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1. An updated framework for SARS-CoV-2 variants reflects the unpredictability of viral evolution

Author

Subissi, Lorenzo, Otieno, James Richard, Worp, Nathalie, Attar Cohen, Homa, Oude Munnink, Bas B., Abu-Raddad, Laith J., Alm, Erik, Barakat, Amal, Barclay, Wendy S., Bhiman, Jinal N., Caly, Leon, Chand, Meera, Chen, Mark, Cullinane, Ann, de Oliveira, Tulio, Drosten, Christian, Druce, Julian, Effler, Paul, El Masry, Ihab, Faye, Adama, Ghedin, Elodie, Grant, Rebecca, Haagmans, Bart L., Happi, Christian, Herring, Belinda L., Hodcroft, Emma B., Ikejezie, Juniorcaius, Katawera, Victoria, Kassamali, Zyleen Alnashir, Leo, Yee-Sin, Leung, Gabriel M., Kondor, Rebecca J., Marklewitz, Marco, Mendez-Rico, Jairo, Melhem, Nada M., Munster, Vincent, Nahapetyan, Karen, Naindoo, Dhamari, Oh, Djin-Ye, Peacock, Thomas P., Peiris, Malik, Peng, Zhibin, Poon, Leo L. M., Rambaut, Andrew, Saha, Senjuti, Shen, Yinzhong, Siqueira, Marilda M., Volz, Erik, Tessema, Sofonias K., Thiel, Volker, Triki, Henda, van der Werf, Sylvie, von Eije, Karin, Cunningham, Jane, Koopmans, Marion P. G., von Gottberg, Anne, Agrawal, Anurag, and Van Kerkhove, Maria D.

Published
2024
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2. Multiplex qPCR Discriminates Variants of Concern to Enhance Global Surveillance of SARS-CoV-2

Author

Vogels, Chantal B. F., primary, Breban, Mallery I., additional, Ott, Isabel M., additional, Alpert, Tara, additional, Petrone, Mary E., additional, Watkins, Anne E., additional, Kalinich, Chaney C., additional, Earnest, Rebecca, additional, Rothman, Jessica E., additional, de Jesus, Jaqueline Goes, additional, Claro, Ingra Morales, additional, Ferreira, Giulia Magalhães, additional, Crispim, Myuki A. E., additional, Singh, Lavanya, additional, Tegally, Houriiyah, additional, Anyaneji, Ugochukwu J., additional, Hodcroft, Emma B., additional, Mason, Christopher E., additional, Khullar, Gaurav, additional, Metti, Jessica, additional, Dudley, Joel T., additional, MacKay, Matthew J., additional, Nash, Megan, additional, Wang, Jianhui, additional, Liu, Chen, additional, Hui, Pei, additional, Murphy, Steven, additional, Neal, Caleb, additional, Laszlo, Eva, additional, Landry, Marie L., additional, Muyombwe, Anthony, additional, Downing, Randy, additional, Razeq, Jafar, additional, de Oliveira, Tulio, additional, Faria, Nuno R., additional, Sabino, Ester C., additional, Neher, Richard A., additional, Fauver, Joseph R., additional, and Grubaugh, Nathan D., additional

Published
2023
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3. Emergence of an early SARS-CoV-2 epidemic in the United States.

Author

Zeller, Mark, Gangavarapu, Karthik, Anderson, Catelyn, Smither, Allison R, Vanchiere, John A, Rose, Rebecca, Snyder, Daniel J, Dudas, Gytis, Watts, Alexander, Matteson, Nathaniel L, Robles-Sikisaka, Refugio, Marshall, Maximilian, Feehan, Amy K, Sabino-Santos, Gilberto, Bell-Kareem, Antoinette R, Hughes, Laura D, Alkuzweny, Manar, Snarski, Patricia, Garcia-Diaz, Julia, Scott, Rona S, Melnik, Lilia I, Klitting, Raphaëlle, McGraw, Michelle, Belda-Ferre, Pedro, DeHoff, Peter, Sathe, Shashank, Marotz, Clarisse, Grubaugh, Nathan D, Nolan, David J, Drouin, Arnaud C, Genemaras, Kaylynn J, Chao, Karissa, Topol, Sarah, Spencer, Emily, Nicholson, Laura, Aigner, Stefan, Yeo, Gene W, Farnaes, Lauge, Hobbs, Charlotte A, Laurent, Louise C, Knight, Rob, Hodcroft, Emma B, Khan, Kamran, Fusco, Dahlene N, Cooper, Vaughn S, Lemey, Phillipe, Gardner, Lauren, Lamers, Susanna L, Kamil, Jeremy P, Garry, Robert F, Suchard, Marc A, and Andersen, Kristian G

Subjects
Humans, Risk Factors, Disease Outbreaks, Phylogeny, Travel, United States, Louisiana, Texas, Databases as Topic, Epidemics, COVID-19, SARS-CoV-2, genomic epidemiology, mobility, phylogenetics, viral emergence, viral sequencing, Emerging Infectious Diseases, Biodefense, Prevention, Vaccine Related, Lung, Developmental Biology, Biological Sciences, Medical and Health Sciences
Abstract

The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.

Published
2021

4. Cryptic transmission of SARS-CoV-2 in Washington state

Author

Bedford, Trevor, Greninger, Alexander L, Roychoudhury, Pavitra, Starita, Lea M, Famulare, Michael, Huang, Meei-Li, Nalla, Arun, Pepper, Gregory, Reinhardt, Adam, Xie, Hong, Shrestha, Lasata, Nguyen, Truong N, Adler, Amanda, Brandstetter, Elisabeth, Cho, Shari, Giroux, Danielle, Han, Peter D, Fay, Kairsten, Frazar, Chris D, Ilcisin, Misja, Lacombe, Kirsten, Lee, Jover, Kiavand, Anahita, Richardson, Matthew, Sibley, Thomas R, Truong, Melissa, Wolf, Caitlin R, Nickerson, Deborah A, Rieder, Mark J, Englund, Janet A, Hadfield, James, Hodcroft, Emma B, Huddleston, John, Moncla, Louise H, Müller, Nicola F, Neher, Richard A, Deng, Xianding, Gu, Wei, Federman, Scot, Chiu, Charles, Duchin, Jeffrey S, Gautom, Romesh, Melly, Geoff, Hiatt, Brian, Dykema, Philip, Lindquist, Scott, Queen, Krista, Tao, Ying, Uehara, Anna, Tong, Suxiang, MacCannell, Duncan, Armstrong, Gregory L, Baird, Geoffrey S, Chu, Helen Y, Shendure, Jay, Jerome, Keith R, Boeckh, Michael, Lutz, Barry R, Thompson, Matthew, Huang, Shichu, Jackson, Michael L, Kimball, Louise E, Logue, Jennifer, Lyon, Victoria, Newman, Kira L, and Suchsland, Monica L Zigman

