Recurrent emergence and transmission of a SARS-CoV-2 spike deletion H69/V70
Author:
Kemp Steven AORCID, Meng Bo, Ferriera Isabella ATM, Datir Rawlings, Harvey William T, Papa Guido, Lytras Spyros, Collier Dami A, Mohamed Ahmed, Gallo Giulia, Thakur Nazia, Carabelli Alessandro M, Kenyon Julia C, Lever Andrew M, De Marco Anna, Saliba Christian, Culap Katja, Cameroni Elisabetta, Piccoli Luca, Corti Davide, James Leo C, Bailey Dalan, Robertson David L, Gupta Ravindra K.ORCID,
Abstract
AbstractSARS-CoV-2 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 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. One of the ΔH69/V70+ N501Y lineages, now known as B.1.1.7, has undergone rapid expansion and includes eight S gene mutations: RBD (N501Y and A570D), S1 (ΔH69/V70 and Δ144) and S2 (P681H, T716I, S982A and D1118H).In vitro, we show that ΔH69/V70 does not reduce serum neutralisation across multiple convalescent sera. However, ΔH69/V70 increases infectivity and is associated with increased incorporation of cleaved spike into virions. ΔH69/V70 is able to compensate for small infectivity defects induced by RBD mutations N501Y, N439K and Y453F. In addition, replacement of H69 and V70 residues in the B.1.1.7 spike reduces its infectivity and spike mediated cell-cell fusion. Based on our data ΔH69/V70 likely acts 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. Vaccines designed to target the deleted spike protein could mitigate against its emergence as increased selective forces from immunity and vaccines increase globally.HighlightsΔH69/V70 is present in at least 28 SARS-CoV-2 lineagesΔH69/V70 does not confer escape from convalescent seraΔH69/V70 increases spike infectivity and compensates for RBD mutationsΔH69/V70 is associated with greater spike cleavageB.1.1.7 requires ΔH69/V70 for optimal spike cleavage and infectivity
Publisher
Cold Spring Harbor Laboratory
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