotoxic T cell, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], Immune response, Receptor, ISARIC4C Investigators, 030304 developmental biology, 0303 health sciences, Multidisciplinary, C100, A300, C900, 3. Good health, Phylogenetics, 030220 oncology & carcinogenesis, Humoral immunity, [SDV.IMM]Life Sciences [q-bio]/Immunology, CD8
Abstract: We identify amino acid variants within dominant SARS-CoV-2 T-cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T-cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T-cell responsiveness was seen due to Q213K in the A*01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215, due to P13L, P13S and P13T in the B*27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17, and due to T362I and P365S in the A*03:01/A*11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T-cell lines unable to recognise variant epitopes have diverse T-cell receptor repertoires. These data demonstrate the potential for T-cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T-cell as well as humoral immunity., Graphical Abstract
Published: 2021

31. Characteristics and outcomes of an international cohort of 400,000 hospitalised patients with Covid-19

Author: Charlotte Summers, Hikombo HITOTO, Anne Sophie Boureau, Pawel Twardowski, Fernando Augusto Bozza, Mark Pritchard, Elias Iosifidis, Jamel Ortoleva, Emanuele Durante-Mangoni, Andreas Lind, Lance Turtle, Paul Le Turnier, Thushan De Silva, Malcolm Gracie Semple, Tom Fletcher, Fakhir Haidri, Sarah Cormican, Ali AIT HSSAIN, Giorgia Montrucchio, Alexandre Gaymard, Gianluigi Li Bassi, Martina Hennessy, Hernando Torres-Zevallos, Waasila Jassat, Oksana Kruglova, Pablo Serrano Balazote, Juan Pablo Horcajada, Christophe Fraser, Mary Catherine Mone, Louise Sigfrid, Patrick Archambault, Jeffrey Javidfar, Francois Lamontagne, Aidan Burrell, Srinivas Murthy, Mauro Panigada, Kevin Bouiller, Helena Barrasa, Hoi Ping Shum, Guillaume Martin-Blondel, Dominique Deplanque, Miguel Pedrera-Jiménez, Clarice Tanaka, William Paxton, Alberto Cucino, Sophie Yacoub, Emmanuelle Denis, Abigail Beane, and Devachandran Jayakumar
Subjects: medicine.medical_specialty, Proportional hazards model, business.industry, Hazard ratio, Respiratory infection, Context (language use), Intensive care unit, law.invention, law, Cohort, Case fatality rate, Emergency medicine, Global health, medicine, business
Abstract: BackgroundPolicymakers need robust data to respond to the COVID-19 pandemic. We describe demographic features, treatments and clinical outcomes in the International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) COVID-19 cohort, the world’s largest international, standardised cohort of hospitalised patients.MethodsThe dataset analysed includes COVID-19 patients hospitalised between January 2020 and May 2021. We investigated how symptoms on admission, comorbidities, risk factors, and treatments varied by age, sex, and other characteristics. We used Cox proportional hazards models to investigate associations between demographics, symptoms, comorbidities, and other factors with risk of death, admission to intensive care unit (ICU), and invasive mechanical ventilation (IMV).Findings439,922 patients with laboratory-confirmed (91.7%) or clinically-diagnosed (8.3%) SARS-CoV-2 infection from 49 countries were enrolled. Age (adjusted hazard ratio [HR] per 10 years 1.49 [95% CI 1.49-1.50]) and male sex (1.26 [1.24-1.28]) were associated with a higher risk of death. Rates of admission to ICU and use of IMV increased with age up to age 60, then dropped. Symptoms, comorbidities, and treatments varied by age and had varied associations with clinical outcomes. Tuberculosis was associated with an 86% higher risk of death, and HIV with an 87% higher risk of death. Case fatality ratio varied by country partly due to differences in the clinical characteristics of recruited patients.InterpretationThe size of our international database and the standardized data collection method makes this study a reliable and comprehensive international description of COVID-19 clinical features. This is a viable model to be applied to future epidemics.FundingUK Foreign, Commonwealth and Development Office, the Bill & Melinda Gates Foundation and Wellcome. See acknowledgements section for funders of sites that contributed data.Research in contextEvidence before this studyTo identify large, international analyses of hospitalised COVID-19 patients that used standardised data collection, we conducted a systematic review of the literature from 1 Jan 2020 to 28 Apr 2020. We identified 78 studies, with data from 77,443 people (1) predominantly from China. We could not find any studies including data from low and middle-income countries. We repeated our search on 18 Aug 2021 but could not identify any further studies that met our inclusion criteria.Added value of this studyOur study uses standardised clinical data collection to collect data from a vast number of patients across the world, including patients from low-, middle-, and high-income countries. The size of our database gives us great confidence in the accuracy of our descriptions of the global impact of COVID-19. We can confirm findings reported by smaller, country-specific studies and compare clinical data between countries. We have demonstrated that it is possible to collect large volumes of standardised clinical data during a pandemic of a novel acute respiratory infection. The results provide a valuable resource for present policymakers and future global health researchers.Implications of all the available evidencePresenting symptoms of SARS-CoV-2 infection in patients requiring hospitalisation are now well-described globally, with the most common being fever, cough, and shortness of breath. Other symptoms also commonly occur, including altered consciousness in older adults and gastrointestinal symptoms in younger patients, and age can influence the likelihood of a patient having symptoms that match one or more case definitions. There are geographic and temporal variations in the case fatality rate (CFR), but overall, CFR was 20.6% in this large international cohort of hospitalised patients with a median age of 60 years (IQR: 45 to 74 years).
Published: 2021

32. PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial

Author: Peter Bock, Estelle Piwowar-Manning, Richard J. Hayes, Sarah Fidler, Robert Hinch, Anne Cori, Rafael Sauter, Hptn (PopART) Study Team, Sian Floyd, Michael Pickles, Deborah Donnell, Christophe Fraser, Ethan Wilson, Helen Ayles, William J. M. Probert, and Medical Research Council (MRC)
Subjects: RNA viruses, Male, Epidemiology, Computer science, Human immunodeficiency virus (HIV), HIV Infections, Pathology and Laboratory Medicine, medicine.disease_cause, Geographical Locations, Immunodeficiency Viruses, Antiretroviral Therapy, Highly Active, Prevalence, Econometrics, Public and Occupational Health, Viral suppression, Biology (General), Hiv transmission, Virus Testing, Ecology, Simulation and Modeling, Incidence, virus diseases, Middle Aged, Vaccination and Immunization, Computational Theory and Mathematics, HIV epidemiology, Medical Microbiology, Viral Pathogens, Modeling and Simulation, Viruses, Disease Progression, Female, Pathogens, Algorithms, Research Article, Adult, Sexual network, Adolescent, Bioinformatics, QH301-705.5, Immunology, Antiretroviral Therapy, Zambia, Context (language use), Research and Analysis Methods, HPTN 071 (PopART) Study Team, Bayesian inference, Microbiology, Young Adult, Cellular and Molecular Neuroscience, Individual based, Antiviral Therapy, Diagnostic Medicine, Retroviruses, Genetics, medicine, Humans, Computer Simulation, IBM, Microbial Pathogens, Molecular Biology, 01 Mathematical Sciences, Ecology, Evolution, Behavior and Systematics, Aged, Medicine and health sciences, Stochastic Processes, Models, Statistical, Lentivirus, Organisms, Hiv epidemiology, Biology and Life Sciences, HIV, Reproducibility of Results, 06 Biological Sciences, Age Groups, Medical Risk Factors, People and Places, Africa, Population Groupings, Preventive Medicine, 08 Information and Computing Sciences
Abstract: Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention., Author summary In this paper we present PopART-IBM, an individual-based model used to simulate HIV transmission in communities in high prevalence settings. We show that PopART-IBM can simulate transmission over a span of decades in a large community in less than a minute. This computational efficiency allows us to calibrate the model within an inference framework, and we show an illustrative example of calibration using an adaptive population Monte Carlo Approximate Bayesian Computation algorithm for a community in Zambia that was part of the HPTN-071 (PopART) trial. We compare the detailed model output to real-world data collected during the trial from this community. Finally, we project how the HIV epidemic would have changed over time in this community if no intervention from the trial had occurred.
Published: 2021

33. Modelling the effectiveness and social costs of daily lateral flow antigen tests versus quarantine in preventing onward transmission of COVID-19 from traced contacts

Author: Michelle Kendall, Robert Hinch, Christophe Fraser, Chris Wymant, Joanna Masel, Lele Zhao, Tim E. A. Peto, John I. Bell, David Bonsall, Anel Nurtay, Susan Hopkins, Luca Ferretti, A. Marm Kilpatrick, and Lucie Abeler-Dörner
Subjects: 2019-20 coronavirus outbreak, education.field_of_study, Coronavirus disease 2019 (COVID-19), business.industry, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Population, law.invention, Transmission (mechanics), law, Environmental health, Quarantine, Medicine, business, education, Contact tracing
Abstract: Quarantining close contacts of individuals infected with SARS-CoV-2 for 10 to 14 days is a key strategy in reducing transmission. However, quarantine requirements are often unpopular, with low adherence, especially when a large fraction of the population has been vaccinated. Daily contact testing (DCT), in which contacts are required to isolate only if they test positive, is an alternative to quarantine for mitigating the risk of transmission from traced contacts. In this study, we developed an integrated model of COVID-19 transmission dynamics and compared the strategies of quarantine and DCT with regard to reduction in transmission and social/economic costs (days of quarantine/self-isolation). Specifically, we compared 10-day quarantine to 7 days of self-testing using rapid lateral flow antigen tests, starting 3 days after exposure to a case. We modelled both incomplete adherence to quarantine and incomplete adherence to DCT. We found that DCT reduces transmission from contacts with similar effectiveness, at much lower social/economic costs, especially for highly vaccinated populations. The findings were robust across a spectrum of scenarios with varying assumptions on the speed of contact tracing, sensitivity of lateral flow antigen tests, adherence to quarantine and uptake of testing. Daily tests would also allow rapid initiation of a new round of tracing from infected contacts.
Published: 2021

34. HIV drug resistance in a community-randomized trial of universal testing and treatment: HPTN 071 (PopART)

Author: Jessica M, Fogel, Ethan A, Wilson, Estelle, Piwowar-Manning, Autumn, Breaud, William, Clarke, Christos, Petropoulos, Ayana, Moore, Christophe, Fraser, Barry, Kosloff, Kwame, Shanaube, Gert, van Zyl, Michelle, Scheepers, Sian, Floyd, Peter, Bock, Helen, Ayles, Sarah, Fidler, Richard, Hayes, Deborah, Donnell, and Susan H, Eshleman
Subjects: Adult, Infectious Diseases, Anti-Retroviral Agents, Public Health, Environmental and Occupational Health, Drug Resistance, Humans, Reverse Transcriptase Inhibitors, HIV Infections, Viremia, Viral Load
Abstract: Universal HIV testing and treatment (UTT) has individual and public health benefits. HPTN 071 (PopART), a community-randomized trial in Zambia and South Africa, demonstrated that UTT decreased HIV incidence. This endpoint was assessed in a cohort of48,000 randomly selected adults in the study communities. We evaluated the impact of UTT on HIV drug resistance in this cohort and compared other resistance-related outcomes in participants with recent versus non-recent HIV infection.Two years after the start of HPTN 071 (2016-2017), 6259 participants were HIV positive and 1902 were viremic (viral load400 copies/ml). HIV genotyping and antiretroviral (ARV) drug testing were performed for viremic participants in three groups: seroconverters (infected1 year), non-seroconverters (infected1 year, random subset) and participants with unknown duration of infection (random subset). A two-stage cluster-based approach was used to assess the impact of the study intervention on drug resistance. Treatment failure was defined as being viremic with ARV drugs detected. Participants were classified as ARV naïve based on self-report and ARV drug testing.Genotyping results were obtained for 758 participants (143 seroconverters; 534 non-seroconverters; and 81 unknown duration of infection). The estimated prevalence of resistance in the study communities was 37% for all viremic persons and 11% for all HIV-positive persons. There was no association between UTT and drug resistance. Resistance was detected in 14.0% of seroconverters and 40.8% of non-seroconverters (non-nucleoside reverse transcriptase inhibitor resistance: 14.0% and 39.9%; nucleoside/nucleotide reverse transcriptase inhibitor resistance: 0.7% and 15.5%; protease inhibitor resistance: 0% and 1.9%; multi-class resistance: 0.7% and 16.1%, respectively). ARV drugs were detected in 2/139 (1.4%) of seroconverters and 94/534 (17.6%) of non-seroconverters tested. These participants were classified as failing ART; 88 (93.6%) of the non-seroconverters failing ART had resistance. Mutations used for surveillance of transmitted drug resistance were detected in 10.5% of seroconverters and 15.1% of non-seroconverters who were ARV naive.UTT was not associated with an increase in drug resistance in this cohort. Higher rates of drug resistance and multi-class resistance were observed in non-seroconverters compared to seroconverters.
Published: 2021

35. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil; an exploratory analysis of a randomised controlled trial

Author: Ana Pitella, Eveline Pipolo Milan, S Bibi, Katherine R. W. Emary, D Jenkin, Merryn Voysey, Jeremy Ratcliff, Sarah C. Gilbert, Lily Yin Weckx, Eduardo Sprinz, P M Folegatti, Simon Kerridge, Christophe Fraser, Andrew J. Pollard, Tanya Golubchik, Yama F Mujadidi, Michelle Fuskova, Alexandre Vargas Schwarzbold, N G Marchevsky, Teresa Lambe, Sue Ann Costa Clemens, Ana Verena Mendes, Emma Plested, Parvinder K. Aley, David Bonsall, Peter Simmonds, Sarah Kelly, and M N Ramasamy
Subjects: medicine.medical_specialty, education.field_of_study, business.industry, Population, Vaccine efficacy, law.invention, Vaccination, Randomized controlled trial, law, Internal medicine, Relative risk, Pandemic, Genotype, Medicine, business, education, Viral load
Abstract: Background Emerging evidence shows the substantial real-world impact of authorised vaccines against COVID-19 and provides insight into the potential role of vaccines in curbing the pandemic. However, there remains uncertainty about the efficacy of vaccines against different variants of the virus. Here we assessed efficacy of ChAdOx1 nCoV-19 (AZD1222) against lineages of SARS-CoV-2 circulating in Brazil from June 2020 until early 2021. Methods Participants aged 18 and above were enrolled into a randomised phase 3 trial of ChAdOx1 nCoV-19 vaccine against symptomatic SARS-CoV-2 infection. Participants received two doses of ChAdOx1 nCoV-19 or control (1st dose: Men ACWY vaccine, 2nd dose: normal saline). Nasopharyngeal and oropharyngeal swabbing was performed if participants developed symptoms of COVID-19 (cough, shortness of breath, fever >37.8°C, ageusia, anosmia). Swabs were tested by nucleic acid amplification (NAAT) for SARS-CoV-2, sequenced, and viral load determined. For those samples where a genotype could not be ascertained from sequencing, allele specific PCR was performed. The efficacy analysis included symptomatic COVID-19 in seronegative participants with a NAAT positive swab more than 14 days after a second dose of vaccine. Participants were unblinded after the vaccine was authorised for use, and the control participants offered vaccination. Infections occurring after unblinding were excluded from analysis. Vaccine efficacy was calculated as 100% x (1 – relative risk (RR)), where RR was estimated from a robust Poisson model. The trial is registered at ISRCTN89951424. Findings 9433 participants were eligible for inclusion in the pre-specified primary efficacy population, having reached more than 14 days after a second dose of ChAdOx1 nCoV-19, of whom 307 were NAAT+, in this post-hoc analysis. From June 2020 to February 2021, the two most frequently identified lineages were P.2 (N=153) and B.1.1.28 (N=49). P.1 emerged during the study (N=18) but became dominant only after study unblinding. Viral loads were highest amongst those with P.1 infection. Vaccine efficacy (VE) for B.1.1.33 (88.2%, 95%CI 5, 99), B.1.1.28 (73%, 95% CI, 46, 86), P.2 (69% 95% CI, 55, 78) and P.1 (64%, 95% CI, -2, 87) was estimated. In participants who had received two doses of vaccine, one COVID-19 hospitalisation occurred in the ChAdOx1 nCoV-19 group and 18 in the control group, with VE against hospitalisation 95% (95% CI 61, 99). There were 2 COVID-19 deaths in the control group and none in the vaccine group. Interpretation ChAdOx1 nCoV-19 provides high efficacy against hospitalisation, severe disease and death from COVID-19 in Brazil and there is strong evidence of protection being maintained against P.2, despite the presence of the spike protein mutation E484K. Real world effectiveness studies are ongoing in Brazil to further establish protection against P.1 and other emerging variants.
Published: 2021

