About: Detection and spike gene characterization in porcine deltacoronavirus in China during 2016

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About: Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018 Goto Sponge NotDistinct Permalink

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018
Creator	Gu, Jinyan Lei, Jing Xing, Gang Zhou, Jiyong Zhang, Yu Yu, Jing Cheng, Yao Du, Liuyang Lian, Xue Liao, Ao
Source	Elsevier; Medline; PMC
abstract	Porcine deltacoronavirus (PDCoV) has been emerging in several swine-producing countries for years. In our study, 719 porcine diarrhoea samples from 18 provinces in China were collected for PDCoV and porcine epidemic diarrhoea virus (PEDV) detection. The epidemiological survey revealed that the positive rates of PDCoV, PEDV and coinfection were 13.07%, 36.72% and 4.73%, respectively. The entire spike (S) genes of eleven detected PDCoV strains were sequenced. Phylogenetic analysis showed that the majority of PDCoVs could be divided into three lineages: the China lineage, the USA/Japan/South Korea lineage and the Viet Nam/Laos/Thailand lineage. The China and the Viet Nam/Laos/Thailand lineages showed much greater genetic divergences than the USA/Japan/South Korea lineage. The present study detected one new monophyletic branch that contained three PDCoVs from China, and this branch was separated from the China lineage but closely related to the Viet Nam/Laos/Thailand lineage. The strain CH-HA2-2017, which belongs to this new branch, had a possible recombination event between positions 27 and 1234. Significant amino acid substitutions of PDCoV S proteins were analysed and displayed with a three-dimensional cartoon diagram. The visual spatial location of these substitutions gave a conformational-based reference for further studies on the significance of critical sites on the PDCoV S protein.
has issue date	2019-04-23(xsd:dateTime)
bibo:doi	10.1016/j.meegid.2019.04.023
bibo:pmid	31026605
has license	no-cc
sha1sum (hex)	0c6ba9dd4563409e699feb39f57f540fd4c4e4f4
schema:url	https://doi.org/10.1016/j.meegid.2019.04.023
resource representing a document's title	Detection and spike gene characterization in porcine deltacoronavirus in China during 2016–2018
has PubMed Central identifier	PMC7106087
has PubMed identifier	31026605
schema:publication	Infect Genet Evol
resource representing a document's body	covid:0c6ba9dd4563409e699feb39f57f540fd4c4e4f4#body_text
is schema:about of	named entity 'Laos' named entity 'The' named entity 'survey' named entity 'SIGNIFICANT' named entity 'LINEAGE' named entity 'SWINE' named entity 'VISUAL' named entity 'REFERENCE' named entity 'STUDIES' named entity 'EVENT' named entity 'PORCINE EPIDEMIC DIARRHOEA VIRUS' named entity 'POSITIONS' named entity 'RATES' named entity 'THESE' named entity 'PRESENT' named entity 'THREE-DIMENSIONAL' named entity 'GAVE' named entity 'PHYLOGENETIC ANALYSIS' named entity 'CRITICAL' named entity 'PROTEINS' covid:arg/0c6ba9dd4563409e699feb39f57f540fd4c4e4f4 named entity 'CHINA' named entity 'DIVIDED' named entity 'SITES' named entity 'CONTAINED' named entity 'CARTOON' named entity 'OUR' named entity 'S PROTEIN' named entity 'DIARRHOEA' named entity 'SEPARATED FROM' named entity 'RECOMBINATION' named entity 'THAILAND' named entity 'STRAIN' named entity 'GENETIC' named entity 'PORCINE DELTACORONAVIRUS' named entity 'DETECTION' named entity 'PORCINE' named entity 'DIAGRAM' named entity 'MAJORITY' named entity 'DETECTED' named entity 'STRAINS' named entity 'PEDV' named entity 'VIET NAM' named entity 'POSITIVE' named entity 'GENES' named entity 'HA2' named entity 'RELATED' named entity 'GREATER' named entity 'NEW BRANCH' named entity 'SPIKE' named entity 'PRODUCING' named entity 'USA' named entity 'BRANCH' named entity '28S' named entity 'AMINO ACID SUBSTITUTIONS' named entity 'SAMPLES' named entity 'REVEALED' named entity 'BASED' named entity 'STUDY' named entity 'COUNTRIES' named entity 'COLLECTED' named entity 'KOREA' named entity 'SIGNIFICANCE' named entity 'DISPLAYED' named entity 'SPATIAL LOCATION' named entity 'COINFECTION' named entity 'EPIDEMIOLOGICAL SURVEY' named entity 'MONOPHYLETIC' named entity 'BUT' named entity 'NEW' named entity 'MUCH' named entity 'ENTIRE'

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