FOI Ref: FOI/2021/2643
You asked
Has the SARS-COV-2 (COVID-19) virus has been isolated? Can you explain how you identify and test for variants of the virus? Do the PCR or Lateral Flow tests test for variants?
We said
Thank you for your request.
The COVID-19 Infection Survey (CIS) is a representative household survey which estimates the number of people testing positive for COVID-19 in the community, with or without symptoms. Community in this instance refers to private residential households and it excludes those in hospitals, care homes and/or other institutional settings.
As a household survey, we do not hold information on the isolation of the COVID-19 virus. For that information, you would need to contact the labs which process our swabs. We use the UK biobank (ukbiobank@ukbiobank.ac.uk) and the lighthouse lab at Glasgow.
In order to detect variants, a sample of the swabs returned by our participants will undergo whole genome sequencing. Through sequencing the whole genome of an individual infection, we can determine the genetic lineage of that infection and this also allows us to determine which variant that infection belongs to. In the technical dataset accompanying our latest bulletin, you can find the genetic lineages and Ct values of a sample of the positive tests returned by the participants in our study on tab 1a.
RT-PCR tests, which we use for testing our survey population, alone cannot distinguish between variants. However, they can be useful indicators of an infection's variant when taken in conjunction with other data. For more information on how we identify variants in our study, please see 'section 3: study design: data we collect' in our methodology article. In the technical dataset accompanying our latest bulletin, on tab 1c, you can find the modelled daily rates of the number of cases compatible with both the alpha and delta variants for each of the four UK nations. More information about our swab procedure can be found in our methodology article or our study protocol.