Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus.
Animals
Biological Evolution
China
/ epidemiology
Coronavirus
/ classification
Coronavirus Infections
/ epidemiology
Genetic Variation
Genome, Viral
Genomics
Humans
Models, Molecular
Molecular Epidemiology
Open Reading Frames
Phylogeny
Phylogeography
Protein Structure, Secondary
Recombination, Genetic
Selection, Genetic
Spike Glycoprotein, Coronavirus
/ chemistry
Swine
/ virology
Swine Diseases
/ epidemiology
Viral Proteins
/ genetics
BEAST
Bayesian inference
evolution
phylogeographic
porcine deltacoronavirus
recombination
Journal
Molecular biology and evolution
ISSN: 1537-1719
Titre abrégé: Mol Biol Evol
Pays: United States
ID NLM: 8501455
Informations de publication
Date de publication:
01 09 2020
01 09 2020
Historique:
pubmed:
15
5
2020
medline:
17
9
2020
entrez:
15
5
2020
Statut:
ppublish
Résumé
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown once again that coronavirus (CoV) in animals are potential sources for epidemics in humans. Porcine deltacoronavirus (PDCoV) is an emerging enteropathogen of swine with a worldwide distribution. Here, we implemented and described an approach to analyze the epidemiology of PDCoV following its emergence in the pig population. We performed an integrated analysis of full genome sequence data from 21 newly sequenced viruses, along with comprehensive epidemiological surveillance data collected globally over the last 15 years. We found four distinct phylogenetic lineages of PDCoV, which differ in their geographic circulation patterns. Interestingly, we identified more frequent intra- and interlineage recombination and higher virus genetic diversity in the Chinese lineages compared with the USA lineage where pigs are raised in different farming systems and ecological environments. Most recombination breakpoints are located in the ORF1ab gene rather than in genes encoding structural proteins. We also identified five amino acids under positive selection in the spike protein suggesting a role for adaptive evolution. According to structural mapping, three positively selected sites are located in the N-terminal domain of the S1 subunit, which is the most likely involved in binding to a carbohydrate receptor, whereas the other two are located in or near the fusion peptide of the S2 subunit and thus might affect membrane fusion. Finally, our phylogeographic investigations highlighted notable South-North transmission as well as frequent long-distance dispersal events in China that could implicate human-mediated transmission. Our findings provide new insights into the evolution and dispersal of PDCoV that contribute to our understanding of the critical factors involved in CoVs emergence.
Identifiants
pubmed: 32407507
pii: 5837118
doi: 10.1093/molbev/msaa117
pmc: PMC7454817
doi:
Substances chimiques
Spike Glycoprotein, Coronavirus
0
Viral Proteins
0
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
2641-2654Subventions
Organisme : NIAID NIH HHS
ID : U19 AI135995
Pays : United States
Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
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