Uneven growth of SARS-CoV-2 clones evidenced by more than 500,000 whole-genome sequences

We have computed the frequencies of the alleles of the “UK variant” (B.1.1.7) and “South Africa variant” (B.1.351) of SARS-CoV-2 from the large GISAID repository. We find that the frequencies of the mutations in UK variant overall rose towards the end of 2020, as widely reported in the literature and in the general press. However, we also find that these frequencies vary in different patterns rather than in concert. For South Africa variant we find a more complex scenario with frequencies of some mutations rising and some remaining close to zero. Our results point to that what is generally reported as one variant is in fact a collection of variants with different genetic characteristics.