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

Yurkovetskiy, L.; Egri, S.; Kurhade, C.; Diaz-Salinas, M. A.; Jaimes, J. A.; Nyalile, T.; Xie, X.; Choudhary, M. C.; Dauphin, A.; Li, J. Z.; Munro, J. B.; Shi, P.-Y.; Shen, K.; Luban, J.

doi:10.1101/2023.03.30.535005

bioRxiv · 10.1101/2023.03.30.535005

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

Yurkovetskiy, L.·Egri, S.·Kurhade, C.·Diaz-Salinas, M. A.·Jaimes, J. A.·Nyalile, T.·Xie, X.·Choudhary, M. C.·Dauphin, A.·Li, J. Z.·Munro, J. B.·Shi, P.-Y.·Shen, K.·Luban, J.

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Abstract

Abstract/SummarySARS-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. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=194 SRC="FIGDIR/small/535005v2_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@8b4864org.highwire.dtl.DTLVardef@3daad9org.highwire.dtl.DTLVardef@9ba446org.highwire.dtl.DTLVardef@3e1a08_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIS:D614G is ubiquitous among SARS-CoV-2 B-lineage Spikes and is required for infectivity of the main Variants of Concern C_LIO_LIIn an example of convergent evolution, SARS-CoV-2 A lineage viruses maintained transmission chains in the absence of S:D614G, but were instead dependent upon S:Q613H or S:H655Y C_LIO_LIS:D614G and S:H655Y are both adaptations to the polybasic S1/S2 cleavage site C_LIO_LIIncreased infectivity of S:D614G and S:H655Y is associated with a more open RBD conformation and increased steady-state levels of virion-associated S1 C_LI

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Yurkovetskiy, L., Egri, S., Kurhade, C., Diaz-Salinas, M. A., Jaimes, J. A., Nyalile, T., Xie, X., Choudhary, M. C., Dauphin, A., Li, J. Z., Munro, J. B., Shi, P.-Y., Shen, K., Luban, J.. 2023-03-31. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. https://doi.org/10.1101/2023.03.30.535005

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