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Journal articleDate
2022-06-14Author
de Klerk, ArneSwanepoel, Phillip
Lourens, Rentia
Zondo, Mpumelelo
Abodunran, Isaac
Lytras, Spyros
MacLean, Oscar A.
Robertson, David
Pond, Sergei
Zehr, Jordan
Kumar, Venkatesh
Stanhope, Michael J.
Harkins, Gordon W.
Murrell, Ben
Martin, Darren P.
Group
Institute for Genomics and Evolutionary Medicine (Temple University)Department
BiologyPermanent link to this record
http://hdl.handle.net/20.500.12613/8081
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https://doi.org/10.1093/ve/veac054Abstract
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 break points 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 break points 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 break-point hotspot locations. We find that while the locations of recombination break points 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 break points most commonly occur, it is evident that selection against misfolded recombinant proteins also strongly impacts observable recombination break-point distributions in coronavirus genomes sampled from nature.Citation
Arné de Klerk, Phillip Swanepoel, Rentia Lourens, Mpumelelo Zondo, Isaac Abodunran, Spyros Lytras, Oscar A MacLean, David Robertson, Sergei L Kosakovsky Pond, Jordan D Zehr, Venkatesh Kumar, Michael J Stanhope, Gordon Harkins, Ben Murrell, Darren P Martin, Conserved recombination patterns across coronavirus subgenera, Virus Evolution, Volume 8, Issue 2, 2022, veac054, https://doi.org/10.1093/ve/veac054Citation to related work
Oxford University PressHas part
Virus Evolution, Vol. 8, No. 2ADA compliance
For Americans with Disabilities Act (ADA) accommodation, including help with reading this content, please contact scholarshare@temple.eduae974a485f413a2113503eed53cd6c53
http://dx.doi.org/10.34944/dspace/8053
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