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2. Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

Author

Thomson, Emma C, Rosen, Laura E, Shepherd, James G, Spreafico, Roberto, da Silva Filipe, Ana, Wojcechowskyj, Jason A, Davis, Chris, Piccoli, Luca, Pascall, David J, Dillen, Josh, Lytras, Spyros, Czudnochowski, Nadine, Shah, Rajiv, Meury, Marcel, Jesudason, Natasha, De Marco, Anna, Li, Kathy, Bassi, Jessica, O’Toole, Aine, Pinto, Dora, Colquhoun, Rachel M, Culap, Katja, Jackson, Ben, Zatta, Fabrizia, Rambaut, Andrew, Jaconi, Stefano, Sreenu, Vattipally B, Nix, Jay, Zhang, Ivy, Jarrett, Ruth F, Glass, William G, Beltramello, Martina, Nomikou, Kyriaki, Pizzuto, Matteo, Tong, Lily, Cameroni, Elisabetta, Croll, Tristan I, Johnson, Natasha, Di Iulio, Julia, Wickenhagen, Arthur, Ceschi, Alessandro, Harbison, Aoife M, Mair, Daniel, Ferrari, Paolo, Smollett, Katherine, Sallusto, Federica, Carmichael, Stephen, Garzoni, Christian, Nichols, Jenna, Galli, Massimo, Hughes, Joseph, Riva, Agostino, Ho, Antonia, Schiuma, Marco, Semple, Malcolm G, Openshaw, Peter JM, Fadda, Elisa, Baillie, J Kenneth, Chodera, John D, Investigators, The ISARIC4C, Consortium, the COVID-19 Genomics UK, Rihn, Suzannah J, Lycett, Samantha J, Virgin, Herbert W, Telenti, Amalio, Corti, Davide, Robertson, David L, and Snell, Gyorgy

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Biological Sciences, Immunology, Biotechnology, Coronaviruses Therapeutics and Interventions, Coronaviruses, Vaccine Related, Infectious Diseases, Immunization, Emerging Infectious Diseases, Prevention, 5.1 Pharmaceuticals, 2.1 Biological and endogenous factors, Infection, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Antibodies, Neutralizing, Antibodies, Viral, COVID-19, Genetic Fitness, Humans, Immune Evasion, Mutation, Phylogeny, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Virulence, ISARIC4C Investigators, COVID-19 Genomics UK (COG-UK) Consortium, N439K, Spike, monoclonal antibody escape, mutation, protein structure, receptor binding motif, variant, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

SARS-CoV-2 can mutate and evade immunity, with consequences for efficacy of emerging vaccines and antibody therapeutics. Here, we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is a highly variable region of S and provide epidemiological, clinical, and molecular characterization of a prevalent, sentinel RBM mutation, N439K. We demonstrate N439K S protein has enhanced binding affinity to the hACE2 receptor, and N439K viruses have similar in vitro replication fitness and cause infections with similar clinical outcomes as compared to wild type. We show the N439K mutation confers resistance against several neutralizing monoclonal antibodies, including one authorized for emergency use by the US Food and Drug Administration (FDA), and reduces the activity of some polyclonal sera from persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

Published
2021

4. Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic

Author

Jackson, Ben, Boni, Maciej F., Bull, Matthew J., Colleran, Amy, Colquhoun, Rachel M., Darby, Alistair C., Haldenby, Sam, Hill, Verity, Lucaci, Anita, McCrone, John T., Nicholls, Samuel M., O’Toole, Áine, Pacchiarini, Nicole, Poplawski, Radoslaw, Scher, Emily, Todd, Flora, Webster, Hermione J., Whitehead, Mark, Wierzbicki, Claudia, Loman, Nicholas J., Connor, Thomas R., Robertson, David L., Pybus, Oliver G., and Rambaut, Andrew

