Investigation of novel SARS-CoV-2 variant

SOCAIL MEDIA

13 May 2021 This briefing provides an update on previous briefings up to 7 May 2021

Summary

There are 5 variants of concern and 7 variants under investigation (Table 1). This report has been published to continue to share detailed surveillance of VOC-21APR02 (B.1.617.2). A separate report is published covering our routine data on all other VOCs and VUIs. These additional specialist technical briefings represent early data and analysis on an emerging variant and findings have a high level of uncertainty. Whilst case numbers in general remain very low, the proportion of cases which are VOC21APR-02 (B.1.617.2) has increased, as monitored through both genomic and S gene target data. This is most pronounced in London and the North West. The proportion of S gene target positives continues to increase rapidly, but the proportion of VOC-21APR-02 (B.1.617.2) genomes amongst all sequenced cases has a slower increase in the most recent data. Genomic data from the most recent period shown is still being produced and this picture may be related to sequencing lag or alternatively to biases in the S gene data related to geographic coverage. In a small number of areas there are both rising incidence rates and a high proportion of VOC-21APR-02 (B.1.617.2). Surveillance of travellers from India shows a predominance of VOC-21APR-02 (B.1.617.2) amongst imported cases. Secondary attack rates for VOC-21APR-02 (B.1.617.2) are similar to those for VOC20DEC-01 (B.1.1.7) in non-travellers and slightly higher for travellers. Small numbers of non-travel VOC-21APR-02 (B.1.617.2) cases mean these results should be interpreted with caution and will be refined with further cases. Routine reinfection surveillance shows a small number of potential reinfection cases with VOC-21APR-02 (B.1.617.2). This would be expected with any prevalent variant; comparative analyses have been initiated. The updated VOC-21APR-02 (B.1.617.2) risk assessment will be published separately on 14 May 2021.

Published information on variants

The collection page gives content on variants, including prior technical briefings. Definitions for variants of concern, variants under investigation and signals in monitoring are detailed in technical briefing 8. Data on variants not detailed here is published in the variant data update. Variant risk assessments are available in prior technical briefings. A repository containing the up-to-date genomic definitions for all variants of concern (VOC) and variants under investigation (VUI) as curated by Public Health England was created 5 March 2021. The repository can be accessed on GitHub.

Published information on variants



Variants under surveillance

Table 1 shows the current variants of concern (VOC) and variants under investigation (VUI). Summary epidemiology on each variant is shown in Table 2, case numbers are also updated online.
Table 1. Variant lineage and designation as of 12 May 2021 (provisionally extinct variants removed)
Lineage Designation First detected in sequence from Status
B.1.1.7 VOC-20DEC01 UK VOC
B.1.351 VOC-20DEC02 South Africa VOC
P1 VOC-21JAN-02 Japan ex Brazil VOC
B1.1.7 with E484K VOC-21FEB02 UK VOC
B.1.617.2 VOC-21APR-02 India VOC
P2 VUI-21JAN-01 Brazil VUI
A.23.1 with E484K VUI-21FEB-01 UK VUI
B.1.525 VUI-21FEB-03 UK VUI
B.1.1.318 VUI-21FEB-04 UK England VUI
P3 VUI-21MAR-02 Philippines VUI
B.1.617.1 with E484Q VUI-21APR-01 India VUI
B.1.617.3 VUI-21APR-03 India VUI
B.1.429 Monitoring
B.1.1.7 with S494P Monitoring
A.27 Monitoring
B.1.526 Monitoring
B.1.1.7 with Q677H Monitoring
B.1.620 Monitoring
B1.214.2 Monitoring
B.1.1.1 with L452Q and F490S Monitoring
R.1 Monitoring
B.1.1.28 with N501T and E484Q Monitoring
C.36 Monitoring
B.1.621 Monitoring
B.1 with 214insQAS Monitoring
AV.1 Monitoring


Sequencing coverage

Figure 1 shows the proportion of cases which are sequenced in England. Figure 1. Coverage of sequencing: percentage of SARS-CoV-2 cases sequenced over time as of 12 May 2021(Find accessible data used in this graph in underlying data)F1.

