Clare McCann

Search results

• 2024

  Lineage frequency time series reveal elevated levels of genetic drift in SARS-CoV-2 transmission in England

  The COVID-19 Genomics UK (COG-UK) Consortium, Yu, Q., Ascensao, J. A., Okada, T., Boyd, O., Volz, E., Hallatschek, O., Bashton, M., Smith, D., Nelson, A. & McCann, C., 15 Apr 2024, In: PLoS Pathogens. 20, 4, 37 p., e1012090.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  1 Citation (Scopus)

  1 Downloads (Pure)

• Prevalence of persistent SARS-CoV-2 in a large community surveillance study

  Ghafari, M., Hall, M., Golubchik, T., Ayoubkhani, D., House, T., MacIntyre-Cockett, G., Fryer, H. R., Thomson, L., Nurtay, A., Kemp, S. A., Ferretti, L., Buck, D., Green, A., Trebes, A., Lonie, L. J., Piazza, P., Studley, R., Rourke, E., Smith, D. L., Bashton, M., & 16 othersNelson, A., Crown, M., McCann, C., Young, G. R., Santos, R. A. N. D., Richards, Z., Tariq, M. A., Cahuantzi, R., Wellcome Sanger Institute COVID-19 Surveillance Team, COVID-19 Infection Survey Group, The COVID-19 Genomics UK (COG-UK) Consortium, Barrett, J., Fraser, C., Bonsall, D., Walker, A. S. & Lythgoe, K., 29 Feb 2024, In: Nature. 626, 8001, p. 1094-1101 25 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  29 Citations (Scopus)

  25 Downloads (Pure)

• Spatial and temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of socio-economic deprivation, weather, and lockdown on lineage dynamics

  Moss, E. D., Rushton, S. P., Baker, P., Bashton, M., Crown, M. R., Dos Santos, R. N., Nelson, A., O’Brien, S. J., Richards, Z., Sanderson, R. A., Yew, W. C., Young, G. R., McCann, C. M. & Smith, D. L., 4 Sept 2024, In: Peer Community Journal. 4, p. 1-22 22 p., e84.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  7 Downloads (Pure)
• 2023

  Does pre-enrichment of anodes with acetate to select for Geobacter spp. enhance performance of microbial fuel cells when switched to more complex substrates?

  Christgen, B., Spurr, M., Milner, E. M., Izadi, P., McCann, C., Yu, E. H., Curtis, T., Scott, K. & Head, I. M., 23 Nov 2023, In: Frontiers in Microbiology. 14, 12 p., 1199286.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  2 Citations (Scopus)

  29 Downloads (Pure)

• Investigating Variability in Microbial Fuel Cells

  Leicester, D. D., Settle, S., McCann, C. M. & Heidrich, E. S., 29 Mar 2023, In: Applied and Environmental Microbiology. 89, 3, p. 1-17 17 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  5 Citations (Scopus)

  27 Downloads (Pure)

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

  Cotton, S., McHugh, M. P., Dewar, R., Haas, J. G., Templeton, K., The COVID-19 Genomics UK (COG-UK) Consortium, Robson, S. C., Connor, T. R., Loman, N. J., Golubchik, T., Martinez Nunez, R. T., Bonsall, D., Rambaut, A., Snell, L. B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., & 31 othersPrieto, J. A., Saeed, K., Jackson, D. K., Houlihan, C., Frampton, D., Hamilton, W. L., Witney, A. A., Bucca, G., Pope, C. F., Moore, C., Thomson, E. C., Cutino-Moguel, T., Harrison, E. M., Smith, C. P., Rogan, F., Beckwith, S. M., Murray, A., Singleton, D., Eastick, K., Sheridan, L. A., Randell, P., Jackson, L. M., Ariani, C. V., Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., Henderson, J. H. & Yew, W. C., 1 May 2023, In: Journal of Hospital Infection. 135, p. 28-36 9 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  2 Citations (Scopus)

  22 Downloads (Pure)

• Lineage replacement and evolution captured by 3 years of the United Kingdom Coronavirus (COVID-19) Infection Survey