Subjects
Infectious Diseases, Pneumonia & Influenza, Lung, Prevention, Emerging Infectious Diseases, Biodefense, Vaccine Related, Pneumonia, Infection, Good Health and Well Being, Bayes Theorem, Betacoronavirus, COVID-19, Coronavirus Infections, Genome, Viral, Humans, Likelihood Functions, Pandemics, Phylogeny, Pneumonia, Viral, SARS-CoV-2, Washington, Seattle Flu Study Investigators, General Science & Technology
Abstract

After its emergence in Wuhan, China, in late November or early December 2019, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus rapidly spread globally. Genome sequencing of SARS-CoV-2 allows the reconstruction of its transmission history, although this is contingent on sampling. We analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington state in the United States. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020, which subsequently spread locally before active community surveillance was implemented.

Published
2020

7. Epidemiological and clinical insights into the enterovirus D68 upsurge in Europe 2021/22 and the emergence of novel B3-derived lineages, ENPEN multicentre study

Author

Simoes, Margarida Pires, primary, Hodcroft, Emma B, additional, Simmonds, Peter, additional, Albert, Jan, additional, Alidjinou, Enagon K, additional, Ambert-Balay, Katia, additional, Andrés, Cristina, additional, Antón, Andrés, additional, Auvray, Christelle, additional, Bailly, Jean-Luc, additional, Baldanti, Fausto, additional, Bastings, Capser, additional, Beard, Stuart, additional, Pereira, Carla Berengua, additional, Berginc, Natasa, additional, Bloemen, Mandy, additional, Blomqvist, Soile, additional, Bosma, Froukje, additional, Böttcher, Sindy, additional, Bubba, Laura, additional, Buderus, Stafan, additional, Cabrerizo, Maria, additional, Calvo, Christina, additional, Celma, Christina, additional, Ceriotti, Ferruccio, additional, Clark, Gemma, additional, Costa, Inës, additional, Coste-Burel, Marianne, additional, Couderé, Karen, additional, Cremer, Jeroen, additional, del Cuerpo Casas, Margarita, additional, Daehne, Theo, additional, de Beer, Jessica, additional, de Ceano-Vivas, Maria, additional, De Gascun, Cillian, additional, de Rougemont, Alexis, additional, Dean, Johnathan, additional, Dembinski, Jennifer L, additional, Diedrich, Sabine, additional, Diez-Domingo, Javier, additional, Dillner, Lena, additional, Dorenberg, Dagny H, additional, Ducancelle, Alexandra, additional, Dudman, Susanne, additional, Dyrdak, Robert, additional, Eis-Huebinger, Anna-Maria, additional, Falces-Romero, Iker, additional, Farkas, Agnes, additional, Feeney, Susan, additional, Fernandez-Garcia, Maria D, additional, Flipse, Jacky, additional, Franck, Kristina T, additional, Galli, Cristina, additional, Garrigue, Isabelle, additional, Geeraedts, Felix, additional, Georgieva, Irina, additional, Giardina, Federica, additional, Guiomar, Raquel, additional, Hauzenberger, Elenor, additional, Heikens, Esther, additional, Henquell, Cécille, additional, Hober, Didier, additional, Hönemann, Amrio, additional, Howson-Wells, Hannah, additional, Hruškar, Željka, additional, Ikonen, Niina, additional, Imbert, Berthemarie, additional, Jansz, Arjan R, additional, Jeannoël, Marion, additional, Jiřincová, Helena, additional, Josset, Laurence, additional, Keeren, Kathrin, additional, Kramer-Lindhout, Naomie, additional, Krokstad, Sidsel, additional, Lazrek, Mouna, additional, Le Guillou-Guillemette, Hélène, additional, Lefeuvre, Caroline, additional, Lind, Andreas, additional, Lunar, Maja M, additional, Maier, Melanie, additional, Marque-Juillet, Stéphanie, additional, McClure, C Patrick, additional, McKenna, James, additional, Meijer, Adam, additional, Menasalvas Ruiz, Ana, additional, Mengual-Chuliá, Beatriz, additional, Midgley, Sofie, additional, Mirand, Audrey, additional, Molenkamp, Richard, additional, Montes, Milagrosa, additional, Moreno-Docón, Antonio, additional, Morley, Ursula, additional, Murk, Jean-Luc, additional, Navascués-Ortega, Ana, additional, Nijhuis, Roel, additional, Nikolaeva-Glomb, Lubomira, additional, Nordbø, Svein A, additional, Numanovic, Sanela, additional, Oggioni, Massimo, additional, Oñate Vergara, Eider, additional, Pacaud, Jordi, additional, Pacreau, Marie L, additional, Panning, Marcus, additional, Pariani, Elena, additional, Pekova, Lili, additional, Pellegrinelli, Laura, additional, Petrovec, Miroslav, additional, Pietsch, Corinna, additional, Pilorge, Léa, additional, Piñeiro, Luis, additional, Piralla, Antonio, additional, Poljak, Mario, additional, Prochazka, Birgit, additional, Rabella, Nuria, additional, Rahamat-Langendoen, Janette C, additional, Rainetova, petra, additional, Reynders, Marijke, additional, Riezebos-Brilman, Annelies, additional, Roorda, Lieuwe, additional, Savolainen-Kopra, Carita, additional, Schuffenecker, Isabelle, additional, Smeets, Leo C, additional, Stoyanova, Ayse, additional, Stefic, Karl, additional, Swanink, Caroline, additional, Tabain, Irena, additional, Tjhie, Jeroen, additional, Thouault, Luc, additional, Tumiotto, Camille, additional, Uceda Renteria, Sara, additional, Uršič, Tina, additional, Vallet, Sophie, additional, Van Ranst, Marc, additional, Van Wunnik, Peter, additional, Verweij, Jaco J, additional, Vila, Jorgina, additional, Wintermans, Bas, additional, Wollants, Elke, additional, Wolthers, Katja C, additional, Xavier López-Labrado, F, additional, Fischer, Thea Kolsen, additional, Harvala, Heli, additional, and Benschop, Kimberley S M, additional

Published
2024
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9. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Author

Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Vaughan, Timothy G., Crawford, Katharine H. D., Althaus, Christian L., and Reichmuth, Martina L.

