Reduced sequencing
From late March 2023 onwards, due to the low number of sequenced samples, the UK SARS-CoV-2 sequencing surveillance data is not updated on the Wellcome Sanger Institute COVID-19 Genomic surveillance dashboard.
Updates
Reduced sequencing
From 1 April 2022, the number of samples the Wellcome Sanger Institute processes for Covid-19 virus genome sequencing has reduced. The Institute now sequences samples from the ONS study but does not receive time and location data associated with these samples and therefore is unable to display them here.
Reduced coverage in some regions
Wellcome Sanger Institute currently receives samples from fewer Lighthouse Labs, which will reduce coverage in some regions including the South West of England.
Update (14 March 2022): Sample reception from all Lighthouse Labs has resumed.
North East sampling error
Due to a metadata issue, recent releases have reported Omicron proportions as artificially low in the North East. We have now excluded the affected samples from the period to avoid this bias.
Aggregation window and estimated cases
We have changed our aggregation window from two weeks to one week, in order to better reflect rapid changes in proportions.
We have added an estimate of total cases of each lineage by combining genome proportions with total case numbers from api.coronavirus.data.gov.uk.
Additionally, charts may now be downloaded in CSV format. These downloads are generated client-side to reflect the selection of lineage, area and date.
Sampling of S-gene target failure
To ensure Omicron cases are identified for public health reasons, S-gene target failure (SGTF) samples are currently prioritised for sequencing. To avoid this bias affecting the results seen here, we have downsampled SGTF samples in this data such that the proportion of SGTF sequences approximates the proportion of overall SGTF cases for each LTLA-day.
Update: SGTF-based prioritisation ceased on 10 December.
Assigning AY.4.2
Because lineage-defining mutations of AY.4.2, including Y145H, are affected by amplicon dropout, we have used Pangolin in Usher mode with the latest decision tree, and supplemented it with predictions of AY.4.2 from an alternative approach to increase sensitivity.
Sub-lineages of Delta
In order to better track diversity within the Delta variant, we are now showing the most common sub-lineages in the UK (at present AY.4, AY.5, AY.6 and AY.9). These assignments are based on recent updates from the Pango network. These lineages remain the Delta variant, just as B.1.617.2 does, and their designation does not imply any functional biological difference from B.1.617.2.
We now assign lineages with UShER, as implemented in pangolin, which calculates lineages by placing sequences on a phylogenetic tree.
Change in source of time and place data
The source of locations and dates has been updated. The new source is used for samples from 22 May 2021 onwards, and may result in small changes in counts for some LTLA-weeks.
Dark mode
We have added a “dark mode” style to the site. This will be automatically applied based on your system preference, and can be chosen manually using the main menu.
New features
We have added two new features to the Raw and Modelled lineage pages. You can now search by postcode, as well as by entering a local authority name. You can also drag horizontally on any graph to zoom in on a specific date range.