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Mutation Sites Are Distant from Remdesivir Binding Site in Human SARS-CoV-2 RNA-Dependent RNA Polymerase

The
comparison of 10,929 human SARS-CoV-2 RdRp protein sequences representing six
geographical locations with the reference protein sequence in human SARS-CoV-2
genome isolate from Wuhan, China, identified 222 distinct mutation sites in the
RdRp protein. The NiRAN and interface domains, Fingers, Palm and Thumb
sub-domains were each associated with ~20% or more mutations compared to mutations
in N-terminal, beta-hairpin or C-terminal regions of the protein. The
Pro4715Leu mutation was predominantly observed in RdRp proteins from all six
geographical locations; Africa, Asia, Europe, North America, Oceania and South
America. None of the mutation site
residues were within 3.2 Å interacting distance from remdesivir as observed in the
three-dimensional cryo-electron microscopy structures of RdRp protein complexes
available in the Protein Data Bank. Therefore, the mutations in human
SARS-CoV-2 RdRp proteins, described in the present work, are not likely to
cause resistance to remdesivir binding. Further, the mutations were also not
associated with functionally important residues that would affect the enzyme’s
function.