Role of Q675H Mutation in Improving SARS-CoV-2 Spike Interaction with the Furin Binding Pocket

Abstract

Genotype screening was implemented in Italy and showed a significant prevalence of new SARS-CoV-2 mutants carrying Q675H mutation, near the furin cleavage site of spike protein. Currently, this mutation, which is expressed on different SARS-CoV-2 lineages circulating worldwide, has not been thoughtfully investigated. Therefore, we performed phylogenetic and biocomputational analysis to better understand SARS-CoV-2 Q675H mutants’ evolutionary relationships with other circulating lineages and Q675H function in its molecular context. Our studies reveal that Q675H spike mutation is the result of parallel evolution because it arose independently in separate evolutionary clades. In silico data show that the Q675H mutation gives rise to a hydrogen-bonds network in the spike polar region. This results in an optimized directionality of arginine residues involved in interaction of spike with the furin binding pocket, thus improving proteolytic exposure of the viral protein. Furin was predicted to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation could confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we have shown that Q675H spike mutation is documented in all the VOCs. This finding highlights that VOCs are still evolving to enhance viral fitness and to adapt to the human host. At the same time, it may suggest Q675H spike mutation involvement in SARS-CoV-2 evolution.

Evolution of SARS-CoV-2 during the first year of the COVID-19 pandemic in Northwestern Argentina

“… EPI_ISL_2136033, EPI_ISL_4082236 N.5 L452R EPI_ISL_2135314 N.5 Delta, Epsilon, Kappa, and Omicron (lineages BA.4 and BA.5) Associated with low-level reductions in susceptibility of convalescent and vaccine plasma samples ( Ferreira et al., 2021 ; Greaney et al., 2021 ). Q675H EPI_ISL_4003459 C.26 P.6 Improves proteolytic exposure of SARS-CoV-2 Spike in the Furin Binding Pocket ( Bertelli et al., 2021 ). L18F EPI_ISL_4082302 C.37 Beta and Gamma Associated with reduced susceptibility to several NTD-binding mAbs but by itself does not appear to reduce CP or VP susceptibility ( McCallum et al., 2021 ; Wang et al., 2021 ).…”

Evidence for coordinated evolution at amino acid sites of SARS-CoV-2 spike

“…Although experiments suggested a positive effect of Q677H on the background of VOCs Alpha and Gamma both carrying N501Y (Zeng et al, 2021, p. 2), this fact is in disagreement with very low population frequencies of Q677H in these VOCs (Gangavarapu et al, 2022a, 2022b, 2022c). The same is true for the Q675H mutation: while it was observed in some isolates of VOCs with the N501Y lineage-defining mutation, the population frequencies of these strains were also very low (Bertelli et al, 2021).…”

“…Among the four predicted discordantly evolving pairs, two pairs (501, 677) and (501, 675) are between the three sites whose effects of mutations were assessed experimentally or computationally (figure 4). The N501Y mutation increases the binding affinity of Spike to ACE2 up to 15-fold (Starr et al, 2022) and increases infectivity (Liu et al, 2022); the Q677H mutation increases infectivity, propensity to syncytium formation and escape of neutralization by serum of vaccinated people (Zeng et al, 2021, p. 2); and the Q675H mutation is predicted to increase furin binding affinity (Bertelli et al, 2021). Although experiments suggested a positive effect of Q677H on the background of VOCs Alpha and Gamma both carrying N501Y (Zeng et al, 2021, p. 2), this fact is in disagreement with very low population frequencies of Q677H in these VOCs (Gangavarapu et al, 2022a, 2022b, 2022c).…”

Spike Mutation Profiles Associated With SARS-CoV-2 Breakthrough Infections in Delta Emerging and Predominant Time Periods in British Columbia, Canada

“…These mutations increase the spike protein's stability ( 31 , 35 ). Other in-silico studies show Q675H is associated with decrease protein stability ( 31 ), but provides increased furin affinity ( 36 ). Lastly, we identified P812S to be positively associated with BTIs, but an in-silico study suggests this mutation decreases spike-TMPRSS2 binding ( 37 ).…”