SARS-CoV-2 Point Mutation and Deletion Spectra, and Their Association with Different Disease Outcome

Abstract

Mutant spectra of RNA viruses are important to understand viral pathogenesis, and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultra-deep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of thirty nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19.

Point mutations at specific sites of the nsp12–nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2

“…All genomic sequences for the phylogenetic analysis and associated metadata are published in Global Initiative on Sharing All Influenza Data (GISAID’s EpiCoV database) ( https://gisaid.org ) (GISAID Identifier: EPI_SET_231009qw; https://doi.org/10.55876/gis8.231009qw ) ( 43 ). The Fastq files for all SARS-CoV-2 ultradeep sequences used in the present study are available at ENA (ID PRJEB48766 ) ( 44 ).…”