Research and analysis

Variants: distribution of case data, 13 June 2022

Updated 24 June 2022

Changes to variant classification system

The UK Health Security Agency (UKHSA) amended its variant classification system to give a clearer indication of which variants have significant changes in biological properties compared to the current dominant variant(s).

In the new system, the variant of concern (VOC) label will be assigned to variants which are currently emerging or circulating, and for which we have confirmed or can predict:

  • a detrimental change in biological properties (changes in transmissibility, severity or immune evasion) compared to the current dominant variant(s); and

  • a growth rate potentially compatible with maintaining transmission and/or displacing the current dominant variant.

There is no other categorisation of variants, including no variant under investigation (VUI) category. UKHSA will continue to designate new variants based on genomic features and growth, and these will receive a variant number (V-date-number).

Previous variants of concern which no longer meet the criteria above have been redesignated. These changes took effect as of 1 April 2022.

As of 20 May Omicron BA.4 and Omicron BA.5 have been designated variants of concern (VOCs) in the UK.

Surveillance overview

From 31 January 2022, the UKHSA has reported episodes of infection in its coronavirus (COVID-19) surveillance. Previous surveillance of COVID-19 in England was 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.

The ‘episode’ definition introduced groups positive results up to and including 90 days apart into episodes. Positive test results which are more than 90 days apart will be classed as separate episodes.

The UKHSA methodology for reporting of COVID-19 cases varies between England and the devolved authorities. England and Scotland report 90-day infection episodes. Wales reports 42-day infection episodes. Northern Ireland reports data at individual level (only one infection episode is reported per person) but is working towards reporting 90-day infection episodes.

Information pertaining to V-21MAR-01, B1.324.1 with E484K has been removed as this variant has been reclassified as provisionally extinct. Variants V-21FEB-01 (A.23.1 with E484K), and V-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 V-21MAY-01, AV.1 has been removed as of 3 December 2021 as it has been classified as provisionally extinct. Variant V-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 1 June)
VOC-21NOV-01 Omicron BA.1 (B.1.1.529.1) 2,135,001 -338
VOC-22JAN-01 Omicron BA.2 (B.1.1.529.2) 475,420 2,548
V-22APR-02 Omicron XE 2,054 18
VOC-22APR-03 Omicron BA.4 (B.1.1.529.4) 637 162
VOC-22APR-04 Omicron BA.5 (B.1.1.529.5) 716 287

*Numbers based on UKHSA definitions, so these have replaced WHO naming in the variant column.

**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, Delta, Gamma, Mu and Omicron. Since mid-December genotyping has only been able to detect Omicron BA1 only with all other variants being labelled as undetermined.

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$
V-20DEC-01 Alpha B.1.1.7 281,104 28 April 2022
V-20DEC-02$ Beta B.1.351 1,061$ 12 November 2021
V-21JAN-02 Gamma P.1 294 17 March 2022
V-21APR-02+*** Delta B.1.617.2 AY.1 AY.2 1,732,374+ 6 May 2022
V-21OCT-01*** V-21OCT-01 A.Y 4.2 123,517 13 March 2022
V-21JAN-01 Zeta P.2 50 14 April 2021
V-21APR-01 Kappa B.1.617.1 464 14 September 2021
V-21MAY-02 V-21MAY-02 C.36.3 136 26 June 2021
V-21JUN-01 Lambda C.37 8 18 June 2021
V-22APR-01 V-22APR-01 XD 0  

*Numbers based on UKHSA definitions, so these have replaced WHO naming in the variant column.

**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, Delta, Gamma, Mu and Omicron. Since mid-December genotyping has only been able to detect Omicron BA1 only with all other variants being labelled as undetermined.

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

+Of which 790 had the K417N mutation.

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

Note on Omicron (VOC-21NOV-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 230,187
Northern Ireland 9,365
Scotland 29,108
Wales 12,444
Total cases 281,104

Case definitions

Genomic match Criteria
Confirmed (sequencing) COVID-19* confirmed case with at least 5 V-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 945
Northern Ireland 9
Scotland 64
Wales 43
Total cases 1,061

Case definitions

Genomic match Criteria
Confirmed (sequencing) COVID-19* confirmed case where:
• at least 4 V-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 polymerase chain reaction (PCR).

Gamma

Surveillance overview

Total confirmed and probable cases
England 269
Northern Ireland 0
Scotland 23
Wales 2
Total cases 294

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 polymerase chain reaction (PCR).

Delta

Surveillance overview

Total confirmed and probable cases
England 1,413,852
Northern Ireland 93,796
Scotland 133,581
Wales 91,145
Total cases 1,732,374

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 polymerase chain reaction (PCR).

V-21OCT-01

Surveillance overview

Total confirmed and probable cases
England 94,024
Northern Ireland 754
Scotland 13,699
Wales 15,040
Total cases 123,517

Case definitions

Genomic match Criteria
Confirmed (sequencing) COVID-19* confirmed case that are confirmed VOC-21APR-02 with at least 2 V-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).

VOC-21NOV-01 (Omicron sub-lineage BA.1)

Surveillance overview

Total confirmed and probable cases
England 1,724,987
Northern Ireland 106,557
Scotland 246,343
Wales 57,114
Total cases 2,135,001

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 polymerase chain reaction (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 V-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 polymerase chain reaction (PCR).

Kappa

Surveillance overview

Total confirmed and probable cases
England 417
Northern Ireland 5
Scotland 27
Wales 15
Total cases 464

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 polymerase chain reaction (PCR).

V-21MAY-02

Surveillance overview

Total confirmed and probable cases
England 125
Northern Ireland 3
Scotland 4
Wales 4
Total cases 136

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 polymerase chain reaction (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 V-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).

VOC-22JAN-01 (Omicron sub-lineage BA.2)

Surveillance overview

Total confirmed and probable cases
England 338,867
Northern Ireland 11,083
Scotland 96,824
Wales 28,646
Total cases 475,420

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
Probable (genotyping) COVID-19* confirmed case with a confirmed sequencing result.

*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

VOC-22APR-03 (Omicron sub-lineage BA.4)

Surveillance overview

Total confirmed and probable cases
England 532
Northern Ireland 4
Scotland 83
Wales 18
Total cases 637

Case definitions

Genomic match Criteria
Confirmed (sequencing) COVID-19* confirmed case with at least 3 lineage defining mutations called as alternate base and no defining positions called as wild-type
Probable (genotyping) COVID-19* confirmed case with a confirmed sequencing result.

*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).

VOC-22APR-04 (Omicron sub-lineage BA.5)

Surveillance overview

Total confirmed and probable cases
England 566
Northern Ireland 8
Scotland 117
Wales 25
Total cases 716

Case definitions

Genomic match Criteria
Confirmed (sequencing) COVID-19* confirmed case with at least 3 lineage defining mutations called as alternate base and no defining positions called as wild-type
Probable (genotyping) COVID-19* confirmed case with a confirmed sequencing result.

*A confirmed COVID-19 case: a case where the individual is confirmed to be infected with SARS-CoV-2 by polymerase chain reaction (PCR).