Understanding COVID-19 Variants – What Can The Coronavirus Infection Survey Tell Us?

The ONS is reporting signs of a recent increase in COVID-19 infection rates in much of the UK. There are also indications of the first cases of the newer B.1.617.2 variant. The ONS survey repeatedly tests a large, randomised sample of the entire community population. In this post Sarah Crofts explains what it can tell us about the spread of COVID-19 variants.


It is well understood that coronaviruses mutate and produce different variants which can impact different traits of the virus, such as the transmissibility or severity of disease caused.

First established in April 2020 the Coronavirus (COVID-19) Infection Survey has since expanded to measure the spread of the pandemic across the UK.

To provide the latest estimates of the number of people testing positive for SARS-CoV-2, the virus that causes COVID-19, our survey collects nose and throat swabs from participants to test for the presence of 3 coronavirus genes, the N gene, S gene and ORF1ab gene.

In Autumn 2020, the combination of these genes was used to monitor the spread of the new variant first identified in the South East of England (variant B.1.1.7, commonly known as the ‘Kent’ or ‘UK’ variant). Since that variant would only test positive for two of the three genes, it was straightforward to monitor in our sample. You can read more about this in a previously published blog here.

How variants are identified

The only way to precisely identify a variant is from genome sequencing – where the virus detected on a swab undergoes a detailed investigation to work out all the letters in its genetic code. By looking for differences between a sequenced genetic code and previously identified versions of the COVID-19 virus, we can understand how these different strains of the virus are related to one another. We can also group different strains into broad groups by this method when there is enough of the virus to identify its sequence.

We started publishing these data from April 2021. However, it takes longer to process, which causes a lag between these sequenced data and the most up to date estimates of infection.

Specific strains of SARS-CoV-2 may be labelled as “variants under investigation” if they show concerning characteristics, such as increased transmissibility. They can be subsequently reclassified as “variants of concern”. Among the latest “variants of concern” determined by Public Health England are B.1.1.7 (first detected in the UK), B.1.351 (first detected in South Africa) and B.1.617.2 (first detected in India).

Locating the presence of variants

The COVID-19 Infection Survey can identify participants who test positive for these variants if there is enough virus in their swab to sequence and these can provide an estimate of the number of positive cases for these variants among the community. However, our ability to do this depends on how widely a particular variant has spread and whether people with this variant are likely to be participants in our survey (which is unlikely if they have recently arrived from outside the UK).

When an outbreak is localised in specific geographic areas, our survey may not find these cases. For example, whilst we test around 180,000 people each fortnight across the whole of the UK, in any particular area there will be a small number of survey participants – and if infection rates are low, as they are currently, then a very small number may test positive. If only one or two people in a small geographic area test positive for any variant, then it is not possible to produce an estimate.

Public Health England publish separate data that show the numbers of positive tests by variant in local areas. These data are based on PCR tests taken by people who are either experiencing symptoms or are following government guidance to be tested. They also include results from targeted testing in particular areas. Therefore, these data are collected differently to our survey and provide a different measure. The ONS COVID-19 Infection Survey tests participants for the infection regardless of where they live or whether they have symptoms. When there is sufficient spread of a variant to be identified in our survey, it will provide estimates of how many people in the community population test positive for the infection.

Continuous Monitoring

On a weekly basis, we monitor the different gene combinations of our positive results. We know that the variant B.1.617.2 (first detected in India) would test positive on all 3 genes, as would the variant B.1.351 (first detected in South Africa), whereas the B.1.1.7 variant (known as the ‘UK variant’ and the most common infection seen across the UK since December) only tests positive on two genes. If there was a rise among the community population in infections with B.1.617.2, we would identify it within our group classified as ‘not compatible with the UK variant’.

This week, we have seen the estimated number of people testing positive within this group increase. This increase, combined with evidence from other data suggests that variant B.1.617.2 is likely to have caused this increase, but this cannot be confirmed until sequenced data are available. The value of categorising positive results for the infection in this way provides an early indication of a variant in circulation. This classification combined with our sequenced results means that the COVID-19 Infection Survey will pick up any changes in widespread infection levels within the community as a result of new variants.

Picture of Sarah Crofts

Sarah Crofts is Head of Analytical Outputs for the COVID-19 Infection Survey at the Office for National Statistics