COG-UK Publications

How to cite COG-UK as an author and acknowledge COG-UK funding

Manuscripts which use and cite COG-UK’s funding and or data no longer need to be reviewed and approved by COG-UK prior to publication. However, please continue to use the citation and acknowledgement detailed below. For any questions on future papers please contact Professor Sharon Peacock.

Cite COG-UK as an author with the following:

Author Name: The COVID-19 Genomics UK (COG-UK) consortium
Footnote: Full list of consortium names and affiliations included.
Contact Email Address: Professor Sharon Peacock.
Author Affiliation Address: Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom

The full list of consortium names and affiliations can be downloaded here, and must either be copied into the appendices or uploaded alongside the paper as a supplementary material.

Acknowledge COG-UK funding as follows:

“COG-UK is supported by funding from the Medical Research Council (MRC) part of UK Research & Innovation (UKRI), the National Institute of Health Research (NIHR) [grant code: MC_PC_19027], and Genome Research Limited, operating as the Wellcome Sanger Institute. The authors acknowledge use of data generated through the COVID-19 Genomics Programme funded by the Department of Health and Social Care. The views expressed are those of the author and not necessarily those of the Department of Health and Social Care or UKHSA.”

For an automate update list of COG-UK publications you can visit this PubMed page.

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December 2022

O’Toole, Á., Hill, V., Jackson, B., Dewar, R., Sahadeo, N., Colquhoun, R., … Rambaut, A. (2022). Genomics-informed outbreak investigations of SARS-CoV-2 using civet. PLOS Global Public Health, 2(12), e0000704. https://doi.org/10.1371/journal.pgph.0000704

November 2022

Zhao, L., Hall, M., de Cesare, M., MacIntyre-Cockett, G., Lythgoe, K., Fraser, C., … Ferretti, L. (2022). The mutational spectrum of SARS-CoV-2 genomic and antigenomic RNA. Proceedings of the Royal Society B: Biological Sciences, 289(1987). https://doi.org/10.1098/rspb.2022.1747

Hettle, D., Hutchings, S., The COVID-9 Genomics UK (COG-UK) consortium, Muir, P., & Moran, E. (2022). Persistent SARS-CoV-2 infection in immunocompromised patients facilitates rapid viral evolution: Retrospective cohort study and literature review. Clinical Infection in Practice, 16, 100210. https://doi.org/10.1016/j.clinpr.2022.100210

Brunner, F. S., Brown, M. R., Bassano, I., Denise, H., Khalifa, M. S., Wade, M. J., … Paterson, S. (2022). City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants. Water Research, 226(119306). https://doi.org/10.1016/j.watres.2022.119306

October 2022

Cox, M., Peacock, T. P., Harvey, W. T., Hughes, J., Wright, D. W., COVID-19 Genomics UK (COG-UK) Consortium., … Carabelli, A. M. (2022). SARS-CoV-2 variant evasion of monoclonal antibodies based on in vitro studies. Nature Reviews Microbiology, 21(02), 112–124. https://doi.org/10.1038/s41579-022-00809-7

Colton, H., Parker, M. D., Stirrup, O., Blackstone, J., Loose, M., McClure, C. P., … de Silva, T. I. (2022). Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: Analysis of data from the COG-UK HOCI study. Journal of Hospital Infection. https://doi.org/10.1016/j.jhin.2022.09.022

McCrone, J. T., Hill, V., Bajaj, S., Pena, R. E., Lambert, B. C., Inward, R., … Kraemer, M. U. G. (2022). Context-specific emergence and growth of the SARS-CoV-2 Delta variant. Nature, 610(7930), 154–160. https://doi.org/10.1038/s41586-022-05200-3

September 2022

Hill, V., Du Plessis, L., Peacock, T. P., Aggarwal, D., Colquhoun, R., Carabelli, A. M., … Rambaut, A. (2022). The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. Virus Evolution, 8(02). https://doi.org/10.1093/ve/veac080

Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., … Breuer, J. (2022). Effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control for hospital-onset COVID-19 infection: Multicentre, prospective study. eLife, 11, e78427. https://doi.org/10.7554/eLife.78427

August 2022

Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, R., Campbell, A., … Thomson, E. C. (2022). Inconsistent directions of change in case severity across successive SARS-CoV-2 variant waves suggests an unpredictable future. medRxiv. https://doi.org/10.1101/2022.03.24.22272915

Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R. M., … The COVID-19 Genomics UK (COG-UK) Consortium. (2022). Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233). https://doi.org/10.1098/rsta.2021.0315

Hinch, R., Panovska-Griffiths, J., Probert, W. J. M., Ferretti, L., Wymant, C., Di Lauro, F., … Fraser, C. (2022). Estimating SARS-CoV-2 variant fitness and the impact of interventions in England using statistical and geo-spatial agent-based models. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 380(2233). https://doi.org/10.1098/rsta.2021.0304

Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, A., Campbell, R., … Thomson, E. C. (2021). The SARS-CoV-2 Alpha variant is associated with increased clinical severity of COVID-19 in Scotland: a genomics-based retrospective cohort analysis. medRxiv. https://doi.org/10.1101/2021.08.17.21260128

Wilkinson, S. A. J., Richter, A., Casey, A., Osman, H., Mirza, J. D., Stockton, J., … Loman, N. J. (2022). Recurrent SARS-CoV-2 mutations in immunodeficient patients. Virus Evolution, 08(02). https://doi.org/10.1093/ve/veac050 ‌

Dolton, G., Rius, C., Hasan, M. S., Wall, A., Szomolay, B., Behiry, E., … Sewell, A. K. (2022). Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell, 185(16), 2936-2951.e19. https://doi.org/10.1016/j.cell.2022.07.002

Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., De Lorenzo, G., Furnon, W., … Thomson, E. C. (2022). SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology, 7(08), 1161–1179. https://doi.org/10.1038/s41564-022-01143-7

July 2022

Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., … Elliott, P. (2022). 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. BMC Infectious Diseases, 22(01). https://doi.org/10.1186/s12879-022-07628-4

Smallman-Raynor, M. R., Cliff, A. D., & The COVID-19 Genomics UK (COG-UK) Consortium. (2022). Spatial growth rate of emerging SARS-CoV-2 lineages in England, September 2020–December 2021. Epidemiology and Infection, 150, e145. https://doi.org/10.1017/s0950268822001285 ‌

Nickbakhsh, S., Hughes, J., Christofidis, N., Griffiths, E., Shaaban, S., Enright, J., … Smith-Palmer, A. (2022). Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports, 12(01). https://doi.org/10.1038/s41598-022-15661-1

Parker, M. D., Stewart, H., Shehata, O. M., Lindsey, B. B., Shah, D. R., Hsu, S., … de Silva, T. I. (2022). Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B.1.1.7/Alpha variant infections. Communications Biology, 5(01). https://doi.org/10.1038/s42003-022-03565-9

June 2022

Kläser, K., Molteni, E., Graham, M., Canas, L. S., Österdahl, M. F., Antonelli, M., … Duncan, E. L. (2022). 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. Scientific Reports, 12(01). https://doi.org/10.1038/s41598-022-14016-0

May 2022

Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Donovan-Banfield, I., … Hiscox, J. A. (2022). Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers. GigaScience, 11, giac045. https://doi.org/10.1093/gigascience/giac045

Dabrera, G., Allen, H., Zaidi, A., Flannagan, J., Twohig, K., Thelwall, S., … the COG-UK Consortium. (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. Eurosurveillance, 27(20). https://doi.org/10.2807/1560-7917.es.2022.27.20.2100377

Krutikov, M., Stirrup, O., Nacer-Laidi, H., Azmi, B., Fuller, C., Tut, G., … The COVID-19 Genomics UK consortium. (2022). Outcomes of SARS-CoV-2 omicron infection in residents of long-term care facilities in England (VIVALDI): a prospective, cohort study. The Lancet Healthy Longevity, 03(05), e347–e355. https://doi.org/10.1016/s2666-7568(22)00093-9

April 2022

Blackstone, J., Stirrup, O., Mapp, F., Panca, M., Copas, A., Flowers, P., … Breuer, J. (2022). Protocol for the COG-UK hospital-onset COVID-19 infection (HOCI) multicentre interventional clinical study: evaluating the efficacy of rapid genome sequencing of SARS-CoV-2 in limiting the spread of COVID-19 in UK NHS hospitals. BMJ Open, 12(04), e052514. https://doi.org/10.1136/bmjopen-2021-052514