36. OpenABM-Covid19-An agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

Author: Robert Hinch, Katie Bentley, Anthony Finkelstein, Lele Zhao, Tommaso Ristori, Thomas Mead, Lucie Abeler-Dörner, Matthew Hall, Olivier Legat, Daniel Montero, Christophe Fraser, Chris Wymant, James Warren, Ana Bulas Cruz, William J. M. Probert, Andrea Stewart, David Bonsall, Matthew Abueg, Luca Ferretti, Nicole Mather, Katrina A. Lythgoe, Dylan Feldner-Busztin, Kelvin Van-Vuuren, Neo Wu, Michelle Kendall, and Anel Nurtay
Subjects: 0301 basic medicine, Viral Diseases, Systems Analysis, Epidemiology, Computer science, Inference, Geographical locations, Disease Outbreaks, COVID-19 Testing, Medical Conditions, 0302 clinical medicine, Documentation, Epidemiological Statistics, Medicine and Health Sciences, Public and Occupational Health, Biology (General), Virus Testing, Agent-based model, Vaccines, education.field_of_study, Computational model, Ecology, Vaccination and Immunization, Europe, Infectious Diseases, England, Computational Theory and Mathematics, Risk analysis (engineering), Modeling and Simulation, Transparency (graphic), Quarantine, Epidemiological Methods and Statistics, Research Article, COVID-19 Vaccines, Infectious Disease Control, QH301-705.5, Physical Distancing, Immunology, Population, Modularity, Infectious Disease Epidemiology, 03 medical and health sciences, Cellular and Molecular Neuroscience, Diagnostic Medicine, Genetics, Humans, European Union, education, Molecular Biology, Ecology, Evolution, Behavior and Systematics, SARS-CoV-2, COVID-19, Biology and Life Sciences, Covid 19, United Kingdom, 030104 developmental biology, Systems analysis, Age Groups, People and Places, Population Groupings, Preventive Medicine, Contact Tracing, 030217 neurology & neurosurgery
Abstract: SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with computational models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing, and vaccination programmes. It can simulate a population of 1 million people in seconds per day, allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 are its Python and R interfaces, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic., Author summary Throughout the COVID-19 pandemic, computational modelling has been used to inform key uncertainties facing policymakers such as the number of cases and deaths, hospital capacity, tests and contact tracers. Models need to be: sufficiently complex to yield realistic predictions; computationally efficient to allow calibrations; and easy to use so that various policy mixes can be evaluated. OpenABM-Covid19 is a detailed epidemic model of the spread of COVID-19, simulating every individual in a population. Our model enables scientists and policymakers to quickly compare the effectiveness of non-pharmaceutical interventions like lockdowns, testing, quarantine, and digital and manual contact tracing. The model considers a hypothetical city with a default population of 1 million people whose ages and contact patterns are parameterised according to UK demographics. All of the parameters are openly documented and modifiable so that they can be adapted to fit other countries’ data, and refined to match our understanding of COVID-19 as the epidemic progresses. The computer model simulates people’s movement between their homes, workplaces, schools, and social interactions. OpenABM-Covid19 is open source and has been developed collaboratively by teams from academia and industry. Its modularity, documentation, testing framework, and accessibility via Python and R have provided validation, invited contributions, and encouraged wide adoption.
Published: 2021

37. Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

Author: Bo Meng, Steven A. Kemp, Guido Papa, Rawlings Datir, Isabella A.T.M. Ferreira, Sara Marelli, William T. Harvey, Spyros Lytras, Ahmed Mohamed, Giulia Gallo, Nazia Thakur, Dami A. Collier, Petra Mlcochova, Lidia M. Duncan, Alessandro M. Carabelli, Julia C. Kenyon, Andrew M. Lever, Anna De Marco, Christian Saliba, Katja Culap, Elisabetta Cameroni, Nicholas J. Matheson, Luca Piccoli, Davide Corti, Leo C. James, David L. Robertson, Dalan Bailey, Ravindra K. Gupta, Samuel C. Robson, Nicholas J. Loman, Thomas R. Connor, Tanya Golubchik, Rocio T. Martinez Nunez, Catherine Ludden, Sally Corden, Ian Johnston, David Bonsall, Colin P. Smith, Ali R. Awan, Giselda Bucca, M. Estee Torok, Kordo Saeed, Jacqui A. Prieto, David K. Jackson, William L. Hamilton, Luke B. Snell, Catherine Moore, Ewan M. Harrison, Sonia Goncalves, Derek J. Fairley, Matthew W. Loose, Joanne Watkins, Rich Livett, Samuel Moses, Roberto Amato, Sam Nicholls, Matthew Bull, Darren L. Smith, Jeff Barrett, David M. Aanensen, Martin D. Curran, Surendra Parmar, Dinesh Aggarwal, James G. Shepherd, Matthew D. Parker, Sharon Glaysher, Matthew Bashton, Anthony P. Underwood, Nicole Pacchiarini, Katie F. Loveson, Kate E. Templeton, Cordelia F. Langford, John Sillitoe, Thushan I. de Silva, Dennis Wang, Dominic Kwiatkowski, Andrew Rambaut, Justin O’Grady, Simon Cottrell, Matthew T.G. Holden, Emma C. Thomson, Husam Osman, Monique Andersson, Anoop J. Chauhan, Mohammed O. Hassan-Ibrahim, Mara Lawniczak, Alex Alderton, Meera Chand, Chrystala Constantinidou, Meera Unnikrishnan, Alistair C. Darby, Julian A. Hiscox, Steve Paterson, Inigo Martincorena, Erik M. Volz, Andrew J. Page, Oliver G. Pybus, Andrew R. Bassett, Cristina V. Ariani, Michael H. Spencer Chapman, Kathy K. Li, Rajiv N. Shah, Natasha G. Jesudason, Yusri Taha, Martin P. McHugh, Rebecca Dewar, Aminu S. Jahun, Claire McMurray, Sarojini Pandey, James P. McKenna, Andrew Nelson, Gregory R. Young, Clare M. McCann, Scott Elliott, Hannah Lowe, Ben Temperton, Sunando Roy, Anna Price, Sara Rey, Matthew Wyles, Stefan Rooke, Sharif Shaaban, Mariateresa de Cesare, Laura Letchford, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Myra Hosmillo, Áine O’Toole, Andrew R. Hesketh, Richard Stark, Louis du Plessis, Chris Ruis, Helen Adams, Yann Bourgeois, Stephen L. Michell, Dimitris Grammatopoulos, Jonathan Edgeworth, Judith Breuer, John A. Todd, Christophe Fraser, David Buck, Michaela John, Gemma L. Kay, Steve Palmer, Sharon J. Peacock, David Heyburn, Danni Weldon, Esther Robinson, Alan McNally, Peter Muir, Ian B. Vipond, John Boyes, Venkat Sivaprakasam, Tranprit Salluja, Samir Dervisevic, Emma J. Meader, Naomi R. Park, Karen Oliver, Aaron R. Jeffries, Sascha Ott, Ana da Silva Filipe, David A. Simpson, Chris Williams, Jane A.H. Masoli, Bridget A. Knight, Christopher R. Jones, Cherian Koshy, Amy Ash, Anna Casey, Andrew Bosworth, Liz Ratcliffe, Li Xu-McCrae, Hannah M. Pymont, Stephanie Hutchings, Lisa Berry, Katie Jones, Fenella Halstead, Thomas Davis, Christopher Holmes, Miren Iturriza-Gomara, Anita O. Lucaci, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Kathryn Ann Harris, Julianne Rose Brown, Tabitha W. Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Steven Liggett, Clive Graham, Emma Swindells, Jennifer Collins, Gary Eltringham, Sharon Campbell, Patrick C. McClure, Gemma Clark, Tim J. Sloan, Carl Jones, Jessica Lynch, Ben Warne, Steven Leonard, Jillian Durham, Thomas Williams, Sam T. Haldenby, Nathaniel Storey, Nabil-Fareed Alikhan, Nadine Holmes, Christopher Moore, Matthew Carlile, Malorie Perry, Noel Craine, Ronan A. Lyons, Angela H. Beckett, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, Robert Davies, Beth Blane, Sophia T. Girgis, Mathew A. Beale, Katherine L. Bellis, Matthew J. Dorman, Eleanor Drury, Leanne Kane, Sally Kay, Samantha McGuigan, Rachel Nelson, Liam Prestwood, Shavanthi Rajatileka, Rahul Batra, Rachel J. Williams, Mark Kristiansen, Angie Green, Anita Justice, Adhyana I.K. Mahanama, Buddhini Samaraweera, Nazreen F. Hadjirin, Joshua Quick, Radoslaw Poplawski, Leanne M. Kermack, Nicola Reynolds, Grant Hall, Yasmin Chaudhry, Malte L. Pinckert, Iliana Georgana, Robin J. Moll, Alicia Thornton, Richard Myers, Joanne Stockton, Charlotte A. Williams, Wen C. Yew, Alexander J. Trotter, Amy Trebes, George MacIntyre-Cockett, Alec Birchley, Alexander Adams, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Ember Hilvers, Hannah Jones, Hibo Asad, Jason Coombes, Johnathan M. Evans, Laia Fina, Lauren Gilbert, Lee Graham, Michelle Cronin, Sara Kumziene-Summerhayes, Sarah Taylor, Sophie Jones, Danielle C. Groves, Peijun Zhang, Marta Gallis, Stavroula F. Louka, Igor Starinskij, Chris Jackson, Marina Gourtovaia, Gerry Tonkin-Hill, Kevin Lewis, Jaime M. Tovar-Corona, Keith James, Laura Baxter, Mohammad T. Alam, Richard J. Orton, Joseph Hughes, Sreenu Vattipally, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Olivia Boyd, Lily Geidelberg, Alex E. Zarebski, Jayna Raghwani, Moritz U.G. Kraemer, Joel Southgate, Benjamin B. Lindsey, Timothy M. Freeman, Jon-Paul Keatley, Joshua B. Singer, Leonardo de Oliveira Martins, Corin A. Yeats, Khalil Abudahab, Ben E.W. Taylor, Mirko Menegazzo, John Danesh, Wendy Hogsden, Sahar Eldirdiri, Anita Kenyon, Jenifer Mason, Trevor I. Robinson, Alison Holmes, James Price, John A. Hartley, Tanya Curran, Alison E. Mather, Giri Shankar, Rachel Jones, Robin Howe, Sian Morgan, Elizabeth Wastenge, Michael R. Chapman, Siddharth Mookerjee, Rachael Stanley, Wendy Smith, Timothy Peto, David Eyre, Derrick Crook, Gabrielle Vernet, Christine Kitchen, Huw Gulliver, Ian Merrick, Martyn Guest, Robert Munn, Declan T. Bradley, Tim Wyatt, Charlotte Beaver, Luke Foulser, Sophie Palmer, Carol M. Churcher, Ellena Brooks, Kim S. Smith, Katerina Galai, Georgina M. McManus, Frances Bolt, Francesc Coll, Lizzie Meadows, Stephen W. Attwood, Alisha Davies, Elen De Lacy, Fatima Downing, Sue Edwards, Garry P. Scarlett, Sarah Jeremiah, Nikki Smith, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K. Gill, Joana Dias, Ellen E. Higginson, Mailis Maes, Jamie Young, Michelle Wantoch, Dorota Jamrozy, Stephanie Lo, Minal Patel, Verity Hill, Claire M. Bewshea, Sian Ellard, Cressida Auckland, Ian Harrison, Chloe Bishop, Vicki Chalker, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Richard Hopes, Patawee Asamaphan, Marc O. Niebel, Rory N. Gunson, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Antony D. Hale, Louissa R. Macfarlane-Smith, Katherine L. Harper, Holli Carden, Nicholas W. Machin, Kathryn A. Jackson, Shazaad S.Y. Ahmad, Ryan P. George, Lance Turtle, Elaine O’Toole, Joanne Watts, Cassie Breen, Angela Cowell, Adela Alcolea-Medina, Themoula Charalampous, Amita Patel, Lisa J. Levett, Judith Heaney, Aileen Rowan, Graham P. Taylor, Divya Shah, Laura Atkinson, Jack C.D. Lee, Adam P. Westhorpe, Riaz Jannoo, Helen L. Lowe, Angeliki Karamani, Leah Ensell, Wendy Chatterton, Monika Pusok, Ashok Dadrah, Amanda Symmonds, Graciela Sluga, Zoltan Molnar, Paul Baker, Stephen Bonner, Sarah Essex, Edward Barton, Debra Padgett, Garren Scott, Jane Greenaway, Brendan A.I. Payne, Shirelle Burton-Fanning, Sheila Waugh, Veena Raviprakash, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Jonathan Moore, Susanne Stonehouse, Louise Smith, Rose K. Davidson, Luke Bedford, Lindsay Coupland, Victoria Wright, Joseph G. Chappell, Theocharis Tsoleridis, Jonathan Ball, Manjinder Khakh, Vicki M. Fleming, Michelle M. Lister, Hannah C. Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Nichola Duckworth, Sarah Walsh, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Stephen Kidd, Rebecca Williams, Laura Gifford, Kelly Bicknell, Sarah Wyllie, Allyson Lloyd, Robert Impey, Cassandra S. Malone, Benjamin J. Cogger, Nick Levene, Lynn Monaghan, Alexander J. Keeley, David G. Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Emma Betteridge, Ben W. Farr, Scott Goodwin, Michael A. Quail, Carol Scott, Lesley Shirley, Scott A.J. Thurston, Diana Rajan, Iraad F. Bronner, Louise Aigrain, Nicholas M. Redshaw, Stefanie V. Lensing, Shane McCarthy, Alex Makunin, Carlos E. Balcazar, Michael D. Gallagher, Kathleen A. Williamson, Thomas D. Stanton, Michelle L. Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W. Harrison, Christine M. Sambles, David J. Studholme, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Hassan Hartman, Nikos Manesis, Vineet Patel, Juan Ledesma, Katherine A. Twohig, Elias Allara, Clare Pearson, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Paul E. Brown, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N. Carmichael, Katherine L. Smollett, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Seema Nickbakhsh, Edith E. Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J. Webster, Chloe L. Fisher, Adrian W. Signell, Gilberto Betancor, Harry D. Wilson, Gaia Nebbia, Flavia Flaviani, Alberto C. Cerda, Tammy V. Merrill, Rebekah E. Wilson, Marius Cotic, Nadua Bayzid, Thomas Thompson, Erwan Acheson, Steven Rushton, Sarah O’Brien, David J. Baker, Steven Rudder, Alp Aydin, Fei Sang, Johnny Debebe, Sarah Francois, Tetyana I. Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, Angela Marchbank, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Mari Morgan, Robert Beer, Safiah Afifi, Trudy Workman, William Fuller, Catherine Bresner, Adrienn Angyal, Luke R. Green, Paul J. Parsons, Rachel M. Tucker, Rebecca Brown, Max Whiteley, James Bonfield, Christoph Puethe, Andrew Whitwham, Jennifier Liddle, Will Rowe, Igor Siveroni, Thanh Le-Viet, Amy Gaskin, Rob Johnson, Irina Abnizova, Mozam Ali, Laura Allen, Ralph Anderson, Cristina Ariani, Siobhan Austin-Guest, Sendu Bala, Jeffrey Barrett, Andrew Bassett, Kristina Battleday, James Beal, Mathew Beale, Sam Bellany, Tristram Bellerby, Katie Bellis, Duncan Berger, Matt Berriman, Paul Bevan, Simon Binley, Jason Bishop, Kirsty Blackburn, Nick Boughton, Sam Bowker, Timothy Brendler-Spaeth, Iraad Bronner, Tanya Brooklyn, Sarah Kay Buddenborg, Robert Bush, Catarina Caetano, Alex Cagan, Nicola Carter, Joanna Cartwright, Tiago Carvalho Monteiro, Liz Chapman, Tracey-Jane Chillingworth, Peter Clapham, Richard Clark, Adrian Clarke, Catriona Clarke, Daryl Cole, Elizabeth Cook, Maria Coppola, Linda Cornell, Clare Cornwell, Craig Corton, Abby Crackett, Alison Cranage, Harriet Craven, Sarah Craw, Mark Crawford, Tim Cutts, Monika Dabrowska, Matt Davies, Joseph Dawson, Callum Day, Aiden Densem, Thomas Dibling, Cat Dockree, David Dodd, Sunil Dogga, Matthew Dorman, Gordon Dougan, Martin Dougherty, Alexander Dove, Lucy Drummond, Monika Dudek, Laura Durrant, Elizabeth Easthope, Sabine Eckert, Pete Ellis, Ben Farr, Michael Fenton, Marcella Ferrero, Neil Flack, Howerd Fordham, Grace Forsythe, Matt Francis, Audrey Fraser, Adam Freeman, Anastasia Galvin, Maria Garcia-Casado, Alex Gedny, Sophia Girgis, James Glover, Oliver Gould, Andy Gray, Emma Gray, Coline Griffiths, Yong Gu, Florence Guerin, Will Hamilton, Hannah Hanks, Ewan Harrison, Alexandria Harrott, Edward Harry, Julia Harvison, Paul Heath, Anastasia Hernandez-Koutoucheva, Rhiannon Hobbs, Dave Holland, Sarah Holmes, Gary Hornett, Nicholas Hough, Liz Huckle, Lena Hughes-Hallet, Adam Hunter, Stephen Inglis, Sameena Iqbal, Adam Jackson, David Jackson, Carlos Jimenez Verdejo, Matthew Jones, Kalyan Kallepally, Keely Kay, Jon Keatley, Alan Keith, Alison King, Lucy Kitchin, Matt Kleanthous, Martina Klimekova, Petra Korlevic, Ksenia Krasheninnkova, Greg Lane, Cordelia Langford, Adam Laverack, Katharine Law, Stefanie Lensing, Amanah Lewis-Wade, Jennifer Liddle, Quan Lin, Sarah Lindsay, Sally Linsdell, Rhona Long, Jamie Lovell, Jon Lovell, James Mack, Mark Maddison, Aleksei Makunin, Irfan Mamun, Jenny Mansfield, Neil Marriott, Matt Martin, Matthew Mayho, Jo McClintock, Sandra McHugh, Liz MapcMinn, Carl Meadows, Emily Mobley, Robin Moll, Maria Morra, Leanne Morrow, Kathryn Murie, Sian Nash, Claire Nathwani, Plamena Naydenova, Alexandra Neaverson, Ed Nerou, Jon Nicholson, Tabea Nimz, Guillaume G. Noell, Sarah O’Meara, Valeriu Ohan, Charles Olney, Doug Ormond, Agnes Oszlanczi, Yoke Fei Pang, Barbora Pardubska, Naomi Park, Aaron Parmar, Gaurang Patel, Maggie Payne, Sharon Peacock, Arabella Petersen, Deborah Plowman, Tom Preston, Michael Quail, Richard Rance, Suzannah Rawlings, Nicholas Redshaw, Joe Reynolds, Mark Reynolds, Simon Rice, Matt Richardson, Connor Roberts, Katrina Robinson, Melanie Robinson, David Robinson, Hazel Rogers, Eduardo Martin Rojo, Daljit Roopra, Mark Rose, Luke Rudd, Ramin Sadri, Nicholas Salmon, David Saul, Frank Schwach, Phil Seekings, Alison Simms, Matt Sinnott, Shanthi Sivadasan, Bart Siwek, Dale Sizer, Kenneth Skeldon, Jason Skelton, Joanna Slater-Tunstill, Lisa Sloper, Nathalie Smerdon, Chris Smith, Christen Smith, James Smith, Katie Smith, Michelle Smith, Sean Smith, Tina Smith, Leighton Sneade, Carmen Diaz Soria, Catarina Sousa, Emily Souster, Andrew Sparkes, Michael Spencer-Chapman, Janet Squares, Robert Stanley, Claire Steed, Tim Stickland, Ian Still, Mike Stratton, Michelle Strickland, Allen Swann, Agnieszka Swiatkowska, Neil Sycamore, Emma Swift, Edward Symons, Suzanne Szluha, Emma Taluy, Nunu Tao, Katy Taylor, Sam Taylor, Stacey Thompson, Mark Thompson, Mark Thomson, Nicholas Thomson, Scott Thurston, Dee Toombs, Benjamin Topping, Jaime Tovar-Corona, Daniel Ungureanu, James Uphill, Jana Urbanova, Philip Jansen Van, Valerie Vancollie, Paul Voak, Danielle Walker, Matthew Walker, Matt Waller, Gary Ward, Charlie Weatherhogg, Niki Webb, Alan Wells, Eloise Wells, Luke Westwood, Theo Whipp, Thomas Whiteley, Georgia Whitton, Sara Widaa, Mia Williams, Mark Wilson, Sean Wright, and Apollo - University of Cambridge Repository
Subjects: 0301 basic medicine, Resistance, MC UU 1201412, Plasma protein binding, Antibodies, Viral, medicine.disease_cause, MR/R024758/1, 0302 clinical medicine, Recurrence, Chlorocebus aethiops, deletion, Biology (General), Receptor, Phylogeny, Infectivity, Mutation, biology, infectivity, MC_UU_12014/12, C500, C700, UKRI, MRC, Antibody Escape, Spike Glycoprotein, Coronavirus, antibody escape, Antibody, Protein Binding, QH301-705.5, Sars-cov-2, Alpha (ethology), Article, General Biochemistry, Genetics and Molecular Biology, Virus, Cell Line, resistance, Deletion, 03 medical and health sciences, spike mutation, medicine, Alpha Variant, Animals, Humans, neutralizing antibodies, B.1.1.7, Vero Cells, Pandemics, Immune Evasion, SARS-CoV-2, Biochemistry, Genetics and Molecular Biology(all), COVID-19, MR/P008801/1, Antibodies, Neutralizing, Virology, body regions, HEK293 Cells, 030104 developmental biology, Alpha variant, Spike Mutation, biology.protein, Vero cell, Neutralizing Antibodies, 030217 neurology & neurosurgery
Abstract: We report severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike ΔH69/V70 in multiple independent lineages, often occurring after acquisition of receptor binding motif replacements such as N439K and Y453F, known to increase binding affinity to the ACE2 receptor and confer antibody escape. In vitro, we show that, although ΔH69/V70 itself is not an antibody evasion mechanism, it increases infectivity associated with enhanced incorporation of cleaved spike into virions. ΔH69/V70 is able to partially rescue infectivity of spike proteins that have acquired N439K and Y453F escape mutations by increased spike incorporation. In addition, replacement of the H69 and V70 residues in the Alpha variant B.1.1.7 spike (where ΔH69/V70 occurs naturally) impairs spike incorporation and entry efficiency of the B.1.1.7 spike pseudotyped virus. Alpha variant B.1.1.7 spike mediates faster kinetics of cell-cell fusion than wild-type Wuhan-1 D614G, dependent on ΔH69/V70. Therefore, as ΔH69/V70 compensates for immune escape mutations that impair infectivity, continued surveillance for deletions with functional effects is warranted., Graphical abstract, Meng et al. report that the SARS-CoV-2 spike ΔH69/V70 has arisen multiple times. The deletion increases entry efficiency associated with increased cleaved spike in virions and can compensate for loss of infectivity. The B.1.1.7 spike requires ΔH69/V70 for efficient cell entry and cell-cell fusion activity.
Published: 2021

38. Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 lineages circulating in Brazil

Author: Tanya Golubchik, Ana Pittella, Katherine R. W. Emary, Sarah C. Gilbert, Parvinder K. Aley, Jeremy Ratcliff, Sue Ann Costa Clemens, Simon Kerridge, P M Folegatti, N G Marchevsky, Teresa Lambe, Lily Yin Weckx, Sarah Kelly, Eveline Pipolo Milan, S Bibi, Christophe Fraser, Yama F Mujadidi, Michelle Fuskova, Merryn Voysey, Alexandre Vargas Schwarzbold, Emma Plested, Peter Simmonds, Andrew J. Pollard, M N Ramasamy, D Jenkin, Ana Verena Mendes, David Bonsall, Eduardo Sprinz, Project, AMPHEUS, and Team, Oxford COVID Vaccine Trial
Subjects: Adult, Male, medicine.medical_specialty, COVID-19 Vaccines, Adolescent, Science, Dose-Response Relationship, Immunologic, General Physics and Astronomy, General Biochemistry, Genetics and Molecular Biology, Article, law.invention, Cohort Studies, Young Adult, Randomized controlled trial, law, Throat, Internal medicine, ChAdOx1 nCoV-19, medicine, Humans, Genotyping, Nose, Phylogeny, Aged, Vaccines, Multidisciplinary, business.industry, SARS-CoV-2, Vaccination, COVID-19, General Chemistry, Middle Aged, Viral Load, Vaccine efficacy, Clinical trial, Hospitalization, medicine.anatomical_structure, Treatment Outcome, Viral infection, Infectious diseases, Female, business, Brazil, Cohort study
Abstract: Several COVID-19 vaccines have shown good efficacy in clinical trials, but there remains uncertainty about the efficacy of vaccines against different variants. Here, we investigate the efficacy of ChAdOx1 nCoV-19 (AZD1222) against symptomatic COVID-19 in a post-hoc exploratory analysis of a Phase 3 randomised trial in Brazil (trial registration ISRCTN89951424). Nose and throat swabs were tested by PCR in symptomatic participants. Sequencing and genotyping of swabs were performed to determine the lineages of SARS-CoV-2 circulating during the study. Protection against any symptomatic COVID-19 caused by the Zeta (P.2) variant was assessed in 153 cases with vaccine efficacy (VE) of 69% (95% CI 55, 78). 49 cases of B.1.1.28 occurred and VE was 73% (46, 86). The Gamma (P.1) variant arose later in the trial and fewer cases (N = 18) were available for analysis. VE was 64% (−2, 87). ChAdOx1 nCoV-19 provided 95% protection (95% CI 61%, 99%) against hospitalisation due to COVID-19. In summary, we report that ChAdOx1 nCoV-19 protects against emerging variants in Brazil despite the presence of the spike protein mutation E484K., Emerging variants of SARS-CoV-2 raise concerns about vaccine efficiency. Here, the authors present a post-hoc analysis for the ChAdOx1 nCoV-19 (AZD1222) vaccine trial in Brazil and provide efficacy against symptomatic COVID-19 caused by the Zeta (P.2) and other variants.
Published: 2021

39. Deep-sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial – BCPP/ Ya Tsie trial

Author: Myron Essex, Christophe Fraser, Yingze Zhang, Golubchick T, Pretorius Holme M, Pamela Bachanas, Novitsky, Tchetgen Tchetgen Ej, Lebelonyane R, Lerato E Magosi, Shahin Lockman, Janet Moore, Segolodi T, Sikhulile Moyo, De Gruttola, Marc Lipsitch, and Joseph Makhema
Subjects: education.field_of_study, business.industry, Incidence (epidemiology), Population, Human immunodeficiency virus (HIV), virus diseases, Context (language use), medicine.disease_cause, Treatment trial, Phylogenetics, Medicine, Prevention trials, business, Hiv transmission, education, Demography
Abstract: Mathematical models predict that community-wide access to HIV testing-and-treatment can rapidly and substantially reduce new HIV infections. Yet several large universal test-and-treat HIV prevention trials in high-prevalence epidemics demonstrated variable reduction in population-level incidence. To elucidate patterns of HIV spread in universal test-and-treat trials we quantified the contribution of geographic-location, gender, age and randomized-HIV- intervention to HIV transmissions in the 30-community Ya Tsie trial in Botswana (estimated trial population: 175,664). Deep-sequence phylogenetic analysis revealed that most inferred HIV transmissions within the trial occurred within the same or between neighboring communities, and between similarly-aged partners. Transmissions into intervention communities from control communities were more common than the reverse post-baseline (30% [12.2 – 56.7] versus 3% [0.1 – 27.3]) than at baseline (7% [1.5 – 25.3] versus 5% [0.9 – 22.9]) compatible with a benefit from treatment-as-prevention. Our findings suggest that population mobility patterns are fundamental to HIV transmission dynamics and to the impact of HIV control strategies.
Published: 2021

40. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Author: Mark S Graham, Carole H Sudre, Anna May, Michela Antonelli, Benjamin Murray, Thomas Varsavsky, Kerstin Kläser, Liane S Canas, Erika Molteni, Marc Modat, David A Drew, Long H Nguyen, Lorenzo Polidori, Somesh Selvachandran, Christina Hu, Joan Capdevila, Alexander Hammers, Andrew T Chan, Jonathan Wolf, Tim D Spector, Claire J Steves, Sebastien Ourselin, Cherian Koshy, Amy Ash, Emma Wise, Nathan Moore, Matilde Mori, Nick Cortes, Jessica Lynch, Stephen Kidd, Derek J Fairley, Tanya Curran, James P McKenna, Helen Adams, Christophe Fraser, Tanya Golubchik, David Bonsall, Mohammed O Hassan-Ibrahim, Cassandra S Malone, Benjamin J Cogger, Michelle Wantoch, Nicola Reynolds, Ben Warne, Joshua Maksimovic, Karla Spellman, Kathryn McCluggage, Michaela John, Robert Beer, Safiah Afifi, Sian Morgan, Angela Marchbank, Anna Price, Christine Kitchen, Huw Gulliver, Ian Merrick, Joel Southgate, Martyn Guest, Robert Munn, Trudy Workman, Thomas R Connor, William Fuller, Catherine Bresner, Luke B Snell, Amita Patel, Themoula Charalampous, Gaia Nebbia, Rahul Batra, Jonathan Edgeworth, Samuel C Robson, Angela H Beckett, David M Aanensen, Anthony P Underwood, Corin A Yeats, Khalil Abudahab, Ben EW Taylor, Mirko Menegazzo, Gemma Clark, Wendy Smith, Manjinder Khakh, Vicki M Fleming, Michelle M Lister, Hannah C Howson-Wells, Louise Berry, Tim Boswell, Amelia Joseph, Iona Willingham, Carl Jones, Christopher Holmes, Paul Bird, Thomas Helmer, Karlie Fallon, Julian Tang, Veena Raviprakash, Sharon Campbell, Nicola Sheriff, Victoria Blakey, Lesley-Anne Williams, Matthew W Loose, Nadine Holmes, Christopher Moore, Matthew Carlile, Victoria Wright, Fei Sang, Johnny Debebe, Francesc Coll, Adrian W Signell, Gilberto Betancor, Harry D Wilson, Sahar Eldirdiri, Anita Kenyon, Thomas Davis, Oliver G Pybus, Louis du Plessis, Alex E Zarebski, Jayna Raghwani, Moritz UG Kraemer, Sarah Francois, Stephen W Attwood, Tetyana I Vasylyeva, Marina Escalera Zamudio, Bernardo Gutierrez, M. Estee Torok, William L Hamilton, Ian G Goodfellow, Grant Hall, Aminu S Jahun, Yasmin Chaudhry, Myra Hosmillo, Malte L Pinckert, Iliana Georgana, Samuel Moses, Hannah Lowe, Luke Bedford, Jonathan Moore, Susanne Stonehouse, Chloe L Fisher, Ali R Awan, John BoYes, Judith Breuer, Kathryn Ann Harris, Julianne Rose Brown, Divya Shah, Laura Atkinson, Jack CD Lee, Nathaniel Storey, Flavia Flaviani, Adela Alcolea-Medina, Rebecca Williams, Gabrielle Vernet, Michael R Chapman, Lisa J Levett, Judith Heaney, Wendy Chatterton, Monika Pusok, Li Xu-McCrae, Darren L Smith, Matthew Bashton, Gregory R Young, Alison Holmes, Paul Anthony Randell, Alison Cox, Pinglawathee Madona, Frances Bolt, James Price, Siddharth Mookerjee, Manon Ragonnet-Cronin, Fabricia F. Nascimento, David Jorgensen, Igor Siveroni, Rob Johnson, Olivia Boyd, Lily Geidelberg, Erik M Volz, Aileen Rowan, Graham P Taylor, Katherine L Smollett, Nicholas J Loman, Joshua Quick, Claire McMurray, Joanne Stockton, Sam Nicholls, Will Rowe, Radoslaw Poplawski, Alan McNally, Rocio T Martinez Nunez, Jenifer Mason, Trevor I Robinson, Elaine O'Toole, Joanne Watts, Cassie Breen, Angela Cowell, Graciela Sluga, Nicholas W Machin, Shazaad S Y Ahmad, Ryan P George, Fenella Halstead, Venkat Sivaprakasam, Wendy Hogsden, Chris J Illingworth, Chris Jackson, Emma C Thomson, James G Shepherd, Patawee Asamaphan, Marc O Niebel, Kathy K Li, Rajiv N Shah, Natasha G Jesudason, Lily Tong, Alice Broos, Daniel Mair, Jenna Nichols, Stephen N Carmichael, Kyriaki Nomikou, Elihu Aranday-Cortes, Natasha Johnson, Igor Starinskij, Ana da Silva Filipe, David L Robertson, Richard J Orton, Joseph Hughes, Sreenu Vattipally, Joshua B Singer, Seema Nickbakhsh, Antony D Hale, Louissa R Macfarlane-Smith, Katherine L Harper, Holli Carden, Yusri Taha, Brendan AI Payne, Shirelle Burton-Fanning, Sheila Waugh, Jennifer Collins, Gary Eltringham, Steven Rushton, Sarah O'Brien, Amanda Bradley, Alasdair Maclean, Guy Mollett, Rachel Blacow, Kate E Templeton, Martin P McHugh, Rebecca Dewar, Elizabeth Wastenge, Samir Dervisevic, Rachael Stanley, Emma J Meader, Lindsay Coupland, Louise Smith, Clive Graham, Edward Barton, Debra Padgett, Garren Scott, Emma Swindells, Jane Greenaway, Andrew Nelson, Clare M McCann, Wen C Yew, Monique Andersson, Timothy Peto, Anita Justice, David Eyre, Derrick Crook, Tim J Sloan, Nichola Duckworth, Sarah Walsh, Anoop J Chauhan, Sharon Glaysher, Kelly Bicknell, Sarah Wyllie, Scott Elliott, Allyson Lloyd, Robert Impey, Nick Levene, Lynn Monaghan, Declan T Bradley, Tim Wyatt, Elias Allara, Clare Pearson, Husam Osman, Andrew Bosworth, Esther Robinson, Peter Muir, Ian B Vipond, Richard Hopes, Hannah M Pymont, Stephanie Hutchings, Martin D Curran, Surendra Parmar, Angie Lackenby, Tamyo Mbisa, Steven Platt, Shahjahan Miah, David Bibby, Carmen Manso, Jonathan Hubb, Meera Chand, Gavin Dabrera, Mary Ramsay, Daniel Bradshaw, Alicia Thornton, Richard Myers, Ulf Schaefer, Natalie Groves, Eileen Gallagher, David Lee, David Williams, Nicholas Ellaby, Ian Harrison, Hassan Hartman, Nikos Manesis, Vineet Patel, Chloe Bishop, Vicki Chalker, Juan Ledesma, Katherine A Twohig, Matthew T.G. Holden, Sharif Shaaban, Alec Birchley, Alexander Adams, Alisha Davies, Amy Gaskin, Amy Plimmer, Bree Gatica-Wilcox, Caoimhe McKerr, Catherine Moore, Chris Williams, David Heyburn, Elen De Lacy, Ember Hilvers, Fatima Downing, Giri Shankar, Hannah Jones, Hibo Asad, Jason Coombes, Joanne Watkins, Johnathan M Evans, Laia Fina, Laura Gifford, Lauren Gilbert, Lee Graham, Malorie Perry, Mari Morgan, Matthew Bull, Michelle Cronin, Nicole Pacchiarini, Noel Craine, Rachel Jones, Robin Howe, Sally Corden, Sara Rey, Sara Kumziene-SummerhaYes, Sarah Taylor, Simon Cottrell, Sophie Jones, Sue Edwards, Justin O'Grady, Andrew J Page, Alison E Mather, David J Baker, Steven Rudder, Alp Aydin, Gemma L Kay, Alexander J Trotter, Nabil-Fareed Alikhan, Leonardo de Oliveira Martins, Thanh Le-Viet, Lizzie Meadows, Anna Casey, Liz Ratcliffe, David A Simpson, Zoltan Molnar, Thomas Thompson, Erwan Acheson, Jane AH Masoli, Bridget A Knight, Sian Ellard, Cressida Auckland, Christopher R Jones, Tabitha W Mahungu, Dianne Irish-Tavares, Tanzina Haque, Jennifer Hart, Eric Witele, Melisa Louise Fenton, Ashok Dadrah, Amanda Symmonds, Tranprit Saluja, Yann Bourgeois, Garry P Scarlett, Katie F Loveson, Salman Goudarzi, Christopher Fearn, Kate Cook, Hannah Dent, Hannah Paul, David G Partridge, Mohammad Raza, Cariad Evans, Kate Johnson, Steven Liggett, Paul Baker, Stephen Bonner, Sarah Essex, Ronan A Lyons, Kordo Saeed, Adhyana I.K Mahanama, Buddhini Samaraweera, Siona Silveira, Emanuela Pelosi, Eleri Wilson-Davies, Rachel J Williams, Mark Kristiansen, Sunando Roy, Charlotte A Williams, Marius Cotic, Nadua Bayzid, Adam P Westhorpe, John A Hartley, Riaz Jannoo, Helen L Lowe, Angeliki Karamani, Leah Ensell, Jacqui A Prieto, Sarah Jeremiah, Dimitris Grammatopoulos, Sarojini Pandey, Lisa Berry, Katie Jones, Alex Richter, Andrew Beggs, Angus Best, Benita Percival, Jeremy Mirza, Oliver Megram, Megan Mayhew, Liam Crawford, Fiona Ashcroft, Emma Moles-Garcia, Nicola Cumley, Colin P Smith, Giselda Bucca, Andrew R Hesketh, Beth Blane, Sophia T Girgis, Danielle Leek, Sushmita Sridhar, Sally Forrest, Claire Cormie, Harmeet K Gill, Joana Dias, Ellen E Higginson, Mailis Maes, Jamie Young, Leanne M Kermack, Ravi Kumar Gupta, Catherine Ludden, Sharon J Peacock, Sophie Palmer, Carol M Churcher, Nazreen F Hadjirin, Alessandro M Carabelli, Ellena Brooks, Kim S Smith, Katerina Galai, Georgina M McManus, Chris Ruis, Rose K Davidson, Andrew Rambaut, Thomas Williams, Carlos E Balcazar, Michael D Gallagher, Áine O'Toole, Stefan Rooke, Verity Hill, Kathleen A Williamson, Thomas D Stanton, Stephen L Michell, Claire M Bewshea, Ben Temperton, Michelle L Michelsen, Joanna Warwick-Dugdale, Robin Manley, Audrey Farbos, James W Harrison, Christine M Sambles, David J Studholme, Aaron R Jeffries, Alistair C Darby, Julian A Hiscox, Steve Paterson, Miren Iturriza-Gomara, Kathryn A Jackson, Anita O Lucaci, Edith E Vamos, Margaret Hughes, Lucille Rainbow, Richard Eccles, Charlotte Nelson, Mark Whitehead, Lance Turtle, Sam T Haldenby, Richard Gregory, Matthew Gemmell, Claudia Wierzbicki, Hermione J Webster, Thushan I de Silva, Nikki Smith, Adrienn Angyal, Benjamin B Lindsey, Danielle C Groves, Luke R Green, Dennis Wang, Timothy M Freeman, Matthew D Parker, Alexander J Keeley, Paul J Parsons, Rachel M Tucker, Rebecca Brown, Matthew Wyles, Max Whiteley, Peijun Zhang, Marta Gallis, Stavroula F Louka, Chrystala Constantinidou, Meera Unnikrishnan, Sascha Ott, Jeffrey K.J. Cheng, Hannah E. Bridgewater, Lucy R. Frost, Grace Taylor-Joyce, Richard Stark, Laura Baxter, Mohammad T. Alam, Paul E Brown, Dinesh Aggarwal, Alberto C Cerda, Tammy V Merrill, Rebekah E Wilson, Patrick C McClure, Joseph G Chappell, Theocharis Tsoleridis, Jonathan Ball, David Buck, John A Todd, Angie Green, Amy Trebes, George MacIntyre-Cockett, Mariateresa de Cesare, Alex Alderton, Roberto Amato, Cristina V Ariani, Mathew A Beale, Charlotte Beaver, Katherine L Bellis, Emma Betteridge, James Bonfield, John Danesh, Matthew J Dorman, Eleanor Drury, Ben W Farr, Luke Foulser, Sonia Goncalves, Scott Goodwin, Marina Gourtovaia, Ewan M Harrison, David K Jackson, Dorota Jamrozy, Ian Johnston, Leanne Kane, Sally Kay, Jon-Paul Keatley, Dominic Kwiatkowski, Cordelia F Langford, Mara Lawniczak, Laura Letchford, Rich Livett, Stephanie Lo, Inigo Martincorena, Samantha McGuigan, Rachel Nelson, Steve Palmer, Naomi R Park, Minal Patel, Liam Prestwood, Christoph Puethe, Michael A Quail, Shavanthi Rajatileka, Carol Scott, Lesley Shirley, John Sillitoe, Michael H Spencer Chapman, Scott AJ Thurston, Gerry Tonkin-Hill, Danni Weldon, Diana Rajan, Iraad F Bronner, Louise Aigrain, Nicholas M Redshaw, Stefanie V Lensing, Robert Davies, Andrew Whitwham, Jennifier Liddle, Kevin Lewis, Jaime M Tovar-Corona, Steven Leonard, Jillian Durham, Andrew R Bassett, Shane McCarthy, Robin J Moll, Keith James, Karen Oliver, Alex Makunin, Jeff Barrett, Rory N Gunson, Sudre, Carole H [0000-0001-5753-428X], Molteni, Erika [0000-0001-7773-8140], Apollo - University of Cambridge Repository, and Medical Research Council (MRC)
Subjects: Adult, Male, medicine.medical_specialty, Adolescent, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), B100, B200, 01 natural sciences, Spearman's rank correlation coefficient, 03 medical and health sciences, Young Adult, 0302 clinical medicine, COVID-19 Genomics UK (COG-UK) Consortium, Epidemiology, medicine, Humans, 030212 general & internal medicine, 0101 mathematics, Young adult, Aged, business.industry, SARS-CoV-2, Incidence (epidemiology), Public health, Comment, 010102 general mathematics, Public Health, Environmental and Occupational Health, Ecological study, COVID-19, C500, Articles, Middle Aged, C700, Transmissibility (vibration), United Kingdom, Reinfection, Female, Public aspects of medicine, RA1-1270, business, Demography
Abstract: Background: The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods: We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, R t, for the two incidence estimates. Findings: From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the R t of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, R t fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation: The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding: Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society.
Published: 2021

