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  • 2021

    Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England

    Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., Hinsley, W. R., Laydon, D. J., Dabrera, G., O’Toole, Á., Amato, R., Ragonnet-Cronin, M., Harrison, I., Jackson, B., Ariani, C. V., Boyd, O., Loman, N. J., McCrone, J. T., Gonçalves, S., Jorgensen, D. & 35 others, Myers, R., Hill, V., Jackson, D. K., Gaythorpe, K., Groves, N., Sillitoe, J., Kwiatkowski, D. P., Koshy, C., Ash, A., Wise, E., Moore, N., Mori, M., Cortes, N., Lynch, J., Kidd, S., Fairley, D. J., Curran, T., McKenna, J. P., Adams, H., Fraser, C., The COVID-19 Genomics UK (COG-UK) Consortium, Smith, D. L., Bashton, M., Young, G. R., Nelson, A., McCann, C. M., Yew, W. C., Jones, H., Flaxman, S., Ratmann, O., Bhatt, S., Hopkins, S., Gandy, A., Rambaut, A. & Ferguson, N. M., 13 May 2021, In: Nature. 593, 7858, p. 266-269 4 p.

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    122 Citations (Scopus)
  • Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

    The COVID-19 Genomics UK (COG-UK) Consortium, 1 May 2021, In: The Lancet Public Health. 6, 5, p. e335-e345

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  • Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England

    The COVID-19 Genomics UK (COG-UK) Consortium, Mishra, S., Mindermann, S., Sharma, M., Whittaker, C., Mellan, T. A., Wilton, T., Klapsa, D., Mate, R., Fritzsche, M., Zambon, M., Ahuja, J., Howes, A., Miscouridou, X., Nason, G. P., Ratmann, O., Semenova, E., Leech, G., Sandkühler, J. F., Rogers-Smith, C. & 16 others, Vollmer, M., Unwin, H. J. T., Gal, Y., Chand, M., Gandy, A., Martin, J., Volz, E., Ferguson, N. M., Bhatt, S., Brauner, J. M., Flaxman, S., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 1 Sep 2021, In: EClinicalMedicine. 39, 9 p., 101064.

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    6 Citations (Scopus)
  • Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity

    The ISARIC4C Investigators, The COVID-19 Genomics UK (COG-UK) Consortium, Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., Davis, C., Piccoli, L., Pascall, D. J., Dillen, J., Lytras, S., Czudnochowski, N., Shah, R., Meury, M., Jesudason, N., De Marco, A., Li, K., Bassi, J. & 38 others, O'Toole, A., Pinto, D., Colquhoun, R. M., Culap, K., Jackson, B., Zatta, F., Rambaut, A., Jaconi, S., Sreenu, V. B., Nix, J., Zhang, I., Jarrett, R. F., Glass, W. G., Beltramello, M., Nomikou, K., Pizzuto, M., Tong, L., Cameroni, E., Croll, T. I., Johnson, N., Di Iulio, J., Wickenhagen, A., Ceschi, A., Harbison, A. M., Mair, D., Ferrari, P., Smollett, K., Sallusto, F., Carmichael, S., Garzoni, C., Nichols, J., Galli, M., Robertson, D. L., Snell, G., Bashton, M., Smith, D., Nelson, A. & Young, G., 4 Mar 2021, In: Cell. 184, 5, p. 1171-1187.e20

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    139 Citations (Scopus)
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  • CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

    The COVID-19 Genomics UK (COG-UK) Consortium, Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., Taylor, B., Colquhoun, R. M., Rowe, W. P. M., Jackson, B., Hill, V., O’Toole, Á., Rey, S., Southgate, J., Amato, R., Livett, R., Gonçalves, S., Harrison, E. M., Peacock, S. J. & 9 others, Aanensen, D. M., Rambaut, A., Connor, T. R., Loman, N. J., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., Dec 2021, In: Genome Biology. 22, 1, 21 p., 196.

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  • Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission

    The COVID-19 Genomics UK (COG-UK) Consortium, Snell, L. B., Fisher, C. L., Taj, U., Stirrup, O., Merrick, B., Alcolea-Medina, A., Charalampous, T., Signell, A. W., Wilson, H. D., Betancor, G., Kia Ik, M. T., Cunningham, E., Cliff, P. R., Pickering, S., Galao, R. P., Batra, R., Neil, S. J. D., Malim, M. H., Doores, K. J. & 9 others, Douthwaite, S. T., Nebbia, G., Edgeworth, J. D., Awan, A. R., Bashton, M., Nelson, A., McCann, C., Young, G. & Smith, D., 13 Aug 2021, (E-pub ahead of print) In: Clinical Microbiology and Infection.

