(LONDON) JUST IN: GOVUK Press Statement Report: Variants Surveillance Overview UK Total Distribution on December 4th 2021: #AceHealthDesk report

#CoronavirusNewsDesk Variants: distribution of case data, 03 December 2021

Surveillance overview

UK total distribution

Variant*Other names by which this variant may be known**LineageTotal confirmed (sequencing) and probable (genotyping) cases‡New cases since last update (data up to 24 Nov)AlphaVOC-20DEC-01B.1.1.7277,563-22Beta§VOC-20DEC-02B.1.3511,107§+1GammaVOC-21JAN-02P.12910DeltaVOC-21APR-02B.1.617.2 AY.1 AY.21,452,519+82,000VUI-21OCT-01***VUI-21OCT-01A.Y 4.265,922+12,292OmicronVOC-21NOV-01B.1.1.52932+32ZetaVUI-21JAN-01P.2570EtaVUI-21FEB-03B.1.525 (previously designated UK1188)5140VUI-21FEB-04VUI-21FEB-04B.1.1.318366-1ThetaVUI-21MAR-02P.3100KappaVUI-21APR-01B.1.617.15200VUI-21APR-03VUI-21APR-03B.1.617.3180VUI-21MAY-02VUI-21MAY-02C.36.31580LambdaVUI-21JUN-01C.379+1Mu§VUI-21JUL-01B.1.62158§+1

*Information pertaining to VUI-21MAR-01, B1.324.1 with E484K has been removed as this variant has been reclassified as provisionally extinct. Variants VUI-21FEB-01 (A.23.1 with E484K), and VOC-21FEB-02 (Alpha with E484K) are provisionally extinct (not detected for 12 weeks in the UK or in GISAID) therefore they will no longer be included in the publication from 12 November 2021. Variant VUI-21MAY-01, AV.1 has been removed as of 3 December 2021 as it has been classified as provisionally extinct.

**WHO naming has been included where available.

† Of which 475 had the K417N mutation.

Confirmed individuals are confirmed COVID-19 cases with a validated sequencing result meeting the confirmed case definitions outlined in the sections below. Probable individuals are confirmed COVID-19 cases with a genotyping result where sequencing confirmation is awaited or not available. Published figures include genotyping assay data for England, using a combination of highly specific mutations as an indicator of a probable variant. Genotyping assay data is currently only available for Alpha, Beta (for specimen dates up to and including 30 June 2021), Delta and Gamma.

§Due to having identical genotyping profiles, since 1 July Beta and Mu cases identified by genotyping have been categorised as ‘Beta or Mu’. In addition to the above numbers, a further 12 ‘Beta or Mu’ provisional genotyping cases have been identified.

***Confirmed VOC-21APR-02 with at least 2 VUI-21OCT-01 lineage defining positions called as alternate (variant) base and all other defining positions reported as N (unknown) or mixed bases.

****Due to an earlier data reporting issue, 13 cases of Gamma reported in October 2021 have been removed from this week’s total.

Differences between a variant of concern and a variant under investigation

SARS-CoV-2 variants, if considered to have concerning epidemiological, immunological or pathogenic properties, are raised for formal investigation. At this point they are designated variant under investigation (VUI) with a year, month, and number. Following a risk assessment with the relevant expert committee, they may be designated variant of concern (VOC).

Changes in nomenclature

The previous variant names frequently include similar numbers with similar or repeating patterns. This makes referring to them verbally challenging. To overcome this challenge, a revised nomenclature has been agreed involving dropping the first 2 numbers of the year and replacing the 2-month numbers with a 3-letter abbreviation. This shortens the name and reduces the degree of repeated sequences of numbers. The table containing surveillance overview ‘UK total distribution’ contains a list of new variant names alongside previous or other names in use for VOCs and VUIs.

Alpha

Surveillance overview

This variant was first detected in the UK and was first sequenced in the UK in September 2020.Total confirmed and probable casesEngland226,790Northern Ireland9,176Scotland29,129Wales12,468Total cases277,563

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with at least 5 VOC-20DEC-01 lineage defining positions are called as alternate (variant) base and all other defining positions reported as N (unknown) or mixed basesProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Beta

Surveillance overview

This variant was first detected in South Africa and was first sequenced in the UK in December 2020.Total confirmed and probable casesEngland992Northern Ireland10Scotland62Wales43Total cases1,107

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case where:
• at least 4 VOC-20DEC-02 lineage defining positions are called as alternate (variant) base, and 
• all other defining positions reported as N (unknown) or mixed bases 
or
• at least 5 of the 9 non-synonymous changesProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Gamma

Surveillance overview

This variant was first detected in Japan in travellers from Brazil in January 2021 and was first detected in the UK in February 2021.Total confirmed and probable casesEngland266Northern Ireland0Scotland23Wales2Total cases291