41. Associations between baseline characteristics, CD4 cell count response and virological failure on first-line efavirenz + tenofovir + emtricitabine for HIV

Author: Oliver T. Stirrup, Caroline A. Sabin, Andrew N. Phillips, Ian Williams, Duncan Churchill, Anna Tostevin, Teresa Hill, David T. Dunn, David Asboe, Anton Pozniak, Patricia Cane, David Chadwick, Duncan Clark, Simon Collins, Valerie Delpech, Samuel Douthwaite, David Dunn, Esther Fearnhill, Kholoud Porter, Oliver Stirrup, Christophe Fraser, Anna Maria Geretti, Rory Gunson, Antony Hale, Stéphane Hué, Linda Lazarus, Andrew Leigh-Brown, Tamyo Mbisa, Nicola Mackie, Chloe Orkin, Eleni Nastouli, Deenan Pillay, Andrew Phillips, Caroline Sabin, Erasmus Smit, Kate Templeton, Peter Tilston, Erik Volz, Hongyi Zhang, Keith Fairbrother, Justine Dawkins, Siobhan O’Shea, Jane Mullen, Alison Cox, Richard Tandy, Tracy Fawcett, Mark Hopkins, Clare Booth, Lynne Renwick, Matthias L. Schmid, Brendan Payne, Jonathan Hubb, Simon Dustan, Stuart Kirk, Amanda Bradley-Stewart, Sophie Jose, Alicia Thornton, Susie Huntington, Adam Glabay, Shaadi Shidfar, Janet Lynch, James Hand, Carl de Souza, Nicky Perry, Stuart Tilbury, Elaney Youssef, Brian Gazzard, Mark Nelson, Tracey Mabika, Sundhiya Mandalia, Jane Anderson, Sajid Munshi, Frank Post, Ade Adefisan, Chris Taylor, Zachary Gleisner, Fowzia Ibrahim, Lucy Campbell, Kirsty Baillie, Richard Gilson, Nataliya Brima, Jonathan Ainsworth, Achim Schwenk, Sheila Miller, Chris Wood, Margaret Johnson, Mike Youle, Fiona Lampe, Colette Smith, Rob Tsintas, Clinton Chaloner, Samantha Hutchinson, John Walsh, Nicky Mackie, Alan Winston, Jonathan Weber, Farhan Ramzan, Mark Carder, Clifford Leen, Alan Wilson, Sheila Morris, Mark Gompels, Sue Allan, Adrian Palfreeman, Adam Lewszuk, Stephen Kegg, Akin Faleye, Victoria Ogunbiyi, Sue Mitchell, Phillip Hay, Christian Kemble, Fabiola Martin, Sarah Russell-Sharpe, Janet Gravely, Sris Allan, Andrew Harte, Anjum Tariq, Hazel Spencer, Ron Jones, Jillian Pritchard, Shirley Cumming, Claire Atkinson, Dushyant Mital, Veronica Edgell, Juli Allen, Andy Ustianowski, Cynthia Murphy, Ilise Gunder, Roy Trevelion, and Abdel Babiker
Subjects: 0301 basic medicine, NNRTI, medicine.medical_specialty, Efavirenz, Epidemiology, Immunology, antiretroviral therapy, Drug resistance, Emtricitabine, Microbiology, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, Virology, Internal medicine, Medicine, Cumulative incidence, 030212 general & internal medicine, drug resistance, business.industry, Hazard ratio, Public Health, Environmental and Occupational Health, HIV, Resistance mutation, QR1-502, 030104 developmental biology, Infectious Diseases, chemistry, NRTI, Cohort, Public aspects of medicine, RA1-1270, business, Viral load, ART, medicine.drug
Abstract: Objectives The aim of this study was to investigate associations between baseline characteristics and CD4 cell count response on first-line antiretroviral therapy and risk of virological failure (VF) with or without drug resistance. Methods We conducted an analysis of UK Collaborative HIV Cohort data linked to the UK HIV Drug Resistance Database. Inclusion criteria were viral sequence showing no resistance prior to initiation of first-line efavirenz + tenofovir disoproxil fumarate + emtricitabine and virological suppression within 6 months. Outcomes of VF (≥200 copies/mL) with or without drug resistance were assessed using a competing risks approach fitted jointly with a model for CD4 cell count recovery. Hazard ratios for each VF outcome were estimated for baseline CD4 cell count and viral load and characteristics of CD4 cell count response using latent variables on a standard normal scale. Results A total of 3640 people were included with 338 VF events; corresponding viral sequences were available in 134 with ≥1 resistance mutation in 36. VF with resistance was associated with lower baseline CD4 (0.30, 0.09–0.62), lower CD4 recovery (0.04, 0.00–0.17) and higher CD4 variability (4.40, 1.22–12.68). A different pattern of associations was observed for VF without resistance, but the strength of these results was less consistent across sensitivity analyses. Cumulative incidence of VF with resistance was estimated to be >2% at 3 years for baseline CD4 ≥350 cells/μL. Conclusion Lower baseline CD4 cell count and suboptimal CD4 recovery are associated with VF with drug resistance. People with low CD4 cell count before ART or with suboptimal CD4 recovery on treatment should be a priority for regimens with high genetic barrier to resistance.
Published: 2019

42. HIV-1 Transmission Patterns in Men Who Have Sex with Men: Insights from Genetic Source Attribution Analysis

Author: Alison E Brown, Delpech, David Dunn, Oliver Ratmann, Anna Tostevin, Christophe Fraser, S Le Vu, Erik M. Volz, Noel Gill, Medical Research Council (MRC), National Institute for Health Research, and Bill & Melinda Gates Foundation
Subjects: Adult, Male, 0301 basic medicine, Adolescent, Genotype, Epidemiology, Immunology, Human immunodeficiency virus (HIV), Attribution analysis, HIV Infections, medicine.disease_cause, Men who have sex with men, Sexual and Gender Minorities, Young Adult, 03 medical and health sciences, 0302 clinical medicine, immune system diseases, Virology, HIV Seropositivity, Ethnicity, Humans, Medicine, Genetic Testing, 030212 general & internal medicine, Homosexuality, Male, Phylogeny, reproductive and urinary physiology, Aged, Aged, 80 and over, Models, Statistical, business.industry, Age Factors, Hiv epidemiology, virus diseases, 1103 Clinical Sciences, Middle Aged, phylodynamics, United Kingdom, 3. Good health, 030104 developmental biology, Infectious Diseases, Viral phylodynamics, Hiv 1 transmission, HIV epidemiology, HIV-1, age-mixing, phylogenetic, business, Demography
Abstract: BACKGROUND:Near 60% of new HIV infections in the United Kingdom are estimated to occur in men who have sex with men (MSM). Age-disassortative partnerships in MSM have been suggested to spread the HIV epidemics in many Western developed countries and to contribute to ethnic disparities in infection rates. Understanding these mixing patterns in transmission can help to determine which groups are at a greater risk and guide public health interventions. METHODS:We analyzed combined epidemiologic data and viral sequences from MSM diagnosed with HIV at the national level. We applied a phylodynamic source attribution model to infer patterns of transmission between groups of patients. RESULTS:From pair probabilities of transmission between 14 603 MSM patients, we found that potential transmitters of HIV subtype B were on average 8 months older than recipients. We also found a moderate overall assortativity of transmission by ethnic group and a stronger assortativity by region. CONCLUSIONS:Our findings suggest that there is only a modest net flow of transmissions from older to young MSM in subtype B epidemics and that young MSM, both for Black or White groups, are more likely to be infected by one another than expected in a sexual network with random mixing.
Published: 2019