Published
2021
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5. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Koshy, Cherian, Wise, Emma, Cortes, Nick, Lynch, Jessica, Kidd, Stephen, Mori, Matilde, Fairley, Derek J., Curran, Tanya, McKenna, James P., Adams, Helen, Fraser, Christophe, Golubchik, Tanya, Bonsall, David, Moore, Catrin, Caddy, Sarah L., Khokhar, Fahad A., 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., Charalampous, Themoula, Nebbia, Gaia, Batra, Rahul, Edgeworth, Jonathan, Robson, Samuel C., Beckett, Angela, Loveson, Katie F., Aanensen, David M., Underwood, Anthony P., Yeats, Corin A., Abudahab, Khalil, Taylor, Ben E.W., 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, Bird, Paul, Helmer, Thomas, Fallon, Karlie, Holmes, Christopher, Tang, Julian, Raviprakash, Veena, Campbell, Sharon, Sheriff, Nicola, 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., Feltwell, Theresa, Houldcroft, Charlotte J., Eldirdiri, Sahar, Kenyon, Anita, Davis, Thomas, Pybus, Oliver, du Plessis, Louis, Zarebski, Alex, Raghwani, Jayna, Kraemer, Moritz, Francois, Sarah, Attwood, Stephen, Vasylyeva, Tetyana, Torok, M. Estee, Hamilton, William L., Goodfellow, Ian G., Hall, Grant, Jahun, Aminu S., Chaudhry, Yasmin, Hosmillo, Myra, Pinckert, Malte L., Georgana, Iliana, Yakovleva, Anna, Meredith, Luke W., Moses, Samuel, Lowe, Hannah, Ryan, Felicity, Fisher, Chloe L., Awan, Ali R., Boyes, John, Breuer, Judith, Harris, Kathryn Ann, Brown, Julianne Rose, Shah, Divya, Atkinson, Laura, Lee, Jack C.D., Alcolea-Medina, Adela, Moore, Nathan, Cortes, Nicholas, Williams, Rebecca, Chapman, Michael R., Levett, Lisa J., Heaney, Judith, Smith, Darren L., Bashton, Matthew, Young, Gregory R., Allan, John, Loh, Joshua, Randell, Paul A., Cox, Alison, Madona, Pinglawathee, Holmes, Alison, Bolt, Frances, Price, James, Mookerjee, Siddharth, Rowan, Aileen, Taylor, Graham P., Ragonnet-Cronin, Manon, Nascimento, Fabricia F., Jorgensen, David, Siveroni, Igor, Johnson, Rob, Boyd, Olivia, Geidelberg, Lily, Volz, Erik M., Brunker, Kirstyn, Smollett, Katherine L., Loman, Nicholas J., Quick, Joshua, McMurray, Claire, Stockton, Joanne, Nicholls, Sam, Rowe, Will, Poplawski, Radoslaw, Martinez-Nunez, Rocio T., Mason, Jenifer, Robinson, Trevor I., O'Toole, Elaine, Watts, Joanne, Breen, Cassie, Cowell, Angela, Ludden, Catherine, Sluga, Graciela, Machin, Nicholas W., Ahmad, Shazaad S.Y., George, Ryan P., Halstead, Fenella, Sivaprakasam, Venkat, Thomson, Emma C., Shepherd, James G., Asamaphan, Patawee, Niebel, Marc O., Li, Kathy K., Shah, Rajiv N., Jesudason, Natasha G., Parr, Yasmin A., 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., Hale, Antony D., Macfarlane-Smith, Louissa R., Harper, Katherine L., Taha, Yusri, Payne, Brendan A.I., Burton-Fanning, Shirelle, Waugh, Sheila, Collins, Jennifer, Eltringham, Gary, Templeton, Kate E., McHugh, Martin P., Dewar, Rebecca, Wastenge, Elizabeth, Dervisevic, Samir, Stanley, Rachael, Prakash, Reenesh, Stuart, Claire, Elumogo, Ngozi, Sethi, Dheeraj K., Meader, Emma J., Coupland, Lindsay J., Potter, Will, Graham, Clive, Barton, Edward, Padgett, Debra, Scott, Garren, Swindells, Emma, Greenaway, Jane, Nelson, Andrew, Yew, Wen C., Resende Silva, Paola C., Andersson, Monique, Shaw, Robert, Peto, Timothy, Justice, Anita, Eyre, David, Crooke, Derrick, Hoosdally, Sarah, Sloan, Tim J., Duckworth, Nichola, Walsh, Sarah, Chauhan, Anoop J., Glaysher, Sharon, Bicknell, Kelly, Wyllie, Sarah, Butcher, Ethan, Elliott, Scott, Lloyd, Allyson, Impey, Robert, Levene, Nick, Monaghan, Lynn, Bradley, Declan T., Allara, Elias, Pearson, Clare, 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, Osman, Husam, Bosworth, Andrew, Robinson, Esther, 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., Wain, John, Webber, Mark A., Mather, Alison E., Baker, David J., Rudder, Steven, Yasir, Muhammad, Thomson, Nicholas M., Aydin, Alp, Tedim, Ana P., Kay, Gemma L., Trotter, Alexander J., Gilroy, Rachel A.J., Alikhan, Nabil-Fareed, de Oliveira Martins, Leonardo, Le-Viet, Thanh, Meadows, Lizzie, Kolyva, Anastasia, Diaz, Maria, Bell, Andrew, Gutierrez, Ana Victoria, Charles, Ian G., Adriaenssens, Evelien M., Kingsley, Robert A., Casey, Anna, Simpson, David A., Molnar, Zoltan, Thompson, Thomas, Acheson, Erwan, Masoli, Jane A.H., Knight, Bridget A., Hattersley, Andrew, Ellard, Sian, Auckland, Cressida, Mahungu, Tabitha W., Irish-Tavares, Dianne, Haque, Tanzina, Bourgeois, Yann, Scarlett, Garry P., Partridge, David G., Raza, Mohammad, Evans, Cariad, Johnson, Kate, Liggett, Steven, Baker, Paul, Essex, Sarah, Lyons, Ronan A., Caller, Laura G., Castellano, Sergi, Williams, Rachel J., Kristiansen, Mark, Roy, Sunando, Williams, Charlotte A., Dyal, Patricia L., Tutill, Helena J., Panchbhaya, Yasmin N., Forrest, Leysa M., Niola, Paola, Findlay, Jacqueline, Brooks, Tony T., Gavriil, Artemis, Mestek-Boukhibar, Lamia, Weeks, Sam, Pandey, Sarojini, Berry, Lisa, Jones, Katie, Richter, Alex, Beggs, Andrew, Smith, Colin P., Bucca, Giselda, Hesketh, Andrew R., Harrison, Ewan M., Peacock, Sharon J., Palmer, Sophie, Churcher, Carol M., Bellis, Katherine L., Girgis, Sophia T., Naydenova, Plamena, Blane, Beth, Sridhar, Sushmita, Ruis, Chris, Forrest, Sally, Cormie, Claire, Gill, Harmeet K., Dias, Joana, Higginson, Ellen E., Maes, Mailis, Young, Jamie, Kermack, Leanne M., Hadjirin, Nazreen F., Aggarwal, Dinesh, Griffith, Luke, Swingler, Tracey, Davidson, Rose K., Rambaut, Andrew, Williams, Thomas, Balcazar, Carlos E., Gallagher, Michael D., O'Toole, Áine, Rooke, Stefan, Jackson, Ben, Colquhoun, Rachel, Ashworth, Jordan, Hill, Verity, McCrone, J.T., Scher, Emily, Yu, Xiaoyu, 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, Kwiatkowski, Dominic, 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, 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., McClure, Patrick C., Chappell, Joseph G., Tsoleridis, Theocharis, Ball, Jonathan, Grammatopoulos, Dimitris, Buck, David, Todd, John A., Green, Angie, Trebes, Amy, MacIntyre-Cockett, George, de Cesare, Mariateresa, Langford, Cordelia, Alderton, Alex, Amato, Roberto, Goncalves, Sonia, Jackson, David K., Johnston, Ian, Sillitoe, John, Palmer, Steve, Lawniczak, Mara, Berriman, Matt, Danesh, John, Livett, Rich, Shirley, Lesley, Farr, Ben, Quail, Mike, Thurston, Scott, Park, Naomi, Betteridge, Emma, Weldon, Danni, Goodwin, Scott, Nelson, Rachel, Beaver, Charlotte, Letchford, Laura, Jackson, David A., Foulser, Luke, McMinn, Liz, Prestwood, Liam, Kay, Sally, Kane, Leanne, Dorman, Matthew J., Martincorena, Inigo, Puethe, Christoph, Keatley, Jon-Paul, Tonkin-Hill, Gerry, Smith, Christen, Jamrozy, Dorota, Beale, Mathew A., Patel, Minal, Ariani, Cristina, Spencer-Chapman, Michael, Drury, Eleanor, Lo, Stephanie, Rajatileka, Shavanthi, Scott, Carol, James, Keith, Buddenborg, Sarah K., Berger, Duncan J., Patel, Gaurang, Garcia-Casado, Maria V., Dibling, Thomas, McGuigan, Samantha, Rogers, Hazel A., Hunter, Adam D., Souster, Emily, Neaverson, Alexandra S., Volz, Erik, McCrone, John T., O’Toole, Áine, Johnson, Robert, Rey, Sara M., Nicholls, Samuel M., Colquhoun, Rachel M., Shepherd, James, Pascall, David J., Shah, Rajiv, Jesudason, Natasha, Li, Kathy, Jarrett, Ruth, Goodfellow, Ian, and Pybus, Oliver G.

