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1. A Pandemic of Busywork: Increased Online Coursework Following the Transition to Remote Instruction Is Associated with Reduced Academic Achievement

Author: Motz, Benjamin A., Quick, Joshua D., Wernert, Julie A., and Miles, Tonya A.
Abstract: Under normal circumstances, when students invest more effort in their schoolwork, they generally show evidence of improved academic achievement. But when universities abruptly transitioned to remote instruction in Spring 2020, instructors assigned rapidly-prepared online learning activities, disrupting the normal relationship between effort and outcomes. In this study, we examine this relationship using data observed from a large-scale survey of undergraduate students, from logs of student activity in the online learning management system, and from students' estimated cumulative performance in their courses (n = 4,636). We find that there was a general increase in the number of assignments that students were expected to complete following the transition to remote instruction, and that students who spent more time and reported more effort carrying out this coursework generally had lower course performance and reported feeling less successful. We infer that instructors, under pressure to rapidly put their course materials online, modified their courses to include online busywork that did not constitute meaningful learning activities, which had a detrimental effect on student outcomes at scale. These findings are discussed in contrast with other situations when increased engagement does not necessarily lead to improved learning outcomes, and in comparison with the broader relationship between effort and academic achievement.
Published: 2021

2. The Digital Divide among College Students: Lessons Learned from the COVID-19 Emergency Transition. Policy Report

Author: Midwestern Higher Education Compact, Jaggars, Shanna S., Motz, Benjamin A., Rivera, Marcos D., Heckler, Andrew, Quick, Joshua D., Hance, Elizabeth A., and Karwisch, Caroline
Abstract: This report examines the meaning and impact of the digital divide -- the gap between those who can and cannot access the Internet -- on college students during the COVID-19 emergency shift to remote learning. The assessment is based on several national surveys conducted in the spring or summer of 2020, as well as results from a large-scale survey the authors conducted at Indiana University and The Ohio State University during the same time period. Key findings reveal the prevalence of inadequate technology, the relationship between inadequate technology and student success, and college and state approaches to supporting students with inadequate technology during the emergency transition. [At Indiana University, this research was sponsored by Schmidt Futures and by the Office of the Vice President for Research at Indiana University. At Ohio State, this research was supported by the Office of Student Academic Success, the Office of Student Life, and the Drake Institute for Teaching and Learning.]
Published: 2021

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

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

Author: Béquet, Adolphe J., Hidalgo-Muñoz, Antonio R., Moreau, Fabien, Quick, Joshua, and Jallais, Christophe
Published: 2022
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5. Automated Educative Nudges to Reduce Missed Assignments in College

Author: Motz, Benjamin A., Mallon, Matthew G., and Quick, Joshua D.
Abstract: As institutions of higher education increasingly utilize online learning management systems, college students are asked to submit more assignments online. Under this regime, when most assignments are posted and submitted online, it is possible to know if a student is missing a submission for an imminent deadline, and to intervene proactively to reduce missed assignments and improve student outcomes. Toward this goal, we designed and evaluated a scalable targeted intervention: a mobile app that would deploy push notifications when students were missing submissions for assignments with imminent deadlines. Results from two experimental pilots demonstrate that this intervention system significantly decreased missed assignments compared with control notifications about instructor announcements to the class (in Experiment 1), and improved assignment adherence and course grades compared with courses that were not using the app (in Experiment 2). In this article, we discuss the benefits and theoretical implications of this behavioral guide rail, a purely informative proactive intervention to mitigate risk in advance of a negative outcome.
Published: 2021
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6. Real-time pathogen surveillance systems using DNA sequencing

Author: Quick, Joshua
Subjects: 572.8, QH301 Biology, QH426 Genetics, QR Microbiology
Abstract: Microbiological research has uncovered the basis of fermentation, infectious disease, vaccination and antibiotics. Now, a technological revolution leveraging DNA, the code of life, has allowed us to unravel cellular and evolutionary processes in exquisite detail. Today our need for new innovation is still great. The modern world is a challenging environment: over-population, climate change and highly mobile populations create a high risk of pandemic disease especially from viruses and many bacteria are now resistant to our life saving antibiotic drugs due to overuse. In hospitals, the spread of pathogens can be rapid and life threatening. Whole-genome sequencing has the power to identify the source of infections and determine whether clusters of cases belong to an outbreak. Portable, real-time nanopore sequencing enables sequencing to be performed near the patient, even in resource-limited settings. Integrating with existing datasets allows digital surveillance able to detect outbreaks earlier while they can still be contained. Early demonstrations of the power of whole-genome sequencing for outbreak surveillance have made it an area of intense interest and further development in laboratory methods and infrastructure will make it an important tool that can be deployed in response to future outbreaks.
Published: 2018

7. 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: Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek, Curran, Tanya, McKenna, James, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed, Malone, Cassandra, Cogger, Benjamin, Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas, Fuller, William, Bresner, Catherine, Snell, Luke, Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel, Beckett, Angela, Aanensen, David, Underwood, Anthony, Yeats, Corin, Abudahab, Khalil, Taylor, Ben, Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki, Lister, Michelle, Howson-Wells, Hannah, Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, Loose, Matthew, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian, Betancor, Gilberto, Wilson, Harry, Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Escalera Zamudio, Marina, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William, Goodfellow, Ian, Hall, Grant, Jahun, Aminu, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte, Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe, Awan, Ali, BoYes, John, Breuer, Judith, Harris, Kathryn, Brown, Julianne, Shah, Divya, Atkinson, Laura, Lee, Jack, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael, Levett, Lisa, Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren, Bashton, Matthew, Young, Gregory, Holmes, Alison, Randell, Paul, Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, F. Nascimento, Fabricia, Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik, Rowan, Aileen, Taylor, Graham, Smollett, Katherine, Loman, Nicholas, Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Martinez Nunez, Rocio, Mason, Jenifer, Robinson, Trevor, O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas, Ahmad, Shazaad, George, Ryan, Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris, Jackson, Chris, Thomson, Emma, Shepherd, James, Asamaphan, Patawee, Niebel, Marc, Li, Kathy, Shah, Rajiv, Jesudason, Natasha, Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen, Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David, Orton, Richard, Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua, Nickbakhsh, Seema, Hale, Antony, Macfarlane-Smith, Louissa, Harper, Katherine, Carden, Holli, Taha, Yusri, Payne, Brendan, Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O'Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate, McHugh, Martin, Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma, Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare, Yew, Wen, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim, Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop, Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan, Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Muir, Peter, Vipond, Ian, Hopes, Richard, Pymont, Hannah, Hutchings, Stephanie, Curran, Martin, Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Ledesma, Juan, Twohig, Katherine, Holden, Matthew, Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan, Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-SummerhaYes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O'Grady, Justin, Page, Andrew, Mather, Alison, Baker, David, Rudder, Steven, Aydin, Alp, Kay, Gemma, Trotter, Alexander, Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David, Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane, Knight, Bridget, Ellard, Sian, Auckland, Cressida, Jones, Christopher, Mahungu, Tabitha, Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa, Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry, Loveson, Katie, Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David, Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan, Saeed, Kordo, Mahanama, Adhyana, Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel, Kristiansen, Mark, Roy, Sunando, Williams, Charlotte, Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam, Hartley, John, Jannoo, Riaz, Lowe, Helen, Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui, Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin, Bucca, Giselda, Hesketh, Andrew, Blane, Beth, Girgis, Sophia, Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet, Dias, Joana, Higginson, Ellen, Maes, Mailis, Young, Jamie, Kermack, Leanne, Gupta, Ravi, Ludden, Catherine, Peacock, Sharon, Palmer, Sophie, Churcher, Carol, Hadjirin, Nazreen, Carabelli, Alessandro, Brooks, Ellena, Smith, Kim, Galai, Katerina, McManus, Georgina, Ruis, Chris, Davidson, Rose, Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos, Gallagher, Michael, O'Toole, Áine, Rooke, Stefan, Hill, Verity, Williamson, Kathleen, Stanton, Thomas, Michell, Stephen, Bewshea, Claire, Temperton, Ben, Michelsen, Michelle, Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James, Sambles, Christine, Studholme, David, Jeffries, Aaron, Jackson, Leigh, Darby, Alistair, Hiscox, Julian, Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn, Lucaci, Anita, Vamos, Edith, Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam, Gregory, Richard, Gemmell, Matthew, Wierzbicki, Claudia, Webster, Hermione, de Silva, Thushan, Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin, Groves, Danielle, Green, Luke, Wang, Dennis, Freeman, Timothy, Parker, Matthew, Keeley, Alexander, Parsons, Paul, Tucker, Rachel, Brown, Rebecca, Wyles, Matthew, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey, Bridgewater, Hannah, Frost, Lucy, Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad, Brown, Paul, Aggarwal, Dinesh, Cerda, Alberto, Merrill, Tammy, Wilson, Rebekah, McClure, Patrick, Chappell, Joseph, Tsoleridis, Theocharis, Ball, Jonathan, Buck, David, Todd, John, Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Alderton, Alex, Amato, Roberto, Ariani, Cristina, Beale, Mathew, Beaver, Charlotte, Bellis, Katherine, Betteridge, Emma, Bonfield, James, Danesh, John, Dorman, Matthew, Drury, Eleanor, Farr, Ben, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan, Jackson, David, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia, Lawniczak, Mara, Letchford, Laura, Livett, Rich, Lo, Stephanie, Martincorena, Inigo, McGuigan, Samantha, Nelson, Rachel, Palmer, Steve, Park, Naomi, Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael, Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Spencer Chapman, Michael, Thurston, Scott, Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad, Aigrain, Louise, Redshaw, Nicholas, Lensing, Stefanie, Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime, Leonard, Steven, Durham, Jillian, Bassett, Andrew, McCarthy, Shane, Moll, Robin, James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff, Gunson, Rory, Twohig, Katherine A, Nyberg, Tommy, Zaidi, Asad, Thelwall, Simon, Sinnathamby, Mary A, Aliabadi, Shirin, Seaman, Shaun R, Harris, Ross J, Hope, Russell, Lopez-Bernal, Jamie, Charlett, Andre, De Angelis, Daniela, and Presanis, Anne M
Published: 2022
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8. The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

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

Author: Subissi, Lorenzo, Sousa, Andreza, Ba, Ibrahima, Perrocheau, Anne, Quick, Joshua, Meredith, Luke, Augustinho, Edmilson, Sousa, Beni Carvalho, Lima, Vania, Luiz, Jose, Diallo, Amadou Bailo, Djingarey, Mamoudou Harouna, Da Cruz, Claudina Augusto, Pontes, Feliciana Sousa, Tomé Palmer, Maria, Conceição, Marisa, Santana Gil, Vilfrido, and Fall, Ibrahima Socé
Published: 2021
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10. Resurgence of Ebola virus in 2021 in Guinea suggests a new paradigm for outbreaks

