Recombination events are concentrated in the spike protein region of Betacoronaviruses

• Published in: PLoS genetics Vol. 16; no. 12; p. e1009272
• Main Authors: Bobay, Louis-Marie, O’Donnell, Angela C., Ochman, Howard
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 17.12.2020; Public Library of Science (PLoS)
• Subjects: ACE2; Angiotensin-converting enzyme 2; Betacoronavirus - classification; Betacoronavirus - genetics; Biology and Life Sciences; Coronaviruses; Crossing Over, Genetic - genetics; Divergence; Evolution; Genes, Viral - genetics; Genetic aspects; Genetic recombination; Genome, Viral - genetics; Genomes; Host Specificity - genetics; Medicine and health sciences; Models, Genetic; Mutation; Nucleotide sequence; Physiological aspects; Polymorphism, Genetic; Population structure; Proteins; Recombination; Recombination, Genetic - genetics; SARS-CoV-2 - classification; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Spike Glycoprotein, Coronavirus - genetics; Spike protein; Standard deviation; Transversion; Viral proteins; Viral Tropism - genetics; United States
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1009272

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.