SARS-CoV-2 variant surveillance and assessment: technical briefing 54
Updated 22 September 2023
Applies to England
© Crown copyright 2023
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Summary
This report has been published to share the detailed variant surveillance analyses which contribute to the variant risk assessments and designation of new SARS-CoV-2 variants. This specialist technical briefing contains early data and analysis on emerging variants and findings have a high level of uncertainty. Unless stated otherwise, this technical briefing uses a data cut-off of 11 September 2023 to allow time for analyses.
During periods when technical briefings are being published by the UK Health Security Agency (UKHSA), the routine variant prevalence and growth rate reports will be included in the technical briefing.
Situational assessment BA.2.86 (Variant Technical Group of 12 September 2023)
The variant technical group reviewed available data on 12 September. Although there is additional information, primarily published laboratory data, there is nothing that materially changes the situational assessment of 5 September 2023. There are still insufficient BA.2.86 sequences in any country to make a reliable assessment of growth. The assessment will next be reviewed on 19 September 2023.
Data summary
BA.2.86
As of 11 September 2023, there are 37 BA.2.86 sequenced cases in England, an increase of 3 cases in the last week. Cases were in East of England, London, North East and North West England. Of 37 total cases in England, 7 were hospitalised (1 has unknown hospitalisation status), and no deaths due to COVID-19 have been reported. Most sequenced cases in England are people tested in hospital and the hospitalisation rate cannot be estimated from this data. These cases include 28 sequenced as part of an investigation of an outbreak in a care home which reported a high attack rate. Of the remaining 9 cases, all were sporadic apart from which 2 may be epidemiologically linked.
As of 11 September 2023, 5 BA.2.86 cases have been reported by Public Health Scotland. There are no cases reported by Wales or Northern Ireland.
The global situation is dynamic with new cases identified daily. As of 12 September 2023, there are 99 sequences from human cases identified as BA.2.86 available in GISAID from 14 countries. The earliest collection date is 24 July 2023, and the most recent collection date is 30 August 2023. Of the 99 sequences, 36 are from the UK. The remaining UK sequence data will be uploaded to GISAID in due course. There are also multiple reports of BA.2.86 detected in wastewater in other countries though limited sequence data is available.
Sequence variant prevalence (UKHSA-designated variants)
As of 7 September 2023, for sequences with a specimen date between 21 August 2023 and 27 August 2023 inclusive: 26.3% were classified as V-23JUL-01 (EG.5.1); 22.6% of UK sequences were classified as V-22OCT-02 (XBB); 21.8% were classified as V-23APR-01 (XBB.1.16); 4.0% were classified as V-23JAN-01 (XBB.1.5); 2.6% were classified as V-23AUG-01 (BA.2.86); and 2.5% were classified as V-22DEC-01 (CH.1.1). The remaining sequences (20.2%) were from lineages that have not been designated as a variant by UKHSA or are of insufficient quality to assign.
Horizon scanning
Variant designations are made when variants are considered significant enough to report in routine surveillance and to facilitate variant-specific epidemiological studies. The designation means that UKHSA has confirmed a genomic case definition and will monitor the variant through regular surveillance analyses. Since the last report, no new variants have been designated.
Variants are identified as signals when they show growth or potentially significant mutational profile through a standard horizon scanning process. Lineage XBB.1.16.6 is currently being monitored as part of horizon scanning due to increased growth both within the UK and internationally. The spike mutation combination F455L:L456F is also being investigated as it is associated with several lineages that show increased growth.
Growth rates
Using English sequencing data, only EG.5.1.4, XBB.1.16.6 and EG.5.1.3 were identified, by both the generalised additive model and the logistic regression model, as having positive growth rates relative to other lineages. However, the sample sizes for the majority of lineages are relatively small. The lineage BA.2.86 does not appear in this analysis as it did not meet the criteria of 50 sequenced cases and 1.5% lineage prevalence in the past 6 weeks.