Author: Keita, Alpha Kabinet, Koundouno, Fara R., Faye, Martin, Düx, Ariane, Hinzmann, Julia, Diallo, Haby, Ayouba, Ahidjo, Le Marcis, Frederic, Soropogui, Barré, Ifono, Kékoura, Diagne, Moussa M., Sow, Mamadou S., Bore, Joseph A., Calvignac-Spencer, Sebastien, Vidal, Nicole, Camara, Jacob, Keita, Mamadou B., Renevey, Annick, Diallo, Amadou, Soumah, Abdoul K., Millimono, Saa L., Mari-Saez, Almudena, Diop, Mamadou, Doré, Ahmadou, Soumah, Fodé Y., Kourouma, Kaka, Vielle, Nathalie J., Loucoubar, Cheikh, Camara, Ibrahima, Kourouma, Karifa, Annibaldis, Giuditta, Bah, Assaïtou, Thielebein, Anke, Pahlmann, Meike, Pullan, Steven T., Carroll, Miles W., Quick, Joshua, Formenty, Pierre, Legand, Anais, Pietro, Karla, Wiley, Michael R., Tordo, Noel, Peyrefitte, Christophe, McCrone, John T., Rambaut, Andrew, Sidibé, Youssouf, Barry, Mamadou D., Kourouma, Madeleine, Saouromou, Cé D., Condé, Mamadou, Baldé, Moussa, Povogui, Moriba, Keita, Sakoba, Diakite, Mandiou, Bah, Mamadou S., Sidibe, Amadou, Diakite, Dembo, Sako, Fodé B., Traore, Fodé A., Ki-Zerbo, Georges A., Lemey, Philippe, Günther, Stephan, Kafetzopoulou, Liana E., Sall, Amadou A., Delaporte, Eric, Duraffour, Sophie, Faye, Ousmane, Leendertz, Fabian H., Peeters, Martine, Toure, Abdoulaye, and Magassouba, N’. Faly
Published: 2021
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11. Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Author: Koshy, Cherian, Ash, Amy, Wise, Emma, Moore, Nathan, Mori, Matilde, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Fairley, Derek J, Curran, Tanya, McKenna, James P, Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Hassan-Ibrahim, Mohammed O, Malone, Cassandra S, Cogger, Benjamin J, Wantoch, Michelle, Reynolds, Nicola, Warne, Ben, Maksimovic, Joshua, Spellman, Karla, McCluggage, Kathryn, John, Michaela, Beer, Robert, Afifi, Safiah, Morgan, Sian, Marchbank, Angela, Price, Anna, Kitchen, Christine, Gulliver, Huw, Merrick, Ian, Southgate, Joel, Guest, Martyn, Munn, Robert, Workman, Trudy, Connor, Thomas R, Fuller, William, Bresner, Catherine, Snell, Luke B, Patel, Amita, Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C, Beckett, Angela H, Aanensen, David M, Underwood, Anthony P, Yeats, Corin A, Abudahab, Khalil, Taylor, Ben EW, Menegazzo, Mirko, Clark, Gemma, Smith, Wendy, Khakh, Manjinder, Fleming, Vicki M, Lister, Michelle M, Howson-Wells, Hannah C, Berry, Louise, Boswell, Tim, Joseph, Amelia, Willingham, Iona, Jones, Carl, Holmes, Christopher, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, Blakey, Victoria, Williams, Lesley-Anne, Loose, Matthew W, Holmes, Nadine, Moore, Christopher, Carlile, Matthew, Wright, Victoria, Sang, Fei, Debebe, Johnny, Coll, Francesc, Signell, Adrian W, Betancor, Gilberto, Wilson, Harry D, Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver G, du Plessis, Louis, Zarebski, Alex E, Raghwani, Jayna, Kraemer, Moritz UG, Francois, Sarah, Attwood, Stephen W, Vasylyeva, Tetyana I, Escalera Zamudio, Marina, Gutierrez, Bernardo, Torok, M. Estee, Hamilton, William L, Goodfellow, Ian G, Hall, Grant, Jahun, Aminu S, Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L, Georgana, Iliana, Moses, Samuel, Lowe, Hannah, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Fisher, Chloe L, Awan, Ali R, BoYes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack CD, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Williams, Rebecca, Vernet, Gabrielle, Chapman, Michael R, Levett, Lisa J, Heaney, Judith, Chatterton, Wendy, Pusok, Monika, Xu-McCrae, Li, Smith, Darren L, Bashton, Matthew, Young, Gregory R, Holmes, Alison, Randell, Paul Anthony, Cox, Alison, Madona, Pinglawathee, Bolt, Frances, Price, James, Mookerjee, Siddharth, Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M, Rowan, Aileen, Taylor, Graham P, Smollett, Katherine L, Loman, Nicholas J, Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, McNally, Alan, Martinez Nunez, Rocio T, Mason, Jenifer, Robinson, Trevor I, O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Sluga, Graciela, Machin, Nicholas W, Ahmad, Shazaad S Y, George, Ryan P, Halstead, Fenella, Sivaprakasam, Venkat, Hogsden, Wendy, Illingworth, Chris J, Jackson, Chris, Thomson, Emma C, Shepherd, James G, Asamaphan, Patawee, Niebel, Marc O, Li, Kathy K, Shah, Rajiv N, Jesudason, Natasha G, Tong, Lily, Broos, Alice, Mair, Daniel, Nichols, Jenna, Carmichael, Stephen N, Nomikou, Kyriaki, Aranday-Cortes, Elihu, Johnson, Natasha, Starinskij, Igor, da Silva Filipe, Ana, Robertson, David L, Orton, Richard J, Hughes, Joseph, Vattipally, Sreenu, Singer, Joshua B, Nickbakhsh, Seema, Hale, Antony D, Macfarlane-Smith, Louissa R, Harper, Katherine L, Carden, Holli, Taha, Yusri, Payne, Brendan AI, Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Rushton, Steven, O'Brien, Sarah, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Blacow, Rachel, Templeton, Kate E, McHugh, Martin P, Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Meader, Emma J, Coupland, Lindsay, Smith, Louise, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, McCann, Clare M, Yew, Wen C, Andersson, Monique, Peto, Timothy, Justice, Anita, Eyre, David, Crook, Derrick, Sloan, Tim J, Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J, Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T, Wyatt, Tim, Allara, Elias, Pearson, Clare, Osman, Husam, Bosworth, Andrew, Robinson, Esther, Muir, Peter, Vipond, Ian B, Hopes, Richard, Pymont, Hannah M, Hutchings, Stephanie, Curran, Martin D, Parmar, Surendra, Lackenby, Angie, Mbisa, Tamyo, Platt, Steven, Miah, Shahjahan, Bibby, David, Manso, Carmen, Hubb, Jonathan, Chand, Meera, Dabrera, Gavin, Ramsay, Mary, Bradshaw, Daniel, Thornton, Alicia, Myers, Richard, Schaefer, Ulf, Groves, Natalie, Gallagher, Eileen, Lee, David, Williams, David, Ellaby, Nicholas, Harrison, Ian, Hartman, Hassan, Manesis, Nikos, Patel, Vineet, Bishop, Chloe, Chalker, Vicki, Ledesma, Juan, Twohig, Katherine A, Holden, Matthew T.G., Shaaban, Sharif, Birchley, Alec, Adams, Alexander, Davies, Alisha, Gaskin, Amy, Plimmer, Amy, Gatica-Wilcox, Bree, McKerr, Caoimhe, Moore, Catherine, Williams, Chris, Heyburn, David, De Lacy, Elen, Hilvers, Ember, Downing, Fatima, Shankar, Giri, Jones, Hannah, Asad, Hibo, Coombes, Jason, Watkins, Joanne, Evans, Johnathan M, Fina, Laia, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Perry, Malorie, Morgan, Mari, Bull, Matthew, Cronin, Michelle, Pacchiarini, Nicole, Craine, Noel, Jones, Rachel, Howe, Robin, Corden, Sally, Rey, Sara, Kumziene-SummerhaYes, Sara, Taylor, Sarah, Cottrell, Simon, Jones, Sophie, Edwards, Sue, O'Grady, Justin, Page, Andrew J, Mather, Alison E, Baker, David J, Rudder, Steven, Aydin, Alp, Kay, Gemma L, Trotter, Alexander J, Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Casey, Anna, Ratcliffe, Liz, Simpson, David A, Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane AH, Knight, Bridget A, Ellard, Sian, Auckland, Cressida, Jones, Christopher R, Mahungu, Tabitha W, Irish-Tavares, Dianne, Haque, Tanzina, Hart, Jennifer, Witele, Eric, Fenton, Melisa Louise, Dadrah, Ashok, Symmonds, Amanda, Saluja, Tranprit, Bourgeois, Yann, Scarlett, Garry P, Loveson, Katie F, Goudarzi, Salman, Fearn, Christopher, Cook, Kate, Dent, Hannah, Paul, Hannah, Partridge, David G, Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Bonner, Stephen, Essex, Sarah, Lyons, Ronan A, Saeed, Kordo, Mahanama, Adhyana I.K, Samaraweera, Buddhini, Silveira, Siona, Pelosi, Emanuela, Wilson-Davies, Eleri, Williams, Rachel J, Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A, Cotic, Marius, Bayzid, Nadua, Westhorpe, Adam P, Hartley, John A, Jannoo, Riaz, Lowe, Helen L, Karamani, Angeliki, Ensell, Leah, Prieto, Jacqui A, Jeremiah, Sarah, Grammatopoulos, Dimitris, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Best, Angus, Percival, Benita, Mirza, Jeremy, Megram, Oliver, Mayhew, Megan, Crawford, Liam, Ashcroft, Fiona, Moles-Garcia, Emma, Cumley, Nicola, Smith, Colin P, Bucca, Giselda, Hesketh, Andrew R, Blane, Beth, Girgis, Sophia T, Leek, Danielle, Sridhar, Sushmita, Forrest, Sally, Cormie, Claire, Gill, Harmeet K, Dias, Joana, Higginson, Ellen E, Maes, Mailis, Young, Jamie, Kermack, Leanne M, Gupta, Ravi Kumar, Ludden, Catherine, Peacock, Sharon J, Palmer, Sophie, Churcher, Carol M, Hadjirin, Nazreen F, Carabelli, Alessandro M, Brooks, Ellena, Smith, Kim S, Galai, Katerina, McManus, Georgina M, Ruis, Chris, Davidson, Rose K, Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E, Gallagher, Michael D, O'Toole, Áine, Rooke, Stefan, Hill, Verity, Williamson, Kathleen A, Stanton, Thomas D, Michell, Stephen L, Bewshea, Claire M, Temperton, Ben, Michelsen, Michelle L, Warwick-Dugdale, Joanna, Manley, Robin, Farbos, Audrey, Harrison, James W, Sambles, Christine M, Studholme, David J, Jeffries, Aaron R, Darby, Alistair C, Hiscox, Julian A, Paterson, Steve, Iturriza-Gomara, Miren, Jackson, Kathryn A, Lucaci, Anita O, Vamos, Edith E, Hughes, Margaret, Rainbow, Lucille, Eccles, Richard, Nelson, Charlotte, Whitehead, Mark, Turtle, Lance, Haldenby, Sam T, Gregory, Richard, Gemmell, Matthew, Wierzbicki, Claudia, Webster, Hermione J, de Silva, Thushan I, Smith, Nikki, Angyal, Adrienn, Lindsey, Benjamin B, Groves, Danielle C, Green, Luke R, Wang, Dennis, Freeman, Timothy M, Parker, Matthew D, Keeley, Alexander J, Parsons, Paul J, Tucker, Rachel M, Brown, Rebecca, Wyles, Matthew, Whiteley, Max, Zhang, Peijun, Gallis, Marta, Louka, Stavroula F, Constantinidou, Chrystala, Unnikrishnan, Meera, Ott, Sascha, Cheng, Jeffrey K.J., Bridgewater, Hannah E., Frost, Lucy R., Taylor-Joyce, Grace, Stark, Richard, Baxter, Laura, Alam, Mohammad T., Brown, Paul E, Aggarwal, Dinesh, Cerda, Alberto C, Merrill, Tammy V, Wilson, Rebekah E, McClure, Patrick C, Chappell, Joseph G, Tsoleridis, Theocharis, Ball, Jonathan, Buck, David, Todd, John A, Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Alderton, Alex, Amato, Roberto, Ariani, Cristina V, Beale, Mathew A, Beaver, Charlotte, Bellis, Katherine L, Betteridge, Emma, Bonfield, James, Danesh, John, Dorman, Matthew J, Drury, Eleanor, Farr, Ben W, Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Harrison, Ewan M, Jackson, David K, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F, Lawniczak, Mara, Letchford, Laura, Livett, Rich, Lo, Stephanie, Martincorena, Inigo, McGuigan, Samantha, Nelson, Rachel, Palmer, Steve, Park, Naomi R, Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A, Rajatileka, Shavanthi, Scott, Carol, Shirley, Lesley, Sillitoe, John, Spencer Chapman, Michael H, Thurston, Scott AJ, Tonkin-Hill, Gerry, Weldon, Danni, Rajan, Diana, Bronner, Iraad F, Aigrain, Louise, Redshaw, Nicholas M, Lensing, Stefanie V, Davies, Robert, Whitwham, Andrew, Liddle, Jennifier, Lewis, Kevin, Tovar-Corona, Jaime M, Leonard, Steven, Durham, Jillian, Bassett, Andrew R, McCarthy, Shane, Moll, Robin J, James, Keith, Oliver, Karen, Makunin, Alex, Barrett, Jeff, Gunson, Rory N, Graham, Mark S, Sudre, Carole H, May, Anna, Antonelli, Michela, Murray, Benjamin, Varsavsky, Thomas, Kläser, Kerstin, Canas, Liane S, Molteni, Erika, Modat, Marc, Drew, David A, Nguyen, Long H, Polidori, Lorenzo, Selvachandran, Somesh, Hu, Christina, Capdevila, Joan, Hammers, Alexander, Chan, Andrew T, Wolf, Jonathan, Spector, Tim D, Steves, Claire J, and Ourselin, Sebastien
Published: 2021
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12. Nanopore native RNA sequencing of a human poly(A) transcriptome