Ashford, F., Best, A., Dunn, S. J., Ahmed, Z., Siddiqui, H., Melville, J., … McNally, A. (2022). SARS-CoV-2 Testing in the Community: Testing Positive Samples with the TaqMan SARS-CoV-2 Mutation Panel To Find Variants in Real Time. Journal of Clinical Microbiology. https://doi.org/10.1128/jcm.02408-21

Nyberg, T., Ferguson, N. M., Nash, S. G., Webster, H. H., Flaxman, S., Andrews, N., … Thelwall, T. (2022). 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 Lancet, 399(10332), 1303–1312. https://doi.org/10.1016/s0140-6736(22)00462-7

Chadeau-Hyam, M., Wang, H., Eales, O., Haw, D., Bodinier, B., Whitaker, M., … the COVID-19 Genomics UK consortium. (2022). SARS-CoV-2 infection and vaccine effectiveness in England (REACT-1): a series of cross-sectional random community surveys. The Lancet Respiratory Medicine, 10(04), 355–366. https://doi.org/10.1016/s2213-2600(21)00542-7

March 2022

Wright, D. W., Harvey, W. T., Hughes, J., Cox, M., Peacock, T. P., Colquhoun, R., … Carabelli, A. M. (2022). Tracking SARS-CoV-2 Mutations and Variants Through the COG-UK-Mutation Explorer. Virus Evolution, 8(01). https://doi.org/10.1093/ve/veac023

Rushton, S. P., Moss, E. D., Baker, P., Bashton, M., Crown, M. R., dos Santos, R. N., … Smith, D. L. (2022). Spatio-temporal epidemiology of SARS-CoV-2 virus lineages in Teesside, UK, in 2020: effects of social deprivation, weather and lockdown on lineage dynamics. medRxiv. https://doi.org/10.1101/2022.02.05.22269279

February 2022

Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., … Harrison, E. M. (2022). Genomic assessment of quarantine measures to prevent SARS-CoV-2 importation and transmission. Nature Communications, 13(01), 751. https://doi.org/10.1038/s41467-022-28371-z

Snell, L. B., Wang, W., Alcolea-Medina, A., Charalampous, T., Batra, R., de Jongh, L., … Curcin, V. (2022). Descriptive comparison of admission characteristics between pandemic waves and multivariable analysis of the association of the Alpha variant (B.1.1.7 lineage) of SARS-CoV-2 with disease severity in inner London. BMJ Open Respiratory Research, 12(02), e055474. https://doi.org/10.1136/bmjopen-2021-055474

Aggarwal, D., Warne, B., Jahun, A. S., Hamilton, W. L., Fieldman, T., du Plessis, L., … Goodfellow, I. G. (2022). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Communications, 13(01). https://doi.org/10.1038/s41467-021-27942-w

Lindsey, B. B., Villabona-Arenas, Ch. J., Campbell, F., Keeley, A. J., Parker, M. D., Shah, D. R., … de Silva, T. I. (2022). Characterising within-hospital SARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nature Communications, 13(01). https://doi.org/10.1038/s41467-022-28291-y ‌

Aggarwal, D., Myers, R., Hamilton, W. L., Bharucha, T., Tumelty, N. M., Brown, C. S., … The COVID-19 Genomics UK (COG-UK) Consortium. (2022). The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. The Lancet Microbe, 3(02), e151-e158. https://doi.org/10.1016/s2666-5247(21)00208-1

January 2022

Lythgoe, K. A., Golubchik, T., Hall, M., House, T., MacIntyre-Cockett, G., Fryer, H., … Bonsall, D. (2022). Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey. medRxiv. https://doi.org/10.1101/2022.01.05.21268323

Allen, H., Vusirikala, A., Flannagan, J., Twohig, K. A., Zaidi, A., Chudasama, D., … the COVID-19 Genomics UK (COG-UK) consortium. (2022). Household transmission of COVID-19 cases associated with SARS-CoV-2 delta variant (B.1.617.2): national case-control study. The Lancet Regional Health – Europe, 12, 100252. https://doi.org/10.1016/j.lanepe.2021.100252

Twohig, K. A., Nyberg, T., Zaidi, A., Thelwall, S., Sinnathamby, M. A., Aliabadi, S., … the COVID-19 Genomics UK (COG-UK) consortium. (2022). Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. The Lancet Infectious Diseases, 22(01), 3542. https://doi.org/10.1016/s1473-3099(21)00475-8

