SARSCoV2 variants of concern

 Public Health England.

SARSCoV2 variants of concern variants under investigation in England .

Technical briefing 16.

 18 June 2021 

This briefing provides an update on previous briefings up to 11 June 2021.

Contents  

Summary ..................................................... 3 

Published information on variants ...............................................4 

Part 1: Surveillance overview .................................................. 5 

Variants under surveillance .................................................. 5 

Variant prevalence ................................ 15

 Secondary attack rates ..................................................... 20 

Surveillance of reinfections .................................................... 28 

SARS-CoV-2 Immunity and Reinfection Evaluation (the SIREN study) cohort monitoring .................................................... 32 

Variants linked to suspected SARS-CoV-2 outbreaks ................................................... 35 

Part 2: Delta (B.1.617.2) surveillance.............................. 43 

Severity .................................................... 43 

Monitoring of vaccine effectiveness .................................................. 44 

Surveillance through genomic data .................................................. 46 

Surveillance through S gene detection ............................ 53 

Delta with K417N ................................. 65

 Sources and acknowledgments ...................................69

Summary

 There are 4 current variants of concern and 8 variants under investigation (Table 1). 

 This report has been published to continue to share detailed surveillance of Delta (VOC-21APR-02, B.1.617.2). A separate report is published covering our routine data on all other variants of concern and variants under investigation. These additional specialist technical briefings represent early data and analysis on an emerging variant and findings have a high level of uncertainty. 

 Principal changes and findings this week are: 

 • by combining genotyping and sequencing, more than 80% of cases in England now have a variant test undertaken 

• the most recent data show that the Delta variant comprises 91% of sequenced cases 

• deaths are now presented for those cases which have completed the 28-day follow-up period – the crude case fatality rate remains lower for Delta than other variants at present; however, mortality is a lagged indicator, which means that the number of cases who have completed 28 days of follow up is very low – therefore, it is too early to provide a formal assessment of the case fatality of Delta, stratified by age, compared to other variants 

 • secondary attack rates remain higher for Delta than Alpha – a small reduction in secondary attack rates is observed for Delta in recent weeks 

 • current evidence suggests vaccine effectiveness against hospitalisation is maintained for Delta 

• the most common settings for reported exposures were education settings, for both Alpha and Delta variants – in the latest week presented, hospitality settings were a larger proportion of all common exposures reported by cases with both Alpha and Delta variants, and the proportion of common exposures related to travel also increased. 

 The risk assessment for Delta is published separately and has been updated this week. As Delta is now the dominant variant in the UK, epidemiological data in the weekly surveillance report is highly relevant and available. 

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 on 5 March 2021. The repository can be accessed on GitHub.    

WHO nomenclature as of 31 May 2021 is incorporated. A table incorporating WHO and UK designations and Pango lineages is provided (Table 1); thereafter variants are referred to using their WHO designation where this exists, and the UK designation where it does not.  

Technical Briefing 16 includes variant diagnoses made both by whole-genome sequencing and by a genotyping PCR test, including the categorisation of confirmed and probable variant results and a rules-based decision algorithm (RBDA) to identify variant and mutation (VAM) profiles from genotype assay mutation profiles. Genotyping is used to identify variants Alpha, Beta, Delta and Gamma; targets were updated in mid-May 2021 to prioritise accurate identification of Delta over Alpha.