Author: Workman, Rachael E., Tang, Alison D., Tang, Paul S., Jain, Miten, Tyson, John R., Razaghi, Roham, Zuzarte, Philip C., Gilpatrick, Timothy, Payne, Alexander, Quick, Joshua, Sadowski, Norah, Holmes, Nadine, de Jesus, Jaqueline Goes, Jones, Karen L., Soulette, Cameron M., Snutch, Terrance P., Loman, Nicholas, Paten, Benedict, Loose, Matthew, Simpson, Jared T., Olsen, Hugh E., Brooks, Angela N., Akeson, Mark, and Timp, Winston
Published: 2019
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13. Left Ventricular Assist Device Thrombosis Is Associated With an Increase in the Systolic-to-Diastolic Velocity Ratio Measured at the Inflow and Outflow Cannulae

Author: Jain, Ankit, Rohrer, Ben, Gebhardt, Brian, Breeze, Janis L., Quick, Joshua D., Couper, Gregory, Kiernan, Michael S., Lawrence, Matthew, and Cobey, Frederick C.
Published: 2017
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14. An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar

Author: Grubaugh, Nathan D., Gangavarapu, Karthik, Quick, Joshua, Matteson, Nathaniel L., De Jesus, Jaqueline Goes, Main, Bradley J., Tan, Amanda L., Paul, Lauren M., Brackney, Doug E., Grewal, Saran, Gurfield, Nikos, Van Rompay, Koen K. A., Isern, Sharon, Michael, Scott F., Coffey, Lark L., Loman, Nicholas J., and Andersen, Kristian G.
Published: 2019
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15. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

Author: Quick, Joshua, Grubaugh, Nathan D, Pullan, Steven T, Claro, Ingra M, Smith, Andrew D, Gangavarapu, Karthik, Oliveira, Glenn, Robles-Sikisaka, Refugio, Rogers, Thomas F, Beutler, Nathan A, Burton, Dennis R, Lewis-Ximenez, Lia Laura, de Jesus, Jaqueline Goes, Giovanetti, Marta, Hill, Sarah C, Black, Allison, Bedford, Trevor, Carroll, Miles W, Nunes, Marcio, Alcantara, Jr., Luiz Carlos, Sabino, Ester C, Baylis, Sally A, Faria, Nuno R, Loose, Matthew, Simpson, Jared T, Pybus, Oliver G, Andersen, Kristian G, and Loman, Nicholas J
Published: 2017
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16. Unusual Ebola virus chain of transmission, Conakry, Guinea, 2014-2015

Author: Keita, Mory, Duraffour, Sophie, Loman, Nicholas J., Rambaut, Andrew, Diallo, Boubacar, Magassouba, Nfaly, Carroll, Miles W., Quick, Joshua, Sall, Amadou A., Glynn, Judith R., Formenty, Pierre, Subissi, Lorenzo, and Faye, Ousmane
Subjects: Disease transmission -- Care and treatment, Medical care -- Management -- Sierra Leone -- Guinea -- United Kingdom, Ebola virus -- Research, Company business management, Health
Abstract: As of May 6, 2016, a total of 28,616 Ebola virus disease (EVD) cases, including 11,310 deaths, had been reported since December 2013, mainly from Guinea, Sierra Leone, and Liberia [...]
Published: 2016
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17. Author Correction: Nanopore native RNA sequencing of a human poly(A) transcriptome

Author: Workman, Rachael E., Tang, Alison D., Tang, Paul S., Jain, Miten, Tyson, John R., Razaghi, Roham, Zuzarte, Philip C., Gilpatrick, Timothy, Payne, Alexander, Quick, Joshua, Sadowski, Norah, Holmes, Nadine, de Jesus, Jaqueline Goes, Jones, Karen L., Soulette, Cameron M., Snutch, Terrance P., Loman, Nicholas, Paten, Benedict, Loose, Matthew, Simpson, Jared T., Olsen, Hugh E., Brooks, Angela N., Akeson, Mark, and Timp, Winston
Published: 2020
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18. Detection of human adenovirus F41 in wastewater and its relationship to clinical cases of acute hepatitis of unknown aetiology

Author: Reyne, Marina I., Allen, Danielle M., Levickas, Ashley, Allingham, Pearce, Lock, Jonathan, Fitzgerald, Arthur, McSparron, Cormac, Nejad, Behnam F., McKinley, Jennifer, Lee, Andrew, Bell, Stephen H., Quick, Joshua, Houldcroft, Charlotte J., Bamford, Connor G.G., Gilpin, Deirdre F., and McGrath, John W.
Published: 2023
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19. Blind Disclosure.

Author: Kolb, Aaron, Pease, Marilyn, Sacks, Daniel W., and Quick, Joshua
Published: 2023
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20. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