Snell, L. B., Fisher, C. L., Taj, U., Stirrup, S., Merrick, B., Alcolea-Medina, A., … Arwan, A. R. (2022). Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 infection early in the pandemic and the role of unidentified cases in transmission. Clinical Microbiology and Infection, 28(01), 93–100. https://doi.org/10.1016/j.cmi.2021.07.040

Francis, R. V., Billam, H., Clarke, M., Yates, C., Tsoleridis, T., Berry, L., … COVID-19 Genomics UK (COG-UK) consortium. (2022). The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks. The Journal of Infectious Diseases, 225(01), 10–18. https://doi.org/10.1093/infdis/jiab483

Boshier, F. A. T., Pang, J., Penner, J., Parker, M., Alders, N., Bamford, A., … The COVID-19 Genomics UK (COG-UK) consortium. (2022). Evolution of viral variants in remdesivir treated and untreated SARS‐CoV‐2 infected paediatrics patients. Journal of Medical Virology, 94(01), 161–172. https://doi.org/10.1002/jmv.27285

December 2021

Elliott, P., Haw, D., Wang, H., Eales, O., Walters, C., Ainslie, K., … Riley, S. (2021). Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. Science, 374(6574). https://doi.org/10.1126/science.abl9551

Vöhringer, H. S., Sanderson, T., Sinnott, M., De Maio, N., Nguyen, T., Goater, R., … Gerstung, M. (2021). Genomic reconstruction of the SARS-CoV-2 epidemic in England. Nature, 600, 506–511. https://doi.org/10.1038/s41586-021-04069-y

Davis, C., Logan, N., Tyson, G., Orton, R., Harvey, W. T., Perkins, J. S., … COVID-19 DeplOyed VaccinE (DOVE) Cohort Study investigators. (2021). Reduced neutralisation of the Delta (B.1.617.2) SARS-CoV-2 variant of concern following vaccination. PLOS Pathogens, 17(12), e1010022. https://doi.org/10.1371/journal.ppat.1010022

Mashe, T., Takawira, F. T., Martins, L. de O., Gudza-Mugabe, M., Chirenda, J., Munyanyi, M., … the SARS-CoV-2 Research Group. (2021). 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 Lancet Global Health, 9(12), e1658-e1666. https://doi.org/10.1016/S2214-109X(21)00434-4

Boshier, F. A. T., Venturini, C., Stirrup, O. T., Guerra-Assuncao, J. A., Alcolea-Medina, A., Becket, A. H., … the COVID-19 Genomics UK (COG-UK) consortium. (2021). The Alpha variant was not associated with excess nosocomial SARS-CoV-2 infection in a multi-centre UK hospital study. Journal of Infection, 83(06), 693–700. https://doi.org/10.1016/j.jinf.2021.09.022

November 2021

de Silva, T. I., Liu, G., B Lindsey, B., Dong, D., Shah, D., J. Mentzer, A., … Dong, T. (2021). The impact of viral mutations on recognition by SARS-CoV-2 specific T-cells. iScience, 24(11), 103353. https://doi.org/10.1016/j.isci.2021.103353

September 2021

Martin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., … Kosakovsky Pond, S. L. (2021). The emergence and ongoing convergent evolution of the N501Y lineages coincides with a major global shift in the SARS-CoV-2 selective landscape. Cell, 184(20), 5189–5200e7. https://doi.org/10.1016/j.cell.2021.09.003

Jackson, B., Boni, M. F., Bull, M. J., Colleran, A., Colquhoun, R. M., Darby, A. C., … Rambaut, A. (2021). Generation and transmission of interlineage recombinants in the SARS-CoV-2 pandemic. Cell, 184(20), 5179–5188.e8. https://doi.org/10.1016/j.cell.2021.08.014

Stirrup, O. T., Boshier, F. A. T., Venturini, C., Guerra-Assunção, J. A., Alcolea-Medina, A., Becket, A. H., … Breuer, J. (2021). SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men: multicentre cohort study. BMJ Open Respiratory Research, 8, e001029. https://doi.org/10.1136/bmjresp-2021-001029

O’Toole, Á., Hill, V., Pybus, O. G., Watts, A., Bogoch, I. I., Khan, K., … Kraemer, M. U. G. (2021). Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2. Wellcome Open Research. https://doi.org/10.12688/wellcomeopenres.16661.2

