S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness

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

doi:10.1101/2023.03.30.535005

S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness

bioRxiv [Preprint]. 2023 Apr 24:2023.03.30.535005. doi: 10.1101/2023.03.30.535005.

Authors

Leonid Yurkovetskiy^{1

2

3}, Shawn Egri^{1

3}, Chaitanya Kurhade^{4

3}, Marco A Diaz-Salinas^{5

3}, Javier A Jaimes^{1

2

3}, Thomas Nyalile^{1

2}, Xuping Xie⁴, Manish C Choudhary^{2

6}, Ann Dauphin^{1

2}, Jonathan Z Li^{2

6}, James B Munro^{5

7}, Pei-Yong Shi⁴, Kuang Shen^{1

2}, Jeremy Luban^{1

2

7

8

9}

Affiliations

¹ Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
² Massachusetts Consortium on Pathogen Readiness, Boston, MA, 02115.
³ These authors contributed equally.
⁴ Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.
⁵ Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605, USA.
⁶ Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
⁷ Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
⁸ Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
⁹ Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.

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 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.

Keywords: ACE2; COVID-19; S:D614G; S:H655Y; S:Q613H; SARS-CoV-2; Spike protein; coronavirus; epistasis; evolution; infectivity; pandemic; variants.

Publication types

Preprint

Abstract

Publication types

Grants and funding