BA.2.86 (V-23AUG-01)
UK cases
There are 37 confirmed cases of BA.2.86 in England.
Of these, 28 cases were identified as part of a care home outbreak investigation in the East of England.
There are an additional 9 cases identified through routine surveillance: 6 in London, one in the North West, one in the North East, and one in the East of England. Of 7 cases with known information on epidemiological links, 2 cases may be epidemiologically linked. None of the 7 cases have recent travel history.
Of 37 cases, 7 cases were hospitalised, 2 were tested in an emergency department, and 1 case has unknown hospitalisation status. There were no deaths due to COVID-19 among these cases. These data cannot be used to estimate a hospitalisation rate since most testing and genomic surveillance is amongst people in hospital.
Figure 1. Number of confirmed BA.2.86 cases by specimen date as of 11 September 2023
The data used in this graph can be found in the accompanying spreadsheet.
Figure 2. Age-sex breakdown of BA.2.86 cases as of 11 September 2023
The data used in this graph can be found in the accompanying spreadsheet.
Figure 3. Number of confirmed BA.2.86 cases by property type and specimen date as of 11 September 2023
The data used in this graph can be found in the accompanying spreadsheet.
Scotland have reported 5 confirmed cases of BA.2.86, an increase of 3 since the previous technical briefing. Further information about Scottish cases is published on the Public Health Scotland webpages.
Global cases
As of 12 September 2023, there are 100 sequences from 99 human cases identified as BA.2.86 available in GISAID. The sequences are from 14 countries: Australia (1); Canada (2); Denmark (13); France (7); Germany (1); Israel (3); Japan (1); Portugal (2); South Africa (17); South Korea (1); Spain (4); Sweden (5); UK (36); and USA (7). One sequence from South Africa was produced from an isolate from an existing case. The earliest collection date is 24 July 2023, and the most recent collection date is 30 August 2023. Figure 4 shows the proportion of sequences from human cases in GISAID that are identified as BA.2.86 by week of collection; the duplicate sequence from South Africa has been removed. An additional 5 partial sequences from wastewater samples are available from Thailand.
Figure 4. Proportion of sequences uploaded to GISAID since 1 July 2023 that are identified as BA.2.86
Sequences are grouped by week of collection and coloured by world region. Sequence data from the UK has been shown separately to those from other European countries. Where collection date is not available, submission date has been used. The proportion of sequences which are BA.2.86 is indicated by the bar (left hand axis). The total number of sequences in GISAID per week are shown by the black line (right hand axis), and the total number of BA.2.86 sequences within each week are shown by the number above each bar. Data as of 12 September 2023.
The data used in this graph can be found in the accompanying spreadsheet.
Phylogeny
Figure 5 shows a phylogeny of the BA.2.86 sequences available in GISAID and additional sequence data from cases in England. The phylogeny was generated as previously described in variant technical briefing 53.
The phylogeny shows diversity among the BA.2.86 sequences and suggests multiple introductions to the UK. The clade that has been designated as lineage BA.2.86.1 is labelled and contains most of the available sequence data from European countries, including all but one of the UK cases.
Figure 5. Phylogeny of BA.2.86 sequences available in GISAID and additional UK sequence data. Sequences are shown by country
Data cut off for sequence data is 7am BST 11 September 2023.
Supplementary data is not available for this figure.
Laboratory investigations
The virus bank grown from the material received by UKHSA from King’s College London has been sequenced and confirmed to be representative of the BA.2.86 lineage. UKHSA laboratories are testing this virus against panels of donated vaccinee sera, sera from the SIREN study, and CONSENSUS study samples. Initial results from these analyses are anticipated week beginning 18 September 2023.
Performance of molecular tests and lateral flow devices are currently being assessed in UKHSA laboratories with cultured virus and clinical samples.
