Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7

The SARS-CoV-2 variant of concern B.1.1.7 has quickly spread. To identify its crucial mutations, we explored the B.1.1.7 associated mutations on an evolutionary tree by the Coronavirus GenBrowser and VENAS. We found that a non-coding deletion g.a28271-, at upstream of the nucleocapsid (N) gene, has triggered the high transmissibility of B.1.1.7. The deletion changes the core Kozak site of the N gene and may reduce the expression of N protein and increase that of ORF9b. The expression of ORF9b is also regulated by another mutation (g.gat28280cta) that mutates the core Kozak sites of the ORF9b gene. If both mutations back-mutate, B.1.1.7 variant loses its high transmissibility. Moreover, the deletion may interact with ORF1a:p.SGF3675-, S:p.P681H, and S:p.T716I to increase the viral transmissibility. Overall, these results demonstrate the importance of the non-coding deletion and provide evolutionary insight into the crucial mutations of B.1.1.7.