VOC and VUI case numbers, proportion, deaths and case fatality rate

The number of cases of variants of concern and variant under investigation are shown in Table 2. including the proportion of variant cases compared to all sequenced cases, deaths and case fatality rate. Figure 2 shows the cumulative number of cases per variant indexed by days since first report.
Table 2. Case number, proportion, death and case fatality rate of variants of concern and variant under investigation from 1 October 2020 to 12 May 2021
Variant Case Number Case Proportion Deaths Case Fatality
VOC-20DEC-01 202,229 98.425% 4,103 2.0%(2.0-2.1%)
VOC-20DEC-02 772 0.376% 12 1.6%(0.8-2.7%)
VOC-21FEB-02 43 0.021% 1 2.3%(0.1-12.3%)
VOC-21JAN-02 102 0.05% 0 0.0%(0.0-3.6%)
VUI-21APR-01 330 0.161% 0 0.0%(0.0-1.1%)
VOC-21APR-02 1,255 0.611% 4 0.3%(0.1-0.8%)
VUI-21APR-03 11 0.005% 0 0.0%(0.0-28.5%)
VUI-21FEB-01 79 0.038% 2 2.5%(0.3-8.8%)
VUI-21FEB-03 393 0.191% 12 3.1%(1.6-5.3%)
VUI-21FEB-04 190 0.092% 1 0.5%(0.0-2.9%)
VUI-21JAN-01 54 0.026% 1 1.9%(0.0-9.9%)
VUI-21MAR-02 6 0.003% 0 0.0%(0.0-45.9%)
Excludes variant cases not linked to a known COVID-19 case or with provisional sequencing/genotyping results. aCase number England genomic cases 12 May 2021. bDeaths As of 12 May 2021 (within 28 days) with confirmed or probable VOC or total cases. c95% Confidence Intervals calculated with Clopper–Pearson exact method, using R package PropCIs. Figure 2. Cumulative cases in England of variants indexed by days since first reported, data as of 12 May 2021 (Find accessible data used in this graph in underlying data). Figure 2 demonstrates the rapid identification of B.1.617.2 cases over a short period of time.F2.

Variant prevalence

The prevalence of different variants amongst all sequenced cases is presented in Figure 3, split by region in Figure 4 and by travel status in Figure 5. The ‘Other’ category in Figure 3 and Figure 4 includes genomes where the quality is insufficient to determine variant status and genomes that do not meet the current definition for any designated variant under investigation or variant of concern. The total genomic dataset used for this assessment includes enhanced testing and sequencing from individuals who have travelled, and surge testing and sequencing in outbreak areas. Sequencing numbers and coverage fall in the last week shown due partly to sequencing lag time, and new sequences are still being produced relating to sample dates in that week. The supplementary data for figures is available. Figure 3. Variant prevalence for all England available case data from 1 February 2021 as of 12 May 2021 (Excluding cases where the specimen date was unknown). (Find accessible data used in this graph in underlying data).F3. Figure 4. Variant prevalence for all England available case data from 1 February 2021 as of 12 May 2021 by region (Excluding cases where the region or specimen date were unknown). Black line indicates total number of cases sequenced (Find accessible data used in this graph in underlying data). Data for most recent 2 weeks is incomplete.F4. Figure 5. Prevalence of variants over time: all sequenced cases in England, split by travel status as of 12 May 2021(Find accessible data used in this graph in underlying data). Travel status includes cases matched to Passenger Locator Form data and samples taken as part of the managed quarantine service or through private testing following travel. The total number of sequenced cases in each week is shown in the bars below, split by travel status.F5.