Variant prevalence
Testing policy and sequencing should be considered when interpreting variant data. Information about surveillance systems for England are reported by 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 6. Lineages are shown if there are more than or equal to 5,000 sequences since 20 March 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 7 shows the relationship between all lineages shown in Figure 6. 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 6 is shown next to the relevant lineage labels in Figure 7. Where a sublineage has a percentage in Figure 7, 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 7. The colours in Figure 7 correspond to the lineage colours in Figure 6.
Figure 6. Prevalence of Pango lineages in the UK sequence data with a specimen date from week beginning 20 March 2023 to week beginning 28 August 2023, as of 7 September 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. BA.2.86 and lineages present in at least 2% of sequences in the most recent week are labelled to the right of the plot.
The data used in this graph can be found in the accompanying spreadsheet.
Figure 7. Sankey diagram showing the relationship between Pangolin lineages observed in UK sequence data since 20 March 2023
Proportions are given for lineages that are observed in sequences with a specimen date between 28 August 2023 and 3 September 2023. Data shown as of 7 September 2023. Lineage colours match those in Figure 6.
Supplementary data is not available for this figure.
Variant modelling
Methods used for variant modelling have previously been described in the UKHSA prevalence and growth rate briefings.
Growth rates were based on sequences sampled through Pillar 1 testing (primarily positive tests conducted in hospital) in England (Table 1). The sampling range for both the logistic regression generalised linear model (GLM) and generalised additive model (GAM) are from 17 March 2023 to 1 September 2023. The model fit for any lineage with a positive growth rate advantage (with 95% confidence intervals (CIs) that do not cross zero) are shown in Figure 8. The lineages that had an estimated weekly positive growth rate with reasonable confidence are EG.5.1.4 (29.28%, GAM), XBB.1.16.6 (27.01%, GAM), XBB.1.16.15 (26.60%, GAM), EG.5.1.3 (14.46%, GAM), FL.1.5.1 (13.45%, GAM) and EG.5.1 (12.00%, GAM).
Table 1. Growth rate (GR) of English sequence lineages as of 1 September 2023†
| Lineage* | Lineage Group Composition** | Pillar 1 Sample Size*** | Weekly growth rate advantage (GAM) | Estimated prevalence¥ (GAM) | Weekly growth rate advantage (GLM) |
|---|---|---|---|---|---|
| EG.5.1.4 (XBB.1.9.2.5.1.4) | EG.5.1.4 (100%) | 100 | 29.28% (95% CI: 26.08 to 32.48) | 6.44% (95% CI: 4.83 to 8.52) | 42.23% (95% CI: 10.75 to 73.71) |
| XBB.1.16.6 | XBB.1.16.6 (100%) | 134 | 27.01% (95% CI: 22.65 to 31.37) | 6.89% (95% CI: 4.46 to 10.5) | 37.85% (95% CI: 13.18 to 62.52) |