Subjects
Epidemics -- Causes of -- Distribution -- Europe, Disease transmission -- Causes of -- 2020 AD, Company distribution practices, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Following its emergence in late 2019, the spread of SARS-CoV-2.sup.1,2 has been tracked by phylogenetic analysis of viral genome sequences in unprecedented detail.sup.3-5. Although the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, travel within Europe resumed in the summer of 2020. Here we report on a SARS-CoV-2 variant, 20E (EU1), that was identified in Spain in early summer 2020 and subsequently spread across Europe. We find no evidence that this variant has increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant's success. Despite travel restrictions, we estimate that 20E (EU1) was introduced hundreds of times to European countries by summertime travellers, which is likely to have undermined local efforts to minimize infection with SARS-CoV-2. Our results illustrate how a variant can rapidly become dominant even in the absence of a substantial transmission advantage in favourable epidemiological settings. Genomic surveillance is critical for understanding how travel can affect transmission of SARS-CoV-2, and thus for informing future containment strategies as travel resumes. Analysis of the spread of the 20E (EU1) variant of SARS-CoV-2 through Europe suggests that international travel and insufficient containment, rather than increased transmissibility, led to a resurgence of infections., Author(s): Emma B. Hodcroft [sup.1] [sup.2] [sup.3] , Moira Zuber [sup.1] , Sarah Nadeau [sup.2] [sup.4] , Timothy G. Vaughan [sup.2] [sup.4] , Katharine H. D. Crawford [sup.5] [sup.6] [sup.7] [...]

Published
2021
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11. Identifying Transmission Clusters with Cluster Picker and HIV-TRACE

Author

Rose, Rebecca, Lamers, Susanna L, Dollar, James J, Grabowski, Mary K, Hodcroft, Emma B, Ragonnet-Cronin, Manon, Wertheim, Joel O, Redd, Andrew D, German, Danielle, and Laeyendecker, Oliver

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Genetics, HIV/AIDS, Good Health and Well Being, Adolescent, Adult, Cluster Analysis, Disease Transmission, Infectious, Female, HIV, HIV Infections, Humans, Male, Middle Aged, Molecular Epidemiology, Sequence Analysis, DNA, Young Adult, viral clustering, Uganda, Virology, Clinical sciences
Abstract

We compared the behavior of two approaches (Cluster Picker and HIV-TRACE) at varying genetic distances to identify transmission clusters. We used three HIV gp41 sequence datasets originating from the Rakai Community Cohort Study: (1) next-generation sequence (NGS) data from nine linked couples; (2) NGS data from longitudinal sampling of 14 individuals; and (3) Sanger consensus sequences from a cross-sectional dataset (n = 1,022) containing 91 epidemiologically linked heterosexual couples. We calculated the optimal genetic distance threshold to separate linked versus unlinked NGS datasets using a receiver operating curve analysis. We evaluated the number, size, and composition of clusters detected by Cluster Picker and HIV-TRACE at six genetic distance thresholds (1%-5.3%) on all three datasets. We further tested the effect of using all NGS, versus only a single variant for each patient/time point, for datasets (1) and (2). The optimal gp41 genetic distance threshold to distinguish linked and unlinked couples and individuals was 5.3% and 4%, respectively. HIV-TRACE tended to detect larger and fewer clusters, whereas Cluster Picker detected more clusters containing only two sequences. For NGS datasets (1) and (2), HIV-TRACE and Cluster Picker detected all linked pairs at 3% and 4% genetic distances, respectively. However, at 5.3% genetic distance, 20% of couples in dataset (3) did not cluster using either program, and for >1/3 of couples cluster assignment were discordant. We suggest caution in choosing thresholds for clustering analyses in a generalized epidemic.

Published
2017

13. Estimating the heritability of virulence in HIV

Author

Hodcroft, Emma B., Leigh Brown, Andrew, and Rambaut, Andrew

Subjects
616.97, HIV, viral load, heritability, virulence, AIDS, phylogenetics
Abstract

The rate that HIV-infected individuals progress to AIDS and death varies greatly. Viral load taken during the asymptomatic phase of the disease is one of the best-known predictors of HIV progression rate and transmission risk, and is known to be in uenced by both host and environmental factors. However, the role that the virus itself plays in determining the viral load is less clear. Previous studies have attempted to quantify the amount the viral genome in uences viral load, or the heritability of viral load, using transmission pairs and phylogenetic signal in small sample sizes, but have produced highly disparate estimates. E cient and accurate methods to estimate heritability have been utilised by quantitative geneticists for years, but are rarely applied to non-pedigree data. Here, I present a novel application of a population-scale method based in quantitative genetics to estimate the heritability of viral load in HIV using a viral phylogeny. This new phylogenetic method allows the inclusion of more samples than ever previously used, and avoids confounding e ects associated with transmission pair studies. This new method was applied to the two largest HIV subtypes found in the UK, subtypes B and C, using sequences and clinical data from UK-wide HIV databases. For subtype B (n=8,483) and C (n=1,821), I estimated that 5.7% (CI 2.8{8.6%) and 29.7% (CI 14.8{44.7%) of the variance in viral load is determined by the viral genome, respectively. These estimates suggest that viral in uence on viral load varies greatly between subtypes, with subtype C having much larger viral control over viral load than subtype B. I expanded the phylogenetic method to test whether the component of the viral load determined by the virus has changed over time. In subtype B, I foundevidence of a small but signi cant decrease in the viral component of viral load of -0.05 log10 copies/mL/yr. I built a stochastic, individual-based model capable of simulating a realistic HIV epidemic, with heritable viral loads that in uence transmission and disease progression, capable of generating data sets to assess the accuracy of phylogenetic methods. This was successfully used to generate epidemics approximating those in a small African village and a Western `men who have sex with men' community under a variety of conditions. To test the accuracy of the new phylogenetic heritability estimation method, simulated datasets were generated with the heritability of viral load set at values of 30%, 50%, 70%, and 90%. Unfortunately, complications in the heritability equation used prevented full assessment of the new phylogenetic method on the simulated data. Future development of the model will enable simulation of realistic viral loads under varying heritability values, enabling simulation of data sets that can be used to test this and other heritability estimation methods. This new phylogenetic method allows accurate estimation of heritability in large datasets, and has provided valuable insight into the viral in uence on viral load in HIV.