Author: Aggarwal, Dinesh, Warne, Ben, Jahun, Aminu S., Hamilton, William L., Fieldman, Thomas, du Plessis, Louis, Hill, Verity, Blane, Beth, Watkins, Emmeline, Wright, Elizabeth, Hall, Grant, Ludden, Catherine, Myers, Richard, Hosmillo, Myra, Chaudhry, Yasmin, Pinckert, Malte L., Georgana, Iliana, Izuagbe, Rhys, Leek, Danielle, Nsonwu, Olisaeloka, Hughes, Gareth J., Packer, Simon, Page, Andrew J., Metaxaki, Marina, Fuller, Stewart, Weale, Gillian, Holgate, Jon, Brown, Christopher A., Orton, Alexandra, Douthwaite, Julie, Rees, Steve, Brown, Christopher, Clark, Roger, Jones, Daniel R., Kuenzi, Fred, Rankin, Jennifer, Waddell, Ian, Maxwell, Patrick, Matheson, Nicholas, Abell, Chris, Braithwaite, Vickie, Brierley, Craig, Crowcroft, Jon, Dahal, Aastha, Faulkner, Kathryn, Glover, Michael, Goodfellow, Ian, Greatorex, Jane, James, Laura, Lehner, Paul, Leslie, Ian, Liddell, Kathleen, Margolis, Ben, Morgan, Sally, Sheridan, Linda, Valletta, Sally, Vignoles, Anna, Vinnell, Martin, Wills, Mark, Hilborne, Sarah, Berry, Sarah, Kahkeshi, Mahin Bagheri, Hancock, Dawn, Winster, Jennifer, Enright, Jessica, Samworth, Richard, Samtani, Vijay, Ahmadi-Assalemi, Gabriela, Feather, Tom, Goodall, Robin, Hoensch, Steve, Johnson, Dean, Hunt, Martin, Mathieson, Nick, Nikitina, Katya, Sheldrake, Zara, Keen, Martin, Sato, Aris, Connor, David, Tolhurst, Jonathan, Williman, Jack, Hollamby, Victoria, Jordan, Sinead, Fatseas, Tania, Taylor, Peter, Georgiou, Christine, Caspersz, Michelle, McNulty, Claire, Davies, Richard, Clarke, Rebecca, Danaei, Darius, Dyer, Rory, Glew, Rob, Lambson, Oliver, Gibbs, Karen, Mozdzen, Barbara, Raub, Gabor, Radecki, Asako, White, Phil, Hughes, Robert, Gransden, Lucie, Ceaser, Matt, Sing, Robert, Wilson, Karl, Parlikad, Ajith, Dhada, Maharshi, Ridgman, Tom, Mungovan, Diane, Matthews, Steve, Searle, Paul, Mills, John, Neely, Andy, Henderson, Robert, Murphy, Edna, Russell, Matthew, Freeling, Anthony, Poppitt, Steve, Tynan, Jo, Knapton, James, Marchetti, Filippo, Angelis, Daniela De, Feltwell, Theresa, Hadjirin, Nazreen F., Jahun, Aminu, Pinckert, Malte, Shaw, Ashley, Chaudhry, Afzal, Brown, Nicholas M., Mactavous, Lenette, Hannan, Sophie, Hosaja, Aleksandra, Leong, Clare, Wright, Jo, Quinnell, Natalie, Workman, Chris, Ferris, Mark, Wright, Giles, Brooks, Ellena, Carabelli, Alessandro M., Churcher, Carol M., Galai, Katerina, Girgis, Sophia T., Gupta, Ravi K., McManus, Georgina M., Palmer, Sophie, Peacock, Sharon J., Smith, Kim S., Allara, Elias, Bibby, David, Bishop, Chloe, Bosworth, Andrew, Bradshaw, Daniel, Chalker, Vicki, Chand, Meera, Dabrera, Gavin, Ellaby, Nicholas, Gallagher, Eileen, Groves, Natalie, Harrison, Ian, Hartman, Hassan, Hopes, Richard, Hubb, Jonathan, Hutchings, Stephanie, Lackenby, Angie, Ledesma, Juan, Lee, David, Manesis, Nikos, Manso, Carmen, Mbisa, Tamyo, Miah, Shahjahan, Muir, Peter, Osman, Husam, Patel, Vineet, Pearson, Clare, Platt, Steven, Pymont, Hannah M., Ramsay, Mary, Robinson, Esther, Schaefer, Ulf, Thornton, Alicia, Twohig, Katherine A., Vipond, Ian B., Williams, David, Aigrain, Louise, Alderton, Alex, Amato, Roberto, Ariani, Cristina V., Barrett, Jeff, Bassett, Andrew R., Beale, Mathew A., Beaver, Charlotte, Bellis, Katherine L., Betteridge, Emma, Bonfield, James, Bronner, Iraad F., Chapman, Michael H. S., Danesh, John, Davies, Robert, Dorman, Matthew J., Drury, Eleanor, Durham, Jillian, Farr, Ben W., Foulser, Luke, Goncalves, Sonia, Goodwin, Scott, Gourtovaia, Marina, Jackson, David K., James, Keith, Jamrozy, Dorota, Johnston, Ian, Kane, Leanne, Kay, Sally, Keatley, Jon-Paul, Kwiatkowski, Dominic, Langford, Cordelia F., Lawniczak, Mara, Lensing, Stefanie V., Leonard, Steven, Letchford, Laura, Lewis, Kevin, Liddle, Jennifier, Livett, Rich, Lo, Stephanie, Makunin, Alex, Martincorena, Inigo, McCarthy, Shane, McGuigan, Samantha, Moll, Robin J., Nelson, Rachel, Oliver, Karen, Palmer, Steve, Park, Naomi R., Patel, Minal, Prestwood, Liam, Puethe, Christoph, Quail, Michael A., Rajan, Diana, Rajatileka, Shavanthi, Redshaw, Nicholas M., Scott, Carol, Shirley, Lesley, Sillitoe, John, Thurston, Scott A. J., Tonkin-Hill, Gerry, Tovar-Corona, Jaime M., Weldon, Danni, Whitwham, Andrew, Attwood, Stephen W., Zamudio, Marina Escalera, Francois, Sarah, Gutierrez, Bernardo, Kraemer, Moritz U. G., Raghwani, Jayna, Vasylyeva, Tetyana I., Zarebski, Alex E., Alikhan, Nabil-Fareed, Aydin, Alp, Baker, David J., de Oliveira Martins, Leonardo, Kay, Gemma L., Le-Viet, Thanh, Mather, Alison E., Meadows, Lizzie, O’Grady, Justin, Rudder, Steven, Trotter, Alexander J., Illingworth, Chris J., Jackson, Chris, Aranday-Cortes, Elihu, Asamaphan, Patawee, Broos, Alice, Carmichael, Stephen N., da Silva Filipe, Ana, Hughes, Joseph, Jesudason, Natasha G., Johnson, Natasha, Li, Kathy K., Mair, Daniel, Nichols, Jenna, Nickbakhsh, Seema, Niebel, Marc O., Nomikou, Kyriaki, Orton, Richard J., Robertson, David L., Shah, Rajiv N., Shepherd, James G., Singer, Joshua B., Starinskij, Igor, Thomson, Emma C., Tong, Lily, Vattipally, Sreenu, Ash, Amy, Koshy, Cherian, Cortes, Nick, Kidd, Stephen, Lynch, Jessica, Moore, Nathan, Mori, Matilde, Wise, Emma, Curran, Tanya, Fairley, Derek J., McKenna, James P., Adams, Helen, Bonsall, David, Fraser, Christophe, Golubchik, Tanya, Cogger, Benjamin J., Hassan-Ibrahim, Mohammed O., Malone, Cassandra S., Reynolds, Nicola, Wantoch, Michelle, Afifi, Safiah, Beer, Robert, John, Michaela, Maksimovic, Joshua, McCluggage, Kathryn, Morgan, Sian, Spellman, Karla, Bresner, Catherine, Connor, Thomas R., Fuller, William, Guest, Martyn, Gulliver, Huw, Kitchen, Christine, Marchbank, Angela, Merrick, Ian, Munn, Robert, Price, Anna, Southgate, Joel, Workman, Trudy, Patel, Amita, Snell, Luke B., Batra, Rahul, Charalampous, Themoula, Edgeworth, Jonathan, Nebbia, Gaia, Beckett, Angela H., Robson, Samuel C., Aanensen, David M., Abudahab, Khalil, Menegazzo, Mirko, Taylor, Ben E. W., Underwood, Anthony P., Yeats, Corin A., Berry, Louise, Boswell, Tim, Clark, Gemma, Fleming, Vicki M., Howson-Wells, Hannah C., Jones, Carl, Joseph, Amelia, Khakh, Manjinder, Lister, Michelle M., Smith, Wendy, Willingham, Iona, Bird, Paul, Fallon, Karlie, Helmer, Thomas, Holmes, Christopher, Tang, Julian, Blakey, Victoria, Campbell, Sharon, Raviprakash, Veena, Sheriff, Nicola, Williams, Lesley-Anne, Carlile, Matthew, Debebe, Johnny, Holmes, Nadine, Loose, Matthew W., Moore, Christopher, Sang, Fei, Wright, Victoria, Coll, Francesc, Betancor, Gilberto, Signell, Adrian W., Wilson, Harry D., Davis, Thomas, Eldirdiri, Sahar, Kenyon, Anita, Torok, M. Estee, Lowe, Hannah, Moses, Samuel, Bedford, Luke, Moore, Jonathan, Stonehouse, Susanne, Awan, Ali R., Fisher, Chloe L., BoYes, John, Atkinson, Laura, Breuer, Judith, Brown, Julianne R., Harris, Kathryn A., Lee, Jack C. D., Shah, Divya, Storey, Nathaniel, Flaviani, Flavia, Alcolea-Medina, Adela, Vernet, Gabrielle, Williams, Rebecca, Chapman, Michael R., Chatterton, Wendy, Heaney, Judith, Levett, Lisa J., Pusok, Monika, Xu-McCrae, Li, Bashton, Matthew, Smith, Darren, Young, Greg, Bolt, Frances, Cox, Alison, Holmes, Alison, Madona, Pinglawathee, Mookerjee, Siddharth, Price, James, Randell, Paul A., Boyd, Olivia, Nascimento, Fabricia F., Geidelberg, Lily, Johnson, Rob, Jorgensen, David, Ragonnet-Cronin, Manon, Rowan, Aileen, Siveroni, Igor, Taylor, Graham P., Volz, Erik M., Smollett, Katherine L., Loman, Nicholas J., McMurray, Claire, McNally, Alan, Nicholls, Sam, Poplawski, Radoslaw, Quick, Joshua, Rowe, Will, Stockton, Joanne, Nunez, Rocio T. Martinez, Breen, Cassie, Cowell, Angela, Mason, Jenifer, O’Toole, Elaine, Robinson, Trevor I., Watts, Joanne, Sluga, Graciela, Ahmad, Shazaad S. Y., George, Ryan P., Machin, Nicholas W., Halstead, Fenella, Hogsden, Wendy, Sivaprakasam, Venkat, Carden, Holli, Hale, Antony D., Harper, Katherine L., Macfarlane-Smith, Louissa R., Burton-Fanning, Shirelle, Collins, Jennifer, Eltringham, Gary, Payne, Brendan AI., Taha, Yusri, Waugh, Sheila, O’Brien, Sarah, Rushton, Steven, Blacow, Rachel, Bradley, Amanda, Maclean, Alasdair, Mollett, Guy, Dewar, Rebecca, McHugh, Martin P., Templeton, Kate E., Wastenge, Elizabeth, Coupland, Lindsay, Dervisevic, Samir, Meader, Emma J., Stanley, Rachael, Smith, Louise, Barton, Edward, Graham, Clive, Padgett, Debra, Scott, Garren, Greenaway, Jane, Swindells, Emma, McCann, Clare, Nelson, Andrew, Yew, Wen Chyin, Andersson, Monique, Crook, Derrick, Eyre, David, Justice, Anita, Peto, Timothy, Duckworth, Nichola, Sloan, Tim J., Walsh, Sarah, Bicknell, Kelly, Chauhan, Anoop J., Elliott, Scott, Glaysher, Sharon, Impey, Robert, Lloyd, Allyson, Wyllie, Sarah, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Wyatt, Tim, Curran, Martin D., Parmar, Surendra, Holden, Matthew T. G., Shaaban, Sharif, Adams, Alexander, Asad, Hibo, Birchley, Alec, Bull, Matthew, Coombes, Jason, Corden, Sally, Cottrell, Simon, Craine, Noel, Cronin, Michelle, Davies, Alisha, Lacy, Elen De, Downing, Fatima, Edwards, Sue, Evans, Johnathan M., Fina, Laia, Gaskin, Amy, Gatica-Wilcox, Bree, Gifford, Laura, Gilbert, Lauren, Graham, Lee, Heyburn, David, Hilvers, Ember, Howe, Robin, Jones, Hannah, Jones, Rachel, Jones, Sophie, Kumziene-SummerhaYes, Sara, McKerr, Caoimhe, Moore, Catherine, Morgan, Mari, Pacchiarini, Nicole, Perry, Malorie, Plimmer, Amy, Rey, Sara, Shankar, Giri, Taylor, Sarah, Watkins, Joanne, Williams, Chris, Casey, Anna, Ratcliffe, Liz, Acheson, Erwan, Molnar, Zoltan, Simpson, David A., Thompson, Thomas, Auckland, Cressida, Ellard, Sian, Jones, Christopher R., Knight, Bridget A., Masoli, Jane A. H., Haque, Tanzina, Hart, Jennifer, Irish-Tavares, Dianne, Mahungu, Tabitha W., Witele, Eric, Dadrah, Ashok, Fenton, Melisa L., Saluja, Tranprit, Symmonds, Amanda, Bourgeois, Yann, Scarlett, Garry P., Cook, Kate, Dent, Hannah, Fearn, Christopher, Goudarzi, Salman, Loveson, Katie F., Paul, Hannah, Evans, Cariad, Johnson, Kate, Partridge, David G., Raza, Mohammad, Baker, Paul, Bonner, Stephen, Essex, Sarah, Liggett, Steven, Lyons, Ronan A., Mahanama, Adhyana I. K., Saeed, Kordo, Samaraweera, Buddhini, Silveira, Siona, Wilson-Davies, Eleri, Emanuela, P., Bayzid, Nadua, Cotic, Marius, Ensell, Leah, Hartley, John A., Jannoo, Riaz, Karamani, Angeliki, Kristiansen, Mark, Lowe, Helen L., Roy, Sunando, Westhorpe, Adam P., Williams, Rachel J., Williams, Charlotte A., Jeremiah, Sarah, Prieto, Jacqui A., Berry, Lisa, Grammatopoulos, Dimitris, Jones, Katie, Pandey, Sarojini, Beggs, Andrew, Richter, Alex, Ashcroft, Fiona, Best, Angus, Crawford, Liam, Cumley, Nicola, Mayhew, Megan, Megram, Oliver, Mirza, Jeremy, Moles-Garcia, Emma, Percival, Benita, Bucca, Giselda, Hesketh, Andrew R., Smith, Colin P., Davidson, Rose K., Balcazar, Carlos E., Gallagher, Michael D., O’Toole, Áine, Rambaut, Andrew, Rooke, Stefan, Stanton, Thomas D., Williams, Thomas, Williamson, Kathleen A., Bewshea, Claire M., Farbos, Audrey, Harrison, James W., Jeffries, Aaron R., Manley, Robin, Michell, Stephen L., Michelsen, Michelle L., Sambles, Christine M., Studholme, David J., Temperton, Ben, Warwick-Dugdale, Joanna, Darby, Alistair C., Eccles, Richard, Gemmell, Matthew, Gregory, Richard, Haldenby, Sam T., Hiscox, Julian A., Hughes, Margaret, Iturriza-Gomara, Miren, Jackson, Kathryn A., Lucaci, Anita O., Nelson, Charlotte, Paterson, Steve, Rainbow, Lucille, Turtle, Lance, Vamos, Edith E., Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Angyal, Adrienn, Brown, Rebecca, de Silva, Thushan I., Freeman, Timothy M., Gallis, Marta, Green, Luke R., Groves, Danielle C., Keeley, Alexander J., Lindsey, Benjamin B., Louka, Stavroula F., Parker, Matthew D., Parsons, Paul J., Smith, Nikki, Tucker, Rachel M., Wang, Dennis, Whiteley, Max, Wyles, Matthew, Zhang, Peijun, Alam, Mohammad T., Baxter, Laura, Bridgewater, Hannah E., Brown, Paul E., Cheng, Jeffrey K. J., Constantinidou, Chrystala, Frost, Lucy R., Ott, Sascha, Stark, Richard, Taylor-Joyce, Grace, Unnikrishnan, Meera, Cerda, Alberto C., Merrill, Tammy V., Wilson, Rebekah E., Ball, Jonathan, Chappell, Joseph G., McClure, Patrick C., Tsoleridis, Theocharis, Buck, David, de Cesare, Mariateresa, Green, Angie, MacIntyre-Cockett, George, Todd, John A., Trebes, Amy, Gunson, Rory N., Cormie, Claire, Dias, Joana, Forrest, Sally, Gill, Harmeet K., Higginson, Ellen E., Kermack, Leanne M., Maes, Mailis, Ruis, Chris, Sridhar, Sushmita, Young, Jamie, Howes, Rob, McFarlane, Duncan, Dougan, Gordon, Pybus, Oliver G., Maxwell, Patrick H., Weekes, Michael P., Illingworth, Chris, Harrison, Ewan M., Matheson, Nicholas J., Goodfellow, Ian G., The Cambridge Covid-19 testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programm, The COVID-19 Genomics UK (COG-UK) Consortium, Aggarwal, Dinesh [0000-0002-5938-8172], Warne, Ben [0000-0003-1326-0373], Hill, Verity [0000-0002-3509-8146], Pinckert, Malte [0000-0002-6072-5949], Leek, Danielle [0000-0001-5367-3354], Pybus, Oliver [0000-0001-6619-6112], Weekes, Michael [0000-0002-0030-2784], Apollo - University of Cambridge Repository, Jahun, Aminu S [0000-0002-4585-1701], Hamilton, William L [0000-0002-3330-353X], du Plessis, Louis [0000-0003-0352-6289], Blane, Beth [0000-0002-0996-9091], Wright, Elizabeth [0000-0002-8378-9072], Hall, Grant [0000-0003-3928-3979], Chaudhry, Yasmin [0000-0002-2386-3269], Pinckert, Malte L [0000-0002-6072-5949], Izuagbe, Rhys [0000-0001-8080-2510], Nsonwu, Olisaeloka [0000-0002-3024-700X], Hughes, Gareth J [0000-0002-3781-0117], Packer, Simon [0000-0002-9157-3650], Page, Andrew J [0000-0001-6919-6062], Metaxaki, Marina [0000-0002-4552-1622], Weale, Gillian [0000-0003-4728-5915], Brown, Christopher A [0000-0001-7773-0878], Peacock, Sharon J [0000-0002-1718-2782], Pybus, Oliver G [0000-0002-8797-2667], Weekes, Michael P [0000-0003-3196-5545], Harrison, Ewan M [0000-0003-2720-0507], Matheson, Nicholas J [0000-0002-3318-1851], Goodfellow, Ian G [0000-0002-9483-510X], Jahun, Aminu [0000-0002-4585-1701], Hosmillo, Myra [0000-0002-3514-7681], McFarlane, Duncan [0000-0002-1558-7823], Dougan, Gordon [0000-0003-0022-965X], Peacock, Sharon [0000-0002-1718-2782], Weekes, Michael [0000-0003-3196-5545], Illingworth, Christopher [0000-0002-0030-2784], Harrison, Ewan [0000-0003-2720-0507], Matheson, Nicholas [0000-0002-3318-1851], and Goodfellow, Ian [0000-0002-9483-510X]
Subjects: Universities, 631/326/325/2483, Science, education, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, General Physics and Astronomy, Cambridge Covid-19 testing Centre, 45/23, Genome, Viral, General Biochemistry, Genetics and Molecular Biology, COVID-19 Genomics UK (COG-UK) Consortium, Risk Factors, The COVID-19 Genomics UK (COG-UK) Consortium, Humans, Students, Phylogeny, 631/326/596/4130, Multidisciplinary, SARS-CoV-2, article, COVID-19, virus diseases, C500, General Chemistry, Genomics, C700, 692/700/478/174, United Kingdom, The Cambridge Covid-19 testing Centre, RNA, Viral, 631/326/596/2562, Contact Tracing, 631/326/596/2563
Abstract: Understanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics., Nature Communications, 13, ISSN:2041-1723
Published: 2022

