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COG-UK Publications

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June 2022

Kläser, K., Molteni, E., Graham, M., Canas, L. S., Österdahl, M. F., Antonelli, M., … Aggarwal, D. (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(1). 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., … Darby, A. C. (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. https://doi.org/10.1093/gigascience/giac045

Krutikov, M., Stirrup, O., Nacer-Laidi, H., Azmi, B., Fuller, C., Tut, G., … Shallcross, L. (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

Pascall, D. J., Vink, E., Blacow, R., Bulteel, N., Campbell, R., Campbell, A., … Lewis, T. (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

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., … Chand, M. (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., … Riley, S. (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 & 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

Hill, V., Louis du Plessis, Alexander, T. P., Aggarwal, D., Carabelli, A., Colquhoun, R., … Barrett, J. (2022). The origins and molecular evolution of SARS-CoV-2 lineage B.1.1.7 in the UK. bioRxiv. https://doi.org/10.1101/2022.03.08.481609

Wilkinson, S. A., Richter, A., Casey, A., Osman, H., Mirza, J. D., Stockton, J., … Loman, N. J. (2022). Recurrent SARS-CoV-2 Mutations in Immunodeficient Patients. medRxiv. https://doi.org/10.1101/2022.03.02.22271697

February 2022

Aggarwal, D., Page, A. J., Schaefer, U., Savva, G. M., Myers, R., Volz, E., … Wise, E. (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

Brunner, F. S., Brown, M. R., Bassano, I., Denise, H., Khalifa, M. S., Wade, M., … Paterson, S. (2022). City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants. medRxiv. https://doi.org/10.1101/2022.02.16.22269810

Stirrup, O., Blackstone, J., Mapp, F., MacNeil, A., Panca, M., Holmes, A., … Robertson, D. (2022). Evaluating the effectiveness of rapid SARS-CoV-2 genome sequencing in supporting infection control teams: the COG-UK hospital-onset COVID-19 infection study. medRxiv. https://doi.org/10.1101/2022.02.10.22270799

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

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. medRxiv. https://doi.org/10.1101/2022.02.02.22270110

Aggarwal, D., Myers, R., Hamilton, W. L., Bharucha, T., Tumelty, N. M., Brown, C. S., … Page, A. J. (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

Krutikov, M., Stirrup, O., Nacer-Laidi, H., Azmi, B., Fuller, C., Tut, G., … Shallcross, L. (2022). Outcomes of SARS-CoV-2 Omicron infection in residents of Long-Term Care. medRxiv. https://doi.org/10.1101/2022.01.21.22269605

Willett, B. J., Grove, J., MacLean, O. A., Wilkie, C., Logan, N., Lorenzo, G. D., … Puxty, K. (2022). The hyper-transmissible SARS-CoV-2 Omicron variant exhibits significant antigenic change, vaccine escape and a switch in cell entry mechanism. medRxiv. https://doi.org/10.1101/2022.01.03.21268111

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

Panovska-Griffiths, J., Swallow, B., Hinch, R., Cohen, J., Rosenfeld, K., Stuart, R. M., … Kerr, C. C. (2022). Statistical and agent-based modelling of the transmissibility of different SARS-CoV-2 variants in England and impact of different interventions. medRxiv. https://doi.org/10.1101/2021.12.30.21267090

Allen, H., Vusirikala, A., Flannagan, J., Twohig, K. A., Zaidi, A., Chudasama, D., … Kall, M. (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., … Mori, M. (2021). 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., Merrick, B., Alcolea-Medina, A., Charalampous, T., … Nebbia, G. (2021). 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., … McClure, C. P. (2021). 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., … Breuer, J. (2021). 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

McCrone, J. T., Hill, V., Bajaj, S., Pena, R. E., Lambert, B. C., Inward, R., … O’Toole, Á. (2021). Context-specific emergence and growth of the SARS-CoV-2 Delta variant. medRxiv. https://doi.org/10.1101/2021.12.14.21267606

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

Eales, O., Page, A. J., de Oliveira Martins, L., Wang, H., Bodinier, B., Haw, D., … Elliott, P. (2021). 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. medRxiv. https://doi.org/10.1101/2021.12.17.21267925

Davis, C., Logan, N., Tyson, G., Orton, R., Harvey, W. T., Perkins, J. S., … Willett, B. J. (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., … Mukeredzi, I. (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., … Roy, S. (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