Published
2015

17. Functional SARS-CoV-2 cross-reactive CD4 + T cells established in early childhood decline with age

Author

Humbert, Marion, primary, Olofsson, Anna, additional, Wullimann, David, additional, Niessl, Julia, additional, Hodcroft, Emma B., additional, Cai, Curtis, additional, Gao, Yu, additional, Sohlberg, Ebba, additional, Dyrdak, Robert, additional, Mikaeloff, Flora, additional, Neogi, Ujjwal, additional, Albert, Jan, additional, Malmberg, Karl-Johan, additional, Lund-Johansen, Fridtjof, additional, Aleman, Soo, additional, Björkhem-Bergman, Linda, additional, Jenmalm, Maria C., additional, Ljunggren, Hans-Gustaf, additional, Buggert, Marcus, additional, and Karlsson, Annika C., additional

Published
2023
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20. Spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Author

Swiss National Science Foundation, European Commission, University of Basel, ETH Zurich, National Institute of General Medical Sciences (US), National Institute of Allergy and Infectious Diseases (US), Burroughs Wellcome Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Hodcroft, Emma B. [0000-0002-0078-2212], Zuber, Moira [0000-0002-4275-8739], Nadeau, Sarah [0000-0003-1008-8918], Vaughan, Timothy G. [0000-0001-6220-2239], Crawford, Katharine H. D. [0000-0002-6223-4019], Althaus, Christian L. [0000-0002-5230-6760], Reichmuth, Martina L. [0000-0001-9345-851X], Bowen, John E. [0000-0003-3590-9727], Walls, Alexandra C. [0000-0002-9636-8330], Corti, Davide [0000-0002-5797-1364], Bloom, Jesse D. [0000-0003-1267-3408], Veesler, David [0000-0002-6019-8675], Mateo, David [0000-0002-1590-4163], Hernando de Castro, Alberto [0000-0003-1180-1068], Comas, Iñaki [0000-0001-5504-9408], González-Candelas, Fernando [0000-0002-0879-5798], Stadler, Tanja [0000-0001-6431-535X], Neher, Richard A. [0000-0003-2525-1407], Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Vaughan, Timothy G., Crawford, Katharine H. D., Althaus, Christian L., Reichmuth, Martina L., Bowen, John E., Walls, Alexandra C., Corti, Davide, Bloom, Jesse D., Veesler, David, Mateo, David, Hernando de Castro, Alberto, Comas, Iñaki, González-Candelas, Fernando, Seqcovid-Spain Consortium, Stadler, Tanja, Neher, Richard A., Swiss National Science Foundation, European Commission, University of Basel, ETH Zurich, National Institute of General Medical Sciences (US), National Institute of Allergy and Infectious Diseases (US), Burroughs Wellcome Fund, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Research Council, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Howard Hughes Medical Institute, Hodcroft, Emma B. [0000-0002-0078-2212], Zuber, Moira [0000-0002-4275-8739], Nadeau, Sarah [0000-0003-1008-8918], Vaughan, Timothy G. [0000-0001-6220-2239], Crawford, Katharine H. D. [0000-0002-6223-4019], Althaus, Christian L. [0000-0002-5230-6760], Reichmuth, Martina L. [0000-0001-9345-851X], Bowen, John E. [0000-0003-3590-9727], Walls, Alexandra C. [0000-0002-9636-8330], Corti, Davide [0000-0002-5797-1364], Bloom, Jesse D. [0000-0003-1267-3408], Veesler, David [0000-0002-6019-8675], Mateo, David [0000-0002-1590-4163], Hernando de Castro, Alberto [0000-0003-1180-1068], Comas, Iñaki [0000-0001-5504-9408], González-Candelas, Fernando [0000-0002-0879-5798], Stadler, Tanja [0000-0001-6431-535X], Neher, Richard A. [0000-0003-2525-1407], Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Vaughan, Timothy G., Crawford, Katharine H. D., Althaus, Christian L., Reichmuth, Martina L., Bowen, John E., Walls, Alexandra C., Corti, Davide, Bloom, Jesse D., Veesler, David, Mateo, David, Hernando de Castro, Alberto, Comas, Iñaki, González-Candelas, Fernando, Seqcovid-Spain Consortium, Stadler, Tanja, and Neher, Richard A.

Abstract

Following its emergence in late 2019, the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1,2 has been tracked via phylogenetic analysis of viral genome sequences in unprecedented detail3–5. While the virus spread globally in early 2020 before borders closed, intercontinental travel has since been greatly reduced. However, within Europe travel resumed in the summer of 2020. Here we report on a novel SARS-CoV-2 variant, 20E (EU1), that emerged in Spain in early summer, and subsequently spread across Europe. We find no evidence of increased transmissibility, but instead demonstrate how rising incidence in Spain, resumption of travel, and lack of effective screening and containment may explain the variant’s success. Despite travel restrictions, we estimate 20E (EU1) was introduced hundreds of times to European countries by summertime travelers, likely undermining local efforts to keep SARS-CoV-2 cases low. Our results demonstrate how a variant can rapidly become dominant even in absence of a substantial transmission advantage in favorable epidemiological settings. Genomic surveillance is critical to understanding how travel can impact SARS-CoV-2 transmission, and thus for informing future containment strategies as travel resumes.

