A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic.
Bayes Theorem
Databases, Genetic
Genome, Viral
Humans
Immune Evasion
Middle East Respiratory Syndrome Coronavirus
/ classification
Recombination, Genetic
Severe acute respiratory syndrome-related coronavirus
/ classification
SARS-CoV-2
/ classification
Spike Glycoprotein, Coronavirus
/ genetics
Viral Nonstructural Proteins
/ genetics
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
30 08 2021
30 08 2021
Historique:
received:
17
03
2021
accepted:
09
08
2021
entrez:
31
8
2021
pubmed:
1
9
2021
medline:
14
9
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34462471
doi: 10.1038/s41598-021-96626-8
pii: 10.1038/s41598-021-96626-8
pmc: PMC8405798
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Viral Nonstructural Proteins
0
nonstructural protein, coronavirus
0
Types de publication
Comparative Study
Journal Article
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
17365Subventions
Organisme : Global Emerging Infections Surveillance (GEIS) Branch
ID : ProMIS ID: P0140_20_WR
Organisme : Global Emerging Infections Surveillance (GEIS) Branch
ID : ProMIS ID: P0140_20_WR
Informations de copyright
© 2021. The Author(s).
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