Published
2021
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9. CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

Author

Nicholls, Samuel M., Poplawski, Radoslaw, Bull, Matthew J., Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M., Rowe, Will P. M., Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M., Peacock, Sharon J., Aanensen, David M., Rambaut, Andrew, Connor, Thomas R., Loman, Nicholas J., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, Matthew, Smith, Darren, Nelson, Andrew, Young, Greg, McCann, Clare, Harrison, Ewan [0000-0003-2720-0507], Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository

Subjects
QH301-705.5, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Genomics, Genome, Viral, Biology, QH426-470, Genome, User-Computer Interface, Pandemic, Genetics, Humans, Biology (General), Whole genome sequencing, Whole Genome Sequencing, SARS-CoV-2, C100, fungi, COVID-19, C500, Sequence Analysis, DNA, Cloud Computing, Data science, C900, United Kingdom, Metadata, B900, Editorial, Software deployment, Epidemiological Monitoring
Abstract

In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02395-y.

Published
2021
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10. Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

Author

Lycett, Samantha J, Hughes, Joseph, McHugh, Martin P, Filipe, Ana da Silva, Dewar, Rebecca, Lu, Lu, Doherty, Thomas, Shepherd, Amy, Inward, Rhys, Rossi, Gianluigi, Balaz, Daniel, Kao, Rowland R, Rooke, Stefan, Cotton, Seb, Gallagher, Michael D, Lopez, Carlos Balcazar, O’Toole, Áine, Scher, Emily, Hill, Verity, McCrone, John T, Colquhoun, Rachel M, Jackson, Ben, Williams, Thomas C, Williamson, Kathleen A, Johnson, Natasha, Smollett, Katherine, Mair, Daniel, Carmichael, Stephen, Tong, Lily, Nichols, Jenna, Brunker, Kirstyn, Shepherd, James G, Li, Kathy, Aranday-Cortes, Elihu, Parr, Yasmin A, Broos, Alice, Nomikou, Kyriaki, McDonald, Sarah E, Niebel, Marc, Asamaphan, Patawee, Starinskij, Igor, Jesudason, Natasha, Shah, Rajiv, Sreenu, Vattipally B, Stanton, Tom, Shaaban, Sharif, MacLean, Alasdair, Woolhouse, Mark, Gunson, Rory, Templeton, Kate, Thomson, Emma C, Rambaut, Andrew, Holden, Matthew T.G., and Robertson, David L