Published
2021

22. Evolution, geographic spreading, and demographic distribution of Enterovirus D68

Author

Hodcroft, Emma B., primary, Dyrdak, Robert, additional, Andrés, Cristina, additional, Egli, Adrian, additional, Reist, Josiane, additional, García Martínez de Artola, Diego, additional, Alcoba-Flórez, Julia, additional, Niesters, Hubert G. M., additional, Antón, Andrés, additional, Poelman, Randy, additional, Reynders, Marijke, additional, Wollants, Elke, additional, Neher, Richard A., additional, and Albert, Jan, additional

Published
2022
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23. Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

Author

Fonds National Suisse de la Recherche Scientifique, University of Basel, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Commission, European Research Council, Hodcroft, Emma B. [0000-0002-0078-2212], Nadeau, Sarah [0000-0003-1008-8918], Comas, Iñaki [0000-0001-5504-9408], González-Candelas, Fernando [0000-0002-0879-5798], Stadler, Tanja [0000-0001-6431-535X], Neher, Richard A. [0000-0003-2525-1407], Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Comas, Iñaki, González-Candelas, Fernando, Seqcovid-Spain Consortium, Stadler, Tanja, Neher, Richard A., Fonds National Suisse de la Recherche Scientifique, University of Basel, Instituto de Salud Carlos III, Consejo Superior de Investigaciones Científicas (España), European Commission, European Research Council, Hodcroft, Emma B. [0000-0002-0078-2212], Nadeau, Sarah [0000-0003-1008-8918], Comas, Iñaki [0000-0001-5504-9408], González-Candelas, Fernando [0000-0002-0879-5798], Stadler, Tanja [0000-0001-6431-535X], Neher, Richard A. [0000-0003-2525-1407], Hodcroft, Emma B., Zuber, Moira, Nadeau, Sarah, Comas, Iñaki, González-Candelas, Fernando, Seqcovid-Spain Consortium, Stadler, Tanja, and Neher, Richard A.

Abstract

A variant of SARS-CoV-2 emerged in early summer 2020, presumably in Spain, and has since spread to multiple European countries. The variant was first observed in Spain in June and has been at frequencies above 40% since July. Outside of Spain, the frequency of this variant has increased from very low values prior to 15th July to 40-70% in Switzerland, Ireland, and the United Kingdom in September. It is also prevalent in Norway, Latvia, the Netherlands, and France. Little can be said about other European countries because few recent sequences are available. Sequences in this cluster (20A.EU1) differ from ancestral sequences at 6 or more positions, including the mutation A222V in the spike protein and A220V in the nucleoprotein. We show that this variant was exported from Spain to other European countries multiple times and that much of the diversity of this cluster in Spain is observed across Europe. It is currently unclear whether this variant is spreading because of a transmission advantage of the virus or whether high incidence in Spain followed by dissemination through tourists is sufficient to explain the rapid rise in multiple countries.

Published
2020

24. Phylogenetic Tools for Generalized HIV-1 Epidemics: Findings from the PANGEA-HIV Methods Comparison

Author

Ratmann, Oliver, Hodcroft, Emma B., Pickles, Michael, Cori, Anne, Hall, Matthew, Lycett, Samantha, Colijn, Caroline, Dearlove, Bethany, Didelot, Xavier, Frost, Simon, Hossain, A.S. Mukarram, Joy, Jeffrey B., Kendall, Michelle, Kühnert, Denise, Leventhal, Gabriel E., Liang, Richard, Plazzotta, Giacomo, Poon, Art F.Y., Rasmussen, David A., Stadler, Tanja, Volz, Erik, Weis, Caroline, Leigh Brown, Andrew J., and Fraser, Christophe

Published
2017
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26. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2

Author

Vogels, Chantal BF, Breban, Mallery I, Ott, Isabel M, Alpert, Tara, Petrone, Mary E, Watkins, Anne E, Kalinich, Chaney C, Earnest, Rebecca, Rothman, Jessica E, Goes de Jesus, Jaqueline, Morales Claro, Ingra, Magalhães Ferreira, Giulia, Crispim, Myuki AE, Brazil-UK CADDE Genomic Network, Singh, Lavanya, Tegally, Houriiyah, Anyaneji, Ugochukwu J, Network for Genomic Surveillance in South Africa, Hodcroft, Emma B, Mason, Christopher E, Khullar, Gaurav, Metti, Jessica, Dudley, Joel T, MacKay, Matthew J, Nash, Megan, Wang, Jianhui, Liu, Chen, Hui, Pei, Murphy, Steven, Neal, Caleb, Laszlo, Eva, Landry, Marie L, Muyombwe, Anthony, Downing, Randy, Razeq, Jafar, de Oliveira, Tulio, Faria, Nuno R, Sabino, Ester C, Neher, Richard A, Fauver, Joseph R, and Grubaugh, Nathan D

Abstract

With the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants that may increase transmissibility and/or cause escape from immune responses, there is an urgent need for the targeted surveillance of circulating lineages. It was found that the B.1.1.7 (also 501Y.V1) variant, first detected in the United Kingdom, could be serendipitously detected by the Thermo Fisher TaqPath COVID-19 PCR assay because a key deletion in these viruses, spike Δ69-70, would cause a "spike gene target failure" (SGTF) result. However, a SGTF result is not definitive for B.1.1.7, and this assay cannot detect other variants of concern (VOC) that lack spike Δ69-70, such as B.1.351 (also 501Y.V2), detected in South Africa, and P.1 (also 501Y.V3), recently detected in Brazil. We identified a deletion in the ORF1a gene (ORF1a Δ3675-3677) in all 3 variants, which has not yet been widely detected in other SARS-CoV-2 lineages. Using ORF1a Δ3675-3677 as the primary target and spike Δ69-70 to differentiate, we designed and validated an open-source PCR assay to detect SARS-CoV-2 VOC. Our assay can be rapidly deployed in laboratories around the world to enhance surveillance for the local emergence and spread of B.1.1.7, B.1.351, and P.1.