  Wellcome Sanger Institute COVID-19 Surveillance Team, Lythgoe, K. A., Golubchik, T., Hall, M., House, T., Cahuantzi, R., MacIntyre-Cockett, G., Fryer, H., Thomson, L., Nurtay, A., Ghafani, M., Buck, D., Green, A., Trebes, A., Piazza, P., Lonie, L. J., Studley, R., Rourke, E., Smith, D., Bashton, M., & 12 othersNelson, A., Crown, M., McCann, C., Young, G. R., Andre Nunes Dos Santos, R., Richards, Z., Tariq, A., Fraser, C., Diamond, I., Barrett, J., Walker, A. S. & Bonsall, D., 25 Oct 2023, In: Proceedings of the Royal Society B: Biological Sciences. 290, 2009, 10 p., 20231284.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  8 Citations (Scopus)

  13 Downloads (Pure)

• Multiple pathways of SARS-CoV-2 nosocomial transmission uncovered by integrated genomic and epidemiological analyses during the second wave of the COVID-19 pandemic in the UK

  Cook, K. F., Beckett, A. H., Glaysher, S., Goudarzi, S., Fearn, C., Loveson, K. F., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K., Lumley, S., Chauhan, A. J., Robson, S. C., The COVID-19 Genomics UK (COG-UK) Consortium, Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., & 4 othersHenderson, J. H., Hollis, A., Stanley, W. & Yew, W. C., 20 Jan 2023, In: Frontiers in cellular and infection microbiology. 12, p. 1-20 20 p., 1066390.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Patient 100%
  • Hospital 37%
  • Infection 37%
  • Severe Acute Respiratory Syndrome Coronavirus 2 37%
  • COVID-19 37%
  4 Citations (Scopus)

  18 Downloads (Pure)

• Utility of wastewater genomic surveillance compared to clinical surveillance to track the spread of the SARS-CoV-2 Omicron variant across England

  The COVID-19 Genomics UK (COG-UK) Consortium, Brunner, F. S., Payne, A., Cairns, E., Airey, G., Gregory, R., Pickwell, N. D., Wilson, M., Carlile, M., Holmes, N., Hill, V., Child, H., Tomlinson, J., Ahmed, S., Denise, H., Rowe, W., Frazer, J., Aerle, R. V., Evens, N., Porter, J., & 8 othersTempleton, K., Jeffries, A. R., Loose, M., Paterson, S., Bashton, M., Smith, D., Nelson, A. & McCann, C., 1 Dec 2023, In: Water Research. 247, 10 p., 120804.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  5 Citations (Scopus)

• 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

  The COVID-19 Genomics UK (COG-UK) Consortium, Fryer, H. R., Golubchik, T., Hall, M., Fraser, C., Hinch, R., Ferretti, L., Thomson, L., Nurtay, A., Pellis, L., House, T., MacIntyre-Cockett, G., Trebes, A., Buck, D., Piazza, P., Green, A., Lonie, L. J., Smith, D., Bashton, M., Crown, M., & 14 othersNelson, A., McCann, C. M., Tariq, M., Elstob, C., Nunes Dos Santos, R., Richards, Z., Xhang, X., Hawley, J., Lee, M. R., Carrillo-Barragan, P., Chapman, I., Harthern-Flint, S., Bonsall, D. & Lythgoe, K. A., 14 Aug 2023, In: PLoS Pathogens. 19, 8, e1011461.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  4 Citations (Scopus)

  35 Downloads (Pure)
• 2022

  Assessment of mortality and hospital admissions associated with confirmed infection with SARS-CoV-2 Alpha variant: a matched cohort and time-to-event analysis, England, October to December 2020

  COG-UK Consortium, Dabrera, G., Allen, H., Zaidi, A., Flannagan, J., Twohig, K., Thelwall, S., Marchant, E., Aziz, N. A., Lamagni, T., Myers, R., Charlett, A., Capelastegui, F., Chudasama, D., Clare, T., Coukan, F., Sinnathamby, M., Ferguson, N., Hopkins, S., Chand, M., & 7 othersHope, R., Kall, M., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 19 May 2022, In: Eurosurveillance. 27, 20, 11 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Infection 100%
  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Wild Type 100%
  • SARS Coronavirus 100%
  • Mortality 80%
  8 Citations (Scopus)

  16 Downloads (Pure)

• Bioavailability of potentially toxic elements influences antibiotic resistance gene and mobile genetic element abundances in urban and rural soils