21. Real-time, portable genome sequencing for Ebola surveillance

Author: Quick, Joshua, Loman, Nicholas J., Duraffour, Sophie, Simpson, Jared T., Severi, Ettore, Cowley, Lauren, Bore, Joseph Akoi, Koundouno, Raymond, Dudas, Gytis, Mikhail, Amy, Ouédraogo, Nobila, Afrough, Babak, Bah, Amadou, Baum, Jonathan H. J., Becker-Ziaja, Beate, Boettcher, Jan Peter, Cabeza-Cabrerizo, Mar, Camino-Sánchez, Álvaro, Carter, Lisa L., Doerrbecker, Juliane, Enkirch, Theresa, Dorival, Isabel García-, Hetzelt, Nicole, Hinzmann, Julia, Holm, Tobias, Kafetzopoulou, Liana Eleni, Koropogui, Michel, Kosgey, Abigael, Kuisma, Eeva, Logue, Christopher H., Mazzarelli, Antonio, Meisel, Sarah, Mertens, Marc, Michel, Janine, Ngabo, Didier, Nitzsche, Katja, Pallasch, Elisa, Patrono, Livia Victoria, Portmann, Jasmine, Repits, Johanna Gabriella, Rickett, Natasha Y., Sachse, Andreas, Singethan, Katrin, Vitoriano, Inês, Yemanaberhan, Rahel L., Zekeng, Elsa G., Racine, Trina, Bello, Alexander, Sall, Amadou Alpha, Faye, Ousmane, Faye, Oumar, Magassouba, NʼFaly, Williams, Cecelia V., Amburgey, Victoria, Winona, Linda, Davis, Emily, Gerlach, Jon, Washington, Frank, Monteil, Vanessa, Jourdain, Marine, Bererd, Marion, Camara, Alimou, Somlare, Hermann, Camara, Abdoulaye, Gerard, Marianne, Bado, Guillaume, Baillet, Bernard, Delaune, Déborah, Nebie, Koumpingnin Yacouba, Diarra, Abdoulaye, Savane, Yacouba, Pallawo, Raymond Bernard, Gutierrez, Giovanna Jaramillo, Milhano, Natacha, Roger, Isabelle, Williams, Christopher J., Yattara, Facinet, Lewandowski, Kuiama, Taylor, James, Rachwal, Phillip, Turner, Daniel J., Pollakis, Georgios, Hiscox, Julian A., Matthews, David A., Shea, Matthew K. Oʼ, Johnston, Andrew McD., Wilson, Duncan, Hutley, Emma, Smit, Erasmus, Di Caro, Antonino, Wölfel, Roman, Stoecker, Kilian, Fleischmann, Erna, Gabriel, Martin, Weller, Simon A., Koivogui, Lamine, Diallo, Boubacar, Keïta, Sakoba, Rambaut, Andrew, Formenty, Pierre, Günther, Stephan, and Carroll, Miles W.
Published: 2016
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22. Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013–2022).

Author: Lambisia, Arnold W., Makori, Timothy O., Mutunga, Martin, Cheruiyot, Robinson, Murunga, Nickson, Quick, Joshua, Githinji, George, James Nokes, D., Houldcroft, Charlotte J., and Agoti, Charles N.
Abstract: Human enteric adenovirus species F (HAdV-F) is a leading cause of childhood diarrhoeal deaths. The genomic analysis would be key to understanding transmission dynamics, potential drivers of disease severity, and vaccine development. However, currently, there are limited HAdV-F genomic data globally. Here, we sequenced and analysed HAdV-F from stool samples collected in coastal Kenya between 2013 and 2022. The samples were collected at Kilif County Hospital in coastal Kenya from children <13 years of age who reported a history of three or more loose stools in the previous 24 hours. The genomes were analysed together with the data from the rest of the world by phylogenetic analysis and mutational profling. Types and lineages were assigned based on phylogenetic clustering consistent with the previously described criteria and nomenclature. Participant clinical and demographic data were linked to genotypic data. Of ninety-one cases identifed using real-time Polymerase Chain Reaction, eighty-eight near-complete genomes were assembled, and these were classifed into HAdV-F40 (n = 41) and HAdV-F41 (n = 47). These types co-circulated throughout the study period. Three and four distinct lineages were observed for HAdV-F40 (Lineages 1–3) and HAdV-F41 (Lineages 1, 2A, 3A, 3C, and 3D). Types F40 and F41 coinfections were observed in fve samples and F41 and B7 in one sample. Two children with F40 and 41 coinfections were also infected with rotavirus and had moderate and severe diseases as defned using the Vesikari Scoring System, respectively. Intratypic recombination was found in four HAdV-F40 sequences occurring between Lineages 1 and 3. None of the HAdV-F41 cases had jaundice. This study provides evidence of extensive genetic diversity, coinfections, and recombination within HAdV-F40 in a rural coastal Kenya that will inform public health policy, vaccine development that includes the locally circulating lineages, and molecular diagnostic assay development. We recommend future comprehensive studies elucidating on HAdV-F genetic diversity and immunity for rational vaccine development. [ABSTRACT FROM AUTHOR]
Published: 2023
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23. Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