43. The value of open-source clinical science in pandemic response

Author: Ali Abbas, Sheryl Ann Abdukahil, Nurul Najmee Abdulkadir, Ryuzo Abe, Laurent Abel, Lara Absil, Subhash Acharya, Andrew Acker, Shingo Adachi, Elisabeth Adam, Diana Adrião, Saleh Al Ageel, Shakeel Ahmed, Quratul Ain, Kate Ainscough, Tharwat Aisa, Ali Ait Hssain, Younes Ait Tamlihat, Takako Akimoto, Ernita Akmal, Eman Al Qasim, Razi Alalqam, Tanvir Alam, Tala Al-dabbous, Senthilkumar Alegesan, Cynthia Alegre, Marta Alessi, Beatrice Alex, Kévin Alexandre, Abdulrahman Al-Fares, Huda Alfoudri, Imran Ali, Naseem Ali Shah, Kazali Enagnon Alidjnou, Jeffrey Aliudin, Qabas Alkhafajee, Clotilde Allavena, Nathalie Allou, Aneela Altaf, João Alves, João Melo Alves, Rita Alves, Maria Amaral, Nur Amira, Heidi Ammerlaan, Phoebe Ampaw, Roberto Andini, Claire Andrejak, Andrea Angheben, François Angoulvant, Séverine Ansart, Sivanesen Anthonidass, Massimo Antonelli, Carlos Alexandre Antunes de Brito, Kazi Rubayet Anwar, Ardiyan Apriyana, Yaseen Arabi, Irene Aragao, Rajeshwari Arali, Francisco Arancibia, Carolline Araujo, Antonio Arcadipane, Patrick Archambault, Lukas Arenz, Jean-Benoît Arlet, Christel Arnold-Day, Ana Aroca, Lovkesh Arora, Rakesh Arora, Elise Artaud-Macari, Diptesh Aryal, Motohiro Asaki, Angel Asensio, Elizabeth Ashley, Muhammad Ashraf, Sheharyar Ashraf, Mohammad Asim, Jean Baptiste Assie, Amirul Asyraf, Anika Atique, AM Udara Lakshan Attanyake, Johann Auchabie, Hugues Aumaitre, Adrien Auvet, Laurène Azemar, Cecile Azoulay, Benjamin Bach, Delphine Bachelet, Claudine Badr, Nadia Baig, J. Kenneth Baillie, J Kevin Baird, Erica Bak, Agamemnon Bakakos, Nazreen Abu Bakar, Andriy Bal, Mohanaprasanth Balakrishnan, Valeria Balan, Firouzé Bani-Sadr, Renata Barbalho, Nicholas Yuri Barbosa, Wendy S. Barclay, Saef Umar Barnett, Michaela Barnikel, Helena Barrasa, Audrey Barrelet, Cleide Barrigoto, Marie Bartoli, Cheryl Bartone, Joaquín Baruch, Mustehan Bashir, Romain Basmaci, Muhammad Fadhli Hassin Basri, Diego Bastos, Denise Battaglini, Jules Bauer, Diego Fernando Bautista Rincon, Denisse Bazan Dow, Alexandra Bedossa, Ker Hong Bee, Sylvie Behilill, Albertus Beishuizen, Aleksandr Beljantsev, David Bellemare, Anna Beltrame, Beatriz Amorim Beltrão, Marine Beluze, Nicolas Benech, Lionel Eric Benjiman, Dehbia Benkerrou, Suzanne Bennett, Luís Bento, Jan-Erik Berdal, Delphine Bergeaud, Hazel Bergin, José Luis Bernal Sobrino, Giulia Bertoli, Lorenzo Bertolino, Simon Bessis, Adam Betz, Sybille Bevilcaqua, Karine Bezulier, Amar Bhatt, Krishna Bhavsar, Isabella Bianchi, Claudia Bianco, Farah Nadiah Bidin, Moirangthem Bikram Singh, Felwa Bin Humaid, Mohd Nazlin Bin Kamarudin, François Bissuel, Patrick Biston, Laurent Bitker, Pablo Blanco-Schweizer, Catherine Blier, Frank Bloos, Mathieu Blot, Lucille Blumberg, Filomena Boccia, Laetitia Bodenes, Alice Bogaarts, Debby Bogaert, Anne-Hélène Boivin, Pierre-Adrien Bolze, François Bompart, Aurelius Bonfasius, Diogo Borges, Raphaël Borie, Hans Martin Bosse, Elisabeth Botelho-Nevers, Lila Bouadma, Olivier Bouchaud, Sabelline Bouchez, Dounia Bouhmani, Damien Bouhour, Kévin Bouiller, Laurence Bouillet, Camile Bouisse, Anne-Sophie Boureau, John Bourke, Maude Bouscambert, Aurore Bousquet, Jason Bouziotis, Bianca Boxma, Marielle Boyer-Besseyre, Maria Boylan, Fernando Augusto Bozza, Matthew Brack, Axelle Braconnier, Cynthia Braga, Timo Brandenburger, Filipa Brás Monteiro, Luca Brazzi, Dorothy Breen, Patrick Breen, Stephen Brett, Kathy Brickell, Tessa Broadley, Alex Browne, Shaunagh Browne, Nicolas Brozzi, Marjolein Brusse-Keizer, Nina Buchtele, Christian Buesaquillo, Polina Bugaeva, Marielle Buisson, Erlina Burhan, Aidan Burrell, Ingrid G. Bustos, Denis Butnaru, André Cabie, Susana Cabral, Eder Caceres, Cyril Cadoz, Mia Callahan, Kate Calligy, Jose Andres Calvache, João Cam, Valentine Campana, Paul Campbell, Josie Campisi, Cecilia Canepa, Mireia Cantero, Pauline Caraux-Paz, Sheila Cárcel, Chiara Simona Cardellino, Filipa Cardoso, Filipe Cardoso, Nelson Cardoso, Sofia Cardoso, Simone Carelli, Nicolas Carlier, Thierry Carmoi, Gayle Carney, Chloe Carpenter, Inês Carqueja, Marie-Christine Carret, François Martin Carrier, Ida Carroll, Gail Carson, Ed Carton, Maire-Laure Casanova, Mariana Cascão, Siobhan Casey, José Casimiro, Bailey Cassandra, Silvia Castañeda, Nidyanara Castanheira, Guylaine Castor-Alexandre, Henry Castrillón, Ivo Castro, Ana Catarino, François-Xavier Catherine, Paolo Cattaneo, Roberta Cavalin, Giulio Giovanni Cavalli, Alexandros Cavayas, Adrian Ceccato, Minerva Cervantes-Gonzalez, Anissa Chair, Catherine Chakveatze, Adrienne Chan, Meera Chand, Christelle Chantalat Auger, Jean-Marc Chapplain, Julie Chas, Mobin Chaudary, Jonathan Samuel Chávez Iñiguez, Anjellica Chen, Yih-Sharng Chen, Matthew Pellan Cheng, Antoine Cheret, Thibault Chiarabini, Julian Chica, Suresh Kumar Chidambaram, Leong Chin-Tho, Catherine Chirouze, Davide Chiumello, Hwa Jin Cho, Sung-Min Cho, Bernard Cholley, Marie-Charlotte Chopin, Ting Soo Chow, Yock Ping Chow, Hiu Jian Chua, Jonathan Chua, Jose Pedro Cidade, José Miguel Cisneros Herreros, Barbara Wanjiru Citarella, Anna Ciullo, Emma Clarke, Jennifer Clarke, Rolando Claure Del Granado, Sara Clohisey, J. Perren Cobb, Necsoi Coca, Cassidy Codan, Caitriona Cody, Alexandra Coelho, Megan Coles, Gwenhaël Colin, Michael Collins, Sebastiano Maria Colombo, Pamela Combs, Jennifer Connolly, Marie Connor, Anne Conrad, Sofía Contreras, Elaine Conway, Graham S. Cooke, Mary Copland, Hugues Cordel, Amanda Corley, Sarah Cormican, Sabine Cornelis, Alexander Daniel Cornet, Arianne Joy Corpuz, Andrea Cortegiani, Grégory Corvaisier, Emma Costigan, Camille Couffignal, Sandrine Couffin-Cadiergues, Roxane Courtois, Stéphanie Cousse, Rachel Cregan, Charles Crepy D'Orleans, Sabine Croonen, Gloria Crowl, Jonathan Crump, Claudina Cruz, Juan Luis Cruz Berm, Jaime Cruz Rojo, Marc Csete, Alberto Cucino, Ailbhe Cullen, Caroline Cullen, Matthew Cummings, Gerard Curley, Elodie Curlier, Colleen Curran, Paula Custodio, Ana da Silva Filipe, Charlene Da Silveira, Al-Awwab Dabaliz, Andrew Dagens, Darren Dahly, Heidi Dalton, Jo Dalton, Seamus Daly, Federico D'Amico, Nick Daneman, Corinne Daniel, Emmanuelle A Dankwa, Jorge Dantas, Frédérick D’Aragon, Mark de Boer, Gillian de Loughry, Diego de Mendoza, Etienne De Montmollin, Rafael Freitas de Oliveira França, Ana Isabel de Pinho Oliveira, Rosanna De Rosa, Thushan de Silva, Peter de Vries, Jillian Deacon, David Dean, Alexa Debard, Bianca DeBenedictis, Marie-Pierre Debray, Nathalie DeCastro, William Dechert, Lauren Deconninck, Romain Decours, Eve Defous, Isabelle Delacroix, Eric Delaveuve, Karen Delavigne, Nathalie M. Delfos, Ionna Deligiannis, Andrea Dell'Amore, Christelle Delmas, Pierre Delobel, Corine Delsing, Elisa Demonchy, Emmanuelle Denis, Dominique Deplanque, Pieter Depuydt, Mehul Desai, Diane Descamps, Mathilde Desvallée, Santi Dewayanti, Alpha Diallo, Sylvain Diamantis, André Dias, Priscila Diaz, Rodrigo Diaz, Juan Jose Diaz Diaz, Kévin Didier, Jean-Luc Diehl, Wim Dieperink, Jérôme Dimet, Vincent Dinot, Fara Diop, Alphonsine Diouf, Yael Dishon, Devika Dixit, Félix Djossou, Annemarie B. Docherty, Helen Doherty, Arjen M Dondorp, Andy Dong, Christl A. Donnelly, Maria Donnelly, Chloe Donohue, Sean Donohue, Yoann Donohue, Ciara Doran, Peter Doran, Céline Dorival, Eric D'Ortenzio, James Joshua Douglas, Renee Douma, Nathalie Dournon, Triona Downer, Joanne Downey, Mark Downing, Tom Drake, Aoife Driscoll, Murray Dryden, Claudio Duarte Fonseca, Vincent Dubee, François Dubos, Alexandre Ducancelle, Toni Duculan, Susanne Dudman, Abhijit Duggal, Paul Dunand, Jake Dunning, Mathilde Duplaix, Emanuele Durante-Mangoni, Lucian Durham III, Bertrand Dussol, Juliette Duthoit, Xavier Duval, Anne Margarita Dyrhol-Riise, Sim Choon Ean, Marco Echeverria-Villalobos, Siobhan Egan, Carla Eira, Mohammed El Sanharawi, Subbarao Elapavaluru, Brigitte Elharrar, Jacobien Ellerbroek, Philippine Eloy, Tarek Elshazly, Iqbal Elyazar, Isabelle Enderle, Tomoyuki Endo, Chan Chee Eng, Ilka Engelmann, Vincent Enouf, Olivier Epaulard, Martina Escher, Mariano Esperatti, Hélène Esperou, Marina Esposito-Farese, João Estevão, Manuel Etienne, Nadia Ettalhaoui, Anna Greti Everding, Mirjam Evers, Isabelle Fabre, Marc Fabre, Amna Faheem, Arabella Fahy, Cameron J. 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Turtle, Anders Tveita, Pawel Twardowski, Makoto Uchiyama, PG Ishara Udayanga, Andrew Udy, Roman Ullrich, Zubair Umer, Alberto Uribe, Asad Usman, Cristinava Vajdovics, Luís Val-Flores, Ana Luiza Valle, Amélie Valran, Stijn Van de Velde, Marcel van den Berge, Machteld van der Feltz, Paul van der Valk, Nicky Van Der Vekens, Peter Van der Voort, Sylvie Van Der Werf, Marlice van Dyk, Laura van Gulik, Jarne Van Hattem, Steven van Lelyveld, Carolien van Netten, Gitte Van Twillert, Ilonka van Veen, Noémie Vanel, Henk Vanoverschelde, Pooja Varghese, Michael Varrone, Shoban Raj Vasudayan, Charline Vauchy, Helen Vaughan, Shaminee Veeran, Aurélie Veislinger, Sebastian Vencken, Sara Ventura, Annelies Verbon, José Ernesto Vidal, César Vieira, Deepak Vijayan, Joy Ann Villanueva, Judit Villar, Pierre-Marc Villeneuve, Andrea Villoldo, Nguyen Van Vinh Chau, Benoit Visseaux, Hannah Visser, Chiara Vitiello, Harald Vonkeman, Fanny Vuotto, Noor Hidayu Wahab, Suhaila Abdul Wahab, Nadirah Abdul Wahid, Marina Wainstein, Wan Fadzlina Wan Muhd Shukeri, Chih-Hsien Wang, Steven Anthony Webb, Jia Wei, Katharina Weil, Tan Pei Wen, Sanne Wesselius, T. Eoin West, Murray Wham, Bryan Whelan, Nicole White, Paul Henri Wicky, Aurélie Wiedemann, Surya Otto Wijaya, Keith Wille, Suzette Willems, Virginie Williams, Evert-Jan Wils, Ng Wing Yiu, Calvin Wong, Teck Fung Wong, Xin Ci Wong, Yew Sing Wong, Gan Ee Xian, Lim Saio Xian, Kuan Pei Xuan, Ioannis Xynogalas, Sophie Yacoub, Siti Rohani Binti Mohd Yakop, Masaki Yamazaki, Yazdan Yazdanpanah, Nicholas Yee Liang Hing, Cécile Yelnik, Chian Hui Yeoh, Stephanie Yerkovich, Toshiki Yokoyama, Hodane Yonis, Obada Yousif, Saptadi Yuliarto, Akram Zaaqoq, Marion Zabbe, Kai Zacharowski, Masliza Zahid, Maram Zahran, Nor Zaila Binti Zaidan, Maria Zambon, Miguel Zambrano, Alberto Zanella, Konrad Zawadka, Nurul Zaynah, Hiba Zayyad, Alexander Zoufaly, David Zucman, ESTACA'Lab ( ESTACA'Lab ), École Supérieure des Techniques Aéronautiques et de Construction Automobile (ESTACA), Laboratoire d’Ingénierie Circulation Transport et Éco-gestion des systèmes énergétiques pour les transports (LICIT-Eco7), École Nationale des Travaux Publics de l'État (ENTPE)-Université Gustave Eiffel, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Department of Mathematics and Statistics, Wichita State University, Indo-French Center for Groundwater Research (IFCGR), Bureau de Recherches Géologiques et Minières (BRGM) (BRGM)-National Geophysical Research Institute [Hyderabad] (NGRI), National Geophysical Research Institute [Hyderabad] (NGRI), Department of Zoology [Rawalpindi, Pakistan], Pir Mehr Ali Shah Arid Agriculture University = PMAS-Arid Agriculture University Rawalpindi (AAUR), CHU Gabriel Montpied [Clermont-Ferrand], CHU Clermont-Ferrand, Génétique Moléculaire des Virus à ARN - Molecular Genetics of RNA Viruses (GMV-ARN (UMR_3569 / U-Pasteur_2)), Institut Pasteur [Paris] (IP)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), Centre National de Référence des virus des infections respiratoires (dont la grippe) - National Reference Center Virus Influenzae [Paris] (CNR - laboratoire coordonnateur), Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Abbas A., Abdukahil S.A., Abdulkadir N.N., Abe R., Abel L., Absil L., Acharya S., Acker A., Adachi S., Adam E., Adriao D., Ageel S.A., Ahmed S., Ain Q., Ainscough K., Aisa T., Ait Hssain A., Ait Tamlihat Y., Akimoto T., Akmal E., Al Qasim E., Alalqam R., Alam T., Al-dabbous T., Alegesan S., Alegre C., Alessi M., Alex B., Alexandre K., Al-Fares A., Alfoudri H., Ali I., Ali Shah N., Alidjnou K.E., Aliudin J., Alkhafajee Q., Allavena C., Allou N., Altaf A., Alves J., Alves J.M., Alves R., Amaral M., Amira N., Ammerlaan H., Ampaw P., Andini R., Andrejak C., Angheben A., Angoulvant F., Ansart S., Anthonidass S., Antonelli M., Antunes de Brito C.A., Anwar K.R., Apriyana A., Arabi Y., Aragao I., Arali R., Arancibia F., Araujo C., Arcadipane A., Archambault P., Arenz L., Arlet J.-B., Arnold-Day C., Aroca A., Arora L., Arora R., Artaud-Macari E., Aryal D., Asaki M., Asensio A., Ashley E., Ashraf M., Ashraf S., Asim M., Assie J.B., Asyraf A., Atique A., Attanyake A.U.L., Auchabie J., Aumaitre H., Auvet A., Azemar L., Azoulay C., Bach B., Bachelet D., Badr C., Baig N., Baillie J.K., Baird J.K., Bak E., Bakakos A., Bakar N.A., Bal A., Balakrishnan M., Balan V., Bani-Sadr F., Barbalho R., Barbosa N.Y., Barclay W.S., Barnett S.U., Barnikel M., Barrasa H., Barrelet A., Barrigoto C., Bartoli M., Bartone C., Baruch J., Bashir M., Basmaci R., Basri M.F.H., Bastos D., Battaglini D., Bauer J., Bautista Rincon D.F., Bazan Dow D., Bedossa A., Bee K.H., Behilill S., Beishuizen A., Beljantsev A., Bellemare D., Beltrame A., Beltrao B.A., Beluze M., Benech N., Benjiman L.E., Benkerrou D., Bennett S., Bento L., Berdal J.-E., Bergeaud D., Bergin H., Bernal Sobrino J.L., Bertoli G., Bertolino L., Bessis S., Betz A., Bevilcaqua S., Bezulier K., Bhatt A., Bhavsar K., Bianchi I., Bianco C., Bidin F.N., Bikram Singh M., Bin Humaid F., Bin Kamarudin M.N., Bissuel F., Biston P., Bitker L., Blanco-Schweizer P., Blier C., Bloos F., Blot M., Blumberg L., Boccia F., Bodenes L., Bogaarts A., Bogaert D., Boivin A.-H., Bolze P.-A., Bompart F., Bonfasius A., Borges D., Borie R., Bosse H.M., Botelho-Nevers E., Bouadma L., Bouchaud O., Bouchez S., Bouhmani D., Bouhour D., Bouiller K., Bouillet L., Bouisse C., Boureau A.-S., Bourke J., Bouscambert M., Bousquet A., Bouziotis J., Boxma B., Boyer-Besseyre M., Boylan M., Bozza F.A., Brack M., Braconnier A., Braga C., Brandenburger T., Bras Monteiro F., Brazzi L., Breen D., Breen P., Brett S., Brickell K., Broadley T., Browne A., Browne S., Brozzi N., Brusse-Keizer M., Buchtele N., Buesaquillo C., Bugaeva P., Buisson M., Burhan E., Burrell A., Bustos I.G., Butnaru D., Cabie A., Cabral S., Caceres E., Cadoz C., Callahan M., Calligy K., Calvache J.A., Cam J., Campana V., Campbell P., Campisi J., Canepa C., Cantero M., Caraux-Paz P., Carcel S., Cardellino C.S., Cardoso F., Cardoso N., Cardoso S., Carelli S., Carlier N., Carmoi T., Carney G., Carpenter C., Carqueja I., Carret M.-C., Carrier F.M., Carroll I., Carson G., Carton E., Casanova M.-L., Cascao M., Casey S., Casimiro J., Cassandra B., Castaneda S., Castanheira N., Castor-Alexandre G., Castrillon H., Castro I., Catarino A., Catherine F.