About
This website displays SARS-CoV-2 genome data in England. Samples come from Lighthouse Labs covering most of the pillar 2 testing in England, and are sequenced by the Wellcome Sanger Institute's Covid-19 Genomics Initiative. These data are a subset of what is made available by the COVID-19 Genomics UK Consortium.
The Lineages tools allow exploration of how SARS-CoV-2 lineages have changed in frequency over time across England. These data are available in two forms: a modelled version which presents an updated version of the case-count based model of the most common lineages described in Lineage-specific growth of SARS-CoV-2 B.1.1.7 during the English national lockdown, and alternatively raw counts of the number of genomes from each lineage, aggregated by local authority in two-week intervals.
The number of sequences from different pangolin lineages aggregated by week and local authority is available on the downloads page.
Source code for the model and the spatiotemporal viewer are available on GitHub.
This work is a collaboration between the Wellcome Sanger Institute, the European Bioinformatics Institute, the UK Health Security Agency, and the COVID-19 Genomics UK (COG-UK) Consortium.
The data displayed on this website are provisional and non-validated, and not a comprehensive record of SARS-CoV-2 incidence. The Wellcome Sanger Institute releases these data for research and public interest purposes only. Caution should be exercised when reviewing the data as it is easy to misinterpret. Please see our guidance for reporting on this website. The Wellcome Sanger Institute assumes no responsibility arising out of or in connection with the data or its use. Authoritative, validated SARS-CoV-2 genome data is made available by the UK Health Security Agency.