  Robins, K., McCann, C. M., Zhou, X-Y., Su, J-Q., Cooke, M., Knapp, C. W. & Graham, D. W., 15 Nov 2022, In: The Science of the Total Environment. 847, 11 p., 157512.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Nested Gene 100%
  • Gene 100%
  • Antibiotic Resistance 71%
  • Antimicrobial Resistance 71%
  • Mobile Genetic Elements 21%
  10 Citations (Scopus)

  27 Downloads (Pure)

• City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants

  The COVID-19 Genomics UK (COG-UK) Consortium, Brunner, F. S., Brown, M. R., Bassano, I., Denise, H., Khalifa, M. S., Wade, M. J., van Aerle, R., Kevill, J. L., Jones, D. L., Farkas, K., Jeffries, A. R., Cairns, E., Wierzbicki, C., Paterson, S., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 1 Nov 2022, In: Water Research. 226, 9 p., 119306.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Waste Water 100%
  • Severe Acute Respiratory Syndrome Coronavirus 2 75%
  • Surveillance 62%
  • Genomics 50%
  • Metropolitan Area 37%
  19 Citations (Scopus)

  53 Downloads (Pure)

• 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 othersDouthwaite, S. T., Nebbia, G., Edgeworth, J. D., Awan, A. R., Bashton, M., Nelson, A., McCann, C., Young, G. & Smith, D., 1 Jan 2022, In: Clinical Microbiology and Infection. 28, 1, p. 93-100 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Polymerase Chain Reaction 37%
  • Analysis 25%
  • COVID-19 25%
  • Patient 25%
  18 Citations (Scopus)

• Comparative analysis of the risks of hospitalisation and death associated with SARS-CoV-2 omicron (B.1.1.529) and delta (B.1.617.2) variants in England: a cohort study

  The COVID-19 Genomics UK (COG-UK) Consortium, Nyberg, T., Ferguson, N. M., Nash, S. G., Webster, H. H., Flaxman, S., Andrews, N., Hinsley, W., Bernal, J. L., Kall, M., Bhatt, S., Blomquist, P., Zaidi, A., Volz, E., Aziz, N. A., Harman, K., Funk, S., Abbott, S., Lopez Bernal, J., Abdul Aziz, N., & 14 othersHope, R., Charlett, A., Chand, M., Ghani, A. C., Seaman, S. R., Dabrera, G., De Angelis, D., Presanis, A. M., Thelwall, S., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 2 Apr 2022, In: The Lancet. 399, 10332, p. 1303-1312 10 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Infection 100%
  • Hazard Ratio 100%
  • Death 90%
  • Protection 80%
  • Vaccine Efficacy 70%
  852 Citations (Scopus)

  28 Downloads (Pure)

• Context-specific emergence and growth of the SARS-CoV-2 Delta variant

  The COVID-19 Genomics UK (COG-UK) Consortium, McCrone, J. T., Hill, V., Bajaj, S., Pena, R. E., Lambert, B. C., Inward, R., Bhatt, S., Volz, E., Ruis, C., Dellicour, S., Baele, G., Zarebski, A. E., Sadilek, A., Wu, N., Schneider, A., Ji, X., Raghwani, J., Jackson, B., Colquhoun, R., & 26 othersO'Toole, Á., Peacock, T. P., Twohig, K., Thelwall, S., Dabrera, G., Myers, R., Faria, N. R., Huber, C., Bogoch, I. I., Khan, K., du Plessis, L., Barrett, J. C., Aanensen, D. M., Barclay, W. S., Chand, M., Connor, T., Loman, N. J., Suchard, M. A., Pybus, O. G., Rambaut, A., Kraemer, M. U. G., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 6 Oct 2022, In: Nature. 610, 7930, p. 154-160 7 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • UK 100%
  • Intervention 50%
  • Emergence 50%
  • Travel 50%
  • Introduction 33%
  50 Citations (Scopus)

