About: Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus
Creator	Su, Shuo Li, Gairu Xing, Gang Han, Guan-Zhu He, Wei Lemey, Philippe Gilbert, Marius Baele, Guy Ji, Xiang Dellicour, Simon Wang, Shilei Huang, Zhen Veit, Michael He, Wan-Ting Kosakovsky Pond, Sergei Suchard, Marc Zhu, Henan Huang, Yaowei Zhang, Letian
Source	Medline; PMC
abstract	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.
has issue date	2020-05-14(xsd:dateTime)
bibo:doi	10.1093/molbev/msaa117
bibo:pmid	32407507
has license	no-cc
schema:url	https://doi.org/10.1093/molbev/msaa117
resource representing a document's title	Genomic Epidemiology, Evolution, and Transmission Dynamics of Porcine Deltacoronavirus
has PubMed Central identifier	PMC7454817
has PubMed identifier	32407507
schema:publication	Mol Biol Evol
resource representing a document's body	covid:PMC7454817#body_text
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