Skip to main content

Cookies on UKHSA data dashboard

We use some essential cookies to make this service work.

We'd like to set additional cookies so we can remember your settings, understand how people use the service and make improvements.

View cookies
UKHSA data dashboard

BetaThis is a new service - your feedback will help us to improve it.

Information
21 November 2024: COVID-19 positivity metrics not updated

A technical issue has prevented UKHSA from updating COVID-19 positivity. Work is underway to resolve the issue and resume reporting as soon as possible. The data presented was last updated on 7 November 2024.

BackEntry title:

COVID-19 weekly cases by lineage

Last updated on Tuesday, 3 September 2024 at 09:24am

Summary

Topic
COVID-19
Category
cases
API name
COVID-19_cases_lineagePercentByWeek

Methodology

The SARS-CoV-2 virus, which causes COVID-19, frequently mutates as it spreads. Samples that test positive for the SARS-CoV-2 virus via polymerase chain reaction (PCR) testing may also undergo whole-genome sequencing. Sequencing identifies the genetic makeup of the virus in the sample, which allows us to classify the virus into a lineage based on the number and types of mutations observed. Where applicable, each case of COVID-19 is assigned a variant. In England people are counted as new cases if they test positive again more than 90 days after their last positive test.

To simplify this metric, we have grouped genetically related lineages. These groups are as follows:

  • Alpha, which includes B.1.1.7 (V-20DEC-01) and B.1.1.7 with E484K (V-21FEB-01)
  • Delta, which includes B.1.617.2 (V-21APR-02) and AY.4.2 (V-21OCT-01)
  • Omicron BA.1, which includes BA.1 (V-21NOV-01)
  • Omicron BA.2, which includes BA.2 (V-22JAN-01) and CH.1.1 (V-22DEC-01)
  • Omicron BA.2.75, which includes BA.2.75 (V-22JUL-01)
  • Omicron BA.2.86, which includes BA.2.86 (V-23AUG-01)
  • Omicron BA.4, which includes BA.4 (V-22APR-03) and BA.4.6 (V-22SEP-01)
  • Omicron BA.5, which includes BA.5 (V-22APR-04) and BQ.1 (V-22OCT-01)
  • Omicron XBB, which includes XBB (V-22OCT-02), XBB.1.5 (V-23JAN-01), XBB.1.16 (V-23APR-01) and EG.5.1 (V-23JUL-01)
  • Omicron JN.1, which includes JN.1 (V-23DEC-01)
  • Other, which includes B.1.351 (V-20DEC-02), B.1.525 (V-21FEB-03), P.1 (V-21JAN-02), B.1.617.1 (V-21APR-01), P.2 (V-21JAN-01), P.3 (V-21MAR-02), C.37 (V-21JUN-01), A.23.1 with E484K (VOC-21FEB-01), B.1.1.318 (V-21FEB-04), B.1.617.3 (V-21APR-03) AV.1 (V-21MAY-01), C.36.3 (V-21MAY-02), B.1.621 (V-21JUL-01), XE (V-22APR-02), as well as samples that could not be successfully sequenced and samples where successful sequencing did not provide information of a high quality

The value shown for a given week is the number of COVID-19 cases categorised into each lineage group divided by the number of COVID-19 cases where the positive sample was whole-genome sequenced that week, then multiplied by 100. Cases are assigned a calendar week based on the date of specimen collection. 

Caveats

Only samples collected for PCR testing can be sequenced and only a subset of samples are selected for sequencing. Sequencing does not always lead to a lineage being determined.

There is a lag of two to three weeks between sample collection and lineage assignment. Therefore, lineage information for more recently confirmed cases may take several weeks to appear in the data.

Back to top