Abstract
SARS-CoV-2 Spike amino acid replacements occur relatively frequently in the receptor binding domain (RBD) and some have a consequences for immune recognition. Here we report recurrent emergence and significant onward transmission of a six nucleotide deletion in the Spike gene, which results in the loss of two amino acids: ΔH69/V70. Of particular note this deletion often follows the receptor binding motif amino acid replacements N501Y, N439K and Y453F. In addition, we report a sub-lineage of over 350 sequences bearing seven spike mutations across the RBD (N501Y, A570D), S1 (ΔH69/V70) and S2 (P681H, T716I, S982A and D1118H) in England. These mutations have possibly arisen as a result of the virus evolving from immune selection pressure in infected individuals. Enhanced surveillance for the ΔH69/V70 deletion with and without RBD mutations should be considered as a priority.
Competing Interest Statement
RKG has received consulting fees from UMOVIS lab, Gilead Sciences and ViiV Healthcare, and a research grant from InvisiSmart Technologies.