Published
2021

27. Identification of resident memory CD8 + T cells with functional specificity for SARS-CoV-2 in unexposed oropharyngeal lymphoid tissue

Author

Niessl, Julia, primary, Sekine, Takuya, additional, Lange, Joshua, additional, Konya, Viktoria, additional, Forkel, Marianne, additional, Maric, Jovana, additional, Rao, Anna, additional, Mazzurana, Luca, additional, Kokkinou, Efthymia, additional, Weigel, Whitney, additional, Llewellyn-Lacey, Sian, additional, Hodcroft, Emma B., additional, Karlsson, Annika C., additional, Fehrm, Johan, additional, Sundman, Joar, additional, Price, David A., additional, Mjösberg, Jenny, additional, Friberg, Danielle, additional, and Buggert, Marcus, additional

Published
2021
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29. Genetic diversity and evolutionary dynamics of respiratory syncytial virus over eleven consecutive years of surveillance in Senegal

Author

Fall, Amary, primary, Elawar, Farah, additional, Hodcroft, Emma B., additional, Jallow, Mamadou Malado, additional, Toure, Cheikh Talibouya, additional, Barry, Mamadou A., additional, Kiori, Davy Evrard, additional, Sy, Sara, additional, Diaw, Yague, additional, Goudiaby, Déborah, additional, Niang, Mbayame Ndiaye, additional, and Dia, Ndongo, additional

Published
2021
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30. A tale of two variants: Spread of SARS-CoV-2 variants Alpha in Geneva, Switzerland, and Beta in South Africa

Author

Althaus, Christian L., primary, Baggio, Stephanie, additional, Reichmuth, Martina L., additional, Hodcroft, Emma B., additional, Riou, Julien, additional, Neher, Richard A., additional, Jacquerioz, Frédérique, additional, Spechbach, Hervé, additional, Salamun, Julien, additional, Vetter, Pauline, additional, Williamson, Carolyn, additional, Hsiao, Nei-yuan, additional, Preiser, Wolfgang, additional, Davies, Mary-Ann, additional, Lessells, Richard J., additional, de Olivera, Tulio, additional, Kaiser, Laurent, additional, and Eckerle, Isabella, additional

Published
2021
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33. Public health actions to control new SARS-CoV-2 variants [commentary]

Author

Grubaugh, Nathan D, Hodcroft, Emma B, Fauver, Joseph R, Phelan, Alexandra L, and Cevik, Muge

Subjects
610 Medicine & health, 360 Social problems & social services
Abstract

Recent reports suggest that some SARS-CoV-2 genetic variants, such as B.1.1.7, might be more transmissible and are quickly spreading around the world. As the emergence of more transmissible variants could exacerbate the pandemic, we provide public health guidance for increased surveillance and measures to reduce community transmission.

Published
2021
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34. Identification of resident memory CD8+ T cells with functional specificity for SARS-CoV-2 in unexposed oropharyngeal lymphoid tissue

Author

Niessl, Julia, Sekine, Takuya, Lange, Joshua, Konya, Viktoria, Forkel, Marianne, Maric, Jovana, Rao, Anna, Mazzurana, Luca, Kokkinou, Efthymia, Weigel, Whitney, Llewellyn-Lacey, Sian, Hodcroft, Emma B., Karlsson, Annika C., Fehrm, Johan, Sundman, Joar, Price, David A., Mjösberg, Jenny, Friberg, Danielle, Buggert, Marcus, Niessl, Julia, Sekine, Takuya, Lange, Joshua, Konya, Viktoria, Forkel, Marianne, Maric, Jovana, Rao, Anna, Mazzurana, Luca, Kokkinou, Efthymia, Weigel, Whitney, Llewellyn-Lacey, Sian, Hodcroft, Emma B., Karlsson, Annika C., Fehrm, Johan, Sundman, Joar, Price, David A., Mjösberg, Jenny, Friberg, Danielle, and Buggert, Marcus

Abstract

Cross-reactive CD4+ T cells that recognize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are more commonly detected in the peripheral blood of unexposed individuals compared with SARS-CoV-2–reactive CD8+ T cells. However, large numbers of memory CD8+ T cells reside in tissues, feasibly harboring localized SARS-CoV-2–specific immune responses. To test this idea, we performed a comprehensive functional and phenotypic analysis of virus-specific T cells in tonsils, a major lymphoid tissue site in the upper respiratory tract, and matched peripheral blood samples obtained from children and adults before the emergence of COVID-19 (coronavirus disease 2019). We found that SARS-CoV-2–specific memory CD4+ T cells could be found at similar frequencies in the tonsils and peripheral blood in unexposed individuals, whereas functional SARS-CoV-2–specific memory CD8+ T cells were almost only detectable in the tonsils. Tonsillar SARS-CoV-2–specific memory CD8+ T cells displayed a follicular homing and tissue-resident memory phenotype, similar to tonsillar Epstein-Barr virus–specific memory CD8+ T cells, but were functionally less potent than other virus-specific memory CD8+ T cell responses. The presence of preexisting tissue-resident memory CD8+ T cells in unexposed individuals could potentially enable rapid sentinel immune responses against SARS-CoV-2., Title in Web of Science: Identification of resident memory CD8(+) T cells with functional specificity for SARS-CoV-2 in unexposed oropharyngeal lymphoid tissue

Published
2021
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35. SARS-CoV-2 N501Y Introductions and Transmissions in Switzerland from Beginning of October 2020 to February 2021—Implementation of Swiss-Wide Diagnostic Screening and Whole Genome Sequencing

Author

Goncalves Cabecinhas, Ana Rita, primary, Roloff, Tim, additional, Stange, Madlen, additional, Bertelli, Claire, additional, Huber, Michael, additional, Ramette, Alban, additional, Chen, Chaoran, additional, Nadeau, Sarah, additional, Gerth, Yannick, additional, Yerly, Sabine, additional, Opota, Onya, additional, Pillonel, Trestan, additional, Schuster, Tobias, additional, Metzger, Cesar M. J. A., additional, Sieber, Jonas, additional, Bel, Michael, additional, Wohlwend, Nadia, additional, Baumann, Christian, additional, Koch, Michel C., additional, Bittel, Pascal, additional, Leuzinger, Karoline, additional, Brunner, Myrta, additional, Suter-Riniker, Franziska, additional, Berlinger, Livia, additional, Søgaard, Kirstine K., additional, Beckmann, Christiane, additional, Noppen, Christoph, additional, Redondo, Maurice, additional, Steffen, Ingrid, additional, Seth-Smith, Helena M. B., additional, Mari, Alfredo, additional, Lienhard, Reto, additional, Risch, Martin, additional, Nolte, Oliver, additional, Eckerle, Isabella, additional, Martinetti Lucchini, Gladys, additional, Hodcroft, Emma B., additional, Neher, Richard A., additional, Stadler, Tanja, additional, Hirsch, Hans H., additional, Leib, Stephen L., additional, Risch, Lorenz, additional, Kaiser, Laurent, additional, Trkola, Alexandra, additional, Greub, Gilbert, additional, and Egli, Adrian, additional