Author: Lauring, Adam S., Hill, Sarah C., de Souza, Renato, Thézé, Julien, Claro, Ingra, Aguiar, Renato S., Abade, Leandro, Santos, Fabiana C. P., Cunha, Mariana S., Nogueira, Juliana S., Salles, Flavia C. S., Rocco, Iray M., Maeda, Adriana Y., Vasami, Fernanda G. S., du Plessis, Louis, Silveira, Paola P., de Jesus, Jaqueline G., Quick, Joshua, Fernandes, Natália C. C. A., Guerra, Juliana M., Réssio, Rodrigo A., Giovanetti, Marta, Alcantara, Luiz C. J., Cirqueira, Cinthya S., Díaz-Delgado, Josué, Macedo, Fernando L. L., Timenetsky, Maria do Carmo S. T., de Paula, Regiane, Spinola, Roberta, Telles de Deus, Juliana, Mucci, Luís F., Tubaki, Rosa Maria, de Menezes, Regiane M. T., Ramos, Patrícia L., de Abreu, Andre L., Cruz, Laura N., Loman, Nick, Dellicour, Simon, Pybus, Oliver G., Sabino, Ester C., and Faria, Nuno R.
Subjects: parasitic diseases, geographic locations
Abstract: São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.
Published: 2020

24. Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 – 2018

Author: Hill, Sarah C., de Souza, Renato, Thézé, Julien, Claro, Ingra, Aguiar, Renato S., Abade, Leandro, Santos, Fabiana C.P., Cunha, Mariana S., Nogueira, Juliana S., Salles, Flavia C.S., Rocco, Iray M., Maeda, Adriana Y., Vasami, Fernanda G.S., du Plessis, Louis, Silveira, Paola P., de Jesus, Jaqueline G., Quick, Joshua, Fernandes, Natália C.C.A., Guerra, Juliana M., and Réssio, Rodrigo A.
Subjects: parasitic diseases, geographic locations
Abstract: São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species., PLoS Pathogens, 16 (8), ISSN:1553-7374, ISSN:1553-7366
Published: 2020

25. Genomic detection of a virus lineage replacement event of dengue virus serotype 2 in Brazil, 2019

Author: Giovanetti, Marta, Faria, Nuno Rodrigues, Lourenço, José, Goes de Jesus, Jaqueline, Xavier, Joilson, Morales Claro, Ingra, Kraemer, Moritz U. G., Fonseca, Vagner, Dellicour, Simon, Thézé, Julien, da Silva Salles, Flavia, Gräf, Tiago, Paz Silveira, Paola, Alves do Nascimento, Valdinete, Costa de Souza, Victor, Campos de Melo Iani, Felipe, Castilho-Martins, Emerson Augusto, Nogueira Cruz, Laura, Wallau, Gabriel, Fabri, Allison, Levy, Flávia, Quick, Joshua, de Azevedo, Vasco, Santana Aguiar, Renato, De Oliveira, Tulio, Bôtto de Menezes, Camila, da Costa Castilho, Marcia, Terra, Tirza Matos, Souza da Silva, Marineide, Bispo de Filippis, Ana Maria, Luiz de Abreu, André, Kleber Oliveira, Wanderson, Croda, Julio, Campelo de Albuquerque, Carlos F., Nunes, Marcio R. T., Sabino, Ester Cerdeira, Loman, Nicholas, Naveca, Felipe Gomes, G.Pybus, Oliver, Alcantara, Luiz Carlos, Department of Infectious Diseases, Istituto Superiore di Sanita [Rome], University of Oxford [Oxford], Instituto Gonçalo Moniz, Partenaires INRAE, Universidade Federal de Minas Gerais, Rega Institute for Medical Research [Leuven, België], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Unité Mixte de Recherche d'Épidémiologie des maladies Animales et zoonotiques (UMR EPIA), VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Fundação Oswaldo Cruz (FIOCRUZ), Réseau International des Instituts Pasteur (RIIP), University of KwaZulu-Natal (UKZN), Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS) Brasília, Distrito Federal, and Secretaria de em Saúde, Ministério da Saúde (SVS-MS), Brasília, Distrito Federal
Subjects: Microbiology (medical), Serotype, lineage replacement, lcsh:Arctic medicine. Tropical medicine, Genotype, lcsh:RC955-962, Lineage (evolution), [SDV]Life Sciences [q-bio], viruses, 030231 tropical medicine, lcsh:QR1-502, Biology, Dengue virus, medicine.disease_cause, Virus, lcsh:Microbiology, Dengue, 03 medical and health sciences, 0302 clinical medicine, Phylogenetics, Caribbean region, parasitic diseases, medicine, Humans, Phylogeny, outbreak, Outbreak, Genetic Variation, virus diseases, Genomics, Dengue Virus, biochemical phenomena, metabolism, and nutrition, Virology, 3. Good health, genomic surveillance, brazil, dengue 2, RNA, Viral, Original Article, Brazil
Abstract: BACKGROUND: Despite efforts to mitigate the impact of DENV epidemics, the virus remains a public health problem in tropical and subtropical regions around the world. Most DENV cases in the Americas between January and July 2019 were reported in Brazil. São Paulo state in the southeast of Brazil has reported nearly half of all DENV infections in the country. OBJECTIVES: To understand the origin and dynamics of the 2019 DENV outbreak. METHODS: Here using portable nanopore sequencing we generated 20 new DENV genome sequences from viremic patients with suspected dengue infection residing in two of the most-affected municipalities of Sao Paulo state, Araraquara and São José do Rio Preto. We conducted a comprehensive phylogenetic analysis with 1,630 global DENV strains to better understand the evolutionary history of the DENV lineages that currently circulate in the region. FINDINGS: The new outbreak strains were classified as DENV2 genotype III (American/Asian genotype). Our analysis shows that the 2019 outbreak is the result of a novel DENV lineage that was recently introduced to Brazil from the Caribbean region. Dating phylogeographic analysis suggests that DENV2-III BR-4 was introduced to Brazil in or around early 2014, possibly from the Caribbean region. MAIN CONCLUSIONS: Our study describes the early detection of a newly introduced and rapidly-expanding DENV2 virus lineage in Brazil.
Published: 2020

26. Genomic epidemiology reveals multiple introductions of Zika virus into the United States

Author: Grubaugh, Nathan D., Ladner, Jason T., Kraemer, Moritz U. G., Dudas, Gytis, Tan, Amanda L., Gangavarapu, Karthik, Wiley, Michael R., White, Stephen, Thz, Julien, Magnani, Diogo M., Prieto, Karla, Reyes, Daniel, Bingham, Andrea M., Paul, Lauren M., Robles-Sikisaka, Refugio, Oliveira, Glenn, Pronty, Darryl, Barcellona, Carolyn M., Metsky, Hayden C., Baniecki, Mary Lynn, Barnes, Kayla G., Chak, Bridget, Freije, Catherine A., Gladden-Young, Adrianne, Gnirke, Andreas, Luo, Cynthia, MacInnis, Bronwyn, Matranga, Christian B., Park, Daniel J., Qu, James, Schaffner, Stephen F., Tomkins-Tinch, Christopher, West, Kendra L., Winnicki, Sarah M., Wohl, Shirlee, Yozwiak, Nathan L., Quick, Joshua, Fauver, Joseph R., Khan, Kamran, Brent, Shannon E., Reiner, Robert C., Jr, Lichtenberger, Paola N., Ricciardi, Michael J., Bailey, Varian K., Watkins, David I., Cone, Marshall R., Kopp, Edgar W., IV, Hogan, Kelly N., Cannons, Andrew C., Jean, Reynald, Monaghan, Andrew J., Garry, Robert F., Loman, Nicholas J., Faria, Nuno R., Porcelli, Mario C., Vasquez, Chalmers, Nagle, Elyse R., Cummings, Derek A. T., Stanek, Danielle, Rambaut, Andrew, Sanchez-Lockhart, Mariano, Sabeti, Pardis C., Gillis, Leah D., Michael, Scott F., Bedford, Trevor, Pybus, Oliver G., Isern, Sharon, Palacios, Gustavo, and Andersen, Kristian G.
Subjects: Zika virus -- Health aspects -- Genetic aspects, Gene expression -- Health aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract: Author(s): Nathan D. Grubaugh [1]; Jason T. Ladner [2]; Moritz U. G. Kraemer [3, 4, 5]; Gytis Dudas [6]; Amanda L. Tan [7]; Karthik Gangavarapu [1]; Michael R. Wiley [2, [...]
Published: 2017
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27. A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104: H4

Author: Loman, Nicholas J., Constantinidou, Chrystala, Christner, Martin, Rohde, Holger, Chan, Jacqueline Z.-M., Quick, Joshua, Weir, Jacqueline C., Quince, Christopher, Smith, Geoffrey P., Betley, Jason R., Aepfelbacher, Martin, and Pallen, Mark J.
Published: 2013
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28. A32 Genomic surveillance of Zika virus transmission in the Amazonas State, Brazil

Author: Quick Joshua, Souza Renato, Sarah C. Hill, Nuno R. Faria, Marta Giovanetti, Simon Dellicour, Nicholas J. Loman, Luiz Carlos Junior Alcantara, Jaqueline Goes de Jesus, Oliver G. Pybus, E.C. Sabino, José Lourenço, Joilson Xavier Junior, Paola Paz, Felipe Gomes Naveca, and Ingra Morales Claro
Subjects: Geography, Transmission (mechanics), biology, law, Virology, Abstract Overview, biology.organism_classification, Microbiology, law.invention, Zika virus
Abstract: Zika virus (ZIKV) has caused an unprecedented epidemic linked to severe congenital syndromes. Transmission of ZIKV in the Americas was first confirmed in May 2015 in northeast Brazil, though the virus was likely introduced 1–2 years prior to its detection. Manaus, the capital city of the Amazonas State, the largest territory of any state in Brazil and the main economic center in the northern region, reported between 2016 and 2017 more than 2,327 suspected cases of ZIKV infection. To gain insights into the timing, source, and likely route(s) of ZIKV introduction in the Amazonas State, we tracked the virus by sequencing ZIKV genomes from infected patients. Using nanopore sequencing technology, we generated 56 Brazilian ZIKV genomes from Manaus city in the Amazonas state, sampled from human cases. On the basis of available sequences of isolates from the Americas, the Manaus sequences, we analyzed fell within a single strongly supported monophyletic clade (bootstrap support = 99%, posterior support = 1.00) that belongs to the Asian genotype. Genetic analysis suggests the outbreak most likely originated from transmission cycles not previously identified in North Brazil and not from a separate introduction into the Americas. Molecular dating analysis indicates that the outbreak was caused by a single founder strain that is estimated to have arrived in Manaus around February 2015. By analyzing surveillance and genetic data, we discovered that ZIKV moved among transmission zones in Manaus. Geographical analysis further indicates that the Northern part of the Manaus regions has a high transmission potential for ZIKV. Our work illustrates that near-real time genomics in the field can augment traditional approaches to infectious disease surveillance and control. Estimated dates for the international spread of ZIKV from the north region indicate the persistence of the virus transmission in recipient regions. Our study provides an understanding of how ZIKV initiates transmission in new regions.
Published: 2019

29. Pseudomonas aeruginosa infection in augmented care: the molecular ecology and transmission dynamics in four large UK hospitals.