Mishra, S., Mindermann, S., Sharma, M., Whittaker, C., Mellan, T. A., Wilton, T., … The COVID-19 Genomics UK (COG-UK) Consortium. (2021). Changing composition of SARS-CoV-2 lineages and rise of Delta variant in England. eClinicalMedicine, 39, 101064. https://doi.org/10.1016/j.eclinm.2021.101064

Wenlock, R. D., Tausan, M., Mann, R., Garr, W., Preston, R., Arnold, A., … Sargent, C. (2021). Nosocomial or not? A combined epidemiological and genomic investigation to understand hospital-acquired COVID-19 infection on an elderly care ward. Infection Prevention in Practice, 3(03), 100165. https://doi.org/10.1016/j.infpip.2021.100165

August 2021

Leary, S., Gaudieri, S., Parker, M. D., Chopra, A., James, I., Pakala, S., … Mallal, S. (2021). Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: Homologous Recombination has Potential to Change SARS-CoV-2 at Both Protein and RNA Level. Pathogens and Immunity, 6(02). https://doi.org/10.20411/pai.v6i2.460

Kraemer, M. U. G., Hill, V., Ruis, C., Dellicour, S., Bajaj, S., McCrone, J. T., … Pybus, O. G. (2021). Spatiotemporal invasion dynamics of SARS-CoV-2 lineage B.1.1.7 emergence. Science, 373(6557), 889–895. https://doi.org/10.1126/science.abj0113

Didelot, X., Geidelberg, L., The COVID-19 Genomics UK (COG-UK) consortium., & Volz, E. M. (2021). Model design for non-parametric phylodynamic inference and applications to pathogen surveillance. bioRxiv. https://doi.org/10.1101/2021.01.18.427056

Tonkin-Hill, G., Martincorena, I., Amato, R., Lawson, A. R. J., Gerstung, M., Johnston, I., … Wellcome Sanger Institute COVID-19 Surveillance Team. (2021). Patterns of within-host genetic diversity in SARS-CoV-2. eLife, 10, e66857. https://doi.org/10.7554/eLife.66857

Eales, O., Walters, C. E., Wang, H., Haw, D., Ainslie, K. E. C., Atchison, C., … Riley, S. (2021). Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2. medRxiv. https://doi.org/10.1101/2021.08.12.21261987

July 2021

Li, K. K., Woo, Y. M., Stirrup, O., Hughes, J., Ho, A., Filipe, A. D. S., … The COVID-19 Genomics UK (COG-UK) consortium. (2021). Genetic epidemiology of SARS-CoV-2 transmission in renal dialysis units – A high risk community-hospital interface. Journal of Infection, 83(01), 96–103. https://doi.org/10.1016/j.jinf.2021.04.020

Nicholls, S. M., Poplawski, R., Bull, M. J., Underwood, A., Chapman, M., Abu-Dahab, K., … The COVID-19 Genomics UK (COG-UK) consortium. (2021). CLIMB-COVID: continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. Genome Biology, 22(01). https://doi.org/10.1186/s13059-021-02395-y

June 2021

Stirrup, O., Hughes, J., Parker, M., Partridge, D. G., Shepherd, J. G., Blackstone, J., … Breuer, J. (2021). Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. eLife, 10, e65828. https://doi.org/10.7554/eLife.65828

Page, A. J., Mather, A. E., Le-Viet, T., Meader, E. J., Alikhan, N.-F., Kay, G. L., … The COVID-19 Genomics UK (COG-UK) consortium. (2021). Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management. Microbial Genomics, 7(06). https://doi.org/10.1099/mgen.0.000589

Meng, B., Kemp, S. A., Papa, G., Datir, R., Ferreira, I. A. T. M., Marelli, S., … Gupta, R. K. (2021). Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. Cell Reports, 35(13), 109292. https://doi.org/10.1016/j.celrep.2021.109292

Riley, S., Wang, H., Eales, O., Haw, D., Walters, C. E., Ainslie, K. E. C., … Elliott, P. (2021). REACT-1 round 12 report: resurgence of SARS-CoV-2 infections in England associated with increased frequency of the Delta variant. medRxiv. https://doi.org/10.1101/2021.06.17.21259103

Chappell, J. G., Tsoleridis, T., Clark, G., Berry, L., Holmes, N., Moore, C., … the COG-UK consortium. (2021). Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. Journal of General Virology, 102(06). https://doi.org/10.1099/jgv.0.001595

