Massachusetts Consortium on Pathogen Readiness (MassCPR)
FP-0034281
United States
Citation
Journal: bioRxiv / Year: 2023 Title: S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. Authors: Leonid Yurkovetskiy / Shawn Egri / Chaitanya Kurhade / Marco A Diaz-Salinas / Javier A Jaimes / Thomas Nyalile / Xuping Xie / Manish C Choudhary / Ann Dauphin / Jonathan Z Li / James B Munro ...Authors: Leonid Yurkovetskiy / Shawn Egri / Chaitanya Kurhade / Marco A Diaz-Salinas / Javier A Jaimes / Thomas Nyalile / Xuping Xie / Manish C Choudhary / Ann Dauphin / Jonathan Z Li / James B Munro / Pei-Yong Shi / Kuang Shen / Jeremy Luban / Abstract: SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and ...SARS-CoV-2 variants bearing complex combinations of mutations that confer increased transmissibility, COVID-19 severity, and immune escape, were first detected after S:D614G had gone to fixation, and likely originated during persistent infection of immunocompromised hosts. To test the hypothesis that S:D614G facilitated emergence of such variants, S:D614G was reverted to the ancestral sequence in the context of sequential Spike sequences from an immunocompromised individual, and within each of the major SARS-CoV-2 variants of concern. In all cases, infectivity of the S:D614G revertants was severely compromised. The infectivity of atypical SARS-CoV-2 lineages that propagated in the absence of S:D614G was found to be dependent upon either S:Q613H or S:H655Y. Notably, Gamma and Omicron variants possess both S:D614G and S:H655Y, each of which contributed to infectivity of these variants. Among sarbecoviruses, S:Q613H, S:D614G, and S:H655Y are only detected in SARS-CoV-2, which is also distinguished by a polybasic S1/S2 cleavage site. Genetic and biochemical experiments here showed that S:Q613H, S:D614G, and S:H655Y each stabilize Spike on virions, and that they are dispensable in the absence of S1/S2 cleavage, consistent with selection of these mutations by the S1/S2 cleavage site. CryoEM revealed that either S:D614G or S:H655Y shift the Spike receptor binding domain (RBD) towards the open conformation required for ACE2-binding and therefore on pathway for infection. Consistent with this, an smFRET reporter for RBD conformation showed that both S:D614G and S:H655Y spontaneously adopt the conformation that ACE2 induces in the parental Spike. Data from these orthogonal experiments demonstrate that S:D614G and S:H655Y are convergent adaptations to the polybasic S1/S2 cleavage site which stabilize S1 on the virion in the open RBD conformation and act epistatically to promote the fitness of variants bearing complex combinations of clinically significant mutations.
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