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  • Detecting SARS-CoV-2 variants with SNP genotyping

    Harper, H., Burridge, A., Winfield, M., Finn, A., Davidson, A., Matthews, D., Hutchings, S., Vipond, B., Jain, N., The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J., Bashton, M., Loh, J., Nelson, A., Smith, D. L., Yew, W. C., Young, G. R., Edwards, K. & Barker, G., 24 Feb 2021, In: PLoS One. 16, 2, p. 1-12 12 p., e0243185.

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  • Detection of SARS-CoV-2 in respiratory samples from cats in the UK associated with human-to-cat transmission

    The COVID-19 Genomics UK (COG-UK) Consortium, Hosie, M. J., Epifano, I., Herder, V., Orton, R. J., Stevenson, A., Johnson, N., MacDonald, E., Dunbar, D., McDonald, M., Howie, F., Tennant, B., Herrity, D., Da Silva Filipe, A., Streicker, D. G., Willett, B. J., Murcia, P. R., Jarrett, R. F., Robertson, D. L., Weir, W. & 4 others, Bashton, M., Nelson, A., Smith, D. & Young, G., Apr 2021, In: Veterinary Record. 188, 8, p. 1-9 9 p., e247.

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    11 Citations (Scopus)
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  • Efficacy of ChAdOx1 nCoV-19 (AZD1222) vaccine against SARS-CoV-2 variant of concern 202012/01 (B.1.1.7): an exploratory analysis of a randomised controlled trial

    The COVID-19 Genomics UK (COG-UK) Consortium, the AMPHEUS Project, Oxford COVID-19 Vaccine Trial Group, Emary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., Blane, B., Bonsall, D., Cicconi, P., Charlton, S., Clutterbuck, E. A., Collins, A. M., Cox, T., Darton, T. C., Dold, C., Douglas, A. D., Duncan, C. J. A. & 37 others, Ewer, K. J., Flaxman, A. L., Faust, S. N., Ferreira, D. M., Feng, S., Finn, A., Folegatti, P. M., Fuskova, M., Galiza, E., Goodman, A. L., Green, C. M., Green, C. A., Greenland, M., Hallis, B., Heath, P. T., Hay, J., Hill, H. C., Jenkin, D., Kerridge, S., Lazarus, R., Libri, V., Lillie, P. J., Ludden, C., Marchevsky, N. G., Minassian, A. M., McGregor, A. C., Mujadidi, Y. F., Phillips, D. J., Plested, E., Pollock, K. M., Robinson, H., Smith, A., Song, R., Bashton, M., Nelson, A., Young, G. & Smith, D., 10 Apr 2021, In: The Lancet. 397, 10282, p. 1351-1362 12 p.

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    117 Citations (Scopus)
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  • Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

    The COVID-19 Genomics UK (COG-UK) Consortium, Du Plessis, L., Mccrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutierrez, B., Raghwani, J., Ashworth, J., Colquhoun, R., Connor, T. R., Faria, N. R., Jackson, B., Loman, N. J., O’toole, Á., Nicholls, S. M., Parag, K. V., Scher, E., Vasylyeva, T. I., Volz, E. M. & 11 others, Watts, A., Bogoch, I. I., Khan, K., Aanensen, D. M., Kraemer, M. U. G., Rambaut, A., Pybus, O. G., Bashton, M., Smith, D., Young, G. & Nelson, A., 12 Feb 2021, In: Science. 371, 6530, p. 708-712 6 p., eabf2946.

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    55 Citations (Scopus)
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  • Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England

    Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., Pearson, C. A. B., Russell, T. W., Tully, D. C., Washburne, A. D., Wenseleers, T., Gimma, A., Waites, W., Wong, K. L. M., van Zandvoort, K., Silverman, J. D., CMMID COVID-19 Working Group, The COVID-19 Genomics UK (COG-UK) Consortium, Diaz-Ordaz, K., Keogh, R. & 9 others, Eggo, R. M., Funk, S., Jit, M., Atkins, K. E., Edmunds, W. J., Bashton, M., Smith, D., Young, G. & Nelson, A., 9 Apr 2021, In: Science. 372, 6538, 16 p., eabg3055.