Williamson, M. K., Hamilton, F., Hutchings, S., Pymont, H. M., Hackett, M., Arnold, D., … Davidson, A. D. (2021). Chronic SARS-CoV-2 infection and viral evolution in a hypogammaglobulinaemic individual. medRxiv. https://doi.org/10.1101/2021.05.31.21257591

Harvey, W. T., Carabelli, A. M., Jackson, B., Gupta, R. K., Thomson, E. C., Harrison, E. M., … Robertson, D. L. (2021). SARS-CoV-2 variants, spike mutations and immune escape. Nature Reviews Microbiology, 19(07), 409–424. https://doi.org/10.1038/s41579-021-00573-0

May 2021

Hsu, S., Parker, M. D., Lindsey, B. B., State, A., Zhang, P., Foulkes, B. H., … de Silva, T. I. (2021). Detection of Spike Mutations; D80G, T95I, G142D, △144, N439K, E484K, P681H, I1130V, and D1139H, in B.1.1.482 Lineage (AV.1) Samples from South Yorkshire, UK. Retrieved from https://virological.org/t/detection-of-spike-mutations-d80g-t95i-g142d-144-n439k-e484k-p681h-i1130v-and-d1139h-in-b-1-1-482-lineage-av-1-samples-from-south-yorkshire-uk/699

Riley, S., Haw, D., Walters, C. E., Wang, H., Eales, O., Ainslie, K. E. C., … Darzi, A. (2021). REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown. medRxiv. https://doi.org/10.1101/2021.05.13.21257144

Eales, O., Page, A. J., Tang, S. N., Walters, C. E., Wang, H., Haw, D., … Riley, S. (2021). SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples. medRxiv. https://doi.org/10.1101/2021.05.08.21256867

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., … Ferguson, N. M. (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. Nature, 593(7858), 266–269. https://doi.org/10.1038/s41586-021-03470-x

Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., … Gupta, R. K. (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature, 593(7857), 136–141. https://doi.org/10.1038/s41586-021-03412-7

Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., … Ourselin, S. (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. The Lancet Public Health, 6(05), e335–e345. https://doi.org/10.1016/s2468-2667(21)00055-4

April 2021

Hosie, M. J., Epifano, I., Herder, V., Orton, R. J., Stevenson, A., Johnson, N., … Weir, W. (2021). Detection of SARS‐CoV‐2 in respiratory samples from cats in the UK associated with human‐to‐cat transmission. Veterinary Record, 188(08). https://doi.org/10.1002/vetr.247

Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., … Golubchik, T. (2021). SARS-CoV-2 within-host diversity and transmission. Science, 372(6539), eabg0821. https://doi.org/10.1126/science.abg0821

Emary, K. R. W., Golubchik, T., Aley, P. K., Ariani, C. V., Angus, B., Bibi, S., … the Oxford COVID-19 Vaccine Trial Group (2021). 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 Lancet, 397(10282), 1351–1362. https://doi.org/10.1016/s0140-6736(21)00628-0

Davies, N. G., Abbott, S., Barnard, R. C., Jarvis, C. I., Kucharski, A. J., Munday, J. D., … Edmunds, J. (2021). Estimated transmissibility and impact of SARS-CoV-2 lineage B.1.1.7 in England. Science, 372(6538), eabg3055. https://doi.org/10.1126/science.abg3055

Kemp, S. A., Collier, D. A., Datir, R. P., Ferreira, I. A. T. M., Gayed, S., Jahun, A., … Gupta, R. K. (2021). SARS-CoV-2 evolution during treatment of chronic infection. Nature, 592(7853), 277–282. https://doi.org/10.1038/s41586-021-03291-y

Parker, M. D., Lindsey, B. B., Leary, S., Gaudieri, S., Chopra, A., Wyles, M., … de Silva, T. I. (2021). Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data. Genome Research, 31(04), 645–658. https://doi.org/10.1101/gr.268110.120

March 2021

Moore, C., Davies, L., Rees, R., Gifford, L., Lewis, H., Plimmer, A., … Connor, T. R. (2021). Localised community circulation of SARS-CoV-2 viruses with an increased accumulation of single nucleotide polymorphisms that adversely affect the sensitivity of real-time reverse transcription assays targeting Nucleocapsid protein. medRxiv. https://doi.org/10.1101/2021.03.22.21254006

