The unusually high number of spike protein mutations, other genomic properties of the variant, and the high sequencing coverage in the UK suggest that the variant has not emerged through gradual accumulation of mutations in the UK. It is also unlikely that the variant could have arisen through selection pressure from ongoing vaccination programmes as the observed increase does not match the timing of such activities.
One possible explanation for the emergence of the variant is prolonged SARS-CoV-2 infection in a single patient, potentially with reduced immunocompetence, similar to what has previously been described [17,18]. Such prolonged infection can lead to accumulation of immune escape mutations at an elevated rate.
Another possible explanation could be adaptation processes in a virus that occur in a different susceptible animal species and is then transmitted back to humans from the animal hosts. This led to the emergence of a variant with multiple spike protein mutations (including RBD mutation Y453F and deletion 69-70) in Denmark during transmission among mink [19]. Several different spike protein mutations associated with mink have also been described in the Netherlands [20]. The UK has reported to ECDC and the WHO Regional Office for Europe that there is no clear epidemiological link to animals for VUI 202012/01, so this explanation is less likely for this variant [1].
Lastly, it is also possible that the variant has emerged through circulation in countries with no or very low sequencing coverage. This hypothesis is less plausible, however, as random mutations acquired during circulation of the virus would not explain the unusually high proportion of spike protein mutations, and undetected circulation for a long enough time for the high number of mutations to accumulate (around 10 months according to current molecular clock estimates) is also not very likely due to global travel patterns.
South Africa reports through the GISAID EpiCoV database [11] and a public press release [21,22] a similar rapid increase since October of a variant with the spike protein mutation N501Y, two additional RBD mutations and multiple additional spike protein mutations. This variant has no close evolutionary relation to VUI 202012/01 but demonstrates that the emergence of successful variants with similar properties may not be rare.
www.bag.admin.ch
and in Germany (one import from the UK):
sozialministerium.baden-wuerttemberg.de
