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McCrone, John T ORCID: 0000-0002-9846-8917, Hill, Verity, Bajaj, Sumali, Pena, Rosario Evans, Lambert, Ben C ORCID: 0000-0003-4274-4158, Inward, Rhys ORCID: 0000-0003-0016-661X, Bhatt, Samir ORCID: 0000-0002-0891-4611, Volz, Erik ORCID: 0000-0001-6268-8937, Ruis, Christopher ORCID: 0000-0003-0977-5534, Dellicour, Simon et al (show 32 more authors) , Baele, Guy ORCID: 0000-0002-1915-7732, Zarebski, Alexander E, Sadilek, Adam ORCID: 0000-0003-0784-7098, Wu, Neo, Schneider, Aaron, Ji, Xiang ORCID: 0000-0002-7243-0865, Raghwani, Jayna, Jackson, Ben ORCID: 0000-0002-9981-0649, Colquhoun, Rachel ORCID: 0000-0002-5577-9897, O'Toole, Áine, Peacock, Thomas P ORCID: 0000-0001-7077-2928, Twohig, Kate, Thelwall, Simon ORCID: 0000-0002-0434-2724, Dabrera, Gavin, Myers, Richard, COVID-19 Genomics UK (COG-UK) Consortium, , Faria, Nuno R ORCID: 0000-0002-9747-8822, Faria, Nuno R ORCID: 0000-0001-8839-2798, Huber, Carmen, Bogoch, Isaac I, Khan, Kamran, du Plessis, Louis ORCID: 0000-0003-0352-6289, Barrett, Jeffrey C, Aanensen, David M, Barclay, Wendy S ORCID: 0000-0002-3948-0895, Chand, Meera, Connor, Thomas ORCID: 0000-0003-2394-6504, Loman, Nicholas J, Suchard, Marc A ORCID: 0000-0001-9818-479X, Pybus, Oliver G ORCID: 0000-0002-8797-2667, Rambaut, Andrew ORCID: 0000-0003-4337-3707 and Kraemer, Moritz UG ORCID: 0000-0001-8838-7147 (2022) Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature, 610 (7930). pp. 154-160.

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Pascall, David J, Vink, Elen ORCID: 0000-0001-8535-6214, Blacow, Rachel, Bulteel, Naomi, Campbell, Alasdair, Campbell, Robyn, Clifford, Sarah, Davis, Chris, da Silva Filipe, Ana, El Sakka, Noha et al (show 28 more authors) , Fjodorova, Ludmila, Forrest, Ruth, Goldstein, Emily, Gunson, Rory, Haughney, John, Holden, Matthew TG ORCID: 0000-0002-4958-2166, Honour, Patrick, Hughes, Joseph, James, Edward, Lewis, Tim, MacLean, Oscar, McHugh, Martin, Mollett, Guy, Nyberg, Tommy, Onishi, Yusuke, Parcell, Ben, Ray, Surajit, Robertson, David L, Seaman, Shaun R, Shabaan, Sharif, Shepherd, James G, Smollett, Katherine, Templeton, Kate, Wastnedge, Elizabeth, Wilkie, Craig, Williams, Thomas, COVID-19 Genomics UK (COG-UK) Consortium, and Thomson, Emma C ORCID: 0000-0003-1482-0889 (2023) Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent. The Journal of infection, 87 (2). pp. 128-135.

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du Plessis, Louis ORCID: 0000-0003-0352-6289, McCrone, John T ORCID: 0000-0002-9846-8917, Zarebski, Alexander E ORCID: 0000-0003-1824-7653, Hill, Verity ORCID: 0000-0002-3509-8146, Ruis, Christopher ORCID: 0000-0003-0977-5534, Gutierrez, Bernardo ORCID: 0000-0002-9220-2739, Raghwani, Jayna ORCID: 0000-0001-8538-4995, Ashworth, Jordan ORCID: 0000-0003-1740-7475, Colquhoun, Rachel ORCID: 0000-0002-5577-9897, Connor, Thomas R ORCID: 0000-0003-2394-6504 et al (show 17 more authors) , Faria, Nuno R ORCID: 0000-0001-8839-2798, Jackson, Ben ORCID: 0000-0002-9981-0649, Loman, Nicholas J ORCID: 0000-0002-9843-8988, O'Toole, Áine ORCID: 0000-0001-8083-474X, Nicholls, Samuel M ORCID: 0000-0003-4081-065X, Parag, Kris V ORCID: 0000-0002-7806-3605, Scher, Emily ORCID: 0000-0002-5401-5879, Vasylyeva, Tetyana I, Volz, Erik M ORCID: 0000-0001-6268-8937, Watts, Alexander ORCID: 0000-0002-2675-3460, Bogoch, Isaac I, Khan, Kamran ORCID: 0000-0003-4367-960X, COVID-19 Genomics UK (COG-UK) Consortium, , Aanensen, David M ORCID: 0000-0001-6688-0854, Kraemer, Moritz UG ORCID: 0000-0001-8838-7147, Rambaut, Andrew ORCID: 0000-0003-4337-3707 and Pybus, Oliver G ORCID: 0000-0002-8797-2667 (2021) Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science (New York, N.Y.), 371 (6530). pp. 708-712.