| XBB.1.16.15 | XBB.1.16.15 (100%) | 102 | 26.6% (95% CI: 23.36 to 29.84) | 6.27% (95% CI: 4.77 to 8.2) | 22.62% (95% CI: -4.63 to 49.86) |
| EG.5.1.3 (XBB.1.9.2.5.1.3) | EG.5.1.3 (100%) | 124 | 14.46% (95% CI: 6.78 to 22.14) | 5.47% (95% CI: 3.59 to 8.23) | 27.95% (95% CI: 2.5 to 53.39) |
| FL.1.5.1 (XBB.1.9.1.1.5.1) | FL.1.5.1 (100%) | 95 | 13.45% (95% CI: 6.12 to 20.79) | 4.13% (95% CI: 2.68 to 6.32) | 27.28% (95% CI: -3.31 to 57.88) |
| EG.5.1 (XBB.1.9.2.5.1) | EG.5.1 (79.36%); EG.5.1.6 (15.14%); EG.5.1.5 (3.21%); EG.5.1.2 (2.29%) | 218 | 12% (95% CI: 5 to 19.01) | 9.09% (95% CI: 6.27 to 13) | 17.5% (95% CI: -2.37 to 37.38) |
| EG.5.1.1 (XBB.1.9.2.5.1.1) | EG.5.1.1 (97.94%); HK.3 (1.8%); HK.2 (0.26%) | 388 | -4.27% (95% CI: -9.62 to 1.07) | 12.73% (95% CI: 8.4 to 18.84) | 18.86% (95% CI: 2.45 to 35.26) |
| XBB.1.9.1 | XBB.1.9.1 (20%); FL.4 (17.5%); FL.15 (12.5%); FL.14 (11.25%); FL.24 (10%)… | 80 | -7.08% (95% CI: -21.38 to 7.23) | 2.05% (95% CI: 1.14 to 3.68) | -18.99% (95% CI: -51.86 to 13.87) |
| EG.6.1 (XBB.1.9.2.6.1) | EG.6.1 (100%) | 62 | -7.82% (95% CI: -21.9 to 6.26) | 1.59% (95% CI: 0.83 to 3.01) | -17.86% (95% CI: -55.42 to 19.7) |
| GE.1 (XBB.2.3.10.1) | GE.1 (100%) | 174 | -8.74% (95% CI: -19.21 to 1.73) | 4.77% (95% CI: 3.07 to 7.33) | -20.71% (95% CI: -43.1 to 1.68) |
| XBB.1.5 | XBB.1.5 (40.65%); XBB.1.5.59 (10.57%); XBB.1.5.28 (6.5%); XBB.1.5.11 (5.69%); XBB.1.5.71 (5.69%)… | 123 | -12.16% (95% CI: -22.71 to -1.62) | 2.57% (95% CI: 1.64 to 4.01) | -16.26% (95% CI: -44.04 to 11.52) |
| XBB.1.16 | XBB.1.16 (69.13%); XBB.1.16.21 (6.68%); XBB.1.16.9 (5.96%); XBB.1.16.19 (4.33%); XBB.1.16.2 (2.71%)… | 554 | -20.73% (95% CI: -29.87 to -11.59) | 9.88% (95% CI: 6.91 to 13.95) | -30.34% (95% CI: -44.57 to -16.12) |
| XBB.1.16.1 | XBB.1.16.1 (65.48%); FU.1 (23.81%); FU.2 (10.71%) | 84 | -22.14% (95% CI: -35.94 to -8.33) | 1.37% (95% CI: 0.74 to 2.51) | -22.9% (95% CI: -57.8 to 12) |
| XBB.1.9.2 | XBB.1.9.2 (39.24%); EG.1 (26.58%); EG.2 (25.32%); EG.7 (5.06%); EG.5 (2.53%)… | 79 | -29.13% (95% CI: -45.14 to -13.12) | 1.03% (95% CI: 0.53 to 2) | -37.45% (95% CI: -72.65 to -2.26) |
| XBB.1.16.11 | XBB.1.16.11 (100%) | 112 | -37.76% (95% CI: -53.43 to -22.1) | 2.14% (95% CI: 0.75 to 5.93) | -7.42% (95% CI: -32.78 to 17.94) |
| XBB.2.3.11 | XBB.2.3.11 (91.92%); GS.1 (8.08%) | 99 | -62% (95% CI: -86.31 to -37.68) | 1.05% (95% CI: 0.4 to 2.78) | -20.28% (95% CI: -48.07 to 7.51) |
*Listed parent lineages include all sub-lineages, other than those explicitly modelled.
** The top 5 contributing lineages to the modelled group in the most recent 6 weeks (21 July 2023 to 1 September 2023). More than 5 sublineages are indicated by “…”
*** Sample size is for Pillar 1 samples in England in the most recent 6 weeks (21 July 2023 to 1 September 2023).
¥ Estimated prevalence for the 1 September 2023.
† Sampling range for both logistic regression and generalised additive models (GAM) is from 17 March 2023 to 1 September 2023.