-X., Cattaneo P., Cavalin R., Cavalli G.G., Cavayas A., Ceccato A., Cervantes-Gonzalez M., Chair A., Chakveatze C., Chan A., Chand M., Chantalat Auger C., Chapplain J.-M., Chas J., Chaudary M., Chavez Iniguez J.S., Chen A., Chen Y.-S., Cheng M.P., Cheret A., Chiarabini T., Chica J., Chidambaram S.K., Chin-Tho L., Chirouze C., Chiumello D., Cho H.J., Cho S.-M., Cholley B., Chopin M.-C., Chow T.S., Chow Y.P., Chua H.J., Chua J., Cidade J.P., Cisneros Herreros J.M., Citarella B.W., Ciullo A., Clarke E., Clarke J., Claure Del Granado R., Clohisey S., Cobb J.P., Coca N., Codan C., Cody C., Coelho A., Coles M., Colin G., Collins M., Colombo S.M., Combs P., Connolly J., Connor M., Conrad A., Contreras S., Conway E., Cooke G.S., Copland M., Cordel H., Corley A., Cormican S., Cornelis S., Cornet A.D., Corpuz A.J., Cortegiani A., Corvaisier G., Costigan E., Couffignal C., Couffin-Cadiergues S., Courtois R., Cousse S., Cregan R., Crepy D'Orleans C., Croonen S., Crowl G., Crump J., Cruz C., Cruz Berm J.L., Cruz Rojo J., Csete M., Cucino A., Cullen A., Cullen C., Cummings M., Curley G., Curlier E., Curran C., Custodio P., da Silva Filipe A., Da Silveira C., Dabaliz A.-A., Dagens A., Dahly D., Dalton H., Dalton J., Daly S., D'Amico F., Daneman N., Daniel C., Dankwa E.A., Dantas J., D'Aragon F., de Boer M., de Loughry G., de Mendoza D., De Montmollin E., de Oliveira Franca R.F., de Pinho Oliveira A.I., De Rosa R., de Silva T., de Vries P., Deacon J., Dean D., Debard A., DeBenedictis B., Debray M.-P., DeCastro N., Dechert W., Deconninck L., Decours R., Defous E., Delacroix I., Delaveuve E., Delavigne K., Delfos N.M., Deligiannis I., Dell'Amore A., Delmas C., Delobel P., Delsing C., Demonchy E., Denis E., Deplanque D., Depuydt P., Desai M., Descamps D., Desvallee M., Dewayanti S., Diallo A., Diamantis S., Dias A., Diaz P., Diaz R., Diaz Diaz J.J., Didier K., Diehl J.-L., Dieperink W., Dimet J., Dinot V., Diop F., Diouf A., Dishon Y., Dixit D., Djossou F., Docherty A.B., Doherty H., Dondorp A.M., Dong A., Donnelly C.A., Donnelly M., Donohue C., Donohue S., Donohue Y., Doran C., Doran P., Dorival C., D'Ortenzio E., Douglas J.J., Douma R., Dournon N., Downer T., Downey J., Downing M., Drake T., Driscoll A., Dryden M., Duarte Fonseca C., Dubee V., Dubos F., Ducancelle A., Duculan T., Dudman S., Duggal A., Dunand P., Dunning J., Duplaix M., Durante-Mangoni E., Durham III L., Dussol B., Duthoit J., Duval X., Dyrhol-Riise A.M., Ean S.C., Echeverria-Villalobos M., Egan S., Eira C., El Sanharawi M., Elapavaluru S., Elharrar B., Ellerbroek J., Eloy P., Elshazly T., Elyazar I., Enderle I., Endo T., Eng C.C., Engelmann I., Enouf V., Epaulard O., Escher M., Esperatti M., Esperou H., Esposito-Farese M., Estevao J., Etienne M., Ettalhaoui N., Everding A.G., Evers M., Fabre I., Fabre M., Faheem A., Fahy A., Fairfield C.J., Fakar Z., Faria P., Farooq A., Farrar J.J., Farshait N., Fateena H., Fatoni A.Z., Faure K., Favory R., Fayed M., Feely N., Feeney L., Fernandes J., Fernandes M., Fernandes S., Ferrand F.-X., Ferrand Devouge E., Ferrao J., Ferraz M., Ferreira B., Ferreira S., Ferrer-Roca R., Ferriere N., Ficko C., Figueiredo-Mello C., Fiorda J., Flament T., Flateau C., Fletcher T., Florio L.L., Flynn B., Flynn D., Foley C., Foley J., Fomin V., Fonseca T., Fontela P., Forsyth S., Foster D., Foti G., Fourn E., Fowler R.A., Fraher D.M., Franch-Llasat D., Fraser C., Fraser J.F., Freire M.V., Freitas Ribeiro A., Friedrich C., Fritz R., Fry S., Fuentes N., Fukuda M., Gaborieau V., Gaci R., Gagliardi M., Gagnard J.-C., Gagne N., Gagneux-Brunon A., Gaiao S., Gail Skeie L., Gallagher P., Gallego Curto E., Gamble C., Gani Y., Garan A., Garcia R., Garcia Barrio N., Garcia-Diaz J., Garcia-Gallo E., Garimella N., Garot D., Garrait V., Gauli B., Gault N., Gavin A., Gavrylov A., Gaymard A., Gebauer J., Geraud E., Gerbaud Morlaes L., Germano N., ghisulal P.K., Ghosn J., Giani M., Giaquinto C., Gibson J., Gigante T., Gilg M., Gilroy E., Giordano G., Girvan M., Gissot V., Gitahi J., Giwangkancana G., Glikman D., Glybochko P., Gnall E., Goco G., Goehringer F., Goepel S., Goffard J.-C., Goh J.Y., Golob J., Gomes R., Gomez K., Gomez-Junyent J., Gominet M., Gonzalez A., Gordon P., Gordon A., Gorenne I., Goubert L., Goujard C., Goulenok T., Grable M., Graf J., Grandin E.W., Granier P., Grasselli G., Grazioli L., Green C.A., Greene C., Greenhalf W., Greffe S., Grieco D.L., Griffee M., Griffiths F., Grigoras I., Groenendijk A., Grosse Lordemann A., Gruner H., Gu Y., Guarracino F., Guedj J., Guego M., Guellec D., Guerguerian A.-M., Guerreiro D., Guery R., Guillaumot A., Guilleminault L., Guimaraes de Castro M., Guimard T., Haalboom M., Haber D., Habraken H., Hachemi A., Hadri N., Haidash O., Haider S., Haidri F., Hakak S., Hall A., Hall M., Halpin S., Hamer A., Hamers R., Hamidfar R., Hammond T., Han L.Y., Haniffa R., Hao K.W., Hardwick H., Harrison E.M., Harrison J., Harrison S.B.E., Hartman A., Hashmi J., Hashmi M., Hayat M., Hayes A., Hays L., Heerman J., Heggelund L., Hendry R., Hennessy M., Henriquez A., Hentzien M., Herekar F., Hernandez-Montfort J., Herr D., Hershey A., Hesstvedt L., Hidayah A., Higgins D., Higgins E., HigginsOKeeffe G., Hinchion R., Hinton S., Hiraiwa H., Hitoto H., Ho A., Ho Y.B., Hoctin A., Hoffmann I., Hoh W.H., Hoiting O., Holt R., Holter J.C., Horby P., Horcajada J.P., Hoshino K., Houas I., Hough C.L., Houltham S., Hsu J.M.-Y., Hulot J.-S., Hussain I., Ijaz S., Illes H.-G., Imbert P., Imran M., Imran Sikander R., Inacio H., Infante Dominguez C., Ing Y.S., Iosifidis E., Ippolito M., Isgett S., Ishani P.G.P.I., Isidoro T., Ismail N., Isnard M., Itai J., Ito A., Ivulich D., Jaafar D., Jaafoura S., Jabot J., Jackson C., Jamieson N., Jaquet P., Jassat W., Jaud-Fischer C., Jaureguiberry S., Javidfar J., Jawad I., Jaworsky D., Jayakumar D., Jego F., Jelani A.M., Jenum S., Jimbo-Sotomayor R., Job V.D.P., Joe O.Y., Jorge Garcia R.N., Joseph C., Joseph M., Joshi S., Jourdain M., Jouvet P., June J., Jung A., Jung H., Juzar D., Kafif O., Kaguelidou F., Kaisbain N., Kaleesvran T., Kali S., Kalicinska A., Kalomoiri S., Kamal S., Kamaluddin M.A.A., Kamaruddin Z.A.C., Kamarudin N., Kandamby D.H., Kandel C., Kang K.Y., Kant R., Kanwal D., Kanyawati D., Karki B., Karpayah P., Karsies T., Kartsonaki C., Kasugai D., Kataria A., Katz K., Kaur A., Kaur Johal S., Kawasaki T., Kay C., Keane H., Keating S., Kellam P., Kelly A., Kelly C., Kelly N., Kelly S., Kelly Y., Kelsey M., Kennedy R., Kennon K., Kernan M., Kerroumi Y., Keshav S., Kestelyn E., Khalid I., Khalid O., Khalil A., Khan C., Khan I., Khanal S., Kho M.E., Khoo D., Khoo R., Khoo S., Khoso N., Kiat K.H., Kida Y., Kiiza P., Kildal A.B., Kim J.B., Kimmoun A., Kindgen-Milles D., King A., Kitamura N., Klenerman P., Klont R., Kloumann Bekken G., Knight S., Kobbe R., Kodippily C., Kohns Vasconcelos M., Koirala S., Komatsu M., Korten V., Kosgei C., Kpangon A., Krawczyk K., Krishnan S., Krishnan V., Kruglova O., Kumar A., Kumar D., Kumar G., Kumar M., Kumar Vecham P., Kuriakose D., Kurtzman E., Kusumastuti N.P., Kutsogiannis D., Kutsyna G., Kyriakoulis K., Lachatre M., Lacoste M., Laffey J.G., Lagrange M., Laine F., Lairez O., Lakhey S., Lalueza A., Lambert M., Lamontagne F., Langelot-Richard M., Langlois V., Lantang E.Y., Lanza M., Laouenan C., Laribi S., Lariviere D., Lasry S., Latif N., Launay O., Laureillard D., Lavie-Badie Y., Law A., Lawrence C., Lawrence T., Le M., Le Bihan C., Le Bris C., Le Falher G., Le Fevre L., Le Hingrat Q., Le Marechal M., Le Mestre S., Le Moal G., Le Moing V., Le Nagard H., Le Turnier P., Leal E., Leal Santos M., Lee B.H., Lee H.G., Lee J., Lee S.H., Lee T.C., Lee Y.L., Leeming G., Lefebvre B., Lefebvre L., Lefevre B., LeGac S., Lelievre J.-D., Lellouche F., Lemaignen A., Lemee V., Lemeur A., Lemmink G., Lene H.S., Lennon J., Leon R., Leone M., Lepiller Q., Lescure F.-X., Lesens O., Lesouhaitier M., Lester-Grant A., Levy B., Levy Y., Levy-Marchal C., Lewandowska K., L'Her E., Li Bassi G., Liang J., Liaquat A., Liegeon G., Lim K.C., Lim W.S., Lima C., Lina B., Lina L., Lind A., Lingas G., Lion-Daolio S., Lissauer S., Liu K., Livrozet M., Lizotte P., Loforte A., Lolong N., Loon L.C., Lopes D., Lopez-Colon D., Loschner A.L., Loubet P., Loufti B., Louis G., Lourenco S., Lovelace-Macon L., Low L.L., Lowik M., Loy J.S., Lucet J.C., Lumbreras Bermejo C., Luna C.M., Lungu O., Luong L., Luque N., Luton D., Lwin N., Lyons R., Maasikas O., Mabiala O., MacDonald S., Machado M., Macheda G., Macias Sanchez J., Madhok J., Maestro de la Calle G., Mahieu R., Mahy S., Maia A.R., Maier L.S., Maillet M., Maitre T., Malfertheiner M., Malik N., Mallon P., Maltez F., Malvy D., Manda V., Mandei J.M., Mandelbrot L., Manetta F., Mangal K., Mankikian J., Manning E., Manuel A., Maria Sant`Ana Malaque C., Marino D., Marino F., Markowicz S., Maroun Eid C., Marques A., Marquis C., Marsh B., Marsh L., Marshal M., Marshall J., Martelli C.T., Martin D.-A., Martin E., Martin-Blondel G., Martinelli A., Martin-Loeches I., Martinot M., Martin-Quiros A., Martins A., Martins J., Martins N., Martins Rego C., Martucci G., Martynenko O., Marwali E.M., Marzukie M., Masa Jimenez J.F., Maslove D., Mason P., Mason S., Masood S., Mat Nor B., Matan M., Mateus Fernandes H., Mathew M., Mathieu D., Mattei M., Matulevics R., Maulin L., Maxwell M., Maynar J., Mazzoni T., Mc Sweeney L., McAndrew L., McArthur C., McCarthy A., McCloskey C., McConnochie R., McDermott S., McDonald S.E., McElroy A., McElwee S., McEneany V., McEvoy N., McGeer A., McKay C., McKeown J., McLean K.A., McNally P., McNicholas B., McPartlan E., Meaney E., Mear-Passard C., Mechlin M., Meher M., Mehkri O., Mele F., Melo L., Memon K., Mendes J.J., Menkiti O., Menon K., Mentre F., Mentzer A.J., Mercier E., Mercier N., Merckx A., Mergeay-Fabre M., Mergler B., Merson L., Mesquita A., Metwally O., Meybeck A., Meyer D., Meynert A.M., Meysonnier V., Meziane A., Mezidi M., Michelagnoli G., Michelanglei C., Michelet I., Mihelis E., Mihnovit V., Miranda-Maldonado H., Misnan N.A., Mohamed N.N.E., Mohamed T.J., Moin A., Molina D., Molinos E., Molloy B., Mone M., Monteiro A., Montes C., Montrucchio G., Moore S., Moore S.C., Morales Cely L., Moro L., Morocho Tutillo D.R., Morton B., Motherway C., Motos A., Mouquet H., Mouton Perrot C., Moyet J., Mudara C., Mufti A.K., Muh N.Y., Muhamad D., Mullaert J., Muller F., Muller K.E., Munblit D., Muneeb S., Munir N., Munshi L., Murphy A., Murphy L., Murris M., Murthy S., Musaab H., Muyandy G., Myrodia D.M., N N., Nagpal D., Nagrebetsky A., Narasimhan M., Narayanan N., Nasim Khan R., Nazerali-Maitland A., Neant N., Neb H., Nekliudov N.A., Nelwan E., Neto R., Neumann E., Neves B., Ng P.Y., Nghi A., Nguyen D., Ni Choileain O., Ni Leathlobhair N., Nichol A., Nitayavardhana P., Nonas S., Noordin N.A.M., Noret M., Norharizam N.F.I., Norman L., Notari A., Noursadeghi M., Nowicka K., Nowinski A., Nseir S., Nunez J.I., Nurnaningsih N., Nyamankolly E., O Brien F., O'Callaghan A., Occhipinti G., OConnor D., O'Donnell M., Ogston T., Ogura T., Oh T.-H., O'Halloran S., O'Hearn K., Ohshimo S., Oldakowska A., Oliveira J., Oliveira L., Olliaro P.L., O'Neil C., Ong D.S.Y., Ong J.Y., Oosthuyzen W., Opavsky A., Openshaw P., Orakzai S., Orozco-Chamorro C.M., Orquera A., Ortoleva J., Osatnik J., O'Shea L., O'Sullivan M., Othman S.Z., Ouamara N., Ouissa R., Owyang C., Oziol E., Pabasara H.M.U., Pagadoy M., Pages J., Palacios A., Palacios M., Palmarini M., Panarello G., Panda P.K., Paneru H., Pang L.H., Panigada M., Pansu N., Papadopoulos A., Parke R., Parker M., Parra B., Parrini V., Pasha T., Pasquier J., Pastene B., Patauner F., Patel J., Pathmanathan M.D., Patrao L., Patricio P., Patrier J., Patterson L., Pattnaik R., Paul C., Paul M., Paulos J., Paxton W.A., Payen J.-F., Peariasamy K., Pedrera Jimenez M., Peek G.J., Peelman F., Peiffer-Smadja N., Peigne V., Pejkovska M., Pelosi P., Peltan I.D., Pereira R., Perez D., Periel L., Perpoint T., Pesenti A., Pestre V., Petrou L., Petrov-Sanchez V., Pettersen F.O., Peytavin G., Pharand S., Piagnerelli M., Picard W., Picone O., de Piero M., Pierobon C., Piersma D., Pimentel C., Pinto R., Pires C., Pironneau I., Piroth L., Pius R., Piva S., Plantier L., Plotkin D., Png H.S., Poissy J., Pokeerbux R., Pokorska-Spiewak M., Poli S., Pollakis G., Ponscarme D., Popielska J., Post A.-M., Postma D.F., Povoa P., Povoas D., Powis J., Prapa S., Preau S., Prebensen C., Preiser J.-C., Prinssen A., Pritchard M.G., Priyadarshani G.D.D., Proenca L., Pudota S., Puechal O., Pujo Semedi B., Pulicken M., Puntoni M., Purcell G., Quesada L., Quinones-Cardona V., Quiros Gonzalez V., Quist-Paulsen E., Quraishi M., Rabaa M., Rabaud C., Rabindrarajan E., Rafael A., Rafiq M., Ragazzo G., Rahman A.K.H.A., Rahman R.A., Rahutullah A., Rainieri F., Rajahram G.S., Rajapakse N., Ralib A., Ramakrishnan N., Ramanathan K., Ramli A.A., Rammaert B., Ramos G.V., Rana A., Rangappa R., Ranjan R., Rapp C., Rashan A., Rashan T., Rasheed G., Rasmin M., Ratsep I., Rau C., Ravi T., Raza A., Real A., Rebaudet S., Redl S., Reeve B., Rehan A., Rehman A., Reid L., Reikvam D.H., Reis R., Rello J., Remppis J., Remy M., Ren H., Renk H., Resende L., Resseguier A.-S., Revest M., Rewa O., Reyes L.F., Reyes T., Ribeiro M.I., Richardson D., Richier L., Ridzuan S.N.A.A., Riera J., Rios A.L., Rishu A., Rispal P., Risso K., Rivera Nunez M.A., Rizer N., Robb D., Robba C., Roberto A., Roberts S., Robertson D.L., Robineau O., Roche-Campo F., Rodari P., Rodeia S., Rodriguez Abreu J., Roessler B., Roger C., Roger 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P., Cisneros Herreros, J. M., Citarella, B. W., Ciullo, A., Clarke, E., Clarke, J., Claure Del Granado, R., Clohisey, S., Cobb, J. P., Coca, N., Codan, C., Cody, C., Coelho, A., Coles, M., Colin, G., Collins, M., Colombo, S. M., Combs, P., Connolly, J., Connor, M., Conrad, A., Contreras, S., Conway, E., Cooke, G. S., Copland, M., Cordel, H., Corley, A., Cormican, S., Cornelis, S., Cornet, A. D., Corpuz, A. J., Cortegiani, A., Corvaisier, G., Costigan, E., Couffignal, C., Couffin-Cadiergues, S., Courtois, R., Cousse, S., Cregan, R., Crepy D'Orleans, C., Croonen, S., Crowl, G., Crump, J., Cruz, C., Cruz Berm, J. L., Cruz Rojo, J., Csete, M., Cucino, A., Cullen, A., Cullen, C., Cummings, M., Curley, G., Curlier, E., Curran, C., Custodio, P., da Silva Filipe, A., Da Silveira, C., Dabaliz, A. -A., Dagens, A., Dahly, D., Dalton, H., Dalton, J., Daly, S., D'Amico, F., Daneman, N., Daniel, C., Dankwa, E. A., Dantas, J., D'Aragon, F., de Boer, M., de Loughry, G., de Mendoza, D., De Montmollin, E., de Oliveira Franca, R. F., de Pinho Oliveira, A. I., De Rosa, R., de Silva, T., de Vries, P., Deacon, J., Dean, D., Debard, A., Debenedictis, B., Debray, M. -P., Decastro, N., Dechert, W., Deconninck, L., Decours, R., Defous, E., Delacroix, I., Delaveuve, E., Delavigne, K., Delfos, N. M., Deligiannis, I., Dell'Amore, A., Delmas, C., Delobel, P., Delsing, C., Demonchy, E., Denis, E., Deplanque, D., Depuydt, P., Desai, M., Descamps, D., Desvallee, M., Dewayanti, S., Diallo, A., Diamantis, S., Dias, A., Diaz, P., Diaz, R., Diaz Diaz, J. J., Didier, K., Diehl, J. -L., Dieperink, W., Dimet, J., Dinot, V., Diop, F., Diouf, A., Dishon, Y., Dixit, D., Djossou, F., Docherty, A. B., Doherty, H., Dondorp, A. M., Dong, A., Donnelly, C. A., Donnelly, M., Donohue, C., Donohue, S., Donohue, Y., Doran, C., Doran, P., Dorival, C., D'Ortenzio, E., Douglas, J. 