2022
DOI: 10.1093/ve/veac054
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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 w… Show more

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Cited by 22 publications
(12 citation statements)
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“…The mapping of these deletions provides an entirely independent data source to evaluate the occurrence of recombination from the commonly used nucleotide-level sequence changes that were also used to test for genomic mosaicism-the consistency between the results from these two data types provides strong evidence for the occurrence of a recombination event in our data. Furthermore, an inferred recombination breakpoint located near the start of the S protein reading frame generally coincides with previously described recombination hotspots for other coronaviruses (de Klerk et al, 2021;Sabir et al, 2016;Yang et al, 2021) and for SARS-CoV-2 (Boni et al, 2020;Jackson et al, 2021;Li et al, 2020;Lytras et al, 2021).…”
Section: Discussionsupporting
confidence: 83%
“…The mapping of these deletions provides an entirely independent data source to evaluate the occurrence of recombination from the commonly used nucleotide-level sequence changes that were also used to test for genomic mosaicism-the consistency between the results from these two data types provides strong evidence for the occurrence of a recombination event in our data. Furthermore, an inferred recombination breakpoint located near the start of the S protein reading frame generally coincides with previously described recombination hotspots for other coronaviruses (de Klerk et al, 2021;Sabir et al, 2016;Yang et al, 2021) and for SARS-CoV-2 (Boni et al, 2020;Jackson et al, 2021;Li et al, 2020;Lytras et al, 2021).…”
Section: Discussionsupporting
confidence: 83%
“…Genomes of different isolates gathered from GenBank and viral RefSeq database [34] were aligned using MUSCLE [51] implemented in MEGA X [52] and checked for possible recombinants in RDP v. 4 [53]. All recombination events with p-val<10 −4 reported by at least four methods were considered significant, based on the methods from related studies [54,55]. Phylogenetic analyses were performed on alignments free of recombinants.…”
Section: Phylogenetic Analysesmentioning
confidence: 99%
“…CoVs are known to extensively recombine ( Banner and Lai 1991 ; Liao and Lai 1992 ; Graham and Baric 2010 ; de Klerk et al. 2022 ; Lytras et al.…”
Section: Resultsmentioning
confidence: 99%