Growth rates

Logistic growth rates (1/week from 1 January 2021 as of 12 May 2021) relative to lineage B.1.1.7 are calculated for each VUI or VOC with more than 20 samples and shown in Table 3. Sample inclusion criteria are: 1) A non-traveller as determined by matching each case against passenger locator forms and managed quarantine service test codes 2) Collected from Pillar 2 testing. 3) If multiple sequences are collected from the same patient which show the same variant, the first sample is retained. Additionally, samples with missing or unknown date of sample collection or upper tier local authority (UTLA) of residence are excluded. A sample of B.1.1.7 is collected for measuring relative growth rates by weighting each B.1.1.7 sample by the proportion of the VUI or VOC which are sampled in each UTLA. Any B.1.1.7 samples collected outside the period of time that the VUI or VOC are observed are excluded as are B.1.1.7 samples collected in UTLAs where the VUI or VOC have not yet been detected. The growth rate is estimated by logistic regression of the variant on time of sample collection. A growth rate of 0 would indicate parity with B.1.1.7. Compared to lineage B.1.1.7, the growth rate for B.1.617.2 displays an increased growth rate. Growth rate is context dependent and cannot be interpreted as a change in biological transmissibility.
Table 3. Growth rate of variants of concern and variants under investigation 1 January 2021 as of 12 May 2021. Sample sizes (n) correspond to the number of VUI or VOC used in the analysis. P values correspond to the null hypothesis that there is no difference in VUI/VOC growth rates and B.1.1.7 growth rates.
Variant Growth rate
VOC-20DEC-02 0.19 (p=4.336e-34,n=283)
VUI-21JAN-01 -0.16 (p=0.01946,n=22)
VOC-21JAN-02 0.62 (p=1.569e-11,n=40)
VUI-21FEB-01 -0.25 (p=0.004,n=55)
VUI-21FEB-03 0.041 (p=0.045,n=150)
VUI-21FEB-04 0.19 (p=1.854e-09,n=90)
VUI-21APR-01 0.61 (p=5.089e-22,n=111)
VOC-21APR-02 1.1 (p=6.591e-142,n=835)


Surveillance of reinfections

Individuals who have 2 positive tests (PCR and/or LFD) at least 90 days apart are classed as possible reinfection cases. A small proportion of reinfections have been sequenced through standard national surveillance sequencing. Table 4 shows the total number of sequences available from second episodes of infection in possible reinfection cases, categorized by variant. Figure 6 shows the number of different variants identified through sequencing that are possible reinfection cases. In recent weeks there have been small numbers of reinfection with VOC-21APR-02. This is expected with any prevalent variant; comparative analyses are underway.
Table 4. Number of sequenced reinfection cases and the variant assigned. (Data as of 12 May 2021)
Variant Total
VOC-20DEC-01 487
VOC-20DEC-02 1
VUI-21JAN-01 0
VOC-21FEB-02 1
VUI-21FEB-03 2
VUI-21FEB-04 2
VUI-21APR-01 2
VOC-21APR-02 13
VUI-21APR-03 0
Total sequenced 714
The total potential reinfection figure includes all tests (for example lateral flow devices as well as PCR tests). Figure 6. The number of reinfections cases from all sample sources, with the total number of reinfections cases with sequences, and the number of variant sequences over time (Find accessible data used in this graph in underlying data)F6.

Part 2: VOC-21APR-02 surveillance



Surveillance through genomic data

Table 5. Number of confirmed and probable VOC-21APR-02 (B.1.617.2) cases, by region of residence as of 12 May 2021
Region Case Number Case Proportion Cases that have travelled Proportion of travellers among cases
East Midlands 129 10.3% 31 24%
East of England 152 12.1% 46 30.3%
London 400 31.9% 106 26.5%
North East 19 1.5% 3 15.8%
North West 319 25.4% 24 7.5%
South East 98 7.8% 46 46.9%
South West 39 3.1% 26 66.7%
West Midlands 62 4.9% 28 45.2%
Yorkshire and Humber 31 2.5% 16 51.6%
Unknown region 6 0.5% NA%
Figure 7. Confirmed and probable VOC-21APR-02 (B.1.617.2) cases by specimen date as of 12 May 2021 Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data)F7. Figure 8. Travel data for confirmed and probable VOC-21APR-02 (B.1.617.2) cases by specimen date as of 12 May 2021 Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data) N/A indicates information is pending or not available.F8.

Spatial variation in risk for variants

The spatial risk surface is estimated by comparing the smoothed intensity of cases (variants of concern) and controls (PCR +ve, non-variants of concern) across a defined geographical area to produce an intensity (or risk) ratio. If the ratio is ~1, this suggests that the risk of infection is unrelated to spatial location. Evidence of spatial variation in risk occurs where the intensities differ. Ratio values >1 indicate an increased risk and values < 1 indicate lower risk. Figure 9 highlights areas of significantly increased risk identified for VOC-21APR-02. Figure 9. Spatial variation in risk for VOC-21APR-02 (B.1.617.2) data from 1 October 2020, as of 12 May 2021, excluding cases that are known to have travelled Supplementary data is not available for this figure). This figure excludes cases in managed quarantine facilities. Supplementary data is not available for this figure.F9.

