Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation.
Animals
Chickens
Coronavirus Infections
/ veterinary
Egypt
Evolution, Molecular
Infectious bronchitis virus
/ classification
Mutation
Phylogeny
Poultry Diseases
/ virology
RNA, Viral
/ genetics
Recombination, Genetic
Sequence Analysis, RNA
Spike Glycoprotein, Coronavirus
/ genetics
Trachea
/ virology
Whole Genome Sequencing
/ methods
Chicken
Coronavirus
Infectious bronchitis
Recombination
Journal
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
ISSN: 1567-7257
Titre abrégé: Infect Genet Evol
Pays: Netherlands
ID NLM: 101084138
Informations de publication
Date de publication:
Nov 2020
Nov 2020
Historique:
received:
18
02
2020
revised:
05
06
2020
accepted:
16
06
2020
pubmed:
6
7
2020
medline:
15
12
2020
entrez:
5
7
2020
Statut:
ppublish
Résumé
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.
Identifiants
pubmed: 32622080
pii: S1567-1348(20)30264-1
doi: 10.1016/j.meegid.2020.104433
pmc: PMC7327463
pii:
doi:
Substances chimiques
RNA, Viral
0
Spike Glycoprotein, Coronavirus
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
104433Informations de copyright
Copyright © 2020 Elsevier B.V. All rights reserved.
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