Variants: distribution of case data, 18 February 2022
Updated 24 June 2022
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Surveillance overview
From 31 January 2022, the UK Health Security Agency (UKHSA) reported episodes of infection in its coronavirus (COVID-19) surveillance. 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. From 31 January 2022, an ‘episode’ definition was introduced, grouping positive results up to and including 90 days apart into single episodes. Positive test results which are more than 90 days apart are classed as separate episodes.
As part of this change, the production of the national Variants and Mutations (VAM) line list has been integrated into the main COVID-19 pipeline, and several enhancements made to VAM data, including new fields and changes to the type of VAM result available. This brief document summarises what data was available on the old person-level VAM line list and how this is changing. It also outlines changes being made to some of the critical fields used for VAM reporting and provides guidance on how these should be interpreted and used.
Please be advised that the table column ‘New cases since last update’ may not be completely accurate. This is due to a comparison between the current (episode level) linelist and the previous (case level) linelist. This should be corrected in the next report.
UK total distribution
| 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 7 February 2022) |
|---|---|---|---|---|
| Alpha | VOC-20DEC-01 | B.1.1.7 | 281,206 | -8 |
| Beta§ | VOC-20DEC-02 | B.1.351 | 1,063§ | 0 |
| Gamma | VOC-21JAN-02 | P.1 | 294 | +2 |
| Delta‡ | VOC-21APR-02 | B.1.617.2 AY.1 AY.2 | 1,729,780‡ | -164 |
| VUI-21OCT-01*** | VUI-21OCT-01 | A.Y 4.2 | 122,818 | +27 |
| Omicron | VOC-21NOV-01 | B.1.1.529 | 1,543,450 | +139,762 |
| Zeta | VUI-21JAN-01 | P.2 | 50 | 0 |
| VUI-21FEB-03 | VUI-21FEB-03 | B.1.525 (previously designated UK1188) | 495 | 0 |
| VUI-21FEB-04 | VUI-21FEB-04 | B.1.1.318 | 374 | 0 |
| Theta | VUI-21MAR-02 | P.3 | 9 | 0 |
| Kappa | VUI-21APR-01 | B.1.617.1 | 465 | 0 |
| VUI-21APR-03 | VUI-21APR-03 | B.1.617.3 | 18 | 0 |
| VUI-21MAY-02 | VUI-21MAY-02 | C.36.3 | 138 | +1 |
| Lambda | VUI-21JUN-01 | C.37 | 8 | 0 |
| Omicron BA.2 | VUI-22JAN-01 | B.1.1.529.BA.2 | 23,544 | +12,581 |
*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.
Variant VUI-21JUL-01 (Mu) has been removed as of 17 February 2022 as it has been classified as provisionally extinct.
**WHO naming has been included where available.
¥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’.
‡Of which 781 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.
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
| Total confirmed and probable cases | |
|---|---|
| England | 230,472 |
| Northern Ireland | 9,162 |
| Scotland | 29,128 |
| Wales | 12,444 |
| Total cases | 281,206 |
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 | 949 |
| Northern Ireland | 9 |
| Scotland | 62 |
| Wales | 43 |
| Total cases | 1,063 |
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 | 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 PCR. |
Delta
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 1,411,793 |
| Northern Ireland | 93,267 |
| Scotland | 133,623 |
| Wales | 91,097 |
| Total cases | 1,729,780 |
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 | 93,423 |
| Northern Ireland | 751 |
| Scotland | 13,627 |
| Wales | 15,017 |
| Total cases | 122,818 |
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 | 1,282,593 |
| Northern Ireland | 75,080 |
| Scotland | 109,466 |
| Wales | 76,311 |
| Total cases | 1,693,610 |
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. |
VUI-21FEB-03
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 443 |
| Northern Ireland | 2 |
| Scotland | 40 |
| Wales | 10 |
| Total cases | 495 |
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. |
VUI-21FEB-04
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 323 |
| Northern Ireland | 40 |
| Scotland | 11 |
| Wales | 0 |
| Total cases | 374 |
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 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 PCR. |
Theta
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 6 |
| Northern Ireland | 0 |
| Scotland | 3 |
| Wales | 0 |
| Total cases | 9 |
Case definitions
| Genomic match | Criteria |
|---|---|
| Confirmed (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 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. |
| **Due to overlap with Delta sequences, the case definition of Kappa sequences was changed on 27 August 2021. |
VUI-21APR-03
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 15 |
| Northern Ireland | 0 |
| Scotland | 0 |
| Wales | 3 |
| Total cases | 18 |
Case definitions
| Genomic match | Criteria |
|---|---|
| Confirmed (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 PCR. |
VUI-21MAY-02
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 128 |
| Northern Ireland | 2 |
| Scotland | 4 |
| Wales | 4 |
| Total cases | 138 |
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
Surveillance overview
| Total confirmed and probable cases | |
|---|---|
| England | 20,534 |
| Northern Ireland | 1,523 |
| Scotland | 893 |
| Wales | 594 |
| Total cases | 23,544 |
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 PCR. |