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W., Granier, P., Grasselli, G., Grazioli, L., Green, C. A., Greene, C., Greenhalf, W., Greffe, S., Grieco, D. L., Griffee, M., Griffiths, F., Grigoras, I., Groenendijk, A., Grosse Lordemann, A., Gruner, H., Gu, Y., Guarracino, F., Guedj, J., Guego, M., Guellec, D., Guerguerian, A. -M., Guerreiro, D., Guery, R., Guillaumot, A., Guilleminault, L., Guimaraes de Castro, M., Guimard, T., Haalboom, M., Haber, D., Habraken, H., Hachemi, A., Hadri, N., Haidash, O., Haider, S., Haidri, F., Hakak, S., Hall, A., Hall, M., Halpin, S., Hamer, A., Hamers, R., Hamidfar, R., Hammond, T., Han, L. Y., Haniffa, R., Hao, K. W., Hardwick, H., Harrison, E. M., Harrison, J., Harrison, S. B. E., Hartman, A., Hashmi, J., Hashmi, M., Hayat, M., Hayes, A., Hays, L., Heerman, J., Heggelund, L., Hendry, R., Hennessy, M., Henriquez, A., Hentzien, M., Herekar, F., Hernandez-Montfort, J., Herr, D., Hershey, A., Hesstvedt, L., Hidayah, A., Higgins, D., Higgins, E., Higginsokeeffe, G., Hinchion, R., Hinton, S., Hiraiwa, H., Hitoto, H., Ho, A., Ho, Y. B., Hoctin, A., Hoffmann, I., Hoh, W. H., Hoiting, O., Holt, R., Holter, J. C., Horby, P., Horcajada, J. P., Hoshino, K., Houas, I., Hough, C. L., Houltham, S., Hsu, J. M. -Y., Hulot, J. -S., Hussain, I., Ijaz, S., Illes, H. -G., Imbert, P., Imran, M., Imran Sikander, R., Inacio, H., Infante Dominguez, C., Ing, Y. S., Iosifidis, E., Ippolito, M., Isgett, S., Ishani, P. G. P. I., Isidoro, T., Ismail, N., Isnard, M., Itai, J., Ito, A., Ivulich, D., Jaafar, D., Jaafoura, S., Jabot, J., Jackson, C., Jamieson, N., Jaquet, P., Jassat, W., Jaud-Fischer, C., Jaureguiberry, S., Javidfar, J., Jawad, I., Jaworsky, D., Jayakumar, D., Jego, F., Jelani, A. M., Jenum, S., Jimbo-Sotomayor, R., Job, V. D. P., Joe, O. Y., Jorge Garcia, R. N., Joseph, C., Joseph, M., Joshi, S., Jourdain, M., Jouvet, P., June, J., Jung, A., Jung, H., Juzar, D., Kafif, O., Kaguelidou, F., Kaisbain, N., Kaleesvran, T., Kali, S., Kalicinska, A., Kalomoiri, S., Kamal, S., Kamaluddin, M. A. A., Kamaruddin, Z. A. C., Kamarudin, N., Kandamby, D. H., Kandel, C., Kang, K. Y., Kant, R., Kanwal, D., Kanyawati, D., Karki, B., Karpayah, P., Karsies, T., Kartsonaki, C., Kasugai, D., Kataria, A., Katz, K., Kaur, A., Kaur Johal, S., Kawasaki, T., Kay, C., Keane, H., Keating, S., Kellam, P., Kelly, A., Kelly, C., Kelly, N., Kelly, S., Kelly, Y., Kelsey, M., Kennedy, R., Kennon, K., Kernan, M., Kerroumi, Y., Keshav, S., Kestelyn, E., Khalid, I., Khalid, O., Khalil, A., Khan, C., Khan, I., Khanal, S., Kho, M. E., Khoo, D., Khoo, R., Khoo, S., Khoso, N., Kiat, K. H., Kida, Y., Kiiza, P., Kildal, A. B., Kim, J. B., Kimmoun, A., Kindgen-Milles, D., King, A., Kitamura, N., Klenerman, P., Klont, R., Kloumann Bekken, G., Knight, S., Kobbe, R., Kodippily, C., Kohns Vasconcelos, M., Koirala, S., Komatsu, M., Korten, V., Kosgei, C., Kpangon, A., Krawczyk, K., Krishnan, S., Krishnan, V., Kruglova, O., Kumar, A., Kumar, D., Kumar, G., Kumar, M., Kumar Vecham, P., Kuriakose, D., Kurtzman, E., Kusumastuti, N. P., Kutsogiannis, D., Kutsyna, G., Kyriakoulis, K., Lachatre, M., Lacoste, M., Laffey, J. G., Lagrange, M., Laine, F., Lairez, O., Lakhey, S., Lalueza, A., Lambert, M., Lamontagne, F., Langelot-Richard, M., Langlois, V., Lantang, E. Y., Lanza, M., Laouenan, C., Laribi, S., Lariviere, D., Lasry, S., Latif, N., Launay, O., Laureillard, D., Lavie-Badie, Y., Law, A., Lawrence, C., Lawrence, T., Le, M., Le Bihan, C., Le Bris, C., Le Falher, G., Le Fevre, L., Le Hingrat, Q., Le Marechal, M., Le Mestre, S., Le Moal, G., Le Moing, V., Le Nagard, H., Le Turnier, P., Leal, E., Leal Santos, M., Lee, B. H., Lee, H. G., Lee, J., Lee, S. H., Lee, T. C., Lee, Y. L., Leeming, G., Lefebvre, B., Lefebvre, L., Lefevre, B., Legac, S., Lelievre, J. -D., Lellouche, F., Lemaignen, A., Lemee, V., Lemeur, A., Lemmink, G., Lene, H. S., Lennon, J., Leon, R., Leone, M., Lepiller, Q., Lescure, F. -X., Lesens, O., Lesouhaitier, M., Lester-Grant, A., Levy, B., Levy, Y., Levy-Marchal, C., Lewandowska, K., L'Her, E., Li Bassi, G., Liang, J., Liaquat, A., Liegeon, G., Lim, K. C., Lim, W. S., Lima, C., Lina, B., Lina, L., Lind, A., Lingas, G., Lion-Daolio, S., Lissauer, S., Liu, K., Livrozet, M., Lizotte, P., Loforte, A., Lolong, N., Loon, L. C., Lopes, D., Lopez-Colon, D., Loschner, A. L., Loubet, P., Loufti, B., Louis, G., Lourenco, S., Lovelace-Macon, L., Low, L. L., Lowik, M., Loy, J. S., Lucet, J. C., Lumbreras Bermejo, C., Luna, C. M., Lungu, O., Luong, L., Luque, N., Luton, D., Lwin, N., Lyons, R., Maasikas, O., Mabiala, O., Macdonald, S., Machado, M., Macheda, G., Macias Sanchez, J., Madhok, J., Maestro de la Calle, G., Mahieu, R., Mahy, S., Maia, A. R., Maier, L. S., Maillet, M., Maitre, T., Malfertheiner, M., Malik, N., Mallon, P., Maltez, F., Malvy, D., Manda, V., Mandei, J. 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A., Mcnally, P., Mcnicholas, B., Mcpartlan, E., Meaney, E., Mear-Passard, C., Mechlin, M., Meher, M., Mehkri, O., Mele, F., Melo, L., Memon, K., Mendes, J. J., Menkiti, O., Menon, K., Mentre, F., Mentzer, A. J., Mercier, E., Mercier, N., Merckx, A., Mergeay-Fabre, M., Mergler, B., Merson, L., Mesquita, A., Metwally, O., Meybeck, A., Meyer, D., Meynert, A. M., Meysonnier, V., Meziane, A., Mezidi, M., Michelagnoli, G., Michelanglei, C., Michelet, I., Mihelis, E., Mihnovit, V., Miranda-Maldonado, H., Misnan, N. A., Mohamed, N. N. E., Mohamed, T. J., Moin, A., Molina, D., Molinos, E., Molloy, B., Mone, M., Monteiro, A., Montes, C., Montrucchio, G., Moore, S., Moore, S. C., Morales Cely, L., Moro, L., Morocho Tutillo, D. R., Morton, B., Motherway, C., Motos, A., Mouquet, H., Mouton Perrot, C., Moyet, J., Mudara, C., Mufti, A. K., Muh, N. Y., Muhamad, D., Mullaert, J., Muller, F., Muller, K. 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M., Orquera, A., Ortoleva, J., Osatnik, J., O'Shea, L., O'Sullivan, M., Othman, S. Z., Ouamara, N., Ouissa, R., Owyang, C., Oziol, E., Pabasara, H. M. U., Pagadoy, M., Pages, J., Palacios, A., Palacios, M., Palmarini, M., Panarello, G., Panda, P. K., Paneru, H., Pang, L. H., Panigada, M., Pansu, N., Papadopoulos, A., Parke, R., Parker, M., Parra, B., Parrini, V., Pasha, T., Pasquier, J., Pastene, B., Patauner, F., Patel, J., Pathmanathan, M. D., Patrao, L., Patricio, P., Patrier, J., Patterson, L., Pattnaik, R., Paul, C., Paul, M., Paulos, J., Paxton, W. A., Payen, J. -F., Peariasamy, K., Pedrera Jimenez, M., Peek, G. J., Peelman, F., Peiffer-Smadja, N., Peigne, V., Pejkovska, M., Pelosi, P., Peltan, I. D., Pereira, R., Perez, D., Periel, L., Perpoint, T., Pesenti, A., Pestre, V., Petrou, L., Petrov-Sanchez, V., Pettersen, F. O., Peytavin, G., Pharand, S., Piagnerelli, M., Picard, W., Picone, O., de Piero, M., Pierobon, C., Piersma, D., Pimentel, C., Pinto, R., Pires, C., Pironneau, I., Piroth, L., Pius, R., Piva, S., Plantier, L., Plotkin, D., Png, H. S., Poissy, J., Pokeerbux, R., Pokorska-Spiewak, M., Poli, S., Pollakis, G., Ponscarme, D., Popielska, J., Post, A. -M., Postma, D. F., Povoa, P., Povoas, D., Powis, J., Prapa, S., Preau, S., Prebensen, C., Preiser, J. -C., Prinssen, A., Pritchard, M. G., Priyadarshani, G. D. D., Proenca, L., Pudota, S., Puechal, O., Pujo Semedi, B., Pulicken, M., Puntoni, M., Purcell, G., Quesada, L., Quinones-Cardona, V., Quiros Gonzalez, V., Quist-Paulsen, E., Quraishi, M., Rabaa, M., Rabaud, C., Rabindrarajan, E., Rafael, A., Rafiq, M., Ragazzo, G., Rahman, A. K. H. A., Rahman, R. A., Rahutullah, A., Rainieri, F., Rajahram, G. S., Rajapakse, N., Ralib, A., Ramakrishnan, N., Ramanathan, K., Ramli, A. A., Rammaert, B., Ramos, G. V., Rana, A., Rangappa, R., Ranjan, R., Rapp, C., Rashan, A., Rashan, T., Rasheed, G., Rasmin, M., Ratsep, I., Rau, C., Ravi, T., Raza, A., Real, A., Rebaudet, S., Redl, S., Reeve, B., Rehan, A., Rehman, A., Reid, L., Reikvam, D. H., Reis, R., Rello, J., Remppis, J., Remy, M., Ren, H., Renk, H., Resende, L., Resseguier, A. -S., Revest, M., Rewa, O., Reyes, L. F., Reyes, T., Ribeiro, M. I., Richardson, D., Richier, L., Ridzuan, S. N. A. A., Riera, J., Rios, A. L., Rishu, A., Rispal, P., Risso, K., Rivera Nunez, M. A., Rizer, N., Robb, D., Robba, C., Roberto, A., Roberts, S., Robertson, D. L., Robineau, O., Roche-Campo, F., Rodari, P., Rodeia, S., Rodriguez Abreu, J., Roessler, B., Roger, C., Roger, P. -M., Roilides, E., Rojek, A., Romaru, J., Roncon-Albuquerque Jr, R., Roriz, M., Rosa-Calatrava, M., Rose, M., Rosenberger, D., Rossanese, A., Rossetti, M., Rossignol, B., Rossignol, P., Rousset, S., Roy, C., Roze, B., Rusmawatiningtyas, D., Russell, C. D., Ryan, M., Ryckaert, S., Rygh Holten, A., Saba, I., Sadaf, S., Sadat, M., Sahraei, V., Saint-Gilles, M., Sakiyalak, P., Salahuddin, N., Salazar, L., Saleem, J., Sales, G., Sallaberry, S., Salmon Gandonniere, C., Salvator, H., Sanchez, O., Sanchez Choez, X., Sanchez de Oliveira, K., Sanchez-Miralles, A., Sancho-Shimizu, V., Sandhu, G., Sandhu, Z., Sandrine, P. -F., Sandulescu, O., Santos, M., Sarfo-Mensah, S., Sarmento Banheiro, B., Sarmiento, I. C. E., Sarton, B., Satyapriya, S., Satyawati, R., Saviciute, E., Savio, R., Savvidou, P., Saw, Y. T., Schaffer, J., Schermer, T., Scherpereel, A., Schneider, M., Schroll, S., Schwameis, M., Schwartz, G., Scott, J. T., Scott-Brown, J., Sedillot, N., Seitz, T., Selvanayagam, J., Selvarajoo, M., Semaille, C., Semple, M. G., Senian, R. B., Senneville, E., Sepulveda, C., Sequeira, F., Sequeira, T., Serpa Neto, A., Serrano Balazote, P., Shadowitz, E., Shahidan, S. A., Shahnaz Hasan, M., Shamsah, M., Shankar, A., Sharjeel, S., Sharma, P., Shaw, C. A., Shaw, V., Shi, H., Shiban, N., Shiekh, M., Shiga, T., Shime, N., Shimizu, H., Shimizu, K., Shimizu, N., Shindo, N., Shrapnel, S., Shum, H. P., Si Mohammed, N., Siang, N. Y., Sibiude, J., Siddiqui, A., Sigfrid, L., Sillaots, P., Silva, C., Silva, M. J., Silva, R., Sim Lim Heng, B., Sin, W. C., Singh, B. C., Singh, P., Sitompul, P. A., Sivam, K., Skogen, V., Smith, S., Smood, B., Smyth, C., Smyth, M., Snacken, M., So, D., Soh, T. V., Solis, M., Solomon, J., Solomon, T., Somers, E., Sommet, A., Song, M. J., Song, R., Song, T., Song Chia, J., Sonntagbauer, M., Soom, A. M., Sotto, A., Soum, E., Sousa, A. C., Sousa, M., Sousa Uva, M., Souza-Dantas, V., Sperry, A., Spinuzza, E., Sri Darshana, B. P. S. R., Sriskandan, S., Stabler, S., Staudinger, T., Stecher, S. -S., Steinsvik, T., Stienstra, Y., Stiksrud, B., Stolz, E., Stone, A., Streinu-Cercel, A., Strudwick, S., Stuart, A., Stuart, D., Subekti, D., Suen, G., Suen, J. Y., Sukumar, P., Sultana, A., Summers, C., Supic, D., Suppiah, D., Surovcova, M., Suwarti, S., Svistunov, A. A., Syahrin, S., Syrigos, K., Sztajnbok, J., Szuldrzynski, K., Tabrizi, S., Taccone, F. S., Tagherset, L., Taib, S. M., Talarek, E., Taleb, S., Talsma, J., Tampubolon, M. L., Tan, K. K., Tan, L. V., Tan, Y. C., Tanaka, C., Tanaka, H., Tanaka, T., Taniguchi, H., Tanveer, H., Taqdees, H., Taqi, A., Tardivon, C., Tattevin, P., Taufik, M. A., Tawfik, H., Tedder, R. S., Tee, T. Y., Teixeira, J., Tejada, S., Tellier, M. -C., Teoh, S. K., Teotonio, V., Teoule, F., Terpstra, P., Terrier, O., Terzi, N., Tessier-Grenier, H., Tey, A., Thabit, A. A. M., Tham, Z. D., Thangavelu, S., Thibault, V., Thiberville, S. -D., Thill, B., Thirumanickam, J., Thompson, S., Thomson, D., Thomson, E. C., Thurai, S. R. T., Thuy, D. B., Thwaites, R. S., Tierney, P., Tieroshyn, V., Timashev, P. S., Timsit, J. -F., Tirupakuzhi Vijayaraghavan, B. K., Tissot, N., Toh, J. Z. Y., Toki, M., Tolppa, T., Tonby, K., Tonnii, S. L., Torres, A., Torres, M., Torres Santos-Olmo, R. M., Torres-Zevallos, H., Towers, M., Trapani, T., Traynor, D., Treoux, T., Trieu, H. T., Tripathy, S., Tromeur, C., Trontzas, I., Trouillon, T., Truong, J., Tual, C., Tubiana, S., Tuite, H., Turmel, J. -M., Turtle, L. C. W., Tveita, A., Twardowski, P., Uchiyama, M., Udayanga, P. I., Udy, A., Ullrich, R., Umer, Z., Uribe, A., Usman, A., Vajdovics, C., Val-Flores, L., Valle, A. L., Valran, A., Van de Velde, S., van den Berge, M., van der Feltz, M., van der Valk, P., Van Der Vekens, N., Van der Voort, P., Van Der Werf, S., van Dyk, M., van Gulik, L., Van Hattem, J., van Lelyveld, S., van Netten, C., Van Twillert, G., van Veen, I., Vanel, N., Vanoverschelde, H., Varghese, P., Varrone, M., Vasudayan, S. R., Vauchy, C., Vaughan, H., Veeran, S., Veislinger, A., Vencken, S., Ventura, S., Verbon, A., Vidal, J. E., Vieira, C., Vijayan, D., Villanueva, J. A., Villar, J., Villeneuve, P. -M., Villoldo, A., Vinh Chau, N. V., Visseaux, B., Visser, H., Vitiello, C., Vonkeman, H., Vuotto, F., Wahab, N. H., Wahab, S. A., Wahid, N. A., Wainstein, M., Wan Muhd Shukeri, W. F., Wang, C. -H., Webb, S. A., Wei, J., Weil, K., Wen, T. P., Wesselius, S., West, T. E., Wham, M., Whelan, B., White, N., Wicky, P. H., Wiedemann, A., Wijaya, S. O., Wille, K., Willems, S., Williams, V., Wils, E. -J., Wing Yiu, N., Wong, C., Wong, T. F., Wong, X. C., Wong, Y. S., Xian, G. E., Xian, L. S., Xuan, K. P., Xynogalas, I., Yacoub, S., Yakop, S. R. B. M., Yamazaki, M., Yazdanpanah, Y., Yee Liang Hing, N., Yelnik, C., Yeoh, C. H., Yerkovich, S., Yokoyama, T., Yonis, H., Yousif, O., Yuliarto, S., Zaaqoq, A., Zabbe, M., Zacharowski, K., Zahid, M., Zahran, M., Zaidan, N. Z. B., Zambon, M., Zambrano, M., Zanella, A., Zawadka, K., Zaynah, N., Zayyad, H., Zoufaly, A., Zucman, D., Intensive Care Medicine, and Group, The ISARIC Clinical Characterisation
Subjects: Biomedical Research, [SDV]Life Sciences [q-bio], Clinical science, Global Health, Corrections, Microbiology, 1117 Public Health and Health Services, 1108 Medical Microbiology, Pandemic, Economics, Humans, ISARIC Clinical Characterisation Group, Pandemics, COVID-19/epidemiology, Actuarial science, Information Dissemination, SARS-CoV-2, Comment, ISARIC, COVID-19, 1103 Clinical Sciences, Communicable Disease Control/methods, Infectious Diseases, Open source, Communicable Disease Control, Value (mathematics), Human
Abstract: International audience
Published: 2021

