SARS-CoV-2 variants of concern and variants under investigation in England

7 May 2021
This briefing provides an update on previous briefings up to 1 April 2021

Summary

•There are 5 variants of concern and 8 variants under investigation (Table 1).
VUI-21APR-02 (B.1.617.2) was escalated to a variant of concern on 6 May 2021 (VOC21APR-02). It is assessed as having at least equivalent transmissibility to B.1.1.7 based on available data (moderate confidence). There are insufficient data currently to assess the potential for immune escape. There has been a steep recent increase in the number of cases identified (N=509 genomically confirmed) of this variant of concern in the UK, which includes both imported (n=157 confirmed after travel) and domestically-acquired cases. Postcodes of residence are most frequently identified as London and the North West.
This technical briefing includes national overview data and surveillance updates for VUI21APR-01 (B.1.617.1), VOC-21APR-02 (B.1.617.2) and VUI-21APR-03 (B.1.617.3), and a new clinical risk assessment for VOC-21APR-02 (B.1.617.2). The full update for each individual variant will be published in the next technical briefing and monthly thereafter.

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.

Variant status

Table 1 shows the current variants of concern and variants under investigation. Summary epidemiology on each variant is shown in Table 4, case numbers are also updated online.

New Variant of Concern VOC-21APR-02

Risk assessment

Case numbers, proportion, deaths and case fatality rate

The number of cases of variants of concern and variant under investigation are shown in Table 4, including the proportion of variant cases compared to all sequenced cases, deaths and case fatality rate.

Excludes variant cases not linked to a known COVID-19 case. *Excludes 33 genomically provisional cases. **Excludes 6 genomically provisional cases. ***Excludes 168 genomically provisional cases aCase number England genomic cases 5 May 2021. bDeaths as of 5 May 2021 (within 28 days) with confirmed or probable VOC or total cases. c 95% Confidence Intervals calculated with Clopper–Pearson exact method, using R package PropCI

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. Prevalence of predicted antigenic change mutations over time is shown in Figure 6 and by travel status in Figure 7 and 8. The supplementary data for figures is available.

Variants in lineage B.1.617

A variant first detected in India was designated under investigation on 1 April 2021 as VUI-21APR-01 (B.1.617.1). VOC-21APR-02 (B.1.617.2) was designated as variant of concern on 6 May 2021. VUI-21APR-03 (B.1.617.3) was designated variant under investigation on 27 April 2021. A repository containing the up-to-date genomic definitions for all VOC and VUI as curated by Public Health England was created 5 March 2021. The repository can be accessed on GitHub.

Genomic Profile for VOC-21APR-02 (B.1.617.2) and VUI-21APR03 (B.1.617.3)

VUI-21APR-01 (B.1.617.1)

VOC-21APR-02 (B.1.617.2)

Trends in S gene detection

The S-gene target in a specific three-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. Figure 13 shows the number of sequenced S gene positive isolates over time since 1 January 2021 (data as of 3 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 15).
Among 354 sequenced S gene positive samples in the second half of April 2021 (specimen dates up to 26 March 2021 due to reporting lag), 95% (n = 337) were variants under investigation or of concern, and 67.2% were VOC-21APR-02. The number of sequenced S gene positive samples (Figure 15) as well as the number and proportion of S gene positive samples nationally (Figure 16) has increased in recent weeks, particularly in London (Figure 17), with data suggesting this growth is driven by the increase in variant cases. Targeted sequencing, for instance of contacts of variant cases, may however result in overrepresentation of variant cases.

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 18 highlights areas of significantly increased risks, areas of significantly increased risk were identified for VUI-21APR-01 and VOC-21APR-02. Supplementary data is not available for this figure.

International surveillance

GISAID includes data on sequences available internationally. As of 4 May 2021 GISAID data indicates 23 countries (including the U.K) have reported at least one case of the VUI21APR-01, VOC-21APR-02 and VUI-21APR-03 variants, which 19 have reported via official or media sources, or via IHR/EWRS. As of 4 May 2021 sequences from the following countries (excluding UK) have been identified on GISAID meeting each of the April Variant Definitions:

• VUI-21APR-01 (B.1.617.1): Australia (16), Bahrain (8), Belgium (5), Canada (2), Czech Republic (2), Germany (23), Greece (1), Guadeloupe (2), Hong Kong (7), India (856), Italy (1), Jordan(3), Malaysia (1), Mexico (1), Netherlands (4), New Zealand (4), Portugal (7), Republic of Ireland (4), Saint Martin (2), Singapore (51), South Korea (5), Sweden (2), Switzerland (3), USA (108)
• VOC-21APR-02 (B.1.617.2): Aruba (1), Australia (30), Bahrain (14), Belgium (4), France (1), Germany (28), Greece (1), Hong Kong (1), India (169), Italy (2), Netherlands (2), New Zealand (7), Poland (1), Republic of Ireland (6), Romania (1), Singapore (72), Spain (3), Sweden (2), Switzerland (6), USA (135)
• VUI-21APR-03 (B.1.617.2): India (36), Russia (2), USA (1)

Secondary attack rates

Secondary attack rates are shown in Table 9. 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.

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 non-travel-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 12 April 2021 in order to allow time for contacts to become cases, hence case counts are lower than other sources.

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