Secondary attack rates

Secondary attack rates for VOC-21APR-02 (B.1.617.2) compared to the other B.1.617.2 lineages and VOC-20DEC-01 (B.1.1.7) are shown in Table 6. These are based on positive tests amongst contacts named to NHS Test and Trace by an original case identified with a confirmed or probable variant of concern or variant under investigation. Secondary attack rates are shown for cases with and without travel history. In non-travel settings, only close contacts (household members, face to face contact, people within 1 metre of the case for 1 minute or longer, or people within 2 metres for 15 minutes) named by the original case are included. In travel settings the contacts reported are not restricted to only close contacts named by the case (for example, they may include contacts on a plane linked by additional contact tracing efforts), leading to likely deflation of secondary attack rates amongst travellers compared to non-travellers. In addition, people recently returning from overseas are subject to stricter quarantine measures and may moderate their behaviour towards contacts. Travel history indicates, but does not confirm, where infection of the original case occurred. Secondary attack rates for contacts of non-travel cases with VUI-21APR-01, VOC-21APR02 or VUI-21APR-03 were not significantly different from that for contacts of non-travel cases with VOC-20DEC-01. Estimates of secondary attack rates for contacts of those that have travelled with variants of concern or variants under investigation were all considerably lower than those that have not travelled. Secondary attack rates for contacts of travel cases with VOC-21APR-02 were higher than those for travel cases with VOC20DEC-01.
Table 6. Secondary attack rates for the 3 B.1.617.2 sublineages, presented with B.1.1.7 for comparison (5 January 2021 to 21 April 2021, data as at 12 May 2021)
Variant Cases in those that have travelled (% with contacts) Cases in those that have not travelled or unknown (% with contacts) Case prop ortion that have trav elled Secondary Attack Rate among contacts of those that have travelled (95% CI) [secondary cases/conta cts] Secondary Attack Rate among contacts of cases that have not travelled or unknown (95% CI) [secondary cases/contacts]
VOC-20DEC01 3663 (78.5% with contacts) 158692 (74.0% with contacts) 2.3% 1.7% (1.6% – 1.8%) [1128/65383] 10.0% (9.9% – 10.1%) [32591/326364]
VUI-21APR-01 171 (80.7% with contacts) 81 (77.8% with contacts) 67.9% 2.0% (1.6% – 2.5%) [70/3469] 12.0% (8.1% – 17.3%) [23/192]
VOC-21APR-02 250 (72.4% with contacts) 287 (80.5% with contacts) 46.6% 3.3% (2.8% – 3.9%) [128/3884] 11.5% (9.6% – 13.9%) [98/850]
VUI-21APR-03 5 (20.0% with contacts) 5 (100.0% with contacts) 50.0% Unavailable [1/3] Unavailable [1/12]
Secondary attack rates are marked as ‘Unavailable’ when count of contacts is less than 50 or count of exposing cases is less than 20. Travel-linked cases for secondary attack rates are identified positively in NHS Test and Trace data using multiple PHE sources. A case is considered as being travel-linked if EpiCell or Health Protection Teams have found evidence of international travel, their NHS Test and Trace record mentions an event associated with international travel, their NHS Test and Trace record was created after notification via IHR NFP or they have been marked for priority contact tracing in NHS Test and Trace for reasons of travel. Some travel-linked cases may be missed by these methods and would be marked as nontravel-linked or unknown. Secondary attack rates from NHS Test and Trace should generally be considered lower bounds due to the nature of contact tracing and testing. Data provided is for period 5 January 2021 to 21 April 2021 in order to allow time for contacts to become cases, hence case counts are lower than other sources. Provisional results are excluded.

Surveillance of cases in travellers from India

Figure 10. Lineages of cases with recent travel history from IndiaEach line shows the count of cases of that lineage with known travel history from India: B.1.1.7 in green, B.1.617.1 in blue, B.1.617.2 in cyan, other lineages as dashed line (22 February 2021 to 2 May 2021).(Find accessible data used in this graph in underlying data).F10. Figure 11. Lineages of cases from selected cities of departure within India.Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data).F11.

