Research and analysis

Variants: distribution of case data, 11 March 2022

Updated 24 June 2022

Surveillance overview

From 31 January 2022, the UK Health Security Agency (UKHSA) has reported episodes of infection in its coronavirus (COVID-19) surveillance. Current surveillance of COVID-19 in England is based on positive samples from the same person grouped together, so that the person is only counted once and reported using the date of the first positive result.

From 31 January 2022, an ‘episode’ definition is introduced, grouping positive results up to and including 90 days apart into episodes. Positive test results which are more than 90 days apart are classed as separate episodes.

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 are no longer being included in the publication since 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. Variant VUI-21JUL-01 (Mu) has been removed as of 17 February 2022 as it has been classified as provisionally extinct.

UK total distribution for variants with new reports in the last 90 days

Variant Other names by which this variant may be known** Lineage Total confirmed (sequencing) and probable (genotyping) cases** ^ New cases since last update (data up to 2 March 2022)
Delta+ VOC-21APR-02 B.1.617.2 AY.1 AY.2 1,730,982+ -71
VUI-21OCT-01*** VUI-21OCT-01 AY.4.2 123,354 +31
Omicron VOC-21NOV-01 B.1.1.529 1,802,857 +83,141
Omicron BA.2 VUI-22JAN-01 B.1.1.529.BA.2 110,830 +38,697

*WHO naming has been included where available.

**Cumulative numbers may be revised up or down as a result of reclassification of results, re-infections and changes to diagnostic tests, new variants or public health management levels.

 ^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.

+Of which 780 had the K417N mutation.

***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.

UK total distribution for variants detected in the UK with no or low$ activity in the last 90 days

Variant Other names by which this variant may be known** Lineage Total confirmed (sequencing) and probable (genotyping) cases** ^ Last reported specimen date$
Alpha VOC-20DEC-01 B.1.1.7 281,125 5 February 2022
Beta¥ VOC-20DEC-02 B.1.351 1,064 12 November 2021
Gamma VOC-21JAN-02 P.1 292 10 February 2022
Zeta VUI-21JAN-01 P.2 50 14 April 2021
Kappa VUI-21APR-01 B.1.617.1 465 14 September 2021
VUI-21MAY-02 VUI-21MAY-02 C.36.3 135 26 June 2021
Lambda VUI-21JUN-01 C.37 8 18 June 2021

**WHO naming has been included where available.

**Cumulative numbers may be revised up or down as a result of reclassification of results, re-infections and changes to diagnostic tests, new variants or public health management levels.

 ^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.

$Fewer than 10 reports in any week during the last 90 days.

¥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 21 ‘Beta or Mu’ provisional genotyping cases have been identified.

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.

Note on Omicron (VOC-21NOV-01 and VUI-22JAN-01)

As genotyping assays cannot distinguish between BA.1 and BA.2 genomes, Omicron (VOC-21NOV-01) includes cases of BA.1 and BA.2 genomes where those genomes were identified by genotyping only and not confirmed by genome sequencing.

Alpha

Surveillance overview

Total confirmed and probable cases
England 230,392
Northern Ireland 9,162
Scotland 29,127
Wales 12,444
Total cases 281,125

Case definitions

Genomic match Criteria
Confirmed
(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 bases
Probable (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

Total confirmed and probable cases
England 950
Northern Ireland 9
Scotland 62
Wales 43
Total cases 1,064

Case definitions

Genomic match Criteria
Confirmed
(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 changes
Probable (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 PCR.

Gamma

Surveillance overview

Total confirmed and probable cases
England 267
Northern Ireland 0
Scotland 23
Wales 2
Total cases 292

Case definitions

Genomic match Criteria
Confirmed
(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 bases
Probable (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 PCR.

Delta

Surveillance overview

Total confirmed and probable cases
England 1,413,078
Northern Ireland 93,280
Scotland 133,502
Wales 91,122
Total cases 1,730,982

Case definitions

Genomic match Criteria
Confirmed
(sequencing)
COVID-19* confirmed case with at least 4 variant defining changes called as alternate base
Probable (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 PCR.

VUI-21OCT-01

Surveillance overview

Total confirmed and probable cases
England 93,950
Northern Ireland 745
Scotland 13,636
Wales 15,023
Total cases 123,354

Case definitions

Genomic match Criteria
Confirmed
(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 PCR.

Omicron

Surveillance overview

Total confirmed and probable cases
England 1,468,887
Northern Ireland 89,308
Scotland 157,393
Wales 87,269
Total cases 1,802,857

Case definitions

Genomic match Criteria
Confirmed
(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-type
Probable (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 PCR.

Zeta

Surveillance overview

Total confirmed and probable cases
England 44
Northern Ireland 0
Scotland 5
Wales 1
Total cases 50

Case definitions

Genomic match Criteria
Confirmed
(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 bases
Probable (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 PCR.

Kappa

Surveillance overview

Total confirmed and probable cases
England 419
Northern Ireland 4
Scotland 27
Wales 15
Total cases 465

Case definitions

Genomic match Criteria
Confirmed
(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 PCR.

VUI-21MAY-02

Surveillance overview

Total confirmed and probable cases
England 125
Northern Ireland 2
Scotland 4
Wales 4
Total cases 135

Case definitions

Genomic match Criteria
Confirmed
(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 PCR.

Lambda

Surveillance overview

Total confirmed and probable cases
England 8
Northern Ireland 0
Scotland 0
Wales 0
Total cases 8

Case definitions

Genomic match Criteria
Confirmed
(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 PCR.

Omicron BA.2 (VUI-22JAN-01)

Surveillance overview

Total confirmed and probable cases
England 85,352
Northern Ireland 4,004
Scotland 16,332
Wales 5,142
Total cases 110,830

Case definitions

Genomic match Criteria
Confirmed
(sequencing)
COVID-19* confirmed case with at least 10 lineage defining non-synonymous changes called as alternate base and no more than 3 defining positions called as wild-type.
*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).