Kläser, K., Molteni, E., Graham, M., Canas, L., Fösterdahl, M., Antonelli, M., … Ourselin, S. (2021). COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: two prospective observational cohort studies. medRxiv. https://doi.org/10.1101/2021.11.24.21266748

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

October 2021

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

September 2021

Martin, D. P., Weaver, S., Tegally, H., San, E. J., Shank, S. D., Wilkinson, E., … Robertson, D. 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., … Loman, N. J. (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., … Weller, S. 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., … Merhi, 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., … Vollmer, M. (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

Pascall, D. J., Mollett, G., Blacow, R., Bulteel, N., Campbell, R., Campbell, A., … Lycett, S. (2021). The The SARS-CoV-2 Alpha variant caused increased clinical severity of disease in Scotland: a genomics-based prospective cohort analysis. medRxiv. https://doi.org/10.1101/2021.08.17.21260128

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. 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., … du Plessis, L. (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., & 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., … Pinckert, M. L. (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., … Elliott, P. (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

Lindsey, B. B., Villabona-Arenas, Ch. J., Campbell, F., Keeley, A. J., Parker, M. D., Shah, D. R., … Cori, A. (2021). Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves. medRxiv. https://doi.org/10.1101/2021.07.15.21260537

Dolton, G., Rius, C., Hasan, M. S., Wall, A., Szomolay, B., Behiry, E., … Sewell, A. K. (2021). Emergence of immune escape at dominant SARS-CoV-2 killer T-cell epitope. medRxiv. https://doi.org/10.1101/2021.06.21.21259010

Li, K. K., Woo, Y. M., Stirrup, O., Hughes, J., Ho, A., Filipe, A. D. S., … Sreenu, V. B. (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., … Aanensen, D. M. (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

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

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., … Bell, A. (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., … Culap, 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., … Barclay, W. (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., … Howson-Wells, H. C. (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

May 2021

Aggarwal, D., Warne, B., Jahun, A., Hamilton, W., Fieldman, T., Plessis, L., … Nsonwu, O. (2021). Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nature Portfolio. https://doi.org/10.21203/rs.3.rs-520627/v1

Hsu, S., Parker, M. D., Lindsey, B. B., State, A., Zhang, P., Foulkes, B. H., … Partridge, D. G. (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., … Elliott, P. (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

Collier, D. A., De Marco, A., Ferreira, I. A. T. M., Meng, B., Datir, R. P., Walls, A. C., … Garzoni, C. (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

Dong, X., Penrice-Randal, R., Goldswain, H., Prince, T., Randle, N., Salguero, J., … Hiscox, J. A. (2021). Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions in nasopharyngeal samples shows phasic transcription in animal models of COVID-19 and dysregulation at later time points that can also be identified in humans. bioRxiv. https://doi.org/10.1101/2021.03.03.433753

Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., … Spector, T. D. (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

Illingworth, C. J. R., Hamilton, W. L., Jackson, C., Popay, A., Meredith, L., Houldcroft, C. J., … Curran, M. (2021). A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events. medRxiv. https://doi.org/10.1101/2020.10.26.20219642

Lythgoe, K. A., Hall, M., Ferretti, L., de Cesare, M., MacIntyre-Cockett, G., Trebes, A., … Ansari, M. A. (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., … Faust, S. N. (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., … Funk, S. (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., … Smith, K. G. C. (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., … Smith, N. (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

Volz, E., Mishra, S., Chand, M., Barrett, J. C., Johnson, R., Geidelberg, L., … Jorgensen, D. (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

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., … Pinto, D. (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

Parker, M. D., Lindsey, B. B., Shah, D. R., Hsu, S., Keeley, A. J., Partridge, D. G., … Foulkes, B. H. (2021). Altered Subgenomic RNA Expression in SARS-CoV-2 B.1.1.7 Infections. bioRxiv. https://doi.org/10.1101/2021.03.02.433156

Hamilton, W. L., Tonkin-Hill, G., Smith, E. R., Dinesh, A., 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., … Watts, A. (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

Baker, D. J., Aydin, A., Le-Viet, T., Kay, G. L., Rudder, S., de Oliveira Martins, L., … Charles, I. G. (2021). CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes. Genome Medicine, 13(01). https://doi.org/10.1186/s13073-021-00839-5

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., … McCrone, J. T. (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., … Jarrett, 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., … Jesudason, N. (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

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: