Mutations in SARS-CoV-2 nsp7 and nsp8 proteins and their predicted impact on replication/transcription complex structure

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) has been identified to be a mutation hot spot, with the P323L mutation being commonly observed in viral genomes isolated from North America. RdRp forms a complex with nonstructural proteins nsp7 and nsp8 to form the minimal replication/transcription machinery required for genome replication. As mutations in RdRp may affect formation of the RdRp-nsp7-nsp8 supercomplex, we analyzed viral genomes to identify mutations in nsp7 and nsp8 protein sequences. Based on in silico analysis of predicted structures of the supercomplex comprising of native and mutated proteins, we demonstrate that specific mutations in nsp7 and nsp8 proteins may have a role in stabilization of the replication/transcription complex.

Keywords: RdRp; SARS-CoV-2; mutation; nsp7; nsp8.

Figure 1

Interactions between residues of (A) native and (B) mutant nsp7 (yellow), nsp8 (orange) and RdRp (green) proteins. The S25L mutation in nsp7 leads to a H‐bond formation between nsp7 S26 and nsp8 D163, which is not observed in the native RdRp–nsp7–nsp8 supercomplex

Figure 2

(A) Interactions between residues of (i) native and (ii) mutant RdRp (green) and nsp8 (orange) proteins. The P323L mutation in RdRp leads to a H‐bond formation with nsp8 N118, which is not observed when native RdRp interacts with nsp8. (B) Interactions between residues of (iii) native and (iv) mutant nsp8 (orange) and RdRp (green) proteins. A steric clash is observed between nsp8 M129 and RdRp N386, which is abolished in the nsp8 M129I mutant