Andrew Nelson

Search results

• 2025

  Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults: potential aerodigestive transmission

  Al-Momani, H., Nelson, A., Al Balawi, H., Al Balawi, D., Aolymat, I., Khasawneh, A. I., Tabl, H., Alsheikh, A., Zueter, A. M., Pearson, J. & Ward, C., 13 Jan 2025, In: Scientific Reports. 15, 1, p. 1-17 17 p., 1811.

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• 2024

  COVID-19 risk mitigation in reopening mass cultural events: population-based observational study for the UK Events Research Programme in Liverpool City Region

  The COVID-19 Genomics UK (COG-UK) Consortium, Burnside, G., Cheyne, C. P., Leeming, G., Humann, M., Darby, A., Green, M. A., Crozier, A., Maskell, S., O'Halloran, K., Musi, E., Carmi, E., Khan, N., Fisher, D., Corcoran, R., Dunning, J., Edmunds, W. J., Tharmaratnam, K., Hughes, D. M. & Malki-Epshtein, L. & 17 others, Cook, M., Roberts, B. M., Gallagher, E., Howell, K., Chand, M., Kemp, R., Boulter, M., Fowler, T., Semple, M. G., Coffey, E., Ashton, M., García-Fiñana, M., Buchan, I. E., Bashton, M., Smith, D., Nelson, A. & Young, G. R., 1 Jan 2024, In: Journal of the Royal Society of Medicine. 117, 1, p. 11-23 13 p.

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  2 Citations (Scopus)

  14 Downloads (Pure)

• Effects of non-digestible carbohydrates on gut microbiota and microbial metabolites: a randomised, controlled dietary intervention in healthy individuals

  Malcomson, F. C., Louca, P., Nelson, A., Willis, N. D., McCallum, I., Xie, L., Ouwehand, A. C., Stowell, J. D., Preston, T., Morrison, D. J., Kelly, S. B., Bradburn, D. M., Belshaw, N. J., Johnson, I. T., Corfe, B. M., Stewart, C. J. & Mathers, J. C., 14 Dec 2024, In: The British Journal of Nutrition. 132, 11, p. 1433-1445 13 p.

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• Influence of maternal folate depletion on Art3 DNA methylation in the murine adult brain: potential consequences for brain and neurocognitive health

  Kok, D. E., Saunders, R., Nelson, A., Smith, D., Ford, D., Mathers, J. C. & McKay, J. A., 1 May 2024, In: Mutagenesis. 39, 3, p. 196-204 9 p., geae007.

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• 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.

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  1 Citation (Scopus)

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• Phylogenomic analyses of multidrug resistant Corynebacterium striatum strains isolated from patients in a tertiary care hospital in the UK

  Sangal, V., Marrs, E. C. L., Nelson, A. & Perry, J. D., 1 Jul 2024, In: European Journal of Clinical Microbiology and Infectious Diseases. 43, 7, p. 1495-1501 7 p.

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• 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 others, Nelson, 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.

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  32 Citations (Scopus)

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• 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.

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• Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence

  Went, S. C., Picton, D. M., Morgan, R. D., Nelson, A., Brady, A., Mariano, G., Dryden, D. T. F., Smith, D. L., Wenner, N., Hinton, J. C. D. & Blower, T. R., 22 Aug 2024, In: Nature Communications. 15, 1, p. 1-18 18 p., 7236.

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• The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies

  Cook, R., Brown, N., Rihtman, B., Michniewski, S., Redgwell, T., Clokie, M., Stekel, D. J., Chen, Y., Scanlan, D. J., Hobman, J. L., Nelson, A., Jones, M. A., Smith, D. & Millard, A., 20 Feb 2024, In: Microbial genomics. 10, 2, p. 1-14 14 p., 001198.

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  10 Citations (Scopus)

  13 Downloads (Pure)
• 2023

  Combining viral genomics and clinical data to assess risk factors for severe COVID-19 (mortality, ICU admission, or intubation) amongst hospital patients in a large acute UK NHS hospital Trust

  The COVID-19 Genomics UK (COG-UK) Consortium, Foxley-Marrable, M., D'Cruz, L., Meredith, P., Glaysher, S., Beckett, A. H., Goudarzi, S., Fearn, C., Cook, K. F., Loveson, K. F., Dent, H., Paul, H., Elliott, S., Wyllie, S., Lloyd, A., Bicknell, K., Lumley, S., McNicholas, J., Prytherch, D. & Lundgren, A. & 7 others, Graur, O., Chauhan, A. J., Robson, S. C., Bashton, M., Smith, D., Nelson, A. & Young, G. R., 23 Mar 2023, In: PLoS One. 18, 3, 29 p., e0283447.