44. Evaluating whole HIV-1 genome sequence for estimation of incidence and migration in a rural South African community

Author: Fabrícia F Nascimento, Manon Ragonnet-Cronin, Tanya Golubchik, Siva Danaviah, Anne Derache, Christophe Fraser, and Erik Volz
Subjects: Medicine (miscellaneous), General Biochemistry, Genetics and Molecular Biology
Abstract: Background: South Africa has the largest number of people living with HIV (PLWHIV) in the world, with HIV prevalence and transmission patterns varying greatly between provinces. Transmission between regions is still poorly understood, but phylodynamics of HIV-1 evolution can reveal how many infections are attributable to contacts outside a given community. We analysed whole genome HIV-1 genetic sequences to estimate incidence and the proportion of transmissions between communities in Hlabisa, a rural South African community. Methods: We separately analysed HIV-1 for gag, pol, and env genes sampled from 2,503 PLWHIV. We estimated time-scaled phylogenies by maximum likelihood under a molecular clock model. Phylodynamic models were fitted to time-scaled trees to estimate transmission rates, effective number of infections, incidence through time, and the proportion of infections imported to Hlabisa. We also partitioned time-scaled phylogenies with significantly different distributions of coalescent times. Results: Phylodynamic analyses showed similar trends in epidemic growth rates between 1980 and 1990. Model-based estimates of incidence and effective number of infections were consistent across genes. Parameter estimates with gag were generally smaller than those estimated with pol and env. When estimating the proportions of new infections in Hlabisa from immigration or transmission from external sources, our posterior median estimates were 85% (95% credible interval (CI) = 78%–92%) for gag, 62% (CI = 40%–78%) for pol, and 77% (CI = 58%–90%) for env in 2015. Analysis of phylogenetic partitions by gene showed that most close global reference sequences clustered within a single partition. This suggests local evolving epidemics or potential unmeasured heterogeneity in the population. Conclusions: We estimated consistent epidemic dynamic trends for gag, pol and env genes using phylodynamic models. There was a high probability that new infections were not attributable to endogenous transmission within Hlabisa, suggesting high inter-connectedness between communities in rural South Africa.
Published: 2022

45. Time to evaluate COVID-19 contact-tracing apps

Author: Lucie Abeler-Dörner, Vittoria Colizza, Luca Ferretti, Steven Riley, Ciro Cattuto, Adam J. Kucharski, Rafael T. Mikolajczyk, Katrina A. Lythgoe, Eva Grill, Michelle Kendall, David Bonsall, Chris Wymant, Christophe Fraser, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Tokyo Institute of Technology [Tokyo] (TITECH), Ludwig-Maximilians-Universität München (LMU), Institute for Scientific Interchange Foundation [Turin, Italy] (ISI Foundation ), London School of Hygiene and Tropical Medicine (LSHTM), Nuffield Department of Medicine [Oxford, UK] (Big Data Institute), University of Oxford, and HAL-SU, Gestionnaire
Subjects: 2019-20 coronavirus outbreak, Infection Control, Coronavirus disease 2019 (COVID-19), COVID-19, Contact Tracing, Evaluation Studies as Topic, Health Policy, Humans, Pandemics, Physical Distancing, Proof of Concept Study, Quarantine, SARS-CoV-2, Mobile Applications, Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), [SDV]Life Sciences [q-bio], General Medicine, Viral infection, General Biochemistry, Genetics and Molecular Biology, [SDV] Life Sciences [q-bio], Human–computer interaction, Contact tracing
Abstract: International audience
Published: 2021

46. Modelling the impact of rapid tests, tracing and distancing in lower-income countries suggest that optimal policies vary with rural-urban settings

Author: Xilin Jiang, Wenfeng Gong, Zlatina Dobreva, Ya Gao, Matthew Quaife, Christophe Fraser, and Chris Holmes
Subjects: Rapid diagnostic test, Inequality, business.industry, Distancing, media_common.quotation_subject, Distribution (economics), law.invention, Geography, Transmission (mechanics), law, Environmental health, Quality (business), business, Contact tracing, Slum, media_common
Abstract: BackgroundNon-pharmaceutical intervention (NPI) remains the most reliable COVID-19 containment tool for low- and middle-income countries (LMICs) given the inequality of vaccine distribution and their vulnerable healthcare systems. We aimed to develop mathematical models that capture LMIC demographic characteristics such as young population and large household size and assess NPI effectiveness in rural and urban communities. MethodsWe constructed synthetic populations for rural, non-slum urban and slum settings to capture LMIC demographic characteristics that vary across communities. We integrated age mixing and household structure into contact networks for each community setting and simulated COVID-19 outbreaks within the networks. Using this agent-based model, we evaluate NPIs including testing and isolation, tracing and quarantine, and physical distancing. We explored the optimal containment strategies for rural and urban communities by designing and simulating setting-specific strategies that deploy rapid diagnostic test, symptom screening, contact tracing and physical distancing. We performed extensive simulations to capture the uncertainty of outbreak trajectories and the impact of varying model parameters. FindingsWe found the impact of testing, tracing and distancing varies with rural-urban settings. In rural communities, we found implementing either high quality (sensitivity > 50%) antigen rapid diagnostic tests or moderate physical distancing could contain the transmission. Additionally, antibody rapid diagnostic tests and symptom-based diagnosis could be useful for mitigating the transmission. In non-slum urban communities, we demonstrated that both physical distancing and case finding are essential for containing COVID-19 (average infection rate < 10%). In slum communities, we found physical distancing is less effective compared to rural and non-slum urban communities. Lastly, for all communities considered, we demonstrated contact quarantine is essential for effective containment and is effective at a low compliance rate (30%). InterpretationOur findings could guide setting-specific strategy design for different communities in LMICs. Our assessments also have implications on applying rapid diagnostic tests and symptom-based diagnosis for case finding, tracing and distancing in lower-income communities.
Published: 2021

47. Modeling the effect of exposure notification and non-pharmaceutical interventions on COVID-19 transmission in Washington state

Author: Paul Eastham, Yusef Shafi, Austin Wu, Robert Hinch, Anel Nurtay, Michael V. McConnell, Neo Wu, Lucie Abeler-Dörner, Luyang Liu, Matt Rosencrantz, Zhao Cheng, Shawn O'Banion, Christophe Fraser, Michael Dikovsky, Matthew Abueg, David Bonsall, and William J. M. Probert
Subjects: Coronavirus disease 2019 (COVID-19), Epidemiology, Computer applications to medicine. Medical informatics, Internet privacy, R858-859.7, Psychological intervention, Medicine (miscellaneous), Health Informatics, 030501 epidemiology, Article, law.invention, Exposure Notification, 03 medical and health sciences, 0302 clinical medicine, Health Information Management, law, 030212 general & internal medicine, Implementation, business.industry, Health policy, Computer Science Applications, Transmission (mechanics), Work (electrical), State (computer science), 0305 other medical science, business, Contact tracing
Abstract: Contact tracing is increasingly used to combat COVID-19, and digital implementations are now being deployed, many based on Apple and Google’s Exposure Notification System. These systems utilize non-traditional smartphone-based technology, presenting challenges in understanding possible outcomes. In this work, we create individual-based models of three Washington state counties to explore how digital exposure notifications combined with other non-pharmaceutical interventions influence COVID-19 disease spread under various adoption, compliance, and mobility scenarios. In a model with 15% participation, we found that exposure notification could reduce infections and deaths by approximately 8% and 6% and could effectively complement traditional contact tracing. We believe this can provide health authorities in Washington state and beyond with guidance on how exposure notification can complement traditional interventions to suppress the spread of COVID-19.
Published: 2021

48. Is HIV short-sighted? Insights from a multistrain nested model

Author: Christophe Fraser, Katrina A. Lythgoe, and Lorenzo Pellis
Subjects: Time Factors, Fitness landscape, Epidemiology, Population, Virulence, HIV Infections, Transmission-virulence trade off, Biology, Virus Replication, Models, Biological, Virus, 03 medical and health sciences, Species Specificity, evolution, Genetics, Humans, Evolutionary dynamics, education, Pathogen, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, QR355, 0303 health sciences, education.field_of_study, Science & Technology, 030306 microbiology, Transmission (medicine), HIV, Original Articles, transmission-virulence trade-off, Virology, Biological Evolution, QR, 3. Good health, Viral replication, Evolutionary biology, Host-Pathogen Interactions, General Agricultural and Biological Sciences, Life Sciences & Biomedicine, nested model, pathogen
Abstract: An important component of pathogen evolution at the population level is evolution within hosts. Unless evolution within hosts is very slow compared to the duration of infection, the composition of pathogen genotypes within a host is likely to change during the course of an infection, thus altering the composition of genotypes available for transmission as infection progresses. We develop a nested modeling approach that allows us to follow the evolution of pathogens at the epidemiological level by explicitly considering within-host evolutionary dynamics of multiple competing strains and the timing of transmission. We use the framework to investigate the impact of short-sighted within-host evolution on the evolution of virulence of human immunodeficiency virus (HIV), and find that the topology of the within-host adaptive landscape determines how virulence evolves at the epidemiological level. If viral reproduction rates increase significantly during the course of infection, the viral population will evolve a high level of virulence even though this will reduce the transmission potential of the virus. However, if reproduction rates increase more modestly, as data suggest, our model predicts that HIV virulence will be only marginally higher than the level that maximizes the transmission potential of the virus.
Published: 2021

49. The epidemiological impact of the NHS COVID-19 app

Author: Chris, Wymant, Luca, Ferretti, Daphne, Tsallis, Marcos, Charalambides, Lucie, Abeler-Dörner, David, Bonsall, Robert, Hinch, Michelle, Kendall, Luke, Milsom, Matthew, Ayres, Chris, Holmes, Mark, Briers, and Christophe, Fraser
Subjects: Wales, England, National Health Programs, Quarantine, Basic Reproduction Number, COVID-19, Humans, Contact Tracing, Mortality, Mobile Applications
Abstract: The COVID-19 pandemic has seen the emergence of digital contact tracing to help to prevent the spread of the disease. A mobile phone app records proximity events between app users, and when a user tests positive for COVID-19, their recent contacts can be notified instantly. Theoretical evidence has supported this new public health intervention
Published: 2021

50. Human Immunodeficiency Virus (HIV) Genetic Diversity Informs Stage of HIV-1 Infection Among Patients Receiving Antiretroviral Therapy in Botswana

Author: Vlad Novitsky, Tanya Golubchik, Christophe Fraser, Manon Ragonnet-Cronin, Erik M. Volz, Max Essex, and Sikhulile Moyo
Subjects: 0301 basic medicine, medicine.medical_specialty, Human immunodeficiency virus (HIV), HIV Infections, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Internal medicine, medicine, Immunology and Allergy, Humans, 030212 general & internal medicine, Stage (cooking), Negative HIV test, Genetic diversity, Botswana, business.industry, Genetic Variation, Viral Load, Antiretroviral therapy, Negative HIV, 030104 developmental biology, Infectious Diseases, Anti-Retroviral Agents, HIV-1, business, Viral load, Diversity (business)
Abstract: Background Human immunodeficiency virus (HIV)-1 genetic diversity increases during infection and can help infer the time elapsed since infection. However, the effect of antiretroviral treatment (ART) on the inference remains unknown. Methods Participants with estimated duration of HIV-1 infection based on repeated testing were sourced from cohorts in Botswana (n = 1944). Full-length HIV genome sequencing was performed from proviral deoxyribonucleic acid. We optimized a machine learning model to classify infections as < or >1 year based on viral genetic diversity, demographic, and clinical data. Results The best predictive model included variables for genetic diversity of HIV-1 gag, pol, and env, viral load, age, sex, and ART status. Most participants were on ART. Balanced accuracy was 90.6% (95% confidence interval, 86.7%–94.1%). We tested the algorithm among newly diagnosed participants with or without documented negative HIV tests. Among those without records, those who self-reported a negative HIV test within 1 year previously. There was no difference in classification between those self-reporting a negative HIV test Conclusions These results indicate that recency of HIV-1 infection can be inferred from viral sequence diversity even among patients on suppressive ART.
Published: 2021

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