Abstract

The second SARS virus, SARS-CoV-2, emerged in December 2019, and within a month was globally distributed. It was first introduced into Scotland in February 2020 associated with returning travellers and visitors. By March it was circulating in communities across the UK, and to control COVID-19 cases, and prevent overwhelming of the National Health Service (NHS), a ‘lockdown’ was introduced on 23rd March 2020 with a restriction of people’s movements. To augment the public health efforts a large-scale genome epidemiology effort (as part of the COVID-19 Genomics UK (COG-UK) consortium) resulted in the sequencing of over 5000 SARS-CoV-2 genomes by 18th August 2020 from Scottish cases, about a quarter of the estimated number of cases at that time. Here we quantify the geographical origins of the first wave introductions into Scotland from abroad and other UK regions, the spread of these SARS-CoV-2 lineages to different regions within Scotland (defined at the level of NHS Health Board) and the effect of lockdown on virus ‘success’. We estimate that approximately 300 introductions seeded lineages in Scotland, with around 25% of these lineages composed of more than five viruses, but by June circulating lineages were reduced to low levels, in line with low numbers of recorded positive cases. Lockdown was, thus, associated with a dramatic reduction in infection numbers and the extinguishing of most virus lineages. Unfortunately since the summer cases have been rising in Scotland in a second wave, with >1000 people testing positive on a daily basis, and hospitalisation of COVID-19 cases on the rise again. Examining the available Scottish genome data from the second wave, and comparing it to the first wave, we find that while some UK lineages have persisted through the summer, the majority of lineages responsible for the second wave are new introductions from outside of Scotland and many from outside of the UK. This indicates that, while lockdown in Scotland is directly linked with the first wave case numbers being brought under control, travel-associated imports (mostly from Europe or other parts of the UK) following the easing of lockdown are responsible for seeding the current epidemic population. This demonstrates that the impact of stringent public health measures can be compromised if following this, movements from regions of high to low prevalence are not minimised.

Published
2021
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11. Additional file 1 of Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs

Author

Colquhoun, Rachel M., Hall, Michael B., Lima, Leandro, Roberts, Leah W., Malone, Kerri M., Hunt, Martin, Letcher, Brice, Hawkey, Jane, George, Sophie, Pankhurst, Louise, and Iqbal, Zamin

Abstract

Additional file 1: A: Supplementary figures 1-13. B: Supplementary tables 1-2. C: Supplementary algorithms 1-3. D: Detailed data availability. E: Supplementary animations 1-2.

Published
2021
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12. Additional file 1 of CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

Author

Nicholls, Samuel M., Poplawski, Radoslaw, Bull, Matthew J., Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M., Rowe, Will P. M., Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M., Peacock, Sharon J., Aanensen, David M., Rambaut, Andrew, Connor, Thomas R., and Loman, Nicholas J.

Abstract

Additional file 1. The COVID-19 Genomics UK (COG-UK) Consortium.

Published
2021
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13. Additional file 2 of CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

Author

Nicholls, Samuel M., Poplawski, Radoslaw, Bull, Matthew J., Underwood, Anthony, Chapman, Michael, Abu-Dahab, Khalil, Taylor, Ben, Colquhoun, Rachel M., Rowe, Will P. M., Jackson, Ben, Hill, Verity, O’Toole, Áine, Rey, Sara, Southgate, Joel, Amato, Roberto, Livett, Rich, Gonçalves, Sónia, Harrison, Ewan M., Peacock, Sharon J., Aanensen, David M., Rambaut, Andrew, Connor, Thomas R., and Loman, Nicholas J.

Abstract

Additional file 2: Table 3. COG-UK full metadata standard.

Published
2021
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15. The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

Author

Thomson, Emma C., Rosen, Laura E., Shepherd, James G., Spreafico, Roberto, da Silva Filipe, Ana, Wojcechowskyj, Jason A., Davis, Chris, Piccoli, Luca, Pascall, David J., Dillen, Josh, Lytras, Spyros, Czudnochowski, Nadine, Shah, Rajiv, Meury, Marcel, Jesudason, Natasha, De Marco, Anna, Li, Kathy, Bassi, Jessica, O’Toole, Aine, Pinto, Dora, Colquhoun, Rachel M., Culap, Katja, Jackson, Ben, Zatta, Fabrizia, Rambaut, Andrew, Jaconi, Stefano, Sreenu, Vattipally B., Nix, Jay, Jarrett, Ruth F., Beltramello, Martina, Nomikou, Kyriaki, Pizzuto, Matteo, Tong, Lily, Cameroni, Elisabetta, Johnson, Natasha, Wickenhagen, Arthur, Ceschi, Alessandro, Mair, Daniel, Ferrari, Paolo, Smollett, Katherine, Sallusto, Federica, Carmichael, Stephen, Garzoni, Christian, Nichols, Jenna, Galli, Massimo, Hughes, Joseph, Riva, Agostino, Ho, Antonia, Semple, Malcolm G., Openshaw, Peter J.M., Baillie, J. Kenneth, Rihn, Suzannah J., Lycett, Samantha J., Virgin, Herbert W., Telenti, Amalio, Corti, Davide, Robertson, David L., Snell, Gyorgy, and Fadda, Elisa

Subjects
Immune system, biology, medicine.drug_class, Immunity, Polyclonal antibodies, biology.protein, medicine, Virulence, Antibody, Monoclonal antibody, Receptor, Virology, Virus
Abstract

SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics. Herein we demonstrate that the immunodominant SARS-CoV-2 spike (S) receptor binding motif (RBM) is the most divergent region of S, and provide epidemiological, clinical, and molecular characterization of a prevalent RBM variant, N439K. We demonstrate that N439K S protein has enhanced binding affinity to the hACE2 receptor, and that N439K virus has similar clinical outcomes and in vitro replication fitness as compared to wild- type. We observed that the N439K mutation resulted in immune escape from a panel of neutralizing monoclonal antibodies, including one in clinical trials, as well as from polyclonal sera from a sizeable fraction of persons recovered from infection. Immune evasion mutations that maintain virulence and fitness such as N439K can emerge within SARS-CoV-2 S, highlighting the need for ongoing molecular surveillance to guide development and usage of vaccines and therapeutics.

