About: Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation

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About: Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation 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	Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation
Creator	Beer, Martin Höper, Dirk Pfaff, Florian Grund, Christian Harder, Timm Sultan, Hesham Hafez, Hafez Hassan, Kareem Shany, Salama Shehata, Awad Ibrahim, Mahmoud Moharam, Ibrahim Abo-Elkhair, Mohammed El Kady, Magdy Kady, E
source	Elsevier; Medline; PMC
abstract	Infectious bronchitis virus (IBV), a gamma-coronavirus, causes infectious bronchitis (IB), a major respiratory disease of chicken. Its high mutation rate in conjunction with recombination of the RNA genome constantly creates IBV variants that are difficult to control by currently available vaccines. In this study, we addressed the question whether small-scale holdings might harbor IBV variants that serve as a reservoir for newly emerging variants. Egyptian IBV isolate EGY/NR725/2016 (NR725/16) from a small-scale broiler farm was assigned to genotype I, clade 23 (S1:GI-23), based on partial S1 gene sequences and corroborated by full genome sequencing. Analysis of the S1 gene established three subclades for historical IBV strains (S1:GI-23.1, S1:GI-23.2.1 and S1:GI-23.2.2) and confirmed NR725/16 as being part of a separate fourth subclade (S1:GI-23.3). Samples from the years 2018 and 2019 revealed that the new subclade prevails in Egypt, carrying fixed mutations within the hypervariable regions (HVR) 1-3 of the S1 protein that affect two neutralization sensitive epitopes at sites 294F, 297S and 306Y (48.2) and 329R (62.1). In addition, recombination was recognized in isolate NR 725/16, with intra-subtype mixing for the entire genes 3ab and E and inter-subtype mixing for the entire gene 6b with a close match to QX like viruses of genotype GI-19. Further analysis of gene 3ab detected the homologous gene pool to NR725/16 in samples from 2013 (3ab:C) and closely related 3ab genotypes in IBV Egyptian isolates from 2016, 2018 and 2019. These data prove a flourishing exchange between poultry holdings with a common gene pool. The continued circulation of viruses harboring genes S1:GI-23.3 and 3ab:C indicates an evolutionary advantage of this combination possibly by combining antigenic escape with modulated pathogenicity to facilitate IBV spread in the vaccinated poultry population in Egypt.
has issue date	2020-07-01(xsd:dateTime)
bibo:doi	10.1016/j.meegid.2020.104433
bibo:pmid	32622080
has license	no-cc
sha1sum (hex)	b2fccd61d98aa0e443f308728956466380c386cd
schema:url	https://doi.org/10.1016/j.meegid.2020.104433
resource representing a document's title	Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation
has PubMed Central identifier	PMC7327463
has PubMed identifier	32622080
schema:publication	Infect Genet Evol
resource representing a document's body	covid:b2fccd61d98aa0e443f308728956466380c386cd#body_text
is schema:about of	named entity 'strains' named entity 'NEW' named entity 'constellation' named entity 'Egypt' named entity 'highly contagious' named entity 'single-stranded' named entity 'poultry' named entity 'Carlsbad, CA' named entity 'gene' named entity 'Israel' named entity 'RNA' named entity 'poultry' named entity 'genome analysis' named entity 'genotype' named entity 'biosecurity' named entity 'nucleotide' named entity 'MCL' named entity 'Egypt' named entity 'partial sequence' named entity 'phylogenetic analysis' named entity 'recombination' named entity 'viruses' named entity 'IBV' named entity 'genotype' named entity 'pathogenicity' named entity 'phylogeny' named entity 'genotype' named entity 'mutation rate' named entity 'viruses' named entity 'gene sequences' named entity 'chicken eggs' named entity 'pathogenicity' named entity 'viruses' named entity 'protein' named entity 'gene' named entity 'gene' named entity 'evolutionary advantage' named entity 'non-essential' named entity 'gene sequences' named entity 'genotyping' named entity 'genome' named entity 'IBV' named entity 'gene' named entity 'gene' named entity 'IBV' named entity 'kidneys' named entity 'IBV' named entity 'host cell' named entity 'virus' named entity 'IBV' named entity 'clade' named entity 'gene' named entity 'infection' named entity 'IBV' named entity 'endemic' named entity 'sequenced' named entity 'rales' named entity 'viruses' named entity 'evolution' named entity 'nucleotides' named entity 'antiviral' named entity 'Egypt' named entity 'virus' named entity 'gene' named entity 'IBV' named entity 'ClustalW' named entity 'Romania'

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