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    392 Citations (Scopus)
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  • Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

    The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Young, G. & Smith, D., 7 Jan 2021, In: Cell. 184, 1, p. 64-75.e11

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    227 Citations (Scopus)
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  • Evolution of viral variants in remdesivir‐treated and untreated SARS‐CoV‐2‐infected pediatrics patients

    Boshier, F. A. T., Pang, J., Penner, J., Parker, M., Alders, N., Bamford, A., Grandjean, L., Grunewald, S., Hatcher, J., Best, T., Dalton, C., Bynoe, P. D., Frauenfelder, C., Köeglmeier, J., Myerson, P., Roy, S., Williams, R., Silva, T. I., Goldstein, R. A., Breuer, J. & 8 others, The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J., Bashton, M., Loh, J., Nelson, A., Smith, D. L., Yew, W. C. & Young, G. R., 1 Jan 2022, In: Journal of Medical Virology. 94, 1, p. 161-172 12 p.

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  • Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant

    Elliott, P., Haw, D., Wang, H., Eales, O., Walters, C. E., Ainslie, K. E. C., Atchison, C., Fronterre, C., Diggle, P. J., Page, A. J., Trotter, A. J., Prosolek, S. J., The COVID-19 Genomics UK (COG-UK) Consortium, Ashby, D., Donnelly, C. A., Barclay, W., Taylor, G., Cooke, G., Ward, H., Darzi, A. & 30 others, Riley, S., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., Corden, S., Johnston, I., Bonsall, D., Smith, C. P., Bucca, G., Torok, M. E., Saeed, K., Prieto, J. A., Jackson, D. K., Hamilton, W. L., Snell, L. B., Moore, C., Harrison, E. M., Williams, R. J., Jones, H., Hartley, J. A., Williams, C., Smith, D. L., Bashton, M., Nelson, A., Young, G. R., McCann, C. M. & Yew, W. C., 2 Nov 2021, (E-pub ahead of print) In: Science. 15 p., abl9551.

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  • Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic

    Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., Haldenby, S., Hill, V., Lucaci, A., McCrone, J. T., Nicholls, S. M., O’toole, Á., Pacchiarini, N., Poplawski, R., Scher, E., Todd, F., Webster, H. J., Whitehead, M., Wierzbicki, C., The COVID-19 Genomics UK (COG-UK) Consortium & 10 others, Loman, N. J., Connor, T. R., Robertson, D. L., Pybus, O. G., Rambaut, A., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 30 Sep 2021, In: Cell. 184, 20, p. 5179-5188.e8 19 p.

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  • 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: SARS-CoV-2 variant changes protein and RNA level

    Leary, S., Gaudieri, S., Parker, M. D., Chopra, A., James, I., Pakala, S., Alves, E., John, M., Lindsey, B. B., Keeley, A. J., Rowland-Jones, S. L., Swanson, M. S., Ostrov, D. A., Bubenik, J. L., Das, S. R., Sidney, J., Sette, A., The COVID-19 Genomics UK (COG-UK) Consortium, De Silva, T., Phillips, E. & 7 others, Mallal, S., Smith, D., Bashton, M., Young, G., Nelson, A., McCann, C. & Yew, W., 20 Aug 2021, In: Pathogens and Immunity. 6, 2, p. 27-49 23 p.

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  • Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface

    The COVID-19 Genomics UK (COG-UK) Consortium, Li, K. K., Woo, Y. M., Stirrup, O., Hughes, J., Ho, A., Filipe, A. D. S., Johnson, N., Smollett, K., Mair, D., Carmichael, S., Tong, L., Nichols, J., Aranday-Cortes, E., Brunker, K., Parr, Y. A., Nomikou, K., McDonald, S. E., Niebel, M., Asamaphan, P. & 27 others, Sreenu, V. B., Robertson, D. L., Taggart, A., Jesudason, N., Shah, R., Shepherd, J., Singer, J., Taylor, A. H. M., Cousland, Z., Price, J., Lees, J. S., Jones, T. P. W., Lopez, C. V., MacLean, A., Starinskij, I., Gunson, R., Morris, S. T. W., Thomson, P. C., Geddes, C. C., Traynor, J. P., Breuer, J., Thomson, E. C., Mark, P. B., Bashton, M., Nelson, A., Smith, D. & Young, G., 1 Jul 2021, In: Journal of Infection. 83, 1, p. 96-103 8 p.