Published
2020
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16. Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Author

Volz, Erik, primary, Hill, Verity, additional, McCrone, John T., additional, Price, Anna, additional, Jorgensen, David, additional, O’Toole, Áine, additional, Southgate, Joel, additional, Johnson, Robert, additional, Jackson, Ben, additional, Nascimento, Fabricia F., additional, Rey, Sara M., additional, Nicholls, Samuel M., additional, Colquhoun, Rachel M., additional, da Silva Filipe, Ana, additional, Shepherd, James, additional, Pascall, David J., additional, Shah, Rajiv, additional, Jesudason, Natasha, additional, Li, Kathy, additional, Jarrett, Ruth, additional, Pacchiarini, Nicole, additional, Bull, Matthew, additional, Geidelberg, Lily, additional, Siveroni, Igor, additional, Goodfellow, Ian, additional, Loman, Nicholas J., additional, Pybus, Oliver G., additional, Robertson, David L., additional, Thomson, Emma C., additional, Rambaut, Andrew, additional, Connor, Thomas R., additional, Koshy, Cherian, additional, Wise, Emma, additional, Cortes, Nick, additional, Lynch, Jessica, additional, Kidd, Stephen, additional, Mori, Matilde, additional, Fairley, Derek J., additional, Curran, Tanya, additional, McKenna, James P., additional, Adams, Helen, additional, Fraser, Christophe, additional, Golubchik, Tanya, additional, Bonsall, David, additional, Moore, Catrin, additional, Caddy, Sarah L., additional, Khokhar, Fahad A., additional, Wantoch, Michelle, additional, Reynolds, Nicola, additional, Warne, Ben, additional, Maksimovic, Joshua, additional, Spellman, Karla, additional, McCluggage, Kathryn, additional, John, Michaela, additional, Beer, Robert, additional, Afifi, Safiah, additional, Morgan, Sian, additional, Marchbank, Angela, additional, Kitchen, Christine, additional, Gulliver, Huw, additional, Merrick, Ian, additional, Guest, Martyn, additional, Munn, Robert, additional, Workman, Trudy, additional, Fuller, William, additional, Bresner, Catherine, additional, Snell, Luke B., additional, Charalampous, Themoula, additional, Nebbia, Gaia, additional, Batra, Rahul, additional, Edgeworth, Jonathan, additional, Robson, Samuel C., additional, Beckett, Angela, additional, Loveson, Katie F., additional, Aanensen, David M., additional, Underwood, Anthony P., additional, Yeats, Corin A., additional, Abudahab, Khalil, additional, Taylor, Ben E.W., additional, Menegazzo, Mirko, additional, Clark, Gemma, additional, Smith, Wendy, additional, Khakh, Manjinder, additional, Fleming, Vicki M., additional, Lister, Michelle M., additional, Howson-Wells, Hannah C., additional, Berry, Louise, additional, Boswell, Tim, additional, Joseph, Amelia, additional, Willingham, Iona, additional, Bird, Paul, additional, Helmer, Thomas, additional, Fallon, Karlie, additional, Holmes, Christopher, additional, Tang, Julian, additional, Raviprakash, Veena, additional, Campbell, Sharon, additional, Sheriff, Nicola, additional, Loose, Matthew W., additional, Holmes, Nadine, additional, Moore, Christopher, additional, Carlile, Matthew, additional, Wright, Victoria, additional, Sang, Fei, additional, Debebe, Johnny, additional, Coll, Francesc, additional, Signell, Adrian W., additional, Betancor, Gilberto, additional, Wilson, Harry D., additional, Feltwell, Theresa, additional, Houldcroft, Charlotte J., additional, Eldirdiri, Sahar, additional, Kenyon, Anita, additional, Davis, Thomas, additional, Pybus, Oliver, additional, du Plessis, Louis, additional, Zarebski, Alex, additional, Raghwani, Jayna, additional, Kraemer, Moritz, additional, Francois, Sarah, additional, Attwood, Stephen, additional, Vasylyeva, Tetyana, additional, Torok, M. Estee, additional, Hamilton, William L., additional, Goodfellow, Ian G., additional, Hall, Grant, additional, Jahun, Aminu S., additional, Chaudhry, Yasmin, additional, Hosmillo, Myra, additional, Pinckert, Malte L., additional, Georgana, Iliana, additional, Yakovleva, Anna, additional, Meredith, Luke W., additional, Moses, Samuel, additional, Lowe, Hannah, additional, Ryan, Felicity, additional, Fisher, Chloe L., additional, Awan, Ali R., additional, Boyes, John, additional, Breuer, Judith, additional, Harris, Kathryn Ann, additional, Brown, Julianne Rose, additional, Shah, Divya, additional, Atkinson, Laura, additional, Lee, Jack C.D., additional, Alcolea-Medina, Adela, additional, Moore, Nathan, additional, Cortes, Nicholas, additional, Williams, Rebecca, additional, Chapman, Michael R., additional, Levett, Lisa J., additional, Heaney, Judith, additional, Smith, Darren L., additional, Bashton, Matthew, additional, Young, Gregory R., additional, Allan, John, additional, Loh, Joshua, additional, Randell, Paul A., additional, Cox, Alison, additional, Madona, Pinglawathee, additional, Holmes, Alison, additional, Bolt, Frances, additional, Price, James, additional, Mookerjee, Siddharth, additional, Rowan, Aileen, additional, Taylor, Graham P., additional, Ragonnet-Cronin, Manon, additional, Johnson, Rob, additional, Boyd, Olivia, additional, Volz, Erik M., additional, Brunker, Kirstyn, additional, Smollett, Katherine L., additional, Quick, Joshua, additional, McMurray, Claire, additional, Stockton, Joanne, additional, Nicholls, Sam, additional, Rowe, Will, additional, Poplawski, Radoslaw, additional, Martinez-Nunez, Rocio T., additional, Mason, Jenifer, additional, Robinson, Trevor I., additional, O'Toole, Elaine, additional, Watts, Joanne, additional, Breen, Cassie, additional, Cowell, Angela, additional, Ludden, Catherine, additional, Sluga, Graciela, additional, Machin, Nicholas