  14 Downloads (Pure)

• COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study

  The COVID-19 Genomics UK (COG-UK) Consortium, Kläser, K., Molteni, E., Graham, M., Canas, L. S., Österdahl, M. F., Antonelli, M., Chen, L., Deng, J., Murray, B., Kerfoot, E., Wolf, J., May, A., Fox, B., Capdevila, J., Aanensen, D. M., Abudahab, K., Adams, H., Adams, A., Afifi, S., & 33 othersAggarwal, D., Ahmad, S. S. Y., Aigrain, L., Alcolea-Medina, A., Alikhan, N. F., Allara, E., Amato, R., Angyal, A., Annett, T., Aplin, S., Ariani, C. V., Asad, H., Ash, A., Ashfield, P., Ashford, F., Atkinson, L., Attwood, S. W., Auckland, C., Aydin, A., Baker, D. J., Baker, P., Bashton, M., Crown, M., Hartley, J. A., Henderson, J. H., Jones, H., McCann, C. M., Nelson, A., Smith, D. L., Yew, W. C., Young, G. R., Hollis, A. & Stanley, W., 1 Dec 2022, In: Scientific Reports. 12, 1, 17 p., 10904.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Symptom 100%
  • Diseases 66%
  • Infection 66%
  • Severe Acute Respiratory Syndrome Coronavirus 2 50%
  • SARS Coronavirus 50%
  41 Citations (Scopus)

  17 Downloads (Pure)

• Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: multicenter, prospective study

  The COVID-19 Genomics UK (COG-UK) Consortium, Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., Machin, N., Shin, G. Y., Mahungu, T. W., Saeed, K., Saluja, T., Taha, Y., Mahida, N., Pope, C. F., Chawla, A., Cutino-Moguel, M. T., Tamuri, A., Williams, R., Darby, A., & 32 othersRobertson, D. L., Flaviani, F., Nastouli, E., Robson, S., Smith, D., Laing, K., Monahan, I. M., Kele, B., Haldenby, S., George, R., Bashton, M., Witney, A. A., Byott, M., Coll, F., Chapman, M., Peacock, S. J., Hughes, J., Nebbia, G., Partridge, D. G., Parker, M., Price, J. R., Peters, C., Roy, S., Snell, L. B., de Silva, T. I., Thomson, E. C., Flowers, P., Copas, A., Breuer, J., McCann, C., Young, G. R. & Nelson, A., 13 Sept 2022, In: eLife. 11, 31 p., e78427.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Sequencing 100%
  • Infection Control 75%
  • Infection Prevention 62%
  • Hospital 50%
  • Incidence 50%
  10 Citations (Scopus)

  48 Downloads (Pure)

• Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope

  The COVID-19 Genomics UK (COG-UK) Consortium, Dolton, G., Rius, C., Hasan, M. S., Wall, A., Szomolay, B., Behiry, E., Whalley, T., Southgate, J., Fuller, A., Morin, T., Topley, K., Tan, L. R., Goulder, P. J. R., Spiller, O. B., Rizkallah, P. J., Jones, L. C., Connor, T. R., Sewell, A. K., Bashton, M., & 4 othersSmith, D., Nelson, A., Young, G. R. & McCann, C., 4 Aug 2022, In: Cell. 185, 16, p. 2936-2951.e19 36 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Cytotoxic T-Cell 33%
  • Epitope 25%
  • Spike 25%
  • Human Leukocyte Antigen 25%
  55 Citations (Scopus)

  29 Downloads (Pure)

• Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models

  The COVID-19 Genomics UK (COG-UK) Consortium, Hinch, R., Panovska-Griffiths, J., Probert, W. J. M., Ferretti, L., Wymant, C., Di Lauro, F., Baya, N., Ghafari, M., Abeler-Dörner, L., Fraser, C., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 3 Oct 2022, In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 380, 2233, 14 p., 20210304.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • England 100%
  • Estimate 66%
  • SARS Coronavirus 66%
  • Model 33%
  • Time 33%
  9 Citations (Scopus)

  21 Downloads (Pure)

• Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission

  Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., Ellaby, N., Platt, S., Groves, N., Gallagher, E., Tumelty, N. M., Le Viet, T., Hughes, G. J., Chen, C., Turner, C., Logan, S., Harrison, A., The COVID-19 Genomics UK (COG-UK) Consortium, Peacock, S. J., Chand, M., & 7 othersHarrison, E. M., Smith, D. L., Bashton, M., Young, G. R., Nelson, A., McCann, C. M. & Yew, W. C., 1 Dec 2022, In: Nature Communications. 13, 1, p. 1-13 13 p., 1012.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Travel 100%
  • Age 25%
  • Genetics 25%
  • Summer 25%
  • Impact 25%
  8 Citations (Scopus)

  29 Downloads (Pure)

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

  Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., Hill, V., Blane, B., Watkins, E., Wright, E., Hall, G., Ludden, C., Myers, R., Hosmillo, M., Chaudhry, Y., Pinckert, M. L., Georgana, I., Izuagbe, R., Leek, D., Nsonwu, O., & 30 othersHughes, G. J., Packer, S., Page, A. J., Metaxaki, M., Fuller, S., Weale, G., Holgate, J., Brown, C. A., The Cambridge Covid-19 testing Centre, University of Cambridge Asymptomatic COVID-19 Screening Programme Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Howes, R., McFarlane, D., Dougan, G., Pybus, O. G., Angelis, D. D., Maxwell, P. H., Peacock, S. J., Weekes, M. P., Illingworth, C., Harrison, E. M., Matheson, N. J., Goodfellow, I. G., Bashton, M., Smith, D. L., Young, G. R., McCann, C. M., Nelson, A., Yew, W. C. & Jones, H., Dec 2022, In: Nature Communications. 13, 1, p. 1-16 16 p., 751.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Student 37%
  • Dynamics 25%
  • Comprehension 12%
  • Cohort Effect 12%
  26 Citations (Scopus)

  23 Downloads (Pure)

• Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning

  Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., Smollett, K., Nomikou, K., Palmalux, N., Tong, L., Carmichael, S., Sreenu, V. B., Orton, R., Goldstein, E. J., Tomb, R. M., The COVID-19 Genomics UK (COG-UK) Consortium, Templeton, K., Gunson, R. N., da Silva Filipe, A., Milosevic, C., & 13 othersThomson, E., Robertson, D. L., Holden, M. T. G., Illingworth, C. J. R., Smith-Palmer, A., Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., Henderson, J. H. & Yew, W. C., Dec 2022, In: Scientific Reports. 12, 1, p. 1-17 17 p., 11735.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Student 50%
  • Students 50%
  • Infection 30%
  • COVID-19 20%
  6 Citations (Scopus)

  24 Downloads (Pure)

• Genomics-informed outbreak investigations of SARS-CoV-2 using civet

  O’Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., Rooke, S., McCrone, J. T., Duggan, K., McHugh, M. P., Nicholls, S. M., Poplawski, R., The COVID-19 Genomics UK (COG-UK) Consortium, COVID-19 Impact Project (Trinidad & Tobago Group), Aanensen, D., Holden, M., Connor, T., Loman, N., Goodfellow, I., Carrington, C. V. F., & 12 othersTempleton, K., Rambaut, A., Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., Henderson, J. H., Hollis, A., Stanley, W. & Yew, W. C., 9 Dec 2022, In: PLOS Global Public Health. 2, 12, 15 p., e0000704.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Virus 100%
  • Health 50%
  • Severe Acute Respiratory Syndrome Coronavirus 2 50%
  • Time 25%
  • Running 25%
  6 Citations (Scopus)

  28 Downloads (Pure)

• 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

  Twohig, K. A., Nyberg, T., Zaidi, A., Thelwall, S., Sinnathamby, M. A., Aliabadi, S., Seaman, S. R., Harris, R. J., Hope, R., Lopez-bernal, J., Gallagher, E., Charlett, A., Angelis, D. D., Presanis, A. M., Dabrera, G., The COVID-19 Genomics UK (COG-UK) Consortium, Koshy, C., Ash, A., Wise, E., Moore, N., & 31 othersMori, M., Cortes, N., Lynch, J., Kidd, S., Fairley, D., Curran, T., Mckenna, J., Adams, H., Fraser, C., Golubchik, T., Bonsall, D., Hassan-ibrahim, M., Malone, C., Cogger, B., Wantoch, M., Reynolds, N., Warne, B., Maksimovic, J., Spellman, K., Mccluggage, K., John, M., Beer, R., Afifi, S., Morgan, S., Marchbank, A., Smith, D., Bashton, M., Young, G., Nelson, A., McCann, C. & Yew, W., 1 Jan 2022, In: The Lancet Infectious Diseases. 22, 1, p. 35-42 8 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Patient 100%
  • Hospital 75%
  • Emergency Care 58%
  • COVID-19 33%
  • Hazard Ratio 25%
  541 Citations (Scopus)

