Recombinant SARS-CoV-2 genomes are currently circulating at low levels.

BioRxiv : the Preprint Server for Biology
David VanInsbergheK. Koelle

Abstract

Viral recombination can generate novel genotypes with unique phenotypic characteristics, including transmissibility and virulence. Although the capacity for recombination among betacoronaviruses is well documented, there is limited evidence of recombination between SARS-CoV-2 strains. By identifying the mutations that primarily determine SARS-CoV-2 clade structure, we developed a lightweight approach for detecting recombinant genomes. Among the over 537,000 genomes queried, we detect 1175 putative recombinants that contain multiple mutational markers from distinct clades. Additional phylogenetic analysis and the observed co-circulation of predicted parent clades in the geographic regions of exposure further support the feasibility of recombination in these detected cases. An analysis of these detected cases did not reveal any evidence for recombination hotspots in the SARS-CoV-2 genome. Although most recombinant genotypes were detected a limited number of times, at least two recombinants are now widely transmitted. Recombinant genomes were also found to contain substitutions of concern for elevated transmissibility and lower vaccine efficacy, including D614G, N501Y, E484K, and L452R. Adjusting for an unequal probability of dete...Continue Reading

Citations

Jan 6, 2021·Journal of Applied Genetics·Szymon HryhorowiczEwa Ziętkiewicz

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Methods Mentioned

BETA
GISAID

Software Mentioned

RAPR
PhyML
GISAID
Nextstrain
MAFFT

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