A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

Abstract The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 r...

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Autores principales:	Simon Pollett, Matthew A. Conte, Mark Sanborn, Richard G. Jarman, Grace M. Lidl, Kayvon Modjarrad, Irina Maljkovic Berry
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/406eea7de06f4c81b9401435935fbf11
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spelling	oai:doaj.org-article:406eea7de06f4c81b9401435935fbf112021-12-02T16:38:49ZA comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic10.1038/s41598-021-96626-82045-2322https://doaj.org/article/406eea7de06f4c81b9401435935fbf112021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96626-8https://doaj.org/toc/2045-2322Abstract The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.Simon PollettMatthew A. ConteMark SanbornRichard G. JarmanGrace M. LidlKayvon ModjarradIrina Maljkovic BerryNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Simon Pollett Matthew A. Conte Mark Sanborn Richard G. Jarman Grace M. Lidl Kayvon Modjarrad Irina Maljkovic Berry A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
description	Abstract The SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.
format	article
author	Simon Pollett Matthew A. Conte Mark Sanborn Richard G. Jarman Grace M. Lidl Kayvon Modjarrad Irina Maljkovic Berry
author_facet	Simon Pollett Matthew A. Conte Mark Sanborn Richard G. Jarman Grace M. Lidl Kayvon Modjarrad Irina Maljkovic Berry
author_sort	Simon Pollett
title	A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
title_short	A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
title_full	A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
title_fullStr	A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
title_full_unstemmed	A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic
title_sort	comparative recombination analysis of human coronaviruses and implications for the sars-cov-2 pandemic
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/406eea7de06f4c81b9401435935fbf11
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A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

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