CI = confidence interval
Figure 8. Modelled prevalence of lineage groups with a growth rate advantage over other circulating lineages
The black line shows the central estimate and blue shaded regions the 95% CIs. Points show the national level proportions, with the size being indicative of the sample size for that particular lineage. The grey portion of the ribbon denotes that this period of time is likely to be backfilled with more sequenced cases, making proportions unreliable.
Supplementary data is not available for this figure.
Published information on variants
On 1 April 2022 UKHSA amended its variant classification system. Further details are available in technical briefing 39.
SARS-CoV-2 routine variant data update covers surveillance data and sequencing coverage data on all other variants up to 25 March 2022.
The collection page gives content on variants, including previous technical briefings. Technical briefings are published periodically.
The UKHSA variant definition repository contains the previous genomic definitions for UKHSA declared variants.
Sources and acknowledgments
Data sources
Data used in this investigation is derived from the CLIMB and UKHSA genomic programme data set, the UKHSA Second Generation Surveillance System, the Secondary Uses Service data set, Emergency Care Data Set, the UKHSA Case and Incident Management System and GISAID.
Authors of this report
Nurin Iwani Binti Abdul Aziz
Wendy Barclay
Jamie Lopez Bernal
Kevin Bewley
Naomi Coombes
Meera Chand
Gavin Dabrera
Katy Davidson
Martyn Fyles
Eileen Gallagher
Rachael Graham
Natalie Groves
Bassam Hallis
Susan Hopkins
Robert Jordan
Meaghan Kall
Amelia Kelly
Nick Loman
Edward Parsons
Laura Lopez Pascua
Rob Patton
Andrew Rambaut
Elise Tessier
Erik Volz
Tom Ward
Deborah Williamson
Variant Technical Group members
Chair
Meera Chand (UKHSA)
Genomics and bioinformatics
Andrew Rambaut (University of Edinburgh)
Thomas Peacock (Pirbright Institute and Imperial College London)
Matt Holden (Public Health Scotland)
Nicholas Loman (UKHSA and University of Birmingham)
Richard Myers (UKHSA)
Eileen Gallagher (UKHSA)
Natalie Groves (UKHSA)
Virology and immunology
Deborah Williamson (UKHSA)
Bassam Hallis (UKHSA)
Derek Smith (University of Cambridge)
Gavin Screaton (University of Oxford)
Lance Turtle (University of Liverpool)
Maria Zambon (UKHSA)
Ravi Gupta (University of Cambridge)
Susanna Dunachie (University of Oxford)
Katie Binley (Northern Ireland Public Health Agency)
Wendy Barclay (Imperial College London)
Emma Thomson (University of Glasgow and London School of Hygiene and Tropical Medicine)
Epidemiology and modelling
Chris Williams (Public Health Wales)
Daniela de Angelis (University of Cambridge)
Erik Volz (UKHSA and Imperial College London)
Fergus Cumming (UKHSA)
Nick Watkins (UKHSA)
Jamie Lopez-Bernal (UKHSA)
John Edmunds (London School of Hygiene and Tropical Medicine)
Julia Gog (Scientific Pandemic Influenza Group on Modelling and University of Cambridge)
Jim McMenamin (Public Health Scotland)
Kimberly Marsh (Public Health Scotland)
Neil Ferguson (Imperial College London)
Meaghan Kall (UKHSA)
Susan Hopkins (UKHSA)
Thomas Finnie (UKHSA)
Tom Ward (UKHSA)
International epidemiology
Chris Lewis (Foreign, Commonwealth and Development Office)
Acknowledgements
The authors are grateful to those teams and groups providing data for these analyses including: NHS, CLIMB, the Wellcome Sanger Institute, Health Protection Data Science teams, the Genotype to Phenotype Consortium, Medical Research Council Biostatistics Unit, the Francis Crick Institute, Cambridge and Imperial College, London.
We are also grateful to the SIREN and CONSENSUS studies as well as Kings College London for providing materials for laboratory analysis.