Surveillance through S gene detection

The S gene target in a specific 3-target assay used in some Lighthouse Laboratories fails in B.1.1.7, previously predominant, but is detected in VUI-21APR-01, VOC-21APR-02 and VUI-21APR-03 variants as well as VOC-20DEC02 (B.1.351) and some others. Specimens with a detectable S gene (also referred to as S gene positive) are defined as those with cycle threshold (CT) values of ≤30 in all 3 gene targets: S, N, and ORF1ab. Figure 12 shows the number of sequenced S gene positive isolates over time since 1 January 2021 (data as of 12 May 2021), as well as the distribution of identified variants among these specimens. Unclassified variants refer to those not considered a VOC or VUI; these dominated the sequenced S gene positive specimens at the beginning of 2021, and decreased in proportion towards the end of April 2021 (Figure 12). Among 789 sequenced S gene positive samples in the second half of April 2021, 96% (n = 754) were variants under investigation or of concern, and 72.2% were VOC-21APR-02 (n=570). Among 397 specimens taken in May so far, 93% are VOC-21APR-02 (n=368). This suggests trends in S gene positive cases may currently capture additional VOC-21APR-02 cases not detected through sequencing, however this proxy is limited by variable TaqPath laboratory coverage across England (Figure 13). Additionally biases in sequencing, for instance targeting of contacts of variant cases in outbreak settings, may result in overrepresentation of variants among the S gene positive sequences. The number of sequenced S gene positive samples (Figure 12) as well as the number and proportion of S gene positive samples nationally (Figure 14) has increased in recent weeks, particularly in North West England and London (Figure 15). Many of the recent S gene positive cases have been detected in a small number of local authorities which have high total case rates, including Bolton, Blackburn with Darwen, Bedford, and Sefton (Figures 13 and 16). Some of these are located in areas where a higher proportion of specimens are tested in laboratories which use the TaqPath PCR assay (Figure 13). Figure 12. Distribution of variants among sequenced S gene positive SARS-CoV-2 specimens, by half-months as of 12 May 2021Figure 12. Distribution of variants among sequenced S gene positive SARS-CoV-2 specimens, by half-months as of 12 May 2021F12. Figure 13. Confirmed and probable VUI-21APR-03 (B.1.617.3) cases by specimen date as of 5 May 2021 Each line shows the count of cases of that lineage with a listed port of departure from a particular city: Mumbai in black, Delhi in red. For each city, the dashed line is B.1.617.1, the solid line B.1.617.2. (22 February 2021 to 2 May 2021).F13. Figure 14. Weekly number and proportion of England Pillar 2 COVID-19 cases with SGTF and detectable S gene among those tested with the TaqPath assay. Specimen dates between 2 September 2020 to 11 May 2021, data as of 12 May 2021 (Find accessible data used in this graph in underlying data).F14. Figure 15. Weekly number and proportion of England Pillar 2 COVID-19 cases with detectable S gene or SGTF among those tested with the TaqPath assay, by region of residence. Specimen dates between 1/1/2021 and 26/04/2021 (latest period incomplete. Find accessible data used in this graph in underlying data).F15. Figure 16. Weekly number and proportion of England Pillar 2 COVID-19 cases with detectable S gene or SGTF among those tested with the TaqPath assay and with S gene detection results (3 February 2021 to 4 May 2021) Specimen dates between 2 May 2021 and 8 May 2021, data as of 12 May 2021 (3 most recent days excluded due to reporting delay). Five UTLAs with highest number of S gene positive cases labelled. Find accessible data used in this graph in underlying data).F16.

Part 3: Other B.1.617 sublineages



VUI-21APR-01 (B.1.617.1)

Table 7. Number of confirmed and probable VUI-21APR-01 (B.1.617.1) cases, by region of residence as of 12 May 2021. Travel status in this table and all subsequent travel data in this document is based on information provided through the Contact Tracing Advisory Service (CTAS) and passenger locator forms where available. Travel status for cases under investigation is confirmed after follow up and is updated regularly.
Region Case Number Case Proportion Cases that have travelled Proportion of travellers among cases
East Midlands 44 13.3% 23 52.3%
East of England 27 8.2% 17 63%
London 145 43.9% 81 55.9%
North East 4 1.2% 2 50%
North West 29 8.8% 20 69%
South East 30 9.1% 19 63.3%
South West 6 1.8% 4 66.7%
West Midlands 30 9.1% 10 33.3%
Yorkshire and Humber 15 4.5% 11 73.3%
Figure 17. Spatial variation in risk for VUI-21APR-01 (B.1.617.1) data from 1 October 2020, as of 12 May 2021, excluding cases that are known to have travelled. Supplementary data is not available for this figure). This figure excludes cases in managed quarantine facilities. Supplementary data is not available for this figure.F17. Figure 18. Confirmed and probable VUI-21APR-01 (B.1.617.1) cases by specimen date as of 12 May 2021. Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data).F18. Figure 19. Travel data for confirmed and probable VUI-21APR-01 (B.1.617.1) cases by specimen date as of 12 May 2021 Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data). N/A indicates information is pending or not available.F19.