W., additional, Ahmad, Shazaad S.Y., additional, George, Ryan P., additional, Halstead, Fenella, additional, Sivaprakasam, Venkat, additional, Shepherd, James G., additional, Asamaphan, Patawee, additional, Niebel, Marc O., additional, Li, Kathy K., additional, Shah, Rajiv N., additional, Jesudason, Natasha G., additional, Parr, Yasmin A., additional, Tong, Lily, additional, Broos, Alice, additional, Mair, Daniel, additional, Nichols, Jenna, additional, Carmichael, Stephen N., additional, Nomikou, Kyriaki, additional, Aranday-Cortes, Elihu, additional, Johnson, Natasha, additional, Starinskij, Igor, additional, Orton, Richard J., additional, Hughes, Joseph, additional, Vattipally, Sreenu, additional, Singer, Joshua B., additional, Hale, Antony D., additional, Macfarlane-Smith, Louissa R., additional, Harper, Katherine L., additional, Taha, Yusri, additional, Payne, Brendan A.I., additional, Burton-Fanning, Shirelle, additional, Waugh, Sheila, additional, Collins, Jennifer, additional, Eltringham, Gary, additional, Templeton, Kate E., additional, McHugh, Martin P., additional, Dewar, Rebecca, additional, Wastenge, Elizabeth, additional, Dervisevic, Samir, additional, Stanley, Rachael, additional, Prakash, Reenesh, additional, Stuart, Claire, additional, Elumogo, Ngozi, additional, Sethi, Dheeraj K., additional, Meader, Emma J., additional, Coupland, Lindsay J., additional, Potter, Will, additional, Graham, Clive, additional, Barton, Edward, additional, Padgett, Debra, additional, Scott, Garren, additional, Swindells, Emma, additional, Greenaway, Jane, additional, Nelson, Andrew, additional, Yew, Wen C., additional, Resende Silva, Paola C., additional, Andersson, Monique, additional, Shaw, Robert, additional, Peto, Timothy, additional, Justice, Anita, additional, Eyre, David, additional, Crooke, Derrick, additional, Hoosdally, Sarah, additional, Sloan, Tim J., additional, Duckworth, Nichola, additional, Walsh, Sarah, additional, Chauhan, Anoop J., additional, Glaysher, Sharon, additional, Bicknell, Kelly, additional, Wyllie, Sarah, additional, Butcher, Ethan, additional, Elliott, Scott, additional, Lloyd, Allyson, additional, Impey, Robert, additional, Levene, Nick, additional, Monaghan, Lynn, additional, Bradley, Declan T., additional, Allara, Elias, additional, Pearson, Clare, additional, Muir, Peter, additional, Vipond, Ian B., additional, Hopes, Richard, additional, Pymont, Hannah M., additional, Hutchings, Stephanie, additional, Curran, Martin D., additional, Parmar, Surendra, additional, Lackenby, Angie, additional, Mbisa, Tamyo, additional, Platt, Steven, additional, Miah, Shahjahan, additional, Bibby, David, additional, Manso, Carmen, additional, Hubb, Jonathan, additional, Chand, Meera, additional, Dabrera, Gavin, additional, Ramsay, Mary, additional, Bradshaw, Daniel, additional, Thornton, Alicia, additional, Myers, Richard, additional, Schaefer, Ulf, additional, Groves, Natalie, additional, Gallagher, Eileen, additional, Lee, David, additional, Williams, David, additional, Ellaby, Nicholas, additional, Harrison, Ian, additional, Hartman, Hassan, additional, Manesis, Nikos, additional, Patel, Vineet, additional, Bishop, Chloe, additional, Chalker, Vicki, additional, Osman, Husam, additional, Bosworth, Andrew, additional, Robinson, Esther, additional, Holden, Matthew T.G., additional, Shaaban, Sharif, additional, Birchley, Alec, additional, Adams, Alexander, additional, Davies, Alisha, additional, Gaskin, Amy, additional, Plimmer, Amy, additional, Gatica-Wilcox, Bree, additional, McKerr, Caoimhe, additional, Moore, Catherine, additional, Williams, Chris, additional, Heyburn, David, additional, De Lacy, Elen, additional, Hilvers, Ember, additional, Downing, Fatima, additional, Shankar, Giri, additional, Jones, Hannah, additional, Asad, Hibo, additional, Coombes, Jason, additional, Watkins, Joanne, additional, Evans, Johnathan M., additional, Fina, Laia, additional, Gifford, Laura, additional, Gilbert, Lauren, additional, Graham, Lee, additional, Perry, Malorie, additional, Morgan, Mari, additional, Cronin, Michelle, additional, Craine, Noel, additional, Jones, Rachel, additional, Howe, Robin, additional, Corden, Sally, additional, Rey, Sara, additional, Kumziene-Summerhayes, Sara, additional, Taylor, Sarah, additional, Cottrell, Simon, additional, Jones, Sophie, additional, Edwards, Sue, additional, O’Grady, Justin, additional, Page, Andrew J., additional, Wain, John, additional, Webber, Mark A., additional, Mather, Alison E., additional, Baker, David J., additional, Rudder, Steven, additional, Yasir, Muhammad, additional, Thomson, Nicholas M., additional, Aydin, Alp, additional, Tedim, Ana P., additional, Kay, Gemma L., additional, Trotter, Alexander J., additional, Gilroy, Rachel A.J., additional, Alikhan, Nabil-Fareed, additional, de Oliveira Martins, Leonardo, additional, Le-Viet, Thanh, additional, Meadows, Lizzie, additional, Kolyva, Anastasia, additional, Diaz, Maria, additional, Bell, Andrew, additional, Gutierrez, Ana Victoria, additional, Charles, Ian G., additional, Adriaenssens, Evelien M., additional, Kingsley, Robert A., additional, Casey, Anna, additional, Simpson, David A., additional, Molnar, Zoltan, additional, Thompson, Thomas, additional, Acheson, Erwan, additional, Masoli, Jane A.H., additional, Knight, Bridget A., additional, Hattersley, Andrew, additional, Ellard, Sian, additional, Auckland, Cressida, additional, Mahungu, Tabitha W., additional, Irish-Tavares, Dianne, additional, Haque, Tanzina, additional, Bourgeois, Yann, additional, Scarlett, Garry