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• Directions of change in intrinsic case severity across successive SARS-CoV-2 variant waves have been inconsistent

  The COVID-19 Genomics UK (COG-UK) Consortium, Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N., Fjodorova, L., Forrest, R., Goldstein, E., Gunson, R., Haughney, J., Holden, M. T. G., Honour, P., Hughes, J. & James, E. & 22 others, Lewis, T., MacLean, O., McHugh, M., Mollett, G., Nyberg, T., Onishi, Y., Parcell, B., Ray, S., Robertson, D. L., Seaman, S. R., Shabaan, S., Shepherd, J. G., Smollett, K., Templeton, K., Wastnedge, E., Wilkie, C., Williams, T., Thomson, E. C., Bashton, M., Smith, D., Nelson, A. & Young, G. R., 1 Aug 2023, In: Journal of Infection. 87, 2, p. 128-135 8 p.

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  12 Citations (Scopus)

  23 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 others, 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., 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.

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  2 Citations (Scopus)

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• 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 others, Nelson, 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.

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  9 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 others, Henderson, 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.

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

  18 Downloads (Pure)

• The core phageome and its interrelationship with preterm human milk lipids

  Yew, W. C., Young, G. R., Nelson, A., Cheung, W., Stewart, C. J., Bridge, S. H., Granger, C., Berrington, J. E., Embleton, N. D. & Smith, D. L., 28 Nov 2023, In: Cell Reports. 42, 11, p. 1-16 1 p., 113373.

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  5 Citations (Scopus)

  32 Downloads (Pure)

• The impact of freezing on the post-mortem human microbiome

  Ogbanga, N., Nelson, A., Gino, S., Wescott, D. J., Mickleburgh, H. L., Gocha, T. P. & Procopio, N., 30 Mar 2023, In: Frontiers in Ecology and Evolution. 11, 1151001.

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  4 Citations (Scopus)

  42 Downloads (Pure)

• The Oral Microbiome for Geographic Origin: An Italian Study

  Ogbanga, N., Nelson, A., Ghignone, S., Voyron, S., Lovisolo, F., Sguazzi, G., Renò, F., Migliario, M., Gino, S. & Procopio, N., 1 May 2023, In: Forensic Science International: Genetics. 64, 9 p., 102841.

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  • Microbiome 100%
  • Oral Microbiome 54%
  • Donor 45%
  • Skin 36%
  • Analysis 27%
  13 Citations (Scopus)

  44 Downloads (Pure)

• The SARS-CoV-2 Alpha variant was associated with increased clinical severity of COVID-19 in Scotland: A genomics-based retrospective cohort analysis

  The COVID-19 Genomics UK (COG-UK) Consortium, Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., Clifford, S., Davis, C., da Silva Filipe, A., El Sakka, N., Fjodorova, L., Forrest, R., Goldstein, E., Gunson, R., Haughney, J., Holden, M. T. G., Honour, P., Hughes, J. & James, E. & 21 others, Lewis, T., Lycett, S., MacLean, O., McHugh, M., Mollett, G., Onishi, Y., Parcell, B., Ray, S., Robertson, D. L., Shabaan, S., Shepherd, J. G., Smollett, K., Templeton, K., Wastnedge, E., Wilkie, C., Williams, T., Thomson, E. C., Bashton, M., Smith, D., Nelson, A. & Young, G. R., 13 Apr 2023, In: PLoS One. 18, 4, 19 p., e0284187.

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  5 Citations (Scopus)

  22 Downloads (Pure)

• Tracheostomy in children is associated with neutrophilic airway inflammation

  Powell, J., Powell, S., Mather, M. W., Beck, L., Nelson, A., Palmowski, P., Porter, A., Coxhead, J., Hedley, A., Scott, J., Rostron, A. J., Hellyer, T. P., Zaidi, F., Davey, T., Garnett, J. P., Agbeko, R., Ward, C., Stewart, C. J., Taggart, C. C. & Brodlie, M. & 1 others, Simpson, A. J., 1 Oct 2023, In: Thorax. 78, 10, p. 1019-1027 9 p.

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  • Tracheostomy 100%
  • Child 80%
  • Serositis 20%
  • Patient 10%
  • Microbiome 10%
  2 Citations (Scopus)

  22 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 others, Templeton, 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.

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  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 others, Nelson, 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.

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  4 Citations (Scopus)

  38 Downloads (Pure)
• 2022

  Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections

  The COVID-19 Genomics UK (COG-UK) Consortium, Bashton, M., Smith, D., Nelson, A. & Young, G. R., 5 Jul 2022, In: Communications Biology. 5, 1, p. 666

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  13 Citations (Scopus)

  9 Downloads (Pure)

• 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 others, Hope, 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

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

  16 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.

