Conserved recombination patterns across coronavirus subgenera

Abstract

Recombination contributes to the genetic diversity found in coronaviruses and is known to be a prominent mechanism whereby they evolve. It is apparent, both from controlled experiments and in genome sequences sampled from nature, that patterns of recombination in coronaviruses are non-random and that this is likely attributable to a combination of sequence features that favour the occurrence of recombination breakpoints at specific genomic sites, and selection disfavouring the survival of recombinants within which favourable intra-genome interactions have been disrupted. Here we leverage available whole-genome sequence data for six coronavirus subgenera to identify specific patterns of recombination that are conserved between multiple subgenera and then identify the likely factors that underlie these conserved patterns. Specifically, we confirm the non-randomness of recombination breakpoints across all six tested coronavirus subgenera, locate conserved recombination hot- and cold-spots, and determine that the locations of transcriptional regulatory sequences are likely major determinants of conserved recombination breakpoint hot-spot locations. We find that while the locations of recombination breakpoints are not uniformly associated with degrees of nucleotide sequence conservation, they display significant tendencies in multiple coronavirus subgenera to occur in low guanine-cytosine content genome regions, in non-coding regions, at the edges of genes, and at sites within the Spike gene that are predicted to be minimally disruptive of Spike protein folding. While it is apparent that sequence features such as transcriptional regulatory sequences are likely major determinants of where the template-switching events that yield recombination breakpoints most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination breakpoint distributions in coronavirus genomes sampled from nature.

Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination

“…1 B and C ). The functional implications of selective Spike recombination has recently been corroborated by multiple independent studies, suggesting this might be a mechanism for antigenic shift utilized by the sarbecoviruses or, more broadly, by all coronavirus groups ( Bobay et al 2020 ; de Klerk et al 2021 ; Goldstein et al 2021 ; Nikolaidis et al 2022 ; Yang et al 2021 ). Our analysis further illustrates the importance of accounting for recombination rather than using whole-genome pairwise similarity to determine the shared evolutionary history of these viruses.…”

Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination

“…With more diversity in circulating SARS-CoV-2 genomes, it will now be possible to track recombinations, characterize the rate of recombination, and identify hot spots for breakpoints (de Klerk et al, 2021). One way to detect these recombinants is the strategy we used.…”

Mucosal Vaccines, Sterilizing Immunity, and the Future of SARS-CoV-2 Virulence

“…That said, increased circulation comes with the serious risk of an attenuated lineage reverting to a more virulent one, via single nucleotide mutations, deletions, or recombination. Multiple coronavirus subgenera have a tendency for recombination in low GC genome regions, non-coding regions, edges of genes, and nondisruptive Spike sites [119]. For SARS-CoV-2, two recombinant lineages are already in circulation (XA and XB).…”