Recurrent Emergence and Transmission of a SARS-CoV-2 Spike Deletion H69/V70

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 out of frame deletion in the S gene, which results in loss of two amino acids: H69 and V70. We show that 𝚫H69/V70 and other common NTD deletions occur at loop structures in RNA where polymerase activity is often compromised. In addition, the same two amino acid deletion is also observed in a set of closely related pangolin sarbecoviruses, but not in the bat sarbecovirus RaTG13. We report that in human infections 𝚫H69/V70 often co-occurs with the receptor binding motif amino acid replacements N501Y, N439K and Y453F, and in the latter two cases has followed the RBD mutation suggesting an epistatic interaction. One of the +.-|.-|.-| N501Y lineages, B.1.1.7, has undergone rapid expansion and includes eight other S gene mutations: RBD (N501Y and A570D), S1 (𝚫H69/V70 and 𝚫144/145) and S2 (P681H, T716I, S982A and D1118H). In vitro, we show that 𝚫H69/V70 does not impact serum neutralisation across multiple convalescent sera. However, the 𝚫H69/V70 does increase infectivity of Spike and is able to compensate for infectivity defects induced by RBD mutations N501Y, N439K and Y453F. In addition replacement of H69 and V70 in B.1.1.7 Spike substantially reduces its infectivity. Mechanistically, we demonstrate that 𝚫H69/V70 is associated with two fold increased Spike incorporation into virions, though it does not increase cell-cell fusion. Based on our data 𝚫H69/V70 increases Spike infectivity, likely acting as a permissive mutation that allows acquisition of otherwise deleterious immune escape mutations. Enhanced surveillance for the 𝚫H69/V70 deletion with and without RBD mutations should be considered as a global priority not only as a marker for the B.1.1.7 variant, but potentially also for other emerging variants of concern. Funding Statement: RKG is supported by a Wellcome Trust Senior Fellowship in Clinical Science (WT108082AIA). COG-UK is supported by funding from the Medical Research Council (MRC) & UK&ch & Innovation (UKRI), the National Institute of Health Research (NIHR) and Genome Research Limited, operating as the Wellcome Sanger Institute. SAK is supported by the Bill and Melinda Gates Foundation via PANGEA grant: OPP1175094. DLR is funded by the MRC (MC UU 1201412). WH is funded by the MRC (MR/R024758/1).We thank Dr James Voss for the kind gift of HeLa cells stably expressing ACE2. SL is funded by Medical Research Council MC_UU_12014/12. This study was also partly funded by Rosetrees Trust. Work in the AML lab is supported by NIHR Biomedical Research Centre Grant RCAG 817. Declaration of Interests: RKG has received consulting fees from UMOVIS lab, Gilead Sciences and ViiV Healthcare, and a research grant from InvisiSmart Technologies. On behalf of COG-UK, there are no other interests to declare. Ethics Approval Statement: Ethical approval for use of serum samples. Controls with COVID-19 were enrolled to the NIHR BioResource Centre Cambridge under ethics review board (17/EE/0025).