Patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate

We sequenced a cohort of SARS-CoV-2 samples in duplicate to develop reliable methods for accurately describing and analysing patterns of within-host variation in the context of ongoing genomic epidemiological studies. Analysis and results are described in the accompanying publication (1). The 1,181 samples were taken as a random subset from a larger prospective study into SARS-CoV-2 infections at Cambridge University Hospitals National Health Service Foundation Trust, a secondary care provider and tertiary referral centre in the East of England (2, 3). Two libraries were sequenced for each sample with separate reverse transcription, PCR amplification and library preparation steps following the COVID-19 ARTIC v3 illumina library construction and sequencing protocol(https://www.protocols.io/view/covid-19-artion-an-be3wjgpe?version_warning=no). Data were generated by the Wellcome Sanger Institute COVID-19 Surveillance Team(https://www.sanger.ac.uk/project/wellcome-sanger-institute-covid-19-surveillance-team/) for the COVID-19 Genomics UK Consortium (https://www.cogconsortium.uk/). These data are available open access. Publications using these data should acknowledge and cite the source using the following format: "This publication uses data generated from the Wellcome Sanger Institute for the COVID-19 Genomics UK Consortium, as described in Tonkin-Hill G, Martincorena I, et al. (2020) https://doi.org/10.1101/2020.12.23.424229". (1) Tonkin-Hill G*, Martincorena I*, Amato R*, Lawson ARJ, Gerstung M, Johnston I, et al. Patterns of within-host genetic diversity in SARS-CoV-2. bioRxiv. Cold Spring Harbor Laboratory Press; 2020; https://doi.org/10.1101/2020.12.23.424229 (2) Hamilton WL, Tonkin-Hill G, Smith E, Houldcroft C, Warne B, Meredith L, et al. COVID-19 infection dynamics in care homes in the East of England: a retrospective genomic epidemiology study. medRxiv. Cold Spring Harbor Laboratory Press; 2020;2020.08.26.20182279. (3) Meredith LW, Hamilton WL, Warne B, Houldcroft CJ, Hosmillo M, Jahun AS, 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;20:1263–72.