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

• Type of Material: Article
• Authors: David VanInsberghe, Emory University; Andrew Neish, Emory University; Anice Lowen, Emory University; Katia Koelle, Emory University
• Language: English
• Date: 2021-03-15
• Publisher: Virus Evolution
• Publication Version: Preprint (Prior to Peer Review)
• Copyright Statement: The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
• License: Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1101/2020.08.05.238386
• Title of Journal or Parent Work: bioRxiv
• Grant/Funding Information: Further support for this study was provided by the US National Institutes of Health National Institute of General Medical Sciences grant 1R01 GM124280-03S1 (supplement).; This study was supported by NIAID Centers of Excellence for Influenza Research and Surveillance (CEIRS) grant HHSN272201400004C and an Emory University MP3 seed grant.
• Keywords: USA; SARS-CoV-2

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 detecting recombinants derived from different parent clades, and for geographic variation in clade abundance, we estimate that at most 5% of circulating viruses in the USA and UK are recombinant. While the phenotypic characterization of detected recombinants was beyond the scope of our analysis, the identification of transmitted recombinants involving substitutions of concern underscores the need to sustain efforts to monitor the emergence of new genotypes generated through recombination.