Coverage reports 

COG-UK captures SARS-CoV-2 samples from COVID-19 infections from across the UK. These weekly summaries include information on sequencing coverage (the number of sequences available in COG-UK out of the total number of people with a COVID-19 infection) across Wales, Scotland, England and Northern Ireland.

Coverage Report 4th January 2020

Coverage Report 30th November 2020

Coverage Report 9th November 2020

Coverage Report 2nd November 2020

Coverage Report 26th October 2020

Coverage Report 19th October 2020


Mutation surveillance reports

These reports provide background context on mutation tracking by COG-UK and describe a priority set of SARS-CoV-2 Spike mutations that are of particular interest based on potential epidemiological significance in the UK and/or biological evidence based on the literature or unpublished work. They provide details on the frequency of mutations, and their potential biological and immunological significance as we currently understand it.

COG-UK report on SARS-CoV-2 Spike mutations of interest in the UK — 15th January 2021.


COG-UK publications and preprints

An integrated national scale SARS-CoV-2 genomic surveillance network. Lancet Microbe 2020; 1(3): e99-e100.

Aggarwal D MR, Hamilton WL. The role of genomics in understanding COVID-19 outbreaks in long term care facilities. . OSFio 2020; : 23. DOI:10.31219.

Augusto J, Menacho K, Andiapen M, et al. Healthcare Workers Bioresource: Study outline and baseline characteristics of a prospective healthcare worker cohort to study immune protection and pathogenesis in COVID-19 [version 1; peer review: 1 approved with reservations]. Wellcome Open Research 2020; 5(179).

Baker DJ, Kay GL, Aydin A, et al. CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing. bioRxiv 2020: 2020.06.24.162156.

Boshier FAT, Pang J, Penner J, et al. Remdesivir induced viral RNA and subgenomic RNA suppression, and evolution of viral variants in SARS-CoV-2 infected patients. medRxiv 2020: 2020.11.18.20230599.

Chappell JG, Tsoleridis T, Clark G, et al. Retrospective screening of routine respiratory samples revealed undetected community transmission and missed intervention opportunities for SARS-CoV-2 in the United Kingdom. medRxiv 2020: 2020.08.18.20174623.

Colton H, Ankcorn M, Yavuz M, et al. Improved sensitivity using a dual target, E and RdRp assay for the diagnosis of SARS-CoV-2 infection: Experience at a large NHS Foundation Trust in the UK. The Journal of infection 2020: S0163-4453(20)30339-X.

du Plessis L, McCrone JT, Zarebski AE, et al. Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK. medRxiv 2020: 2020.10.23.20218446.

Filipe ADS, Shepherd J, Williams T, et al. Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence. medRxiv 2020: 2020.06.08.20124834.

Hamilton WL, Tonkin-Hill G, Smith E, et al. COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study. medRxiv 2020: 2020.08.26.20182279.

Harper H, Burridge AJ, Winfield M, et al. Detecting SARS-CoV-2 variants with SNP genotyping. bioRxiv 2020: 2020.11.18.388140.

Hosie MJ, Epifano I, Herder V, et al. Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK. bioRxiv 2020: 2020.09.23.309948.

Illingworth CJR, Hamilton WL, Jackson CH, et al. A2B-COVID: A method for evaluating potential SARS-CoV-2 transmission events. medRxiv 2020: 2020.10.26.20219642.

Lo SW, Jamrozy D. Genomics and epidemiological surveillance. Nat Rev Microbiol 2020; 18(9): 478.

Lythgoe KA, Hall M, Ferretti L, et al. Shared SARS-CoV-2 diversity suggests localised transmission of minority variants. bioRxiv 2020. 05.28.118992.

Meredith LW, Hamilton WL, Warne B, et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis 2020.

Nicholls SM, Poplawski R, Bull MJ, et al. MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance. bioRxiv 2020: 2020.10.06.328328.

Pang J, Boshier FAT, Alders N, Dixon G, Breuer J. No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS). medRxiv 2020: 2020.07.07.20148213.

Parker MD, Lindsey BB, Leary S, et al. periscope: sub-genomic RNA identification in SARS-CoV-2 ARTIC Network Nanopore Sequencing Data. bioRxiv 2020: 2020.07.01.181867.

Pang J, Boshier FAT, Alders N, Dixon G, Breuer J. No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS). medRxiv 2020: 2020.07.07.20148213.

Rambaut A, Holmes EC, O’Toole Á, et al. A dynamic nomenclature proposal for SARS-CoV-2 lineages to assist genomic epidemiology. Nat Microbiol 2020.

Snell LB, Fisher CL, Taj U, et al. Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks. medRxiv 2020: 2020.11.17.20232827.

Stirrup OT, Hughes J, Parker M, et al. Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data. medRxiv 2020: 2020.11.12.20230326.

Thomson EC, Rosen LE, Shepherd JG, et al. The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. bioRxiv 2020: 2020.11.04.355842.

Tighe PJ, Urbanowicz RA, Fairclough L, et al. Potent anti-SARS-CoV-2 Antibody Responses are Associated with Better Prognosis in Hospital Inpatient COVID-19 Disease. medRxiv 2020: 2020.08.22.20176834.

Volz EM, Hill V, McCrone JT, et al. Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. medRxiv 2020: 2020.07.31.20166082.

Weissman D, Alameh M-G, de Silva T, et al. D614G Spike Mutation Increases SARS CoV-2 Susceptibility to Neutralization. medRxiv 2020: 2020.07.22.20159905.


Read our publications and authorship policy and view the full COG-UK authorship list.

Public Data and Analysis

COG-UK sits at the interface of public health action and academic research. We are committed to open science, and sharing all data that we can as rapidly as possible. This includes sharing data for use by Public Health authorities internationally, to support COVID-19 response, and sharing data in such a way that the academic community can access and use the data and analysis according to FAIR data principles.

Please note that the data that is being shared is the work of hundreds of people and should be treated as unpublished data. If you wish to publish research using the data, please get in contact with COG-UK first to ensure that those who have generated the data can be involved in its analysis.

From this website are aiming to share the results of genomic analysis that feed into weekly updates to the UK Government and Public Health Agencies to help guide its healthcare strategies in responding to, and minimising, the spread of COVID-19 across the UK.


The Centre for Genomic Pathogen Surveillance maintain a Microreact website which permits continuous evaluation of the lineages circulating in the UK (currently updated weekly).


The MRC-University of Glasgow Centre for Virus Research have developed a web application for the analysis of SARS-CoV-2 genome sequences: CoV-GLUE

Latest Sequence Data

Sequences are released rapidly and should be considered draft and subject to change.

All links refer to the latest data build, typically updated daily. The very latest datasets and analysis are available via MRC CLIMB:

We regularly deposit datasets into public databases (GISAID for consensus sequences, ENA for raw data).

GISAID - Global Initiative on Sharing All Influenza Data

The Global Initiative on Sharing All Influenza Data (GISAID) database has emerged as the standard database for sharing of SARS-CoV-2 data internationally.


The COG-UK consortium regularly deposits sequences into this database, which can be viewed in international context via Nextstrain.

INSDC (European Nucleotide Archive)

We are in the process of transferring and uploading raw sequencing reads through the European Nucleotide Archive’s Sequence Read Archive service (BioProject PRJEB37886), with consensus sequences also to follow into ENA/Genbank.