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  • Genomic epidemiology and the role of international and regional travel in the SARS-CoV-2 epidemic in Zimbabwe: a retrospective study of routinely collected surveillance data

    The COVID-19 Genomics UK (COG-UK) Consortium, SARS-CoV-2 Research Group, Mashe, T., Takawira, F. T., De Oliveira Martins, L., Gudza-Mugabe, M., Chirenda, J., Munyanyi, M., Chaibva, B. V., Tarupiwa, A., Gumbo, H., Juru, A., Nyagupe, C., Ruhanya, V., Phiri, I., Manangazira, P., Goredema, A., Danda, S., Chabata, I., Jonga, J. & 22 others, Munharira, R., Masunda, K., Mukeredzi, I., Mangwanya, D., Trotter, A., Le-Viet, T., Rudder, S., Kay, G., Baker, D., Thilliez, G., Gutierrez, A. V., O'Grady, J., Hove, M., Mutapuri-Zinyowera, S., Page, A. J., Kingsley, R. A., Mhlanga, G., Bashton, M., Nelson, A., McCann, C., Smith, D. & Young, G., 1 Dec 2021, In: The Lancet Global Health. 9, 12, p. e1658-e1666 9 p.

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  • Genomic epidemiology of covid-19 in care homes in the east of England

    Hamilton, W. L., Tonkin-Hill, G., Smith, E. R., Aggarwal, D., Houldcroft, C. J., Warne, B., Meredith, L. W., Hosmillo, M., Jahun, A. S., Curran, M. D., Parmar, S., Caller, L. G., Caddy, S. L., Khokhar, F. A., Yakovleva, A., Hall, G., Feltwell, T., Pinckert, M. L., Georgana, I., Chaudhry, Y. & 25 others, Brown, C. S., Gonçalves, S., Amato, R., Harrison, E. M., Brown, N. M., Beale, M. A., Chapman, M. S., Jackson, D. K., Johnston, I., Alderton, A., Sillitoe, J., Langford, C., Dougan, G., Peacock, S. J., Kwiatowski, D. P., Goodfellow, I. G., Estee Torok, M., The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J., Bashton, M., Loh, J., Nelson, A., Smith, D. L., Yew, W. C. & Young, G. R., 2 Sep 2021, In: eLife. 10, p. 1-31 31 p., e64618.

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  • Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

    The COVID-19 Genomics UK (COG-UK) Consortium, Aggarwal, D., Warne, B., Jahun, A., Hamilton, W., Fieldman, T., Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Goodfellow, Y., Pinckert, M., Georgana, I., Izuagbe, R., Leek, D. & 25 others, Nsonwu, O., Hughes, G., Packer, S., Page, A., Metaxaki, M., Fuller, S., Weale, G., Holgate, J., Howes, R., McFarlane, D., Dougan, G., Pybus, O., Angelis, D. D., Maxwell, P., Peacock, S., Weekes, M., Illingworth, C., Harrison, E., Matheson, N., Goodfellow, I. G., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 19 May 2021, (Submitted) 25 p.

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  • Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland

    The COVID-19 Genomics UK (COG-UK) Consortium, da Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., Ashraf, S., Balcazar, C., Brunker, K., Campbell, A., Carmichael, S., Davis, C., Dewar, R., Gallagher, M. D., Gunson, R., Hill, V., Ho, A., Jackson, B., James, E. & 35 others, Jesudason, N., Johnson, N., McWilliam Leitch, E. C., Li, K., MacLean, A., Mair, D., McAllister, D. A., McCrone, J. T., McDonald, S. E., McHugh, M. P., Morris, A. K., Nichols, J., Niebel, M., Nomikou, K., Orton, R. J., O’Toole, Á., Palmarini, M., Parcell, B. J., Parr, Y. A., Rambaut, A., Rooke, S., Shaaban, S., Shah, R., Singer, J. B., Smollett, K., Starinskij, I., Tong, L., Sreenu, V. B., Wastnedge, E., Holden, M. T. G., Robertson, D. L., Bashton, M., Nelson, A., Smith, D. & Young, G., 1 Jan 2021, In: Nature Microbiology. 6, 1, p. 112-122 11 p.

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  • Genomic reconstruction of the SARS-CoV-2 epidemic in England

    The Wellcome Sanger Institute Covid-19 Surveillance Team, The COVID-19 Genomics UK (COG-UK) Consortium, Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, V. T. T., Goater, R., Schwach, F., Harrison, I., Hellewell, J., Ariani, C. V., Gonçalves, S., Jackson, D. K., Johnston, I., Jung, A. W., Saint, C., Sillitoe, J., Suciu, M., Goldman, N. & 14 others, Panovska-Griffiths, J., Birney, E., Volz, E., Funk, S., Kwiatkowski, D. P., Chand, M., Martincorena, I., Barrett, J. C., Gerstung, M., Bashton, M., Nelson, A., McCann, C., Smith, D. & Young, G., 14 Oct 2021, (E-pub ahead of print) In: Nature.

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  • Lactoferrin impact on gut microbiota in preterm infants with late-onset sepsis or necrotising enterocolitis: the MAGPIE mechanisms of action study

    Embleton, N., Berrington, J., Cummings, S., Dorling, J., Ewer, A., Frau, A., Juszczak, E., Kirby, J., Lamb, C., Lanyon, C., Lett, L., McGuire, W., Probert, C., Rushton, S., Shirley, M., Stewart, C. & Young, G. R., 28 Sep 2021, In: Efficacy and Mechanism Evaluation. 8, 14, p. 1-88 88 p.

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  • Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management

    Page, A. J., Mather, A. E., Le-Viet, T., Meader, E. J., Alikhan, N. F., Kay, G. L., De Oliveira Martins, L., Aydin, A., Baker, D. J., Trotter, A. J., Rudder, S., Tedim, A. P., Kolyva, A., Stanley, R., Yasir, M., Diaz, M., Potter, W., Stuart Meadows, C., Bell, A., Gutierrez, A. V. & 27 others, Nicholas, N. M., Adriaenssens, E. M., Swingler, T., Gilroy, R. A. J., Griffith, L., Sethi, D. K., Aggarwal, D., Brown, C. S., Davidson, R. K., Kingsley, R. A., Bedford, L., Coupland, L. J., Charles, I. G., Elumogo, N., Wain, J., Prakash, R., Webber, M. A., Louise Smith, S. J., Chand, M., Dervisevic, S., O’Grady, J., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 29 Jun 2021, In: Microbial genomics. 7, 6, p. 1-15 15 p., 000589.

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  • Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward

    Wenlock, R. D., Tausan, M., Mann, R., Garr, W., Preston, R., Arnold, A., Hoban, J., Webb, L., Quick, C., Beckett, A., Loveson, K., Glaysher, S., Elliott, S., Malone, C., Cogger, B., Easton, L., The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J., Bashton, M., Loh, J. & 7 others, Nelson, A., Smith, D. L., Yew, W. C., Young, G., Robson, S. C., Hassan-ibrahim, M. O. & Sargent, C., 1 Sep 2021, In: Infection Prevention in Practice. 3, 3, 7 p., 100165.

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  • Patterns of within-host genetic diversity in SARS-CoV-2

    Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, A. RJ., Gerstung, M., Johnston, I., Jackson, D. K., Park, N., Lensing, S. V., Quail, M. A., Gonçalves, S., Ariani, C., Spencer Chapman, M., Hamilton, W. L., Meredith, L. W., Hall, G., Jahun, A. S., Chaudhry, Y., Hosmillo, M., Pinckert, M. L. & 25 others, Georgana, I., Yakovleva, A., Caller, L. G., Caddy, S. L., Feltwell, T., Khokhar, F. A., Houldcroft, C. J., Curran, M. D., Parmar, S., The COVID-19 Genomics UK (COG-UK) Consortium, Alderton, A., Nelson, R., Harrison, E. M., Sillitoe, J., Bentley, S. D., Barrett, J. C., Torok, M. E., Goodfellow, I. G., Langford, C., Kwiatkowski, D., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 13 Aug 2021, In: eLife. 10, 25 p.

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  • Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

    The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 29 Jun 2021, In: eLife. 10, 30 p.

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  • Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7

    Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., Harvey, W. T., Lytras, S., Mohamed, A., Gallo, G., Thakur, N., Collier, D. A., Mlcochova, P., The COVID-19 Genomics UK (COG-UK) Consortium, Duncan, L. M., Carabelli, A. M., Kenyon, J. C., Lever, A. M., De Marco, A., Saliba, C. & 31 others, Culap, K., Cameroni, E., Matheson, N. J., Piccoli, L., Corti, D., James, L. C., Robertson, D. L., Bailey, D., Gupta, R. K., Robson, S. C., Loman, N. J., Connor, T. R., Golubchik, T., Martinez Nunez, R. T., Ludden, C., Corden, S., Johnston, I., Bonsall, D., Smith, C. P., Awan, A. R., Bucca, G., Torok, M. E., Saeed, K., Prieto, J. A., Jackson, D. K., Smith, D. L., Bashton, M., Nelson, A., Young, G. R., Mccann, C. M. & Yew, W. C., 29 Jun 2021, In: Cell Reports. 35, 13, 24 p., 109292.

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  • Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV- 2 in the United Kingdom

    Chappell, J. G., Tsoleridis, T., Clark, G., Berry, L., Holmes, N., Moore, C., Carlile, M., Sang, F., Debebe, B. J., Wright, V., Irving, W. L., Thomson, B. J., Boswell, T. C. J., Willingham, I., Joseph, A., Smith, W., Khakh, M., Fleming, V. M., Lister, M. M., Howson-Wells, H. C. & 10 others, Holmes, E. C., Loose, M. W., Ball, J. K., Patrick McClure, C., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 16 Jun 2021, In: Journal of General Virology. 102, 6, p. 1-11 11 p., 001595.

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    1 Citation (Scopus)
  • SARS-CoV-2 evolution during treatment of chronic infection

    The CITIID-NIHR BioResource COVID-19 Collaboration, The COVID-19 Genomics UK (COG-UK) Consortium, Kemp, S. A., Bashton, M., Nelson, A., Young, G. & Smith, D., 8 Apr 2021, In: Nature. 592, 7853, p. 277-282 26 p.

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    170 Citations (Scopus)
  • SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: Multicentre cohort study

    The COVID-19 Genomics UK (COG-UK) Consortium, Stirrup, O., Bashton, M., Nelson, A., McCann, C., Young, G. & Smith, D., 20 Sep 2021, In: BMJ Open Respiratory Research. 8, 1, 10 p., e001029.

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  • SARS-CoV-2 variants, spike mutations and immune escape

    Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., Ludden, C., Reeve, R., Rambaut, A., Peacock, S. J., Robertson, D. L., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 1 Jul 2021, In: Nature Reviews Microbiology. 19, 7, p. 409-424 16 p.

    Research output: Contribution to journalReview articlepeer-review

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    107 Citations (Scopus)
  • SARS-CoV-2 within-host diversity and transmission

    Oxford Virus Sequencing Analysis Group (OVSG), The COVID-19 Genomics UK (COG-UK) Consortium, Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., Andersson, M., Otecko, N., Wise, E. L., Moore, N., Lynch, J., Kidd, S., Cortes, N., Mori, M., Williams, R., Vernet, G., Justice, A., Green, A. & 22 others, Nicholls, S. M., Ansari, M. A., Abeler-Dörner, L., Moore, C. E., Peto, T. E. A., Eyre, D. W., Shaw, R., Simmonds, P., Buck, D., Todd, J. A., Connor, T. R., Ashraf, S., da Silva Filipe, A., Shepherd, J., Thomson, E. C., Bonsall, D., Fraser, C., Golubchik, T., Bashton, M., Nelson, A., Smith, D. & Young, G., 16 Apr 2021, In: Science. 372, 6539, 12 p., eabg0821.

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    9 Citations (Scopus)
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  • Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies

    The CITIID-NIHR BioResource COVID-19 Collaboration, The COVID-19 Genomics UK (COG-UK) Consortium, Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R., Walls, A. C., Kemp S, S. A., Bassi, J., Pinto, D., Fregni, C. S., Bianchi, S., Tortorici, M. A., Bowen, J., Culap, K., Jaconi, S., Cameroni, E., Snell, G., Pizzuto, M. S. & 26 others, Pellanda, A. F., Garzoni, C., Riva, A., Elmer, A., Kingston, N., Graves, B., McCoy, L. E., Smith, K. G. C., Bradley, J. R., Temperton, N., Lourdes Ceron-Gutierrez, L., Barcenas-Morales, G., Harvey, W., Virgin, H. W., Lanzavecchia, A., Piccoli, L., Doffinger, R., Wills, M., Veesler, D., Corti, D., Gupta, R. K., Bashton, M., Young, G., McCann, C., Nelson, A. & Smith, D., 6 May 2021, In: Nature. 593, 7857, p. 136-141 6 p.