  51 Downloads (Pure)

• Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study

  The COVID-19 Genomics UK (COG-UK) Consortium, Allen, H., Vusirikala, A., Flannagan, J., Twohig, K. A., Zaidi, A., Chudasama, D., Lamagni, T., Groves, N., Turner, C., Rawlinson, C., Lopez-Bernal, J., Harris, R., Charlett, A., Dabrera, G., Kall, M., Bashton, M., Nelson, A., Smith, D., Young, G. R., & 1 othersMcCann, C., 1 Jan 2022, In: The Lancet Regional Health - Europe. 12, p. 1-9 9 p., 100252.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • SARS Coronavirus 100%
  • Case-Control Study 66%
  • Comprehension 33%
  • Sex 33%
  • Age 33%
  115 Citations (Scopus)

  17 Downloads (Pure)

• Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study

  The COVID-19 Genomics UK (COG-UK) Consortium, Krutikov, M., Smith, D., Bashton, M., McCann, C., Young, G. R., Nelson, A., Crown, M., Henderson, J., Hollis, A., Stanley, W. & Yew, W., May 2022, In: The Lancet Healthy Longevity. 3, 5, p. e347-e355

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Resident 100%
  • Infection 58%
  • Severe Acute Respiratory Syndrome Coronavirus 2 50%
  • Long-Term Care 50%
  • Hospital 41%
  35 Citations (Scopus)

  24 Downloads (Pure)

• Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review

  The COVID-19 Genomics UK (COG-UK) Consortium, Hettle, D., Hutchings, S., Muir, P., Moran, E., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., Nov 2022, In: Clinical Infection in Practice. 16, 10 p., 100210.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Patient 29%
  • Infection 29%
  • Combination Therapy 16%
  • Persistent Infection 16%
  21 Citations (Scopus)

  18 Downloads (Pure)

• 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

  The COVID-19 Genomics UK (COG-UK) Consortium, Blackstone, J., Stirrup, O., Mapp, F., Panca, M., Copas, A., Flowers, P., Hockey, L., Price, J., Partridge, D., Peters, C., De Silva, T., Nebbia, G., Snell, L. B., McComish, R., Breuer, J., Bashton, M., McCann, C., Nelson, A., Smith, D., & 1 othersYoung, G. R., 19 Apr 2022, In: BMJ Open. 12, 4, 9 p., e052514.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Hospital 100%
  • COVID-19 50%
  • Severe Acute Respiratory Syndrome Coronavirus 2 50%
  • Infection Control 40%
  • Infection Prevention 40%
  8 Citations (Scopus)

  12 Downloads (Pure)

• Recurrent SARS-CoV-2 mutations in immunodeficient patients

  The COVID-19 Genomics UK (COG-UK) Consortium, Wilkinson, S. A. J., Sparks, N., Kele, B., Peacock, T. P., Robson, S. C., Connor, T. R., Loman, N. J., Golubchik, T., Martinez Nunez, R. T., Bonsall, D., Rambaut, A., Snell, L. B., Livett, R., Ludden, C., Corden, S., Nastouli, E., Nebbia, G., Johnston, I., Lythgoe, K., & 31 othersEstee Torok, M., Goodfellow, I. G., Prieto, J. A., Saeed, K., Jackson, D. K., Houlihan, C., Frampton, D., Hamilton, W. L., Witney, A. A., Bucca, G., Pope, C. F., Moore, C., Thomson, E. C., Harrison, E. M., Smith, C. P., Rogan, F., Beckwith, S. M., Murray, A., Singleton, D., Smith, D. L., Bashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., Williams, C., Williams, R. J., Henderson, J. H., Yew, W. C., Jones, H. & Hartley, J. A., 12 Aug 2022, In: Virus Evolution. 8, 2, veac050.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  47 Citations (Scopus)

  20 Downloads (Pure)

• SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys

  The COVID-19 Genomics UK (COG-UK) Consortium, Chadeau-Hyam, M., Wang, H., Eales, O., Haw, D., Bodinier, B., Whitaker, M., Walters, C. E., Ainslie, K. E. C., Atchison, C., Fronterre, C., Diggle, P. J., Page, A. J., Trotter, A. J., Ashby, D., Barclay, W., Taylor, G., Cooke, G., Ward, H., Darzi, A., & 8 othersRiley, S., Donnelly, C. A., Elliott, P., Bashton, M., Smith, D., Young, G. R., Nelson, A. & McCann, C., 1 Apr 2022, In: The Lancet Respiratory Medicine. 10, 4, p. 355-366 12 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Vaccine 100%
  • Prevalence 83%
  • Infection 83%
  • Severe Acute Respiratory Syndrome Coronavirus 2 83%
  • Child 66%
  34 Citations (Scopus)

