SARS-CoV-2 genome sequence prevalence and growth rate update: 25 October 2023
Updated 27 March 2024
Applies to England
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Variant prevalence
Testing policy and sequencing should be considered when interpreting variant data. Information about surveillance systems for England are reported by the UK Health Security Agency (UKHSA) in the National Influenza and COVID-19 surveillance report.
The prevalence of lineages amongst UK sequences by Phylogenetic Assignment of Named Global Outbreak Lineages (Pangolin) designation is presented in Figure 1. Lineages are shown if there are more than or equal to 5,000 sequences since 1 May 2023 or if they represent more than or equal to 1% of sequences within a single week over the last 6 weeks. Lineages that do not meet these criteria are combined with their parent lineage (for example, BA.2.4 is combined with BA.2).
The lineages have been assigned using the accurate Ultrafast Sample placement on Existing tRee (UShER) mode and version 1.22 of the Pangolin data.
Figure 2 shows the relationship between all lineages shown in Figure 1. The figure details the hierarchical relationship of the lineages from left to right, starting with B.1.1.529 through 14 sublineage levels, including aliases and the parent lineages for any recombinants included in the prevalence figures (for example, BJ.1 and BM.1.1.1 are the parent lineages for the XBB recombinant). The percentage of each lineage in the most recent week of data in Figure 1 is shown next to the relevant lineage labels in Figure 2. Where a sublineage has a percentage in Figure 2, it is excluded from the percentage given for any parent lineages. Any lineages that are not present in the most recent week of genomic data will not have a percentage in Figure 2. The colours in Figure 2 correspond to the lineage colours in Figure 1.
Figure 1. Prevalence of Pangolin lineages in the UK sequence data with a specimen date from week beginning 1 May 2023 to week beginning 9 October 2023, as of 19 October 2023
The total number of valid sequence results per week is shown by the black line. The ‘Other’ category in this plot contains all lineages that do not meet the relevant criteria after combining smaller sub-lineages. ‘Unassigned’ are sequences that could not be assigned a lineage by Pangolin. Lineages present in at least 2% of sequences in the most recent week are labelled to the right of the plot.
Figure 2. Sankey diagram showing the relationship between Pangolin lineages observed in UK sequence data since 1 May 2023. Data shown as of 19 October 2023.
Proportions are given for lineages that are observed in sequences with a specimen date between 9 October 2023 and 15 October 2023. Lineage colours match those in Figure 1.
Variant modelling
Growth rate modelling is under review and will be reinstated in future reports.
Sources and acknowledgments
Data sources
Data used in this investigation is derived from the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) data set, the UKHSA genomic programme data set and the UKHSA Second Generation Surveillance System.
Authors of this report
UKHSA Genomics Public Health Analysis Team
UKHSA Infectious Disease Modelling Team
UKHSA TARZET Technical Secretariat