Jackson, B., Rambaut, A., Pybus, O. G., Robertson, D. L., Connor, T., Loman, N. J., & The COVID-19 Genomics UK (COG-UK) consortium. (2021). Recombinant SARS-CoV-2 genomes involving lineage B.1.1.7 in the UK. Retrieved from https://virological.org/t/recombinant-sars-cov-2-genomes-involving-lineage-b-1-1-7-in-the-uk/658

Thomson, E. C., Rosen, L. E., Shepherd, J. G., Spreafico, R., da Silva Filipe, A., Wojcechowskyj, J. A., … Snell, G. (2021). Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity. Cell, 184(05), 1171–1187.e20. https://doi.org/10.1016/j.cell.2021.01.037

Hamilton, W. L., Tonkin-Hill, G., Smith, E. R., Aggarwal, D., Houldcroft, C. J., Warne, B., … Chaudhry, Y. (2021). Genomic epidemiology of COVID-19 in care homes in the East of England. eLife, 10, e64618. https://doi.org/10.7554/eLife.64618

February 2021

Harper, H., Burridge, A., Winfield, M., Finn, A., Davidson, A., Matthews, D., … Barker, G. (2021). Detecting SARS-CoV-2 variants with SNP genotyping. PLOS ONE, 16(02), e0243185. https://doi.org/10.1371/journal.pone.0243185

du Plessis, L., McCrone, J. T., Zarebski, A. E., Hill, V., Ruis, C., Gutierrez, B., … Pybus, O. (2021). Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK. Science, 371(6530), 708–712. https://doi.org/10.1126/science.abf2946

January 2021

Kraemer, M. U. G., Hill, V., Ruis, C., Parag, K. V., Lindstrom Battle, A., O’Toole, Á., … Pybus, O. G. (2021). Spatio-temporal heterogeneity and the spread of lineage B.1.1.7 in the United Kingdom. Retrieved from https://virological.org/t/spatio-temporal-heterogeneity-and-the-spread-of-lineage-b-1-1-7-in-the-united-kingdom/601

Lycett, S. J., Hughes, J., McHugh, M. P., da Silva Filipe, A., Dewar, R., Lu, L., … Robertson, D. L. (2021). Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2. medRxiv. https://doi.org/10.1101/2021.01.08.20248677

Golubchik, T., Lythgoe, K. A., Hall, M., Ferretti, L., Fryer, H. R., MacIntyre-Cockett, G., … Bonsall, D. (2021). Early analysis of a potential link between viral load and the N501Y mutation in the SARS-COV-2 spike protein. medRxiv. https://doi.org/10.1101/2021.01.12.20249080

Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., … Connor, T. R. (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(01), 64–75.e11. https://doi.org/10.1016/j.cell.2020.11.020

de Silva Filipe, A., Shepherd, J. G., Williams, T., Hughes, J., Aranday-Cortes, E., Asamaphan, P., … Thomson, E. C. (2021). Genomic epidemiology reveals multiple introductions of SARS-CoV-2 from mainland Europe into Scotland. Nature Microbiology, 6(01), 112–122. https://doi.org/10.1038/s41564-020-00838-z

December 2020

Vöhringer, H., Sinnott, M., Amato, R., Martincorena, I., Kwiatkowski, D., Barrett, J. C., … The COVID-19 Genomics UK (COG-UK) consortium. (2020). Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown. Retrieved from https://virological.org/t/lineage-specific-growth-of-sars-cov-2-b-1-1-7-during-the-english-national-lockdown/575

October 2020

Ladhani, S. N., Chow, J. Y., Janarthanan, R., Fok, J., Crawley-Boevey, E., Vusirikala, A., … The London Care Home Investigation Team. (2020). Increased risk of SARS-CoV-2 infection in staff working across different care homes: enhanced CoVID-19 outbreak investigations in London care Homes. Journal of Infection, 81(04), 621–624. https://doi.org/10.1016/j.jinf.2020.07.027

July 2020

The COVID-19 Genomics UK (COG-UK) consortium. (2020). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet Microbe, 1(03), e99–e100. https://doi.org/10.1016/s2666-5247(20)30054-9

Selective survey of COVID-19 related research published worldwide

To aid COG-UK consortium research partners, the consortium posted a selected list of genomic research studies published around the world on COVID-19 from May 2020 to March 2021. The files are available in PDF format, click on the links to download:

COG-UK Publications

How to cite COG-UK as an author and acknowledge COG-UK funding