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    141 Citations (Scopus)
  • Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence

    Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., Baele, G., Parag, K. V., Battle, A. L., Gutierrez, B., Jackson, B., Colquhoun, R. M., O'Toole, Á., Klein, B., Vespignani, A., Volz, E., Faria, N. R., Aanensen, D., Loman, N. J., Du Plessis, L. & 10 others, Cauchemez, S., Rambaut, A., Scarpino, S. V., Pybus, O. G., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Nelson, A., Young, G., Smith, D. & McCann, C., 20 Aug 2021, In: Science. 373, 6557, p. 889-895 7 p., eabj0113.

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  • Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data

    The COVID-19 Genomics UK (COG-UK) Consortium, Parker, M. D., Lindsey, B. B., Leary, S., Gaudieri, S., Chopra, A., Wyles, M., Angyal, A., Green, L. R., Parsons, P., Tucker, R. M., Brown, R., Groves, D., Johnson, K., Carrilero, L., Heffer, J., Partridge, D. G., Evans, C., Raza, M., Keeley, A. J. & 21 others, Smith, N., Filipe, A. D. S., Shepherd, J. G., Davis, C., Bennett, S., Sreenu, V. B., Kohl, A., Aranday-Cortes, E., Tong, L., Nichols, J., Thomson, E. C., Wang, D., Mallal, S., de Silva, T. I., Bashton, M., Young, G., Allan, J., Loh, J., Nelson, A., Smith, D. & Yew, W., 1 Apr 2021, In: Genome Research. 31, 4, p. 645-658 14 p.

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    5 Citations (Scopus)
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  • The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study

    COG-UK HOCI Variant Substudy Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Boshier, F. A. T., Venturini, C., Stirrup, O., Guerra-Assunção, J. A., Alcolea-Medina, A., Becket, A. H., Byott, M., Charalampous, T., Filipe, A. D. S., Frampton, D., Glaysher, S., Khan, T., Kulasegara-Shylini, R., Kele, B., Monahan, I. M., Mollett, G., Parker, M., Pelosi, E. & 32 others, Randell, P., Roy, S., Taylor, J. F., Weller, S. J., Wilson-Davies, E., Wade, P., Williams, R., Copas, A. J., Cutino-Moguel, T., Freemantle, N., Hayward, A. C., Holmes, A., Hughes, J., Mahungu, T. W., Nebbia, G., Nastouli, E., Partridge, D. G., Pope, C. F., Price, J. R., Robson, S. C., Saeed, K., Shin, G. Y., de Silva, T. I., Snell, L. B., Thomson, E. C., Witney, A. A., Breuer, J., Bashton, M., Nelson, A., McCann, C., Smith, D. & Young, G., 2 Oct 2021, (E-pub ahead of print) In: Journal of Infection. p. 1-8 8 p.

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  • The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages

    NGS-SA, The COVID-19 Genomics UK (COG-UK) Consortium, Martin, D. P., Weaver, S., Tegally, H., San, J. E., Shank, S. D., Wilkinson, E., Lucaci, A. G., Giandhari, J., Naidoo, S., Pillay, Y., Singh, L., Lessells, R. J., Gupta, R. K., Wertheim, J. O., Nekturenko, A., Murrell, B., Harkins, G. W., Lemey, P. & 9 others, MacLean, O. A., Robertson, D. L., de Oliveira, T., Kosakovsky Pond, S. L., Bashton, M., Nelson, A., McCann, C., Young, G. & Smith, D., 30 Sep 2021, In: Cell. 184, 20, p. 5189-5200.e7 20 p.

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    2 Citations (Scopus)
  • The impact of viral mutations on recognition by SARS-CoV-2 specific T cells

    The COVID-19 Genomics UK (COG-UK) Consortium, ISARIC4C Investigators, de Silva, T. I., Liu, G., Lindsey, B. B., Dong, D., Moore, S. C., Hsu, N. S., Shah, D., Wellington, D., Mentzer, A. J., Angyal, A., Brown, R., Parker, M. D., Ying, Z., Yao, X., Turtle, L., Dunachie, S., Bashton, M., McCann, C. M. & 4 others, Nelson, A., Smith, D. L., Yew, W. C. & Young, G. R., 19 Nov 2021, In: iScience. 24, 11, 16 p., 103353.