Published
2021
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37. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

Author

Braun, Katarina M., primary, Moreno, Gage K., additional, Halfmann, Peter J., additional, Hodcroft, Emma B., additional, Baker, David A., additional, Boehm, Emma C., additional, Weiler, Andrea M., additional, Haj, Amelia K., additional, Hatta, Masato, additional, Chiba, Shiho, additional, Maemura, Tadashi, additional, Kawaoka, Yoshihiro, additional, Koelle, Katia, additional, O’Connor, David H., additional, and Friedrich, Thomas C., additional

Published
2021
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38. Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

Author

Hodcroft, Emma B., primary, Domman, Daryl B., additional, Snyder, Daniel J., additional, Oguntuyo, Kasopefoluwa Y., additional, Van Diest, Maarten, additional, Densmore, Kenneth H., additional, Schwalm, Kurt C., additional, Femling, Jon, additional, Carroll, Jennifer L., additional, Scott, Rona S., additional, Whyte, Martha M., additional, Edwards, Michael W., additional, Hull, Noah C., additional, Kevil, Christopher G., additional, Vanchiere, John A., additional, Lee, Benhur, additional, Dinwiddie, Darrell L., additional, Cooper, Vaughn S., additional, and Kamil, Jeremy P., additional

Published
2021
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39. SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

Author

Cabecinhas, Ana Rita Goncalves, primary, Roloff, Tim, additional, Stange, Madlen, additional, Bertelli, Claire, additional, Huber, Michael, additional, Ramette, Alban, additional, Chen, Chaoran, additional, Nadeau, Sarah, additional, Gerth, Yannick, additional, Yerly, Sabine, additional, Opota, Onya, additional, Pillonel, Trestan, additional, Schuster, Tobias, additional, Metzger, Cesar M.J.A., additional, Sieber, Jonas, additional, Bel, Michael, additional, Wohlwend, Nadia, additional, Baumann, Christian, additional, Koch, Michel C., additional, Bittel, Pascal, additional, Leuzinger, Karoline, additional, Brunner, Myrta, additional, Suter-Riniker, Franziska, additional, Berlinger, Livia, additional, Søgaard, Kirstine K., additional, Beckmann, Christiane, additional, Noppen, Christoph, additional, Redondo, Maurice, additional, Steffen, Ingrid, additional, Seth-Smith, Helena M.B., additional, Mari, Alfredo, additional, Lienhard, Reto, additional, Risch, Martin, additional, Nolte, Oliver, additional, Eckerle, Isabella, additional, Lucchini, Gladys Martinetti, additional, Hodcroft, Emma B., additional, Neher, Richard A., additional, Stadler, Tanja, additional, Hirsch, Hans H., additional, Leib, Stephen L., additional, Risch, Lorenz, additional, Kaiser, Laurent, additional, Trkola, Alexandra, additional, Greub, Gilbert, additional, and Egli, Adrian, additional

Published
2021
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41. Emergence of an early SARS-CoV-2 epidemic in the United States

Author

Zeller, Mark, primary, Gangavarapu, Karthik, additional, Anderson, Catelyn, additional, Smither, Allison R., additional, Vanchiere, John A., additional, Rose, Rebecca, additional, Snyder, Daniel J., additional, Dudas, Gytis, additional, Watts, Alexander, additional, Matteson, Nathaniel L., additional, Robles-Sikisaka, Refugio, additional, Marshall, Maximilian, additional, Feehan, Amy K., additional, Sabino-Santos, Gilberto, additional, Bell-Kareem, Antoinette R., additional, Hughes, Laura D., additional, Alkuzweny, Manar, additional, Snarski, Patricia, additional, Garcia-Diaz, Julia, additional, Scott, Rona S., additional, Melnik, Lilia I., additional, Klitting, Raphaëlle, additional, McGraw, Michelle, additional, Belda-Ferre, Pedro, additional, DeHoff, Peter, additional, Sathe, Shashank, additional, Marotz, Clarisse, additional, Grubaugh, Nathan, additional, Nolan, David J., additional, Drouin, Arnaud C., additional, Genemaras, Kaylynn J., additional, Chao, Karissa, additional, Topol, Sarah, additional, Spencer, Emily, additional, Nicholson, Laura, additional, Aigner, Stefan, additional, Yeo, Gene W., additional, Farnaes, Lauge, additional, Hobbs, Charlotte A., additional, Laurent, Louise C., additional, Knight, Rob, additional, Hodcroft, Emma B., additional, Khan, Kamran, additional, Fusco, Dahlene N., additional, Cooper, Vaughn S., additional, Lemey, Phillipe, additional, Gardner, Lauren, additional, Lamers, Susanna L., additional, Kamil, Jeremy P., additional, Garry, Robert F., additional, Suchard, Marc A., additional, and Andersen, Kristian G., additional

Published
2021
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42. Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

Author

Comas, Iñaki [0000-0001-5504-9408], Alm, Erik, Broberg, Eeva K., Connor, Thomas, Hodcroft, Emma B., Komissarov, Andrey B., Maurer-Stroh, Sebastian, Melidou, Angeliki, Neher, Richard A., O’Toole, Áine, Pereyaslov, Dmitriy, WHO European Region sequencing laboratories, GISAID EpiCoV group, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, Goig, Galo A., Torres-Puente, Manuela, López, Mariana G., González-Candelas, Fernando, Comas, Iñaki [0000-0001-5504-9408], Alm, Erik, Broberg, Eeva K., Connor, Thomas, Hodcroft, Emma B., Komissarov, Andrey B., Maurer-Stroh, Sebastian, Melidou, Angeliki, Neher, Richard A., O’Toole, Áine, Pereyaslov, Dmitriy, WHO European Region sequencing laboratories, GISAID EpiCoV group, Chiner-Oms, Álvaro, Cancino-Muñoz, Irving, Comas, Iñaki, Goig, Galo A., Torres-Puente, Manuela, López, Mariana G., and González-Candelas, Fernando

Abstract

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2.

