L18F substrain of SARS-CoV-2 VOC-202012/01 is rapidly spreading in England

The Variant of Concern (VOC)-202012/01 (also known as B.1.1.7) is a rapidly growing lineage of SARS-CoV-2. In January 2021, VOC-202012/01 constituted about 80% of SARS-CoV-2 genomes sequenced in England and was present in 27 out of 29 countries that reported at least 50 viral genomes. As this strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. Based on GISAID data we systematically estimated growth rates of mutations acquired by the lineage to find that L18F substitution in spike initiated a substrain characterized by replicative advantage of 1.70 [95% CI: 1.56-1.96] in relation to the remaining VOC-202012/01 substrains. We also indicate three mutations in the receptor binding motive of spike, that arose in VOC-202012/01: E484K, F490S, S494P, and may give rise to escape mutants. Such mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine induced seroprevalence.