Phylogenetic analysis and in silico studies link spike Q675H mutation to SARS-CoV-2 adaptive evolution

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 delimiting the conformational space of the highly flexible loop containing the furin cleavage site. 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 found to have a greater affinity for Q675H than Q675 substrate conformations. As a consequence, Q675H mutation is likely to confer a fitness advantage to SARS-CoV-2 by promoting a more efficient viral entry. Interestingly, here we show an ongoing increase in the occurrence of Q675H spike mutation in the most common SARS-CoV-2 variants of concern (VOC). This finding highlights that, VOC are still evolving and start acquiring the Q675H mutation. At the same time, it suggests that our hypothesis of fitness advantage prompted by Q675H could be concrete.

High-depth sequencing characterization of viral dynamics across tissues in fatal COVID-19 reveals compartmentalized infection

“…Moreover, a persistent infection, particularly in an immunosuppressed patient, provides an environment for sustained viral evolution, which can result in the emergence of variants within the infected host 22,41 , and has been hypothesized as a potential source for novel variants of concern 22,41 . The Spike Q675H mutation, an adaptive mutation that has emerged independently in several SARS-CoV-2 lineages 32,33 , arose in a compartmentalized infection in one individual (who was immunocompromised) after just 9 days of infection. The emergence of a functionally advantageous mutation in the heart in a short period of time highlights the potential role of extrapulmonary reservoirs of SARS-CoV-2 in viral evolution within persistently infected hosts.…”

“…We investigated whether these variants have been observed in other studies; GISAID data revealed that one mutation, Spike (S) Q675H, has previously been observed, present at as much as 3% frequency worldwide (January 2021). This mutation was not circulating at the time that this subject contracted SARS-CoV-2, but has since emerged in multiple SARS-CoV-2 lineages, indicating convergent evolution 32,33 . This mutation falls directly upstream of the furin-cleavage site and is predicted to enhance viral entry 32,33 .…”

“…This mutation was not circulating at the time that this subject contracted SARS-CoV-2, but has since emerged in multiple SARS-CoV-2 lineages, indicating convergent evolution 32,33 . This mutation falls directly upstream of the furin-cleavage site and is predicted to enhance viral entry 32,33 . This suggests that this was a functionally advantageous mutation for either infecting the heart specifically, or it may have been broadly advantageous, but did not spread to other tissues because the infection was compartmentalized.…”