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

  56 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 others, Douthwaite, 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 others, Hope, 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.

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  • Infection 100%
  • Hazard Ratio 100%
  • Death 90%
  • Protection 80%
  • Vaccine Efficacy 70%
  871 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 others, O'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.

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  • UK 100%
  • Intervention 50%
  • Emergence 50%
  • Travel 50%
  • Introduction 33%
  59 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 others, Aggarwal, 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

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

  17 Downloads (Pure)

• Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, 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 others, Robertson, 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

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

  51 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 others, Smith, 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%
  58 Citations (Scopus)

  30 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)

• 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.

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

  Open Access

  File

  • Viral Replication 100%
  • Haplotype 100%
  11 Citations (Scopus)

  51 Downloads (Pure)

• Exposure to bile and gastric juice can impact the aerodigestive microbiome in people with cystic fibrosis

  Al-Momani, H., Perry, A., Nelson, A., Stewart, C. J., Jones, R., Krishnan, A., Robertson, A., Bourke, S., Doe, S., Cummings, S., Anderson, A., Forrest, T., Forrest, I., Griffin, M., Wilcox, M., Brodlie, M., Pearson, J. & Ward, C., 30 Jun 2022, In: Scientific Reports. 12, 1, 11 p., 11114.

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

  Open Access

  File

  • Patient 100%
  • Microbiome 100%
  • Lung 100%
  • Pseudomonas aeruginosa 100%
  • Cystic Fibrosis 100%
  5 Citations (Scopus)

  39 Downloads (Pure)

• Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research

  Hockney, R., Orr, C. H., Waring, G. J., Christiaens, I., Taylor, G., Cummings, S. P., Robson, S. C. & Nelson, A., 17 Mar 2022, In: PLoS One. 17, 3, 23 p., e0265441.

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

  Open Access

  File

  • Formaldehyde 100%
  • Fetal Membrane 66%
  • Tissues 33%
  • DNA Extraction 25%
  • Wax 25%
  5 Citations (Scopus)

  26 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 others, Harrison, 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)

  30 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 others, Thomson, 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 others, Templeton, 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%
  7 Citations (Scopus)

  30 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 others, Mori, 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%
  546 Citations (Scopus)

  57 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 others, McCann, 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%
  118 Citations (Scopus)

  17 Downloads (Pure)

• Mixed Tree Nuts, Cognition and Gut Microbiota: a 4-week, Placebo-Controlled, Randomized Crossover Trial in Healthy Non-Elderly Adults

  Haskell-Ramsay, C. F., Dodd, F. L., Smith, D., Cuthbertson, L., Nelson, A., Lodge, J. K. & Jackson, P. A., 1 Dec 2022, In: The Journal of Nutrition. 152, 12, p. 2778-2788 11 p., nxac228.

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

  Open Access

  File

  • Placebo 100%
  • Tree 66%
  • Tree Nut 66%
  • Intestine Flora 33%
  • Lachnospiraceae 33%
  2 Citations (Scopus)

  41 Downloads (Pure)

• Optimisation and application of a novel method to identify bacteriophage in maternal milk and infant stool identifies host-phage communities within preterm infant gut

  Young, G., Yew, W., Nelson, A., Bridge, S., Berrington, J. E., Embleton, N. D. & Smith, D., 26 Apr 2022, In: Frontiers in Pediatrics. 10, 11 p., 856520.

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

  Open Access

  File

  • Sedimentation 100%
  • Inoviridae 100%
  • Baculoviridae 100%
  • Iridoviridae 100%
  2 Citations (Scopus)

  64 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)

  26 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%
  23 Citations (Scopus)

  19 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 others, Young, 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 others, Estee 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
  50 Citations (Scopus)

  22 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 others, Riley, 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 others, Bashton, 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 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time

  The COVID-19 Genomics UK (COG-UK) Consortium, Ashford, F., Best, A., Dunn, S. J., Ahmed, Z., Siddiqui, H., Melville, J., Wilkinson, S., Mirza, J., Cumley, N., Stockton, J., Ferguson, J., Wheatley, L., Ratcliffe, E., Casey, A., Plant, T., Quick, J., Richter, A., Loman, N. & McNally, A. & 4 others, Bashton, M., Smith, D., Nelson, A. & Young, G. R., 4 Apr 2022, In: Journal of Clinical Microbiology. 60, 4, e0240821.

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

  Open Access
  8 Citations (Scopus)

• 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%
  8 Citations (Scopus)

  12 Downloads (Pure)