Published
2020

43. Scientific consensus on the COVID-19 pandemic: we need to act now

Author

Infectieziekten onderzoek3 (Bogaert), Child Health, Infection & Immunity, Alwan, Nisreen A, Burgess, Rochelle Ann, Ashworth, Simon, Beale, Rupert, Bhadelia, Nahid, Bogaert, Debby, Dowd, Jennifer, Eckerle, Isabella, Goldman, Lynn R, Greenhalgh, Trisha, Gurdasani, Deepti, Hamdy, Adam, Hanage, William P, Hodcroft, Emma B, Hyde, Zoë, Kellam, Paul, Kelly-Irving, Michelle, Krammer, Florian, Lipsitch, Marc, McNally, Alan, McKee, Martin, Nouri, Ali, Pimenta, Dominic, Priesemann, Viola, Rutter, Harry, Silver, Joshua, Sridhar, Devi, Swanton, Charles, Walensky, Rochelle P, Yamey, Gavin, Ziauddeen, Hisham, Infectieziekten onderzoek3 (Bogaert), Child Health, Infection & Immunity, Alwan, Nisreen A, Burgess, Rochelle Ann, Ashworth, Simon, Beale, Rupert, Bhadelia, Nahid, Bogaert, Debby, Dowd, Jennifer, Eckerle, Isabella, Goldman, Lynn R, Greenhalgh, Trisha, Gurdasani, Deepti, Hamdy, Adam, Hanage, William P, Hodcroft, Emma B, Hyde, Zoë, Kellam, Paul, Kelly-Irving, Michelle, Krammer, Florian, Lipsitch, Marc, McNally, Alan, McKee, Martin, Nouri, Ali, Pimenta, Dominic, Priesemann, Viola, Rutter, Harry, Silver, Joshua, Sridhar, Devi, Swanton, Charles, Walensky, Rochelle P, Yamey, Gavin, and Ziauddeen, Hisham

Published
2020

44. Transmission of SARS-CoV-2 in domestic cats imposes a narrow bottleneck

Author

Braun, Katarina M., primary, Moreno, Gage K., additional, Halfmann, Peter J., additional, Hodcroft, Emma B., additional, Baker, David A., additional, Boehm, Emma C., additional, Weiler, Andrea M., additional, Haj, Amelia K., additional, Hatta, Masato, additional, Chiba, Shiho, additional, Maemura, Tadashi, additional, Kawaoka, Yoshihiro, additional, Koelle, Katia, additional, O’Connor, David H., additional, and Friedrich, Thomas C., additional

Published
2020
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46. Scientific consensus on the COVID-19 pandemic: we need to act now

Author

Alwan, Nisreen A, primary, Burgess, Rochelle Ann, additional, Ashworth, Simon, additional, Beale, Rupert, additional, Bhadelia, Nahid, additional, Bogaert, Debby, additional, Dowd, Jennifer, additional, Eckerle, Isabella, additional, Goldman, Lynn R, additional, Greenhalgh, Trisha, additional, Gurdasani, Deepti, additional, Hamdy, Adam, additional, Hanage, William P, additional, Hodcroft, Emma B, additional, Hyde, Zoë, additional, Kellam, Paul, additional, Kelly-Irving, Michelle, additional, Krammer, Florian, additional, Lipsitch, Marc, additional, McNally, Alan, additional, McKee, Martin, additional, Nouri, Ali, additional, Pimenta, Dominic, additional, Priesemann, Viola, additional, Rutter, Harry, additional, Silver, Joshua, additional, Sridhar, Devi, additional, Swanton, Charles, additional, Walensky, Rochelle P, additional, Yamey, Gavin, additional, and Ziauddeen, Hisham, additional

Published
2020
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47. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States

Author

Fauver, Joseph R., primary, Petrone, Mary E., additional, Hodcroft, Emma B., additional, Shioda, Kayoko, additional, Ehrlich, Hanna Y., additional, Watts, Alexander G., additional, Vogels, Chantal B.F., additional, Brito, Anderson F., additional, Alpert, Tara, additional, Muyombwe, Anthony, additional, Razeq, Jafar, additional, Downing, Randy, additional, Cheemarla, Nagarjuna R., additional, Wyllie, Anne L., additional, Kalinich, Chaney C., additional, Ott, Isabel M., additional, Quick, Joshua, additional, Loman, Nicholas J., additional, Neugebauer, Karla M., additional, Greninger, Alexander L., additional, Jerome, Keith R., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Huang, Meei-Li, additional, Pitzer, Virginia E., additional, Iwasaki, Akiko, additional, Omer, Saad B., additional, Khan, Kamran, additional, Bogoch, Isaac I., additional, Martinello, Richard A., additional, Foxman, Ellen F., additional, Landry, Marie L., additional, Neher, Richard A., additional, Ko, Albert I., additional, and Grubaugh, Nathan D., additional

Published
2020
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48. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

Author

Fauver, Joseph R., primary, Petrone, Mary E., additional, Hodcroft, Emma B., additional, Shioda, Kayoko, additional, Ehrlich, Hanna Y., additional, Watts, Alexander G., additional, Vogels, Chantal B.F., additional, Brito, Anderson F., additional, Alpert, Tara, additional, Muyombwe, Anthony, additional, Razeq, Jafar, additional, Downing, Randy, additional, Cheemarla, Nagarjuna R., additional, Wyllie, Anne L., additional, Kalinich, Chaney C., additional, Ott, Isabel, additional, Quick, Joshua, additional, Loman, Nicholas J., additional, Neugebauer, Karla M., additional, Greninger, Alexander L., additional, Jerome, Keith R., additional, Roychoudhury, Pavitra, additional, Xie, Hong, additional, Shrestha, Lasata, additional, Huang, Meei-Li, additional, Pitzer, Virginia E., additional, Iwasaki, Akiko, additional, Omer, Saad B., additional, Khan, Kamran, additional, Bogoch, Isaac I., additional, Martinello, Richard A., additional, Foxman, Ellen F., additional, Landry, Marie L., additional, Neher, Richard A., additional, Ko, Albert I., additional, and Grubaugh, Nathan D., additional

Published
2020
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