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with: 
• at least 5 lineage defining non-synonymous changes called as alternate base, and 
• all other positions either N or mixed basesProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Delta

Surveillance overview

Total confirmed and probable casesEngland1,179,127Northern Ireland81,504Scotland116,215Wales75,673Total cases1,452,519

Case definitions

Genomic matchCriteriaConfirmed
(sequencing)COVID-19* confirmed case with at least 4 variant defining changes called as alternate baseProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

VUI-21OCT-01

Surveillance overview

Total confirmed and probable casesEngland49,460Northern Ireland832Scotland7,135Wales8,495Total cases65,922

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case that is confirmed VOC-21APR-02 with at least 2 VUI-21OCT-01 lineage defining positions called as alternate (variant) base and all other defining positions reported as N (unknown) or mixed bases.*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Omicron

Surveillance overview

Total confirmed and probable casesEngland22Northern Ireland-**Scotland10Wales0Total cases32

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with at least 10 lineage defining non-synonymous changes called as alternate base and no more than 7 defining positions called as wild-typeProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR). 

**Northern Ireland data was not available at the time of publishing on 3 December 2021.

Zeta

Surveillance overview

This variant was first detected in Brazil and was first sequenced in the UK in November 2020.Total confirmed and probable casesEngland51Northern Ireland0Scotland5Wales1Total cases57

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* case confirmed as infected with VUI-21JAN-01 through whole genome sequencing (WGS) where: 
• results of all lineage defining non-synonymous changes called as alternate base 
or 
• 6 of 7 non-synonymous changes called as alternate base, and
• remaining position either N or mixed basesProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Eta

Surveillance overview

This variant was first detected in the UK in December 2020.Total confirmed and probable casesEngland462Northern Ireland2Scotland40Wales10Total cases514

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with: 
• at least 5 lineage defining non-synonymous changes called as alternate base, and 
• all other positions either N or mixed basesProbable (genotyping)COVID-19* confirmed case with a genotyping result where sequencing confirmation is awaited or not available*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

VUI-21FEB-04

Surveillance overview

This variant was first detected in the UK (England).Total confirmed and probable casesEngland315Northern Ireland40Scotland11Wales0Total cases366

Case definitions

Genomic matchCriteriaConfirmed
(sequencing)COVID-19* confirmed case with: 
• at least 5 lineage defining non-synonymous changes called as alternate base, and 
• all other positions either N or mixed base
or
• at least 5 of the 9 non-synonymous changes*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Theta

Surveillance overview

This variant was first detected in the Philippines.Total confirmed and probable casesEngland7Northern Ireland0Scotland3Wales0Total cases10

Case definitions

Genomic matchCriteriaConfirmed
(sequencing)COVID-19* confirmed case with: 
• at least 7 variant defining changes called as alternate base, and 
• all other positions either N or mixed base*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Kappa

Surveillance overview

This variant was first detected in India.Total confirmed and probable casesEngland474Northern Ireland4Scotland27Wales15Total cases520

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with: 
• at least 6** variant defining changes called as alternate base, and 
• all other positions either N or mixed base*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).**Due to overlap with Delta sequences, the case definition of Kappa sequences was changed on 27 August 2021.

VUI-21APR-03

Surveillance overview

This variant was first detected in India.Total confirmed and probable casesEngland15Northern Ireland0Scotland0Wales3Total cases18

Case definitions

Genomic matchCriteriaConfirmed  
(sequencing)COVID-19* confirmed case with: 
• at least 8 variant defining changes called as alternate base, and 
• all other positions either N or mixed base*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

VUI-21MAY-02

Surveillance overview

This variant was first detected in Thailand (in travellers from Egypt).Total confirmed and probable casesEngland148Northern Ireland2Scotland4Wales4Total cases158

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with at least 5 variant defining changes called as alternate base, and 
• all other positions either N or mixed base.*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Lambda

Surveillance overview

This variant was first detected in Peru in August 2020.Total confirmed and probable casesEngland8Northern Ireland1Scotland0Wales0Total cases9

Case definitions

Genomic matchCriteriaConfirmed 
(sequencing)COVID-19* confirmed case with at least 5 VUI-21JUN-01 lineage defining positions are called as alternate (variant) base and all other defining positions reported as N (unknown) or mixed bases.*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

Mu

Surveillance overview

Total confirmed and probable casesEngland52Northern Ireland2Scotland3Wales1Total cases58

Case definitions

Genomic matchCriteriaConfirmed
(sequencing)COVID-19* confirmed case with at least 5 VUI-21JUL-01 defining mutations called as alternate (variant) base and all other defining positions reported as N (unknown) or mixed bases.*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

#AceHealthDesk report …………..Published: Dec.04: 2021:

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