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Recombination events are concentrated in the spike protein region of Betacoronaviruses.
Bobay, Louis-Marie; O'Donnell, Angela C; Ochman, Howard.
  • Bobay LM; Department of Biology, University of North Carolina at Greensboro, Greensboro, North Carolina, United States of America.
  • O'Donnell AC; Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America.
  • Ochman H; Department of Integrative Biology, University of Texas at Austin, Austin, Texas, United States of America.
PLoS Genet ; 16(12): e1009272, 2020 12.
Article in English | MEDLINE | ID: covidwho-1388879
ABSTRACT
The Betacoronaviruses comprise multiple subgenera whose members have been implicated in human disease. As with SARS, MERS and now SARS-CoV-2, the origin and emergence of new variants are often attributed to events of recombination that alter host tropism or disease severity. In most cases, recombination has been detected by searches for excessively similar genomic regions in divergent strains; however, such analyses are complicated by the high mutation rates of RNA viruses, which can produce sequence similarities in distant strains by convergent mutations. By applying a genome-wide approach that examines the source of individual polymorphisms and that can be tested against null models in which recombination is absent and homoplasies can arise only by convergent mutations, we examine the extent and limits of recombination in Betacoronaviruses. We find that recombination accounts for nearly 40% of the polymorphisms circulating in populations and that gene exchange occurs almost exclusively among strains belonging to the same subgenus. Although experimental studies have shown that recombinational exchanges occur at random along the coronaviral genome, in nature, they are vastly overrepresented in regions controlling viral interaction with host cells.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Recombination, Genetic / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Topics: Variants Language: English Journal: PLoS Genet Journal subject: Genetics Year: 2020 Document Type: Article Affiliation country: JOURNAL.PGEN.1009272

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Recombination, Genetic / Spike Glycoprotein, Coronavirus / Betacoronavirus Type of study: Diagnostic study / Prognostic study / Randomized controlled trials Topics: Variants Language: English Journal: PLoS Genet Journal subject: Genetics Year: 2020 Document Type: Article Affiliation country: JOURNAL.PGEN.1009272