About: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure

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About: Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure 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
title	Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure
Creator	Wei, Ping Chen, Jiming Dong, Zhihua Fan, Wensheng He, Yining Huang, Teng Li, Meng Mo, Meilan Tang, Ning Wei, Tianchao Wu, Cuilan Zhang, Wen Zhao, Changrun
source	Medline; PMC
abstract	The high mutation rates of infectious bronchitis virus (IBV) pose economic threats to the poultry industry. In order to track the genetic evolutionary of IBV isolates circulating in yellow chickens, we continued to conduct the genetic analyses of the structural genes S1, E, M, and N from 64 IBV isolates in southern China during 2009–2017. The results showed that the dominant genotypes based on the four genes had changed when compared with those during 1985–2008. Based on the S1 gene phylogenetic tree, LX4-type (GI-19) was the most dominant genotype, which was different from that during 1985–2008. The second most dominant genotype was LDT3-A-type, but this genotype disappeared after 2012. New-type 1 (GVI-1) isolates showed increasing tendency and there were four aa (QKEP) located in the hypervariable region (HVR) III and one aa (S) insertion in all the New-type 1 isolates. Both the analyses of amino acid entropy and molecular evolutionary rate revealed that the variations from large to small were S1, E, M, and N. Purifying selection was detected in the S1, E, M, and N gene proteins, which was different from the positive selection during 1985–2008. Six isolates were confirmed to be recombinants, possibly generated from a vaccine virus of the 4/91-type or LDT3-A-type and a circulating virus. The estimated times for the most recent common ancestors based on the S1, E, M, and N genes were the years of 1744, 1893, 1940, and 1945, respectively. Bayesian skyline analysis revealed a sharp decrease in genetic diversity of all the four structural genes after 2010 and since late 2015, the viral population rapidly rose. In conclusion, the IBVs circulating in southern China over the past decade have experienced a remarkable change in genetic diversity, dominant genotypes, and selection pressure, indicating the importance of permanent monitoring of circulating strains and the urgency for developing new vaccines to counteract the emerging LX4-type and New-type IBVs.
has issue date	2019-09-26(xsd:dateTime)
bibo:doi	10.3390/v11100898
bibo:pmid	31561498
has license	cc-by
sha1sum (hex)	0586c9a5cbb333e62fb7e18d5239eae3be34d42a
schema:url	https://doi.org/10.3390/v11100898
resource representing a document's title	Genetic Analysis of Avian Coronavirus Infectious Bronchitis Virus in Yellow Chickens in Southern China over the Past Decade: Revealing the Changes of Genetic Diversity, Dominant Genotypes, and Selection Pressure
has PubMed Central identifier	PMC6833030
has PubMed identifier	31561498
schema:publication	Viruses
resource representing a document's body	covid:0586c9a5cbb333e62fb7e18d5239eae3be34d42a#body_text
is schema:about of	covid:arg/0586c9a5cbb333e62fb7e18d5239eae3be34d42a named entity 'type 1' named entity 'IBVs' named entity 'virus' named entity 'mutation rates' named entity 'genotype' named entity 'China' named entity 'phylogenetic tree' named entity 'IBV' named entity 'positive selection' named entity 'evolutionary rate' named entity 'infectious bronchitis virus' named entity 'gene' named entity 'Southern China' named entity 'Guangxi' named entity 'nucleocapsid' named entity 'sequence identity' named entity 'Yulin' named entity 'IBV' named entity 'vaccine strain' named entity 'IBV' named entity 'prevention and control' named entity 'gene' named entity 'gene' named entity 'nucleocapsid' named entity 'Taiwan' named entity 'Recombination events' named entity 'IBV' named entity 'glycosylation' named entity 'epidemiological' named entity 'IBV' named entity 'China' named entity 'nucleocapsid' named entity 'recombinants' named entity 'pathogenicity' named entity 'glycosylation sites' named entity 'long-term' named entity 'IBV' named entity 'recombination' named entity 'chicken' named entity 'nucleocapsid' named entity 'recombination' named entity 'pathogen' named entity 'co-infection' named entity 'gene' named entity 'cDNA' named entity 'vaccination' named entity 'molecular clock' named entity 'serotype' named entity 'viruses' named entity 'protein' named entity 'structural protein' named entity 'Guangxi' named entity 'pathogenicity' named entity 'IBV' named entity 'genotype' named entity 'type 1' named entity 'positively selected' named entity 'IBVs' named entity 'vaccine' named entity 'vaccine strain' named entity 'IBV' named entity 'genetic diversity' named entity 'dN/dS ratio' named entity 'evolution' named entity 'IBV' named entity 'vaccination programs' named entity 'Yulin' named entity 'nucleocapsid'

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