P., additional, Partridge, David G., additional, Raza, Mohammad, additional, Evans, Cariad, additional, Johnson, Kate, additional, Liggett, Steven, additional, Baker, Paul, additional, Essex, Sarah, additional, Lyons, Ronan A., additional, Caller, Laura G., additional, Castellano, Sergi, additional, Williams, Rachel J., additional, Kristiansen, Mark, additional, Roy, Sunando, additional, Williams, Charlotte A., additional, Dyal, Patricia L., additional, Tutill, Helena J., additional, Panchbhaya, Yasmin N., additional, Forrest, Leysa M., additional, Niola, Paola, additional, Findlay, Jacqueline, additional, Brooks, Tony T., additional, Gavriil, Artemis, additional, Mestek-Boukhibar, Lamia, additional, Weeks, Sam, additional, Pandey, Sarojini, additional, Berry, Lisa, additional, Jones, Katie, additional, Richter, Alex, additional, Beggs, Andrew, additional, Smith, Colin P., additional, Bucca, Giselda, additional, Hesketh, Andrew R., additional, Harrison, Ewan M., additional, Peacock, Sharon J., additional, Palmer, Sophie, additional, Churcher, Carol M., additional, Bellis, Katherine L., additional, Girgis, Sophia T., additional, Naydenova, Plamena, additional, Blane, Beth, additional, Sridhar, Sushmita, additional, Ruis, Chris, additional, Forrest, Sally, additional, Cormie, Claire, additional, Gill, Harmeet K., additional, Dias, Joana, additional, Higginson, Ellen E., additional, Maes, Mailis, additional, Young, Jamie, additional, Kermack, Leanne M., additional, Hadjirin, Nazreen F., additional, Aggarwal, Dinesh, additional, Griffith, Luke, additional, Swingler, Tracey, additional, Davidson, Rose K., additional, Williams, Thomas, additional, Balcazar, Carlos E., additional, Gallagher, Michael D., additional, O'Toole, Áine, additional, Rooke, Stefan, additional, Colquhoun, Rachel, additional, Ashworth, Jordan, additional, McCrone, J.T., additional, Scher, Emily, additional, Yu, Xiaoyu, additional, Williamson, Kathleen A., additional, Stanton, Thomas D., additional, Michell, Stephen L., additional, Bewshea, Claire M., additional, Temperton, Ben, additional, Michelsen, Michelle L., additional, Warwick-Dugdale, Joanna, additional, Manley, Robin, additional, Farbos, Audrey, additional, Harrison, James W., additional, Sambles, Christine M., additional, Studholme, David J., additional, Jeffries, Aaron R., additional, Darby, Alistair C., additional, Hiscox, Julian A., additional, Paterson, Steve, additional, Iturriza-Gomara, Miren, additional, Jackson, Kathryn A., additional, Lucaci, Anita O., additional, Vamos, Edith E., additional, Hughes, Margaret, additional, Rainbow, Lucille, additional, Eccles, Richard, additional, Nelson, Charlotte, additional, Whitehead, Mark, additional, Turtle, Lance, additional, Haldenby, Sam T., additional, Gregory, Richard, additional, Gemmell, Matthew, additional, Kwiatkowski, Dominic, additional, de Silva, Thushan I., additional, Smith, Nikki, additional, Angyal, Adrienn, additional, Lindsey, Benjamin B., additional, Groves, Danielle C., additional, Green, Luke R., additional, Wang, Dennis, additional, Freeman, Timothy M., additional, Parker, Matthew D., additional, Keeley, Alexander J., additional, Parsons, Paul J., additional, Tucker, Rachel M., additional, Brown, Rebecca, additional, Wyles, Matthew, additional, Constantinidou, Chrystala, additional, Unnikrishnan, Meera, additional, Ott, Sascha, additional, Cheng, Jeffrey K.J., additional, Bridgewater, Hannah E., additional, Frost, Lucy R., additional, Taylor-Joyce, Grace, additional, Stark, Richard, additional, Baxter, Laura, additional, Alam, Mohammad T., additional, Brown, Paul E., additional, McClure, Patrick C., additional, Chappell, Joseph G., additional, Tsoleridis, Theocharis, additional, Ball, Jonathan, additional, Grammatopoulos, Dimitris, additional, Buck, David, additional, Todd, John A., additional, Green, Angie, additional, Trebes, Amy, additional, MacIntyre-Cockett, George, additional, de Cesare, Mariateresa, additional, Langford, Cordelia, additional, Alderton, Alex, additional, Amato, Roberto, additional, Goncalves, Sonia, additional, Jackson, David K., additional, Johnston, Ian, additional, Sillitoe, John, additional, Palmer, Steve, additional, Lawniczak, Mara, additional, Berriman, Matt, additional, Danesh, John, additional, Livett, Rich, additional, Shirley, Lesley, additional, Farr, Ben, additional, Quail, Mike, additional, Thurston, Scott, additional, Park, Naomi, additional, Betteridge, Emma, additional, Weldon, Danni, additional, Goodwin, Scott, additional, Nelson, Rachel, additional, Beaver, Charlotte, additional, Letchford, Laura, additional, Jackson, David A., additional, Foulser, Luke, additional, McMinn, Liz, additional, Prestwood, Liam, additional, Kay, Sally, additional, Kane, Leanne, additional, Dorman, Matthew J., additional, Martincorena, Inigo, additional, Puethe, Christoph, additional, Keatley, Jon-Paul, additional, Tonkin-Hill, Gerry, additional, Smith, Christen, additional, Jamrozy, Dorota, additional, Beale, Mathew A., additional, Patel, Minal, additional, Ariani, Cristina, additional, Spencer-Chapman, Michael, additional, Drury, Eleanor, additional, Lo, Stephanie, additional, Rajatileka, Shavanthi, additional, Scott, Carol, additional, James, Keith, additional, Buddenborg, Sarah K., additional, Berger, Duncan J., additional, Patel, Gaurang, additional, Garcia-Casado, Maria V., additional, Dibling, Thomas, additional, McGuigan, Samantha, additional, Rogers, Hazel A., additional, Hunter, Adam D., additional, Souster, Emily, additional, and Neaverson, Alexandra S., additional

