Mutations in SARS-CoV-2 spike protein identified by mass spectrometry based phylogenetics and their structural and functional consequences

The structural and functional consequences of mutations located throughout the S1 and S2 subunit domains of spike protein among omicron and D614G-mutant originating forms of the SARS-CoV-2 virus are examined. These structural mutations were identified by a mass-based phylogenetics approach. The T95I mutation, located in the S1 N-terminal domain, and the T547K mutation of the receptor-binding domain both help to stabilise the spike protein structure and contribute to viral fitness in omicron variants. The D796Y within the N-terminal portion of the S2 subunit, also stabilises the protein, while the effects of Q954H and N969K combine to reduce infectivity through displacement of the backbone of the heptad repeat 2 (HR2) region. The N856K mutation, within the fusion peptide region, introduces a stabilising H-bond at residue T572 that both alters the S1/S2 interaction and hampers conformational change resulting in a mixed stabilisation effect.