Positive selection within the genomes of SARS-CoV-2 and other Coronaviruses independent of impact on protein function

PeerJ
Alejandro BerrioG. A. Wray

Abstract

The emergence of a novel coronavirus (SARS-CoV-2) associated with severe acute respiratory disease (COVID-19) has prompted efforts to understand the genetic basis for its unique characteristics and its jump from non-primate hosts to humans. Tests for positive selection can identify apparently nonrandom patterns of mutation accumulation within genomes, highlighting regions where molecular function may have changed during the origin of a species. Several recent studies of the SARS-CoV-2 genome have identified signals of conservation and positive selection within the gene encoding Spike protein based on the ratio of synonymous to nonsynonymous substitution. Such tests cannot, however, detect changes in the function of RNA molecules. Here we apply a test for branch-specific oversubstitution of mutations within narrow windows of the genome without reference to the genetic code. We recapitulate the finding that the gene encoding Spike protein has been a target of both purifying and positive selection. In addition, we find other likely targets of positive selection within the genome of SARS-CoV-2, specifically within the genes encoding Nsp4 and Nsp16. Homology-directed modeling indicates no change in either Nsp4 or Nsp16 protein struc...Continue Reading

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Citations

Mar 6, 2021·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Necla KoçhanYavuz Oktay
Mar 23, 2021·Journal of Evolutionary Biology·Vincent MontoyaJeffrey B Joy
Apr 18, 2021·Experimental & Molecular Medicine·Devika Singh, Soojin V Yi
Jul 7, 2021·Translational Medicine Communications·Gerald Dieter Griffin

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Datasets Mentioned

BETA
MT121216.1
MT040333.1

Methods Mentioned

BETA
glycosylation

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