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Davies, Nicholas G ORCID: 0000-0002-1740-1412, Abbott, Sam ORCID: 0000-0001-8057-8037, Barnard, Rosanna C ORCID: 0000-0001-7602-0401, Jarvis, Christopher I ORCID: 0000-0002-0812-2446, Kucharski, Adam J, Munday, James D ORCID: 0000-0002-6206-7134, Pearson, Carl AB ORCID: 0000-0003-0701-7860, Russell, Timothy W ORCID: 0000-0001-5610-6080, Tully, Damien C ORCID: 0000-0002-7620-9340, Washburne, Alex D ORCID: 0000-0003-4047-3411 et al (show 15 more authors) , Wenseleers, Tom ORCID: 0000-0002-1434-861X, Gimma, Amy, Waites, William ORCID: 0000-0002-7759-6805, Wong, Kerry LM ORCID: 0000-0002-4400-2257, van Zandvoort, Kevin ORCID: 0000-0002-7770-0537, Silverman, Justin D ORCID: 0000-0002-3063-2098, CMMID COVID-19 Working Group, , COVID-19 Genomics UK (COG-UK) Consortium, , Diaz-Ordaz, Karla ORCID: 0000-0003-3155-1561, Keogh, Ruth ORCID: 0000-0001-6504-3253, Eggo, Rosalind M ORCID: 0000-0002-0362-6717, Funk, Sebastian ORCID: 0000-0002-2842-3406, Jit, Mark ORCID: 0000-0001-6658-8255, Atkins, Katherine E ORCID: 0000-0001-5250-0558 and Edmunds, W John ORCID: 0000-0002-9179-2917 (2021) Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science (New York, N.Y.), 372 (6538). eabg3055-.

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Dong, Xiaofeng, Penrice-Randal, Rebekah ORCID: 0000-0002-0653-2097, Goldswain, Hannah, Prince, Tessa, Randle, Nadine, Salguero, Javier, Tree, Julia, Vamos, Ecaterina, Nelson, Charlotte, Stewart, James ORCID: 0000-0002-8928-2037 et al (show 10 more authors) , Semple, Malcolm ORCID: 0000-0001-9700-0418, Baillie, Kenneth, Openshaw, Peter, Turtle, Lance, Matthews, David, Carroll, Miles, Darby, Alistair ORCID: 0000-0002-3786-6209, Hiscox, Julian ORCID: 0000-0002-6582-0275, ISARIC4C Investigators, and COVID-19 Genomics UK (COG-UK) Consortium, (2021) Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans. bioRxiv. 2021.03.03.433753-.

Cotton, S, McHugh, MP, Dewar, R, Haas, JG, Templeton, K and COVID-19 Genomics UK (COG-UK) Consortium, (2023) Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. The Journal of hospital infection, 135. pp. 28-36.

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Blackstone, James, Stirrup, Oliver, Mapp, Fiona, Panca, Monica, Copas, Andrew, Flowers, Paul, Hockey, Leanne, Price, James, Partridge, David, Peters, Christine et al (show 6 more authors) , de Silva, Thushan, Nebbia, Gaia, Snell, Luke B, McComish, Rachel, COVID-19 Genomics UK (COG-UK) Consortium, and Breuer, Judith (2022) Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals. BMJ open, 12 (4). e052514-e052514.

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Brunner, Franziska S, Payne, Alexander, Cairns, Edward, Airey, George, Gregory, Richard, Pickwell, Natalie D, Wilson, Myles, Carlile, Matthew, Holmes, Nadine, Hill, Verity et al (show 14 more authors) , Child, Harry ORCID: 0000-0002-9127-2647, Tomlinson, Jasmine, Ahmed, Suhel, Denise, Hubert, Rowe, William, Frazer, Jacob, Aerle, Ronny van, Evens, Nicholas, Porter, Jonathan, COVID-19 Genomics UK (COG-UK) Consortium, , Templeton, Kate, Jeffries, Aaron R, Loose, Matt and Paterson, Steve ORCID: 0000-0002-1307-2981 (2023) Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England. Water research, 247. 120804-.

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Aggarwal, Dinesh, Myers, Richard, Hamilton, William L ORCID: 0000-0002-3330-353X, Bharucha, Tehmina, Tumelty, Niamh M ORCID: 0000-0002-9894-6034, Brown, Colin S ORCID: 0000-0003-4776-3403, Meader, Emma J, Connor, Tom ORCID: 0000-0003-2394-6504, Smith, Darren L ORCID: 0000-0003-4925-467X, Bradley, Declan T ORCID: 0000-0003-1468-1823 et al (show 11 more authors) , Robson, Samuel, Bashton, Matthew ORCID: 0000-0002-6847-1525, Shallcross, Laura ORCID: 0000-0003-1713-2555, Zambon, Maria, Goodfellow, Ian, Chand, Meera, O'Grady, Justin, Török, M Estée ORCID: 0000-0001-9098-8590, Peacock, Sharon J, Page, Andrew J and COVID-19 Genomics UK (COG-UK) Consortium, (2022) The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet. Microbe, 3 (2). e151-e158.