Published
2021
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17. Nucleotide-resolution bacterial pan-genomics with reference graphs

Author

Colquhoun, Rachel M, primary, Hall, Michael B, additional, Lima, Leandro, additional, Roberts, Leah W, additional, Malone, Kerri M, additional, Hunt, Martin, additional, Letcher, Brice, additional, Hawkey, Jane, additional, George, Sophie, additional, Pankhurst, Louise, additional, and Iqbal, Zamin, additional

Published
2020
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18. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

Author

Volz, Erik, primary, Hill, Verity, additional, McCrone, John T., additional, Price, Anna, additional, Jorgensen, David, additional, O’Toole, Áine, additional, Southgate, Joel, additional, Johnson, Robert, additional, Jackson, Ben, additional, Nascimento, Fabricia F., additional, Rey, Sara M., additional, Nicholls, Samuel M., additional, Colquhoun, Rachel M., additional, da Silva Filipe, Ana, additional, Shepherd, James, additional, Pascall, David J., additional, Shah, Rajiv, additional, Jesudason, Natasha, additional, Li, Kathy, additional, Jarrett, Ruth, additional, Pacchiarini, Nicole, additional, Bull, Matthew, additional, Geidelberg, Lily, additional, Siveroni, Igor, additional, Goodfellow, Ian, additional, Loman, Nicholas J., additional, Pybus, Oliver G., additional, Robertson, David L., additional, Thomson, Emma C., additional, Rambaut, Andrew, additional, and Connor, Thomas R., additional

Published
2020
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19. CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance.

Author

Nicholls SM, Poplawski R, Bull MJ, Underwood A, Chapman M, Abu-Dahab K, Taylor B, Colquhoun RM, Rowe WPM, Jackson B, Hill V, O'Toole Á, Rey S, Southgate J, Amato R, Livett R, Gonçalves S, Harrison EM, Peacock SJ, Aanensen DM, Rambaut A, Connor TR, and Loman NJ

Subjects
COVID-19 epidemiology, Epidemiological Monitoring, Genome, Viral, Humans, Sequence Analysis, DNA, United Kingdom, User-Computer Interface, Whole Genome Sequencing, Cloud Computing, Genomics organization & administration, SARS-CoV-2 genetics
Abstract

In response to the ongoing SARS-CoV-2 pandemic in the UK, the COVID-19 Genomics UK (COG-UK) consortium was formed to rapidly sequence SARS-CoV-2 genomes as part of a national-scale genomic surveillance strategy. The network consists of universities, academic institutes, regional sequencing centres and the four UK Public Health Agencies. We describe the development and deployment of CLIMB-COVID, an encompassing digital infrastructure to address the challenge of collecting and integrating both genomic sequencing data and sample-associated metadata produced across the COG-UK network.

Published
2021
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