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How do we track and measure new variants of coronavirus?

David Spiegelhalter and Anthony Masters
·2 min read
<span>Photograph: Ben Birchall/PA</span>
Photograph: Ben Birchall/PA

All viruses change through random mutations. Through genomic sequencing we now know that the UK epidemic was seeded by more than 1,000 distinct variants from people returning from Italy, Spain and France in February and March 2020, explaining why we got off to such a bad start.

These tiny changes are mostly inconsequential. Sometimes the virus gets lucky and spreads more easily, or causes more severe illness, in which case it earns the label Variant of Concern (VOC). In December, the rising B.1.1.7 lineage (also snappily known as VOC-202012/01) instigated new restrictions across south-east England, wrecking the tier system and ruining Christmas plans. This became known as the “UK variant” in other countries, while in the UK it is the “Kent variant”. It is unclear what people in Kent call it. More than 100,000 cases have been confirmed by sequencing.

Why is this one variant so concerning? Recent analysis concluded it increases transmission by 43% to 82%. There is also evidence of greater harm, but this is still being explored. Fortunately, there is a proxy measure for this variant, which allows monitoring of its progress without full sequencing, known as S-gene target failure (SGTF). The Office for National Statistics infection survey showed that, of positive cases with sufficient viral load, around 15% in England had SGTF in mid-November. This rose to more than 95% by the middle of February.

This variant showed similarly rapid climbs to dominance outside the UK, rising from 4% of cases in Denmark at the start of the year to 75% at the end of February.

New variants have hit the headlines, including those first identified in South Africa and Brazil. The UK is at the forefront of efforts to track the new variants, and has contributed around half of published sequences to the global Sars-CoV-2 genome repository.

The existing vaccines appear to work well for the UK variant: for others we are still waiting for data on protection against severe illness. Experts express confidence that vaccines can be adapted if necessary, and we must hope they are right.

•David Spiegelhalter is chair of the Winton Centre for Risk and Evidence Communication at Cambridge. Anthony Masters is statistical ambassador for the Royal Statistical Society