Author: Halstead, F.D., Quick, J., Niebel, M., Garvey, M., Cumley, N., Smith, R., Neal, T., Roberts, P., Hardy, K., Shabir, S., Walker, J.T., Hawkey, P., Loman, N.J., Halstead, Fenella D, Quick, Joshua, Niebel, Marc O, Garvey, Mark, Cumley, Nicola, Smith, Robin, and Neal, Timothy
Abstract: Background: Pseudomonas aeruginosa is a common opportunistic pathogen and molecular typing in outbreaks has linked patient acquisition to contaminated hospital water systems.Aim: To elucidate the role of P. aeruginosa transmission rates in non-outbreak augmented care settings in the UK.Methods: Over a 16-week period, all water outlets in augmented care units of four hospitals were sampled for P. aeruginosa and clinical isolates were collected. Outlet and clinical P. aeruginosa isolates underwent whole-genome sequencing (WGS), which with epidemiological data identified acquisition from water as definite (level 1), probable (level 2), possible (level 3), and no evidence (level 4).Findings: Outlets were positive in each hospital on all three occasions: W (16%), X (2.5%), Y (0.9%) and Z (2%); and there were 51 persistently positive outlets in total. WGS identified likely transmission (at levels 1, 2 and 3) from outlets to patients in three hospitals for P. aeruginosa positive patients: W (63%), X (54.5%) and Z (26%). According to the criteria (intimate epidemiological link and no phylogenetic distance), approximately 5% of patients in the study 'definitely' acquired their P. aeruginosa from their water outlets in the intensive care unit. This study found extensive evidence of transmission from the outlet to the patients particularly in the newest hospital (W), which had the highest rate of positive outlets.Conclusions: The overall findings suggest that water outlets are the most likely source of P. aeruginosa nosocomial infections in some settings, and that widespread introduction of control measures would have a substantial impact on infections. [ABSTRACT FROM AUTHOR]
Published: 2021
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30. What college students say, and what they do: aligning self-regulated learning theory with behavioral logs.

Author: Quick, Joshua, Motz, Benjamin, Israel, Jamie, and Kaetzel, Jason
Published: 2020
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31. Importation and early local transmission of COVID-19 in Brazil, 2020.

Author: de Jesus, Jaqueline Goes, Sacchi, Claudio, da Silva Candido, Darlan, Claro, Ingra Morales, Silva Sales, Flávia Cristina, Manuli, Erika Regina, Borges da Silva, Daniela Bernardes, de Paiva, Terezinha Maria, Benega Pinho, Margarete Aparecida, de Oliveira Santos, Katia Correa, Hill, Sarah Catherine, Aguiar, Renato Santana, Romero, Filipe, Pereira dos Santos, Fabiana Cristina, Gonçalves, Claudia Regina, do Carmo Timenetsky, Maria, Quick, Joshua, Rosa Croda, Julio Henrique, de Oliveira, Wanderson, and Rambaut, Andrew
Subjects: COVID-19, PUBLIC health surveillance, NUCLEOTIDE sequencing
Abstract: We conducted the genome sequencing and analysis of the first confirmed COVID-19 infections in Brazil. Rapid sequencing coupled with phylogenetic analyses in the context of travel history corroborate multiple independent importations from Italy and local spread during the initial stage of COVID-19 transmission in Brazil. [ABSTRACT FROM AUTHOR]
Published: 2020
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32. The validity and utility of activity logs as a measure of student engagement.

Author: Motz, Benjamin, Quick, Joshua, Schroeder, Noah, Zook, Jordon, and Gunkel, Matthew
Published: 2019
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33. Deletions in a ribosomal protein-coding gene are associated with tigecycline resistance in Enterococcus faecium

Author: Niebel, Marc, Quick, Joshua, Prieto, Ana Maria Guzman, Hill, Robert L.R., Pike, Rachel, Huber, Damon, David, Miruna, Hornsey, Michael, Wareham, David, Oppenheim, Beryl, Woodford, Neil, van Schaik, Willem, and Loman, Nicholas
Published: 2015
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34. Lightning talks

Author: Fernandez, Obie, Gleason, Lance, Baccigalupo, Claudio, Rigor, Christopher, Kibble, Chris, Morrison, Reid, Quick, Joshua, Arko, André, Defazio, Shane, Evans, Jeremy, Sloan, Isaac, Dean, Joe, Sharma, Nitie, Virata-Stone, Mike, Halley, Gabriel, Harpole, Aaron, Davis, Ryan, Meredith, Elle, Maldonado, Gonzalo, Degen-Portnoy, Peter, Casimir, Jeff, Tse, Ivan, Hsu, Hsing-Hui, and Cuppy, Adam
Subjects: Information Technology
Abstract: 0:12 - Obie Fernandez 1:28 - If you know who this is 2:21 - Lance Gleason 7:10 - Claudio Baccigalupo 12:10 - Christopher Rigor 15:30 - Chris Kibble 17:53 - Reid Morrison 23:17 - Joshua Quick 24:34 - Jason 25:50 - Amy 27:59 - André Arko 31:04 - Shane Defazio 33:16 - Jeremy Evans 37:53 - Isaac Sloan 43:05 - Joe Dean 48:40 - Nitie Sharma 52:12 - Mike Virata-Stone 56:45 - Gabriel Halley 1:00:55 - Aaron Harpole 1:03:05 - Ryan Davis 1:06:47 - Elle Meredith 1:12:04 - Gonzalo Maldonado 1:17:43 - Peter Degen-Portnoy 1:21:56 - Jeff Casimir 1:27:30 - Ivan Tse 1:32:11 - Hsing-Hui Hsu 1:36:57 - Adam Cuppy
Published: 2015
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35. CONCOCT: Clustering cONtigs on COverage and ComposiTion

Author: Alneberg, Johannes, Bjarnason, Brynjar Smari, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z., Loman, Nicholas J., Andersson, Anders F., and Quince, Christopher
Subjects: Genomics (q-bio.GN), FOS: Biological sciences, food and beverages, Quantitative Biology - Genomics
Abstract: Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the same genome, a process referred to as binning, remains a major informatics challenge. Here we present CONCOCT, a computer program that combines three types of information - sequence composition, coverage across multiple sample, and read-pair linkage - to automatically bin contigs into genomes. We demonstrate high recall and precision rates of the program on artificial as well as real human gut metagenome datasets., 28 pages, 14 figures
Published: 2013

36. Field investigation with real-time virus genetic characterisation support of a cluster of Ebola virus disease cases in Dubréka, Guinea, April to June 2015.

Author: Fini, Alessandro, Zomahoun, Delayo, Duraffour, Sophie, Derrough, Tarik, Charles, Myrna, Quick, Joshua, Loman, Nick, Cowley, Lauren, Leno, Mamadou, Ouedraogo, Nobila, Thiam, Oumou, Hernández-Romieu, Alfonso, Iko, Annie, Halimatou Keita, Konate, Djiba, Soumah, Aboubacar Aboubak, Bouchouar, Etran, Ileka-Friouzeau, Samuel, Keita, Sakoba, and Diallo, Boubacar
Published: 2018
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37. Unusual Ebola Virus Chain of Transmission, Conakry, Guinea, 2014-2015.

Author: Mory Keita, Duraffour, Sophie, Loman, Nicholas J., Rambaut, Andrew, Diallo, Boubacar, Magassouba, Nfaly, Carroll, Miles W., Quick, Joshua, Sall, Amadou A., Glynn, Judith R., Formenty, Pierre, Subissi, Lorenzo, Faye, Ousmane, and Keita, Mory
Subjects: EBOLA viral disease transmission, EBOLA virus disease, VIRAL genomes, SEROLOGY, PUBLIC health, DIAGNOSIS
Abstract: In October 2015, a new case of Ebola virus disease in Guinea was detected. Case investigation, serology, and whole-genome sequencing indicated possible transmission of the virus from an Ebola virus disease survivor to another person and then to the case-patient reported here. This transmission chain over 11 months suggests slow Ebola virus evolution. [ABSTRACT FROM AUTHOR]
Published: 2016
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38. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella.

Author: Quick, Joshua, Ashton, Philip, Calus, Szymon, Chatt, Carole, Gossain, Savita, Hawker, Jeremy, Nair, Satheesh, Neal, Keith, Nye, Kathy, Peters, Tansy, Pinna, Elizabeth De, Robinson, Esther, Struthers, Keith, Webber, Mark, Catto, Andrew, Dallman, Timothy J., Hawkey, Peter, and Loman, Nicholas J.
Published: 2015
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39. Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing.

Author: Quick, Joshua, Cumley, Nicola, Wearn, Christopher M., Niebel, Marc, Constantinidou, Chrystala, Thomas, Chris M., Pallen, Mark J., Moiemen, Naiem S., Bamford, Amy, Oppenheim, Beryl, and Loman, Nicholas J.
Abstract: Objectives: Pseudomonas aeruginosa is a common nosocomial pathogen responsible for significant morbidity and mortality internationally. Patients may become colonised or infected with P. aeruginosa after exposure to contaminated sources within the hospital environment. The aim of this study was to determine whether whole-genome sequencing (WGS) can be used to determine the source in a cohort of burns patients at high risk of P. aeruginosa acquisition. Study design: An observational prospective cohort study. Setting: Burns care ward and critical care ward in the UK. Participants: Patients with >7% total burns by surface area were recruited into the study. Methods: All patients were screened for P. aeruginosa on admission and samples taken from their immediate environment, including water. Screening patients who subsequently developed a positive P. aeruginosa microbiology result were subject to enhanced environmental surveillance. All isolates of P. aeruginosa were genome sequenced. Sequence analysis looked at similarity and relatedness between isolates. Results: WGS for 141 P. aeruginosa isolates were obtained from patients, hospital water and the ward environment. Phylogenetic analysis revealed eight distinct clades, with a single clade representing the majority of environmental isolates in the burns unit. Isolates from three patients had identical genotypes compared with water isolates from the same room. There was clear clustering of water isolates by room and outlet, allowing the source of acquisitions to be unambiguously identified. Whole-genome shotgun sequencing of biofilm DNA extracted from a thermostatic mixer valve revealed this was the source of a P. aeruginosa subpopulation previously detected in water. In the remaining two cases there was no clear link to the hospital environment. Conclusions: This study reveals that WGS can be used for source tracking of P. aeruginosa in a hospital setting, and that acquisitions can be traced to a specific source within a hospital ward. [ABSTRACT FROM AUTHOR]
Published: 2014
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40. A complete bacterial genome assembled de novo using only nanopore sequencing data.

Author: Loman, Nicholas J, Quick, Joshua, and Simpson, Jared T
Subjects: *BACTERIAL genomes, *NUCLEOTIDE sequence, *NANOPORES, *NUCLEOTIDES, *ESCHERICHIA coli
Abstract: We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data. Our method has three stages: (i) overlaps are detected between reads and then corrected by a multiple-alignment process; (ii) corrected reads are assembled using the Celera Assembler; and (iii) the assembly is polished using a probabilistic model of the signal-level data. The assembly reconstructs gene order and has 99.5% nucleotide identity. [ABSTRACT FROM AUTHOR]
Published: 2015
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41. Binning metagenomic contigs by coverage and composition.

