SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage

Abstract

For efficient cell entry and membrane fusion, SARS-CoV-2 spike (S) protein needs to be cleaved at two different sites, S1/S2 and S2 by different cellular proteases such as furin and TMPRSS2. Polymorphisms in the S protein can affect cleavage, viral transmission, and pathogenesis. Here, we investigated the role of arising S polymorphisms in vitro and in vivo to understand the emergence of SARS-CoV-2 variants. First, we showed that the S:655Y is selected after in vivo replication in the mink model. This mutation is present in the Gamma Variant Of Concern (VOC) but it also occurred sporadically in early SARS-CoV-2 human isolates. To better understand the impact of this polymorphism, we analyzed the in vitro properties of a panel of SARS-CoV-2 isolates containing S:655Y in different lineage backgrounds. Results demonstrated that this mutation enhances viral replication and spike protein cleavage. Viral competition experiments using hamsters infected with WA1 and WA1-655Y isolates showed that the variant with 655Y became dominant in both direct infected and direct contact animals. Finally, we investigated the cleavage efficiency and fusogenic properties of the spike protein of selected VOCs containing different mutations in their spike proteins. Results showed that all VOCs have evolved to acquire an increased spike cleavage and fusogenic capacity despite having different sets of mutations in the S protein. Our study demonstrates that the S:655Y is an important adaptative mutation that increases viral cell entry, transmission, and host susceptibility. Moreover, SARS-COV-2 VOCs showed a convergent evolution that promotes the S protein processing.

Cell fusion as a link between the SARS-CoV-2 spike protein, COVID-19 complications, and vaccine side effects

“…These observations mean that some SARS-CoV-2 variants can differ in the incidence of cell fusion and thus its consequences, including the ability to persist in the body by using cell-to-cell transmission, [27] a mechanism also used by HIV [28,29]. This prediction is consistent with the report that novel SARS-CoV-2 variants of concern have mutations associated with a gain in syncytia formation [30].…”

Intra-host SARS-CoV-2 evolution in the gut of mucosally-infected Chlorocebus aethiops (African green monkeys)

“…The H655Y mutation which lies immediately adjacent to the furin cleavage site (Figure 1C) and has been detected sporadically in multiple viral lineages with the P.1 (gamma) lineage being most prominent as H655Y is a defining variant of the gamma lineage (nextstrain.org). This variant has also been detected in other animal species disease models including cats and mink [28,29]. A recent report also showed that virus harboring a 655Y amino acid showed enhanced replicative capacity in vitro and spike protein cleavage [29], likely explaining the H655Ymutation in the AGM species.…”

“…This variant has also been detected in other animal species disease models including cats and mink [28,29]. A recent report also showed that virus harboring a 655Y amino acid showed enhanced replicative capacity in vitro and spike protein cleavage [29], likely explaining the H655Ymutation in the AGM species.…”

Cell Fusion as a Link between the SARS-CoV-2 Spike Protein, COVID-19 Complications, and Vaccine Side Effects

“…28,29 This prediction is consistent with the report that novel SARS-CoV-2 variants of concern have mutations associated with a gain in syncytia formation. 30 The pain of (con)fused neuronal networks Neurological manifestations, including pain, are common in COVID-19 patients. 31 While SARS-CoV-2 is likely to contribute to these symptoms in multiple ways, short-circuiting neuronal networks by fusing neurons can explain not only how some CoV-2 is covered by an envelope, which is fused to the cell membrane by spike once this protein is activated by binding to one of its receptors and processed by a membrane protease (both are not shown for simplicity).…”