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  • The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities

    Aggarwal, D., Myers, R., Hamilton, W. L., Bharucha, T., Tumelty, N. M., Brown, C. S., Meader, E. J., Connor, T., Smith, D. L., Bradley, D. T., Robson, S., Bashton, M., Shallcross, L., Zambon, M., Goodfellow, I., Chand, M., O'Grady, J., Török, M. E., Peacock, S. J., Page, A. J. & 6 others, The COVID-19 Genomics UK (COG-UK) Consortium, Allan, J., Loh, J., Nelson, A., Yew, W. C. & Young, G. R., 29 Sep 2021, (E-pub ahead of print) In: The Lancet Microbe. p. 1-9 9 p.

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  • The Stool Volatile Metabolome of Pre-Term Babies

    Frau, A., Lett, L., Slater, R., Young, G. R., Stewart, C. J., Berrington, J., Hughes, D. M., Embleton, N. & Probert, C., 2 Jun 2021, In: Molecules. 26, 11, 11 p., e3341.

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  • Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2

    The COVID-19 Genomics UK (COG-UK) Consortium, O'Toole, Á., Kraemer, M. U. G., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., Messina, J. P., Tegally, H., Lessells, R. R., Giandhari, J., Pillay, S., Tumedi, K. A., Nyepetsi, G., Kebabonye, M., Matsheka, M., Mine, M., Tokajian, S., Hassan, H. & 36 others, Salloum, T., Merhi, G., Koweyes, J., Geoghegan, J. L., de Ligt, J., Ren, X., Storey, M., Freed, N. E., Pattabiraman, C., Prasad, P., Desai, A. S., Vasanthapuram, R., Schulz, T. F., Steinbrück, L., Stadler, T., Parisi, A., Bianco, A., García de Viedma, D., Buenestado-Serrano, S., Borges, V., Isidro, J., Duarte, S., Gomes, J. P., Zuckerman, N. S., Mandelboim, M., Mor, O., Seemann, T., Arnott, A., Draper, J., Gall, M., Rawlinson, W., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 19 May 2021, In: Wellcome Open Research. 6, p. 1-14 14 p., 121.

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    18 Citations (Scopus)
  • 2020

    Acquisition and Development of the Extremely Preterm Infant Microbiota Across Multiple Anatomical Sites

    Young, G. R., van der Gast, C. J., Smith, D. L., Berrington, J. E., Embleton, N. D. & Lanyon, C., 1 Jan 2020, In: Journal of Pediatric Gastroenterology and Nutrition. 70, 1, p. 12-19 8 p.

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    1 Citation (Scopus)
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  • Changes in the gut microbiota of mice orally exposed to methylimidazolium ionic liquids

    Young, G. R., Abdelghany, T. M., Leitch, A. C., Dunn, M. P., Blain, P. G., Lanyon, C. & Wright, M. C., 12 Mar 2020, In: PLoS One. 15, 3, e0229745.

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    5 Citations (Scopus)
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  • Human milk oligosaccharide DSLNT and gut microbiome in preterm infants predicts necrotising enterocolitis

    Masi, A. C., Embleton, N. D., Lamb, C. A., Young, G., Granger, C. L., Najera, J., Smith, D. P., Hoffman, K. L., Petrosino, J. F., Bode, L., Berrington, J. E. & Stewart, C. J., 16 Dec 2020, (E-pub ahead of print) In: Gut. p. gutjnl-2020-322771 322771.

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    14 Citations (Scopus)
    36 Downloads (Pure)
  • 2017

    Development of the neonatal microbiota

    Young, G., Zalewski, S., Cummings, S. & Lanyon, C., 20 Jul 2017, Microbiota in health and disease: from pregnancy to childhood. Browne, P. D., Claassen, E. & Cabana, M. D. (eds.). Wageningen: Wageningen Academic Publishers, p. 39-56 344 p.

    Research output: Chapter in Book/Report/Conference proceedingChapter

  • Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis

    Young, G., Smith, D., Embleton, N., Berrington, J., Schwalbe, E., Cummings, S., van der Gast, C. & Lanyon, C., 6 Jun 2017, In: Frontiers in cellular and infection microbiology. 7, 237.

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    24 Citations (Scopus)
    7 Downloads (Pure)
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