  14 Downloads (Pure)

• SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2

  Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., Jonnerby, J., Atchison, C., The COVID-19 Genomics UK (COG-UK) Consortium, Ashby, D., Barclay, W., Taylor, G., Cooke, G., Ward, H., Darzi, A., Riley, S., Chadeau-Hyam, M., Donnelly, C. A., Elliott, P., Smith, D. L., & 9 othersBashton, M., Young, G. R., McCann, C. M., Nelson, A., Crown, M. R., Henderson, J. H., Hollis, A., Stanley, W. & Yew, W. C., Dec 2022, In: BMC Infectious Diseases. 22, 1, 17 p., 647.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Symptom 50%
  • Immunity 50%
  • Surveillance 33%
  • Polymerase Chain Reaction 33%
  11 Citations (Scopus)

  9 Downloads (Pure)

• SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

  Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., Cantoni, D., Scott, S., Logan, N., Ashraf, S., Manali, M., Szemiel, A., Cowton, V., Vink, E., Harvey, W. T., Davis, C., Asamaphan, P., Smollett, K., Tong, L., Orton, R., & 30 othersHughes, J., Holland, P., Silva, V., Pascall, D. J., Puxty, K., da Silva Filipe, A., Yebra, G., Shaaban, S., Holden, M. T. G., Pinto, R. M., Gunson, R., Templeton, K., Murcia, P. R., Patel, A. H., Klenerman, P., Dunachie, S., PITCH Consortium, The COVID-19 Genomics UK (COG-UK) Consortium, Haughney, J., Robertson, D. L., Palmarini, M., Ray, S., Thomson, E. C., Smith, D. L., Young, G. R., Bashton, M., McCann, C. M., Henderson, J. H., Crown, M. R. & Yew, W. C., 7 Jul 2022, In: Nature Microbiology. 7, 8, p. 1161-1179 19 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Receptor Binding 100%
  • Cells 33%
  • Protein 33%
  • Vaccine 33%
  • In Vitro 33%
  352 Citations (Scopus)

  29 Downloads (Pure)

• Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020-December 2021

  The COVID-19 Genomics UK (COG-UK) Consortium, Smallman-Raynor, M. R., Cliff, A. D., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 20 Jul 2022, In: Epidemiology and Infection. 150, 13 p., e145.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Growth 100%
  • Growth Rate 100%
  • Delta 100%
  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Investigation 66%
  6 Citations (Scopus)

  12 Downloads (Pure)

• Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions

  The COVID-19 Genomics UK (COG-UK) Consortium, Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R. M., Ferretti, L., Di Lauro, F., Wymant, C., Izzo, A., Waites, W., Viner, R., Bonell, C., Fraser, C., Klein, D., Kerr, C. C., Bashton, M., Smith, D., Nelson, A., & 2 othersYoung, G. R. & McCann, C., 3 Oct 2022, In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 380, 2233, 19 p., 20210315.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Mathematical Model 100%
  • Delta 66%
  • Estimate 33%
  • Constriction 33%
  • Epidemic 33%
  12 Citations (Scopus)

  15 Downloads (Pure)

• The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks

  Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., Mahida, N., Irving, W. L., Moore, C., Holmes, N., Ball, J. K., Loose, M. W., McClure, C. P., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Young, G., McCann, C. & Nelson, A., 1 Jan 2022, In: The Journal of Infectious Diseases. 225, 1, p. 10-18

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File
  26 Citations (Scopus)

  18 Downloads (Pure)

• The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA

  Zhao, L., Hall, M., de Cesare, M., MacIntyre-Cockett, G., Lythgoe, K., Fraser, C., Bonsall, D., Golubchik, T., Ferretti, L., The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 30 Nov 2022, In: Proceedings of the Royal Society B: Biological Sciences. 289, 1987, 9 p., 20221747.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Sense 83%
  • RNA 66%
  • Host 66%
  • Patient 16%
  3 Citations (Scopus)

