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Lindsey, Benjamin B, Villabona-Arenas, Ch Julián, Campbell, Finlay, Keeley, Alexander J, Parker, Matthew D, Shah, Dhruv R, Parsons, Helena, Zhang, Peijun, Kakkar, Nishchay, Gallis, Marta et al (show 18 more authors) , Foulkes, Benjamin H, Wolverson, Paige, Louka, Stavroula F, Christou, Stella, State, Amy, Johnson, Katie, Raza, Mohammad, Hsu, Sharon, Jombart, Thibaut, Cori, Anne, Sheffield COVID-19 Genomics Group, , COVID-19 Genomics UK (COG-UK) consortium, , CMMID COVID-19 working group, , Evans, Cariad M, Partridge, David G, Atkins, Katherine E, Hué, Stéphane and de Silva, Thushan I (2022) Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature communications, 13 (1). p. 671.

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Leary, Shay ORCID: 0000-0002-6966-2294, Gaudieri, Silvana, Parker, Matthew D, Chopra, Abha ORCID: 0000-0001-5008-9080, James, Ian, Pakala, Suman, Alves, Eric ORCID: 0000-0002-6072-708X, John, Mina, Lindsey, Benjamin B ORCID: 0000-0003-4227-2592, Keeley, Alexander J ORCID: 0000-0001-9386-1157 et al (show 11 more authors) , Rowland-Jones, Sarah L, Swanson, Maurice S ORCID: 0000-0001-6245-5367, Ostrov, David A, Bubenik, Jodi L, Das, Suman R, Sidney, John, Sette, Alessandro, COVID-19 Genomics UK (COG-UK) consortium, , de Silva, Thushan I ORCID: 0000-0002-6498-9212, Phillips, Elizabeth and Mallal, Simon ORCID: 0000-0002-7036-1309 (2021) Generation of a Novel SARS-CoV-2 Sub-genomic RNA Due to the R203K/G204R Variant in Nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Pathogens & immunity, 6 (2). pp. 27-49.

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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 et al (show 6 more authors) , Gallagher, Eileen, Charlett, Andre, De Angelis, Daniela, Presanis, Anne M, Dabrera, Gavin and COVID-19 Genomics UK (COG-UK) consortium, (2021) 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. The Lancet. Infectious diseases, 22 (1). pp. 35-42.

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Francis, Rodric V, Billam, Harriet, Clarke, Mitch, Yates, Carl, Tsoleridis, Theocharis, Berry, Louise, Mahida, Nikunj, Irving, William L, Moore, Christopher ORCID: 0000-0002-3122-7502, Holmes, Nadine ORCID: 0000-0001-7470-3786 et al (show 4 more authors) , Ball, Jonathan K, Loose, Matthew, McClure, C Patrick ORCID: 0000-0002-1710-1049 and COVID-19 Genomics UK (COG-UK) consortium, (2022) The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. The Journal of infectious diseases, 225 (1). pp. 10-18.

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Wenlock, RD ORCID: 0000-0001-7510-0821, Tausan, M, Mann, R, Garr, W, Preston, R, Arnold, A, Hoban, J, Webb, L, Quick, C, Beckett, A ORCID: 0000-0003-4948-1004 et al (show 10 more authors) , Loveson, K, Glaysher, S ORCID: 0000-0002-9584-0621, Elliott, S, Malone, C, Cogger, B, Easton, L, COVID-19 Genomics UK (COG-UK) consortium, , Robson, SC ORCID: 0000-0001-5702-9160, Hassan-Ibrahim, MO and Sargent, C (2021) Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward. Infection prevention in practice, 3 (3). 100165-.

