Spike protein fusion loop controls SARS-CoV-2 fusogenicity and infectivity (preprint)

ABSTRACT

Compared to the other human coronaviruses, SARS-CoV-2 has a higher reproductive number that is driving the COVID-19 pandemic. The high transmission of SARS-CoV-2 has been attributed to environmental, immunological, and molecular factors. The Spike protein is the foremost molecular factor responsible for virus fusion, entry and spread in the host, and thus holds clues for the rapid viral spread. The dense glycosylation of Spike, its high affinity of binding to the human ACE2 receptor, and the efficient priming by cleavage have already been proposed for driving efficient virus-host entry, but these do not explain its unusually high transmission rate. I have investigated the Spike from six {beta}-coronaviruses, including the SARS-CoV-2, and find that their surface-exposed fusion peptides constituting the defined fusion loop are spatially organized contiguous to each other to work synergistically for triggering the virus-host membrane fusion process. The architecture of the Spike quaternary structure ensures the participation of the fusion peptides in the initiation of the host membrane contact for the virus fusion process. The SARS-CoV-2 fusion peptides have unique physicochemical properties, accrued in part from the presence of consecutive prolines that impart backbone rigidity which aids the virus fusogenicity. The specific contribution of these prolines shows significantly diminished fusogenicity in vitro and associated pathogenesis in vivo, inferred from comparative studies of their deletion-mutant in a fellow murine {beta}-coronavirus MHV-A59. The priming of the Spike by its cleavage and subsequent fusogenic conformational transition steered by the fusion loop may be critical for the SARS-CoV-2 spread. Significance StatementThe three proximal fusion peptides constituting the fusion loop in Spike protein are the membranotropic segments most suitable for engaging the host membrane surface for its disruption. Spikes unique quaternary structure architecture drives the fusion peptides to initiate the protein host membrane contact. The SARS-CoV-2 Spike trimer surface is relatively more hydrophobic among other human coronavirus Spikes, including the fusion peptides that are structurally more rigid owing to the presence of consecutive prolines, aromatic/hydrophobic clusters, a stretch of consecutive {beta}-branched amino acids, and the hydrogen bonds. The synergy accrued from the location of the fusion peptides, their physicochemical features, and the fusogenic conformational transition appears to drive the virus fusion process and may explain the high spread of the SARS-CoV-2.