  30 Downloads (Pure)

• The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK

  The COVID-19 Genomics UK (COG-UK) Consortium, Hill, V., Du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., Ellaby, N., Gallagher, E., Groves, N., Jackson, B., McCrone, J. T., O'Toole, Á., Price, A., Sanderson, T., Scher, E., Southgate, J., Volz, E., Barclay, W. S., Barrett, J. C., & 15 othersChand, M., Connor, T., Goodfellow, I., Gupta, R. K., Harrison, E. M., Loman, N., Myers, R., Robertson, D. L., Pybus, O. G., Rambaut, A., Bashton, M., Smith, D., Nelson, A., Young, G. R. & McCann, C., 26 Aug 2022, In: Virus Evolution. 8, 2, 13 p., veac080.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Evolutionary Rate 100%
  61 Citations (Scopus)

  23 Downloads (Pure)

• Tracking SARS-CoV-2 mutations and variants through the COG-UK-Mutation Explorer

  The COVID-19 Genomics UK (COG-UK) Consortium, Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., Jackson, B., Orton, R., Nielsen, M., Hsu, N. S., Harrison, E. M., De Silva, T. I., Rambaut, A., Peacock, S. J., Robertson, D. L., Carabelli, A. M., Bashton, M., Nelson, A., Smith, D., & 2 othersYoung, G. R. & McCann, C., 18 Mar 2022, In: Virus Evolution. 8, 1, p. 1-14 14 p., veac023.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Mutation 75%
  • Virus 33%
  • Myalgic Encephalomyelitis 33%
  • Combination Therapy 25%
  22 Citations (Scopus)

  63 Downloads (Pure)
• 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 othersMyers, 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.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Gene 83%
  • Diagnosis 33%
  • Polymerase Chain Reaction 33%
  • Age Groups 33%
  755 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

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Reinfection 100%
  • Symptom 81%
  • Infection 45%
  • Severe Acute Respiratory Syndrome Coronavirus 2 36%
  • COVID-19 27%
  233 Citations (Scopus)

  46 Downloads (Pure)

• 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 othersVollmer, 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 Sept 2021, In: EClinicalMedicine. 39, 9 p., 101064.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • SARS Coronavirus 100%
  • Surveillance 66%
  • Clotiazepam 66%
  • Infection 66%
  86 Citations (Scopus)

  36 Downloads (Pure)

• 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 othersRiley, 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., 17 Dec 2021, In: Science. 374, 6574, 15 p., abl9551.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • People 100%
  • Age 66%
  • Prevalence 66%
  • Summer 33%
  89 Citations (Scopus)

  78 Downloads (Pure)

• 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 othersLoman, N. J., Connor, T. R., Robertson, D. L., Pybus, O. G., Rambaut, A., Bashton, M., Smith, D., Nelson, A., Young, G. & McCann, C., 30 Sept 2021, In: Cell. 184, 20, p. 5179-5188.e8 19 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Virus 100%
  • Mutation 75%
  • Recombinant 50%
  • Lineages 50%
  • Severe Acute Respiratory Syndrome Coronavirus 2 50%
  144 Citations (Scopus)

  40 Downloads (Pure)

• 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 othersMallal, 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.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • RNA 64%
  • Genomic RNA 42%
  • Transcription 21%
  • Virus Nucleocapsid 21%
  28 Citations (Scopus)

  11 Downloads (Pure)

• 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 othersMunharira, 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.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Sample 100%
  • SARS Coronavirus 100%
  • Retrospective Study 80%
  • Polymerase Chain Reaction 80%
  16 Citations (Scopus)

  20 Downloads (Pure)

• 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 othersPanovska-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., 16 Dec 2021, In: Nature. 600, 7889, p. 506-511 6 p.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Lineages 66%
  • COVID-19 33%
  • Evolution 16%
  • Dynamics 16%
  56 Citations (Scopus)

  34 Downloads (Pure)

• 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 othersNicholas, 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.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Sample 100%
  • Severe Acute Respiratory Syndrome Coronavirus 2 100%
  • Lineages 62%
  • COVID-19 50%
  • Health 25%
  25 Citations (Scopus)

  19 Downloads (Pure)

• 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 othersGeorgana, 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., e66857.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Purifying Selection 100%
  • Nonsense Mutation 50%
  • RNA Editing 50%
  • Mixed Infection 50%
  • Superinfection 50%
  95 Citations (Scopus)

  26 Downloads (Pure)

• 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.

  Research output: Contribution to journal › Article › peer-review

  Open Access

  File

  • Hospital 100%
  • Infection 90%
  • COVID-19 60%
  • Severe Acute Respiratory Syndrome Coronavirus 2 40%
  • Feedback System 20%
  24 Citations (Scopus)

  14 Downloads (Pure)