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O'Toole, Áine ORCID: 0000-0001-8083-474X, Hill, Verity, Pybus, Oliver G, Watts, Alexander, Bogoch, Issac I ORCID: 0000-0003-1590-6748, Khan, Kamran, Messina, Jane P, COVID-19 Genomics UK (COG-UK) consortium, , Network for Genomic Surveillance in South Africa (NGS-SA), , Brazil-UK CADDE Genomic Network, et al (show 90 more authors) , Tegally, Houriiyah, Lessells, Richard R ORCID: 0000-0003-0926-710X, Giandhari, Jennifer, Pillay, Sureshnee ORCID: 0000-0001-9288-7996, Tumedi, Kefentse Arnold, Nyepetsi, Gape, Kebabonye, Malebogo, Matsheka, Maitshwarelo ORCID: 0000-0002-7124-9343, Mine, Madisa, Tokajian, Sima ORCID: 0000-0002-3653-8940, Hassan, Hamad, Salloum, Tamara ORCID: 0000-0002-2689-4175, Merhi, Georgi ORCID: 0000-0002-5558-4088, Koweyes, Jad ORCID: 0000-0003-2010-6016, Geoghegan, Jemma L, de Ligt, Joep ORCID: 0000-0002-0348-419X, Ren, Xiaoyun, Storey, Matthew, Freed, Nikki E, Pattabiraman, Chitra ORCID: 0000-0002-9707-3358, Prasad, Pramada, Desai, Anita S, Vasanthapuram, Ravi, Schulz, Thomas F ORCID: 0000-0001-8792-5345, Steinbrück, Lars ORCID: 0000-0001-9142-7146, Stadler, Tanja, Swiss Viollier Sequencing Consortium, , Parisi, Antonio, Bianco, Angelica ORCID: 0000-0002-6156-4657, García de Viedma, Darío, Buenestado-Serrano, Sergio ORCID: 0000-0003-1739-4459, Borges, Vítor ORCID: 0000-0003-3767-2209, Isidro, Joana ORCID: 0000-0002-8529-9878, Duarte, Sílvia ORCID: 0000-0003-2943-5975, Gomes, João Paulo ORCID: 0000-0002-2697-2399, Zuckerman, Neta S, Mandelboim, Michal, Mor, Orna, Seemann, Torsten, Arnott, Alicia, Draper, Jenny ORCID: 0000-0002-6916-6442, Gall, Mailie ORCID: 0000-0001-7018-2426, Rawlinson, William, Deveson, Ira ORCID: 0000-0003-3861-0472, Schlebusch, Sanmarié, McMahon, Jamie, Leong, Lex, Lim, Chuan Kok ORCID: 0000-0002-2828-2922, Chironna, Maria ORCID: 0000-0002-1043-1256, Loconsole, Daniela ORCID: 0000-0003-2057-9745, Bal, Antonin, Josset, Laurence, Holmes, Edward, St George, Kirsten, Lasek-Nesselquist, Erica, Sikkema, Reina S, Oude Munnink, Bas, Koopmans, Marion, Brytting, Mia, Sudha Rani, V ORCID: 0000-0002-7161-9527, Pavani, S, Smura, Teemu, Heim, Albert, Kurkela, Satu, Umair, Massab, Salman, Muhammad, Bartolini, Barbara, Rueca, Martina, Drosten, Christian, Wolff, Thorsten ORCID: 0000-0001-7688-236X, Silander, Olin, Eggink, Dirk, Reusken, Chantal, Vennema, Harry, Park, Aekyung, Carrington, Christine ORCID: 0000-0001-6533-9302, Sahadeo, Nikita, Carr, Michael ORCID: 0000-0003-0011-6209, Gonzalez, Gabo, SEARCH Alliance San Diego, , National Virus Reference Laboratory, , SeqCOVID-Spain, , Danish Covid-19 Genome Consortium (DCGC), , Communicable Diseases Genomic Network (CDGN), , Dutch National SARS-CoV-2 surveillance program, , Division of Emerging Infectious Diseases (KDCA), , de Oliveira, Tulio, Faria, Nuno ORCID: 0000-0001-8839-2798, Rambaut, Andrew and Kraemer, Moritz UG (2021) Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch. Wellcome open research, 6. 121-.

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Fryer, Helen R ORCID: 0000-0001-9987-8160, Golubchik, Tanya, Hall, Matthew, Fraser, Christophe, Hinch, Robert, Ferretti, Luca, Thomson, Laura, Nurtay, Anel, Pellis, Lorenzo, House, Thomas et al (show 24 more authors) , MacIntyre-Cockett, George, Trebes, Amy, Buck, David, Piazza, Paolo, Green, Angie, Lonie, Lorne J, Smith, Darren ORCID: 0000-0003-4925-467X, Bashton, Matthew ORCID: 0000-0002-6847-1525, Crown, Matthew, Nelson, Andrew ORCID: 0000-0001-6665-4929, McCann, Clare M, Adnan Tariq, Mohammed, Elstob, Claire J, Nunes Dos Santos, Rui, Richards, Zack, Xhang, Xin, Hawley, Joseph, Lee, Mark R, Carrillo-Barragan, Priscilla ORCID: 0000-0003-2639-264X, Chapman, Isobel, Harthern-Flint, Sarah, COVID-19 Genomics UK (COG-UK) consortium, , Bonsall, David and Lythgoe, Katrina A (2023) Viral burden is associated with age, vaccination, and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection-related sampling bias. PLoS pathogens, 19 (8). e1011461-.