VUI-21APR-03 (B.1.617.3)

Table 8. Number of confirmed and probable VUI-21APR-03 (B.1.617.3) cases, by region of residence as of 12 May 2021
Region Case Number Case Proportion Cases that have travelled Proportion of travellers among cases
London 4 36.4% 2 50%
North West 6 54.5% 2 33.3%
South East 1 9.1% 0 0%
Figure 20. Spatial variation in risk for VUI-21APR-03 (B.1.617.3) data from 1 October 2020, as of 12 May 2021, excluding cases that are known to have travelled Supplementary data is not available for this figure). This figure excludes cases in managed quarantine facilities. Supplementary data is not available for this figure.F20. Figure 21. Confirmed and probable VUI-21APR-03 (B.1.617.3) cases by specimen date as of 12 May 2021 Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data).F21. Figure 22. Travel data for confirmed and probable VUI-21APR-03 (B.1.617.3) cases by specimen date as of 12 May 2021Larger plot includes last 60 days only. (Find accessible data used in this graph in underlying data). N/A indicates information is pending or not available.F22.

International surveillance

In total, 59 countries have reported at least one case of the VUI-21APR-01, VOC-21APR-02 and VUI-21APR-03 variants via GISAID, or official or media sources, or via IHR/EWRS. GISAID includes data on sequences available internationally. As of 12 May 2021 sequences from the following countries (excluding UK) have been identified in GISAID: • VUI-21APR-01 (B.1.617.1) Australia (21), Bahrain (8), Belgium (6), Canada (5), Czech Republic (3), Denmark (21), France (2), Germany (32), Greece (1), Guadeloupe (2), Hong Kong (9), India (1,069), Ireland (9), Italy (1), Japan (9), Jordan (3), Luxembourg (5), Malaysia (1), Mexico (1), Netherlands (6), New Zealand (4), Portugal (7), Saint Martin (2), Singapore (58), South Korea (5), Spain (1), Sweden (4), Switzerland (6), Thailand (1), USA (137), Uganda (1) • VOC-21APR-02 (B.1.617.2) Aruba (3), Australia (64), Austria (1), Bahrain (14), Bangladesh (6), Belgium (15), Canada (1), China (2), Denmark (17), France (13), Germany (46), Greece (1), Hong Kong (3), India (452), Indonesia (4), Ireland (28), Italy (18), Japan (19), Luxembourg (2), Malaysia (1), Mexico (1), Netherlands (5), New Zealand (9), Norway (1), Poland (5), Romania (1), Singapore (100), Slovenia (1), South Korea (1), Spain (5), Sweden (3), Switzerland (13), USA (211), Uganda (3) • VUI-21APR-03 (B.1.617.3) India (47), Russia (2), USA (1)

Sources and acknowledgments

Data sources

Data used in this investigation is derived from the COG-UK dataset, the PHE Second Generation Surveillance System (SGSS), NHS Test and Trace, the Secondary Uses Service (SUS) dataset and Emergency Care Data Set (ECDS).

Variant Technical Group

Authors of this report

PHE Genomics Cell PHE Outbreak Surveillance Team PHE Epidemiology Cell PHE Contact Tracing Data Cell

Variant Technical Group Membership

The PHE Variant Technical Group includes representation from the following organisations: PHE, DHSC, BEIS, Public Health Wales , Public Health Scotland, Public Health Agency Northern Ireland, Imperial College London, London School of Hygiene and Tropical Medicine, University of Birmingham, University of Cambridge, University of Edinburgh, University of Liverpool, the Wellcome Sanger Institute.

Acknowledgements

The authors are grateful to those teams and groups providing data for this analysis including: the Lighthouse Laboratories, COG-UK, the Wellcome Sanger Institute, tthe PHE Epidemiology Cell, Contact Tracing, Genomics and Outbreak Surveillance Teams. Published: May 2021 PHE gateway number: GW-8226