About: Occurrence and sequence analysis of porcine deltacoronaviruses in southern China

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About: Occurrence and sequence analysis of porcine deltacoronaviruses in southern China Goto Sponge NotDistinct Permalink

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	Occurrence and sequence analysis of porcine deltacoronaviruses in southern China
Creator	Zhai, Shao-Lun Li, Feng Wang, Dan Zhou, Xia Li, Xiao-Peng Lv, Dian-Hong Wei, Wen-Kang Wen, Xiao-Hui Zhang, He
Source	Medline; PMC
abstract	BACKGROUND: Following the initial isolation of porcine deltacoronavirus (PDCoV) from pigs with diarrheal disease in the United States in 2014, the virus has been detected on swine farms in some provinces of China. To date, little is known about the molecular epidemiology of PDCoV in southern China where major swine production is operated. RESULTS: To investigate the prevalence of PDCoV in this region and compare its activity to other enteric disease of swine caused by porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis coronavirus (TGEV), and porcine rotavirus group C (Rota C), 390 fecal samples were collected from swine of various ages from 15 swine farms with reported diarrhea. Fecal samples were tested by reverse transcription-PCR (RT-PCR) that targeted PDCoV, PEDV, TGEV, and Rota C, respectively. PDCoV was detected exclusively from nursing piglets with an overall prevalence of approximate 1.28 % (5/390), not in suckling and fattening piglets. Interestingly, all of PDCoV-positive samples were from 2015 rather than 2012–2014. Despite a low detection rate, PDCoV emerged in each province/region of southern China. In addition, compared to TGEV (1.54 %, 5/390) or Rota C (1.28 %, 6/390), there were highly detection rates of PEDV (22.6 %, 88/390) in those samples. Notably, all five PDCoV-positive piglets were co-infected by PEDV. Furthermore, phylogenetic analysis of spike (S) and nucleocapsid (N) gene sequences of PDCoVs revealed that currently circulating PDCoVs in southern China were more closely related to other Chinese strains of PDCoVs than to those reported in United States, South Korea and Thailand. CONCLUSIONS: This study demonstrated that PDCoV was present in southern China despite the low prevalence, and supported an evolutionary theory of geographical clustering of PDCoVs. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12985-016-0591-6) contains supplementary material, which is available to authorized users.
has issue date	2016-08-05(xsd:dateTime)
bibo:doi	10.1186/s12985-016-0591-6
bibo:pmid	27496131
has license	cc-by
sha1sum (hex)	1329ea9b040bdc8af7c30f7ba4b5755e352deae8
schema:url	https://doi.org/10.1186/s12985-016-0591-6
resource representing a document's title	Occurrence and sequence analysis of porcine deltacoronaviruses in southern China
has PubMed Central identifier	PMC4974758
has PubMed identifier	27496131
schema:publication	Virol J
resource representing a document's body	covid:1329ea9b040bdc8af7c30f7ba4b5755e352deae8#body_text
is schema:about of	named entity 'swine' named entity 'fecal' named entity 'caused' named entity 'deltacoronavirus' named entity 'production' named entity 'enteric' named entity 'prevalence' named entity 'farms' covid:arg/1329ea9b040bdc8af7c30f7ba4b5755e352deae8 named entity 'rotavirus' named entity 'Rota' named entity 'phylogenetic analysis' named entity 'suckling' named entity 'nucleocapsid' named entity 'collected' named entity 'addition' named entity 'molecular epidemiology' named entity 'evolutionary theory' named entity 'tested' named entity 'coronavirus' named entity 'RT-PCR' named entity 'PEDV' named entity 'molecular epidemiology' named entity 'swine' named entity 'reverse transcription' named entity 'China' named entity 'phylogenetic analysis' named entity 'nucleocapsid' named entity 'virus' named entity 'PEDV' named entity 'China' named entity 'co-infected' named entity 'China' named entity 'demonstrated' named entity 'Hainan' named entity 'pig' named entity '2, 3' named entity 'PCR' named entity 'PEDV' named entity 'pig' named entity 'pig' named entity 'Shanxi' named entity 'mutation' named entity 'diarrhea' named entity 'protein' named entity 'China' named entity 'nucleocapsid' named entity 'IgG' named entity 'gene sequences' named entity 'Sequence alignment' named entity 'co-infection' named entity 'Beijing Genomics Institute' named entity 'gene sequences' named entity 'pathogenesis' named entity 'feces' named entity 'PEDV' named entity 'nucleocapsid' named entity 'Guangxi autonomous region' named entity 'PEDV' named entity 'Guangdong' named entity 'enteropathogenic' named entity 'enteric viruses' named entity 'recombinant' named entity 'pig' named entity 'nucleocapsid' named entity 'gene' named entity 'gene' named entity 'Phosphate Buffered Saline' named entity 'China' named entity 'nucleocapsid' named entity 'pathogenesis' named entity 'gene' named entity 'Korea'

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