Recurrent emergence and transmission of a SARS-CoV-2 Spike deletion ΔH69/V70

Kemp, Steven; Harvey, William; Datir, Rawlings; Collier, Dami; Ferreira, Isabella; Meng, Bo; consortium, - COVID-19 Genomics UK; Carabelii, Alessandro; Robertson, David L; Gupta, Ravindra K

SARS-CoV-2 Spike amino acid replacements in the receptor binding domain (RBD) occur relatively frequently and some have a consequence for immune recognition. Here we report recurrent emergence and significant onward transmission of a six-nucleotide deletion in the S gene, which results in loss of two amino acids: H69 and V70. Of particular note this deletion,{Delta} H69/V70, often co-occurs with the receptor binding motif amino acid replacements N501Y, N439K and Y453F. One of the{Delta} H69/V70+ N501Y lineages, B.1.1.7, is comprised of over 4000 SARS-CoV-2 genome sequences from the UK and includes eight other S gene mutations: RBD (N501Y and A570D), S1 ({Delta}H69/V70 and{Delta} 144/145) and S2 (P681H, T716I, S982A and D1118H). Some of these mutations have presumably arisen as a result of the virus evolving from immune selection pressure in infected individuals and at least one, lineage B.1.1.7, potentially from a chronic infection. Given our recent evidence that{Delta} H69/V70 enhances viral infectivity (Kemp et al. 2020), its effect on virus fitness appears to be independent to the RBD changes. Enhanced surveillance for the{Delta} H69/V70 deletion with and without RBD mutations should be considered as a priority. Permissive mutations such as{Delta} H69/V70 have the potential to enhance the ability of SARS-CoV-2 to generate new variants, including vaccine escape variants, that would have otherwise significantly reduced viral infectivity.