Author: Alneberg, Johannes, Bjarnason, Brynjar Smári, de Bruijn, Ino, Schirmer, Melanie, Quick, Joshua, Ijaz, Umer Z, Lahti, Leo, Loman, Nicholas J, Andersson, Anders F, and Quince, Christopher
Subjects: SHOTGUN sequencing, GENOMES, NUCLEOTIDE sequencing, ALGORITHMS, DNA analysis
Abstract: Shotgun sequencing enables the reconstruction of genomes from complex microbial communities, but because assembly does not reconstruct entire genomes, it is necessary to bin genome fragments. Here we present CONCOCT, a new algorithm that combines sequence composition and coverage across multiple samples, to automatically cluster contigs into genomes. We demonstrate high recall and precision on artificial as well as real human gut metagenome data sets. [ABSTRACT FROM AUTHOR]
Published: 2014
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42. Human-Centered AI to Support an Adaptive Management of Human-Machine Transitions with Vehicle Automation.

Author: Bellet, Thierry, Banet, Aurélie, Petiot, Marie, Richard, Bertrand, and Quick, Joshua
Subjects: ARTIFICIAL intelligence, AUTOMATION, TRAFFIC safety, AUTOMOBILE driving simulators, VEHICLES
Abstract: This article is about the Human-Centered Design (HCD), development and evaluation of an Artificial Intelligence (AI) algorithm aiming to support an adaptive management of Human-Machine Transition (HMT) between car drivers and vehicle automation. The general principle of this algorithm is to monitor (1) the drivers' behaviors and (2) the situational criticality to manage in real time the Human-Machine Interactions (HMI). This Human-Centered AI (HCAI) approach was designed from real drivers' needs, difficulties and errors observed at the wheel of an instrumented car. Then, the HCAI algorithm was integrated into demonstrators of Advanced Driving Aid Systems (ADAS) implemented on a driving simulator (dedicated to highway driving or to urban intersection crossing). Finally, user tests were carried out to support their evaluation from the end-users point of view. Thirty participants were invited to practically experience these ADAS supported by the HCAI algorithm. To increase the scope of this evaluation, driving simulator experiments were implemented among three groups of 10 participants, corresponding to three highly contrasted profiles of end-users, having respectively a positive, neutral or reluctant attitude towards vehicle automation. After having introduced the research context and presented the HCAI algorithm designed to contextually manage HMT with vehicle automation, the main results collected among these three profiles of future potential end users are presented. In brief, main findings confirm the efficiency and the effectiveness of the HCAI algorithm, its benefits regarding drivers' satisfaction, and the high levels of acceptance, perceived utility, usability and attractiveness of this new type of "adaptive vehicle automation". [ABSTRACT FROM AUTHOR]
Published: 2021
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43. Ultra-deep, long-read nanopore sequencing of mock microbial community standards.

Author: Nicholls, Samuel M, Quick, Joshua C, Tang, Shuiquan, and Loman, Nicholas J
Subjects: *DETECTION limit, *METAGENOMICS, *MICROBIAL communities, *STANDARDS
Abstract: Background Long sequencing reads are information-rich: aiding de novo assembly and reference mapping, and consequently have great potential for the study of microbial communities. However, the best approaches for analysis of long-read metagenomic data are unknown. Additionally, rigorous evaluation of bioinformatics tools is hindered by a lack of long-read data from validated samples with known composition. Findings We sequenced 2 commercially available mock communities containing 10 microbial species (ZymoBIOMICS Microbial Community Standards) with Oxford Nanopore GridION and PromethION. Both communities and the 10 individual species isolates were also sequenced with Illumina technology. We generated 14 and 16 gigabase pairs from 2 GridION flowcells and 150 and 153 gigabase pairs from 2 PromethION flowcells for the evenly distributed and log-distributed communities, respectively. Read length N50 ranged between 5.3 and 5.4 kilobase pairs over the 4 sequencing runs. Basecalls and corresponding signal data are made available (4.2 TB in total). Alignment to Illumina-sequenced isolates demonstrated the expected microbial species at anticipated abundances, with the limit of detection for the lowest abundance species below 50 cells (GridION). De novo assembly of metagenomes recovered long contiguous sequences without the need for pre-processing techniques such as binning. Conclusions We present ultra-deep, long-read nanopore datasets from a well-defined mock community. These datasets will be useful for those developing bioinformatics methods for long-read metagenomics and for the validation and comparison of current laboratory and software pipelines. [ABSTRACT FROM AUTHOR]
Published: 2019
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44. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe.

Author: Kay, Gemma L., Sergeant, Martin J., Zhou, Zhemin, Chan, Jacqueline Z.-M., Millard, Andrew, Quick, Joshua, Szikossy, Ildikó, Pap, Ildikó, Spigelman, Mark, Loman, Nicholas J., Achtman, Mark, Donoghue, Helen D., and Pallen, Mark J.
Published: 2015
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45. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States.

Author: Fauver, Joseph R., Petrone, Mary E., Hodcroft, Emma B., Shioda, Kayoko, Ehrlich, Hanna Y., Watts, Alexander G., Vogels, Chantal B.F., Brito, Anderson F., Alpert, Tara, Muyombwe, Anthony, Razeq, Jafar, Downing, Randy, Cheemarla, Nagarjuna R., Wyllie, Anne L., Kalinich, Chaney C., Ott, Isabel M., Quick, Joshua, Loman, Nicholas J., Neugebauer, Karla M., and Greninger, Alexander L.
Subjects: *SARS-CoV-2, *COVID-19 pandemic, *INTERNATIONAL air travel, *COVID-19, *TRAVEL restrictions
Abstract: The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March. To uncover the sources of SARS-CoV-2 introductions and patterns of spread within the United States, we sequenced nine viral genomes from early reported COVID-19 patients in Connecticut. Our phylogenetic analysis places the majority of these genomes with viruses sequenced from Washington state. By coupling our genomic data with domestic and international travel patterns, we show that early SARS-CoV-2 transmission in Connecticut was likely driven by domestic introductions. Moreover, the risk of domestic importation to Connecticut exceeded that of international importation by mid-March regardless of our estimated effects of federal travel restrictions. This study provides evidence of widespread sustained transmission of SARS-CoV-2 within the United States and highlights the critical need for local surveillance. • Connecticut's COVID-19 outbreak resulted from multiple domestic virus introductions • SARS-CoV-2 genomic data indicate that coast-to-coast spread occurred in the United States • Risk of introduction by domestic air travel exceeded international travel in March • Restrictions on international travel did not significantly alter risk estimates Using genomics and air travel information, the spread of SARS-CoV-2 in the United States from coast to coast is shown to be more a consequence of domestic introductions than of international travel. [ABSTRACT FROM AUTHOR]
Published: 2020
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46. Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.

Author: Mirza JD, de Oliveira Guimarães L, Wilkinson S, Rocha EC, Bertanhe M, Helfstein VC, de-Deus JT, Claro IM, Cumley N, Quick J, Faria NR, Sabino EC, Kirchgatter K, and Loman NJ
Subjects: Animals, Humans, Mosquito Vectors, Brazil, DNA, Culicidae genetics, Arboviruses genetics, Nanopore Sequencing
Abstract: The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.
Published: 2024
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47. Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.

Author: Claro IM, Ramundo MS, Coletti TM, da Silva CAM, Valenca IN, Candido DS, Sales FCS, Manuli ER, de Jesus JG, de Paula A, Felix AC, Andrade PDS, Pinho MC, Souza WM, Amorim MR, Proenca-Modena JL, Kallas EG, Levi JE, Faria NR, Sabino EC, Loman NJ, and Quick J
Abstract: Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work., Competing Interests: No competing interests were disclosed., (Copyright: © 2023 Claro IM et al.)
Published: 2023
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48. Coding-Complete Genome Sequences of Copenhagen and Copenhagen-Derived vP811 Strains of Vaccinia Virus Isolated from Cell Culture.

Author: Landsberger M, Quick J, and Mercer J
Abstract: The coding-complete genomes of laboratory vaccinia virus strain Copenhagen and the Copenhagen-derived deletion strain, vP811, were determined by short-read sequencing. Relative to the NCBI reference genome M35027, seven common coding differences were revealed, including an intact copy of the vaccinia virus immunomodulator A46R in both Cop and vP811.
Published: 2023
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49. Multiplex MinION sequencing suggests enteric adenovirus F41 genetic diversity comparable to pre-COVID-19 era.

Author: Maes M, Khokhar F, Wilkinson SAJ, Smith AD, Kovalenko G, Dougan G, Quick J, Loman NJ, Baker S, Curran MD, Skittrall JP, and Houldcroft CJ
Subjects: Humans, Child, Pandemics, Sequence Analysis, Adenoviridae genetics, Genetic Variation, COVID-19 epidemiology, Adenoviridae Infections
Abstract: Human adenovirus F41 causes acute gastroenteritis in children, and has recently been associated with an apparent increase in paediatric hepatitis of unknown aetiology in the UK, with further cases reported in multiple countries. Relatively little is known about the genetic diversity of adenovirus F41 in UK children; and it is unclear what, if any, impact the COVID-19 pandemic has had on viral diversity in the UK. Methods that allow F41 to be sequenced from clinical samples without the need for viral culture are required to provide the genomic data to address these questions. Therefore, we evaluated an overlapping-amplicon method of sequencing adenovirus genomes from clinical samples using Oxford Nanopore technology. We applied this method to a small sample of adenovirus-species-F-positive extracts collected as part of standard care in the East of England region in January-May 2022. This method produced genomes with >75 % coverage in 13/22 samples and >50 % coverage in 19/22 samples. We identified two F41 lineages present in paediatric patients in the East of England in 2022. Where F41 genomes from paediatric hepatitis cases were available ( n =2), these genomes fell within the diversity of F41 from the UK and continental Europe sequenced before and after the 2020-2021 phase of the COVID-19 pandemic. Our analyses suggest that overlapping amplicon sequencing is an appropriate method for generating F41 genomic data from high-virus-load clinical samples, and currently circulating F41 viral lineages were present in the UK and Europe before the COVID-19 pandemic.
Published: 2023
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50. Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.

Author: Claro IM, Romano CM, Candido DDS, Lima EL, Lindoso JAL, Ramundo MS, Moreira FRR, Barra LAC, Borges LMS, Medeiros LA, Tomishige MYS, Moutinho T, Silva AJDD, Rodrigues CCM, Azevedo LCF, Villas-Boas LS, Silva CAMD, Coletti TM, Manuli ER, O'Toole A, Quick J, Loman N, Rambaut A, Faria NR, Figueiredo-Mello C, and Sabino EC
Subjects: Brazil, Humans, Metagenomics, Mpox (monkeypox) diagnosis, Mpox (monkeypox) epidemiology, Monkeypox virus genetics
Abstract: Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.
Published: 2022
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