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

•New prototype of emerging IBV variant recognized in Egypt.•New IBV strains form a forth subclade within S-genotype GI-23.•Mutations in the S1protein, including two defined neutralizing sites, point to antigenic variation.•Intra-genotypic recombination is recognized for genes S1, 3ab and E, inter-ge...

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Published in:Infection, genetics and evolution genetics and evolution, 2020-11, Vol.85, p.104433-104433, Article 104433
Main Authors: Moharam, Ibrahim, Sultan, Hesham, Hassan, K., Ibrahim, Mahmoud, Shany, Salama, Shehata, Awad A., Abo-ElKhair, Mohammed, Pfaff, Florian, Höper, Dirk, EL Kady, Magdy, Beer, Martin, Harder, Timm, Hafez, Hafez, Grund, Christian
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container_title Infection, genetics and evolution
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creator Moharam, Ibrahim
Sultan, Hesham
Hassan, K.
Ibrahim, Mahmoud
Shany, Salama
Shehata, Awad A.
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Pfaff, Florian
Höper, Dirk
EL Kady, Magdy
Beer, Martin
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Hafez, Hafez
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description •New prototype of emerging IBV variant recognized in Egypt.•New IBV strains form a forth subclade within S-genotype GI-23.•Mutations in the S1protein, including two defined neutralizing sites, point to antigenic variation.•Intra-genotypic recombination is recognized for genes S1, 3ab and E, inter-genotypic recombination for gene 6b (GI-19).•Specific gene 3ab genotype is linked to new IBV emergence of new variants. 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.
doi_str_mv 10.1016/j.meegid.2020.104433
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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.</description><identifier>ISSN: 1567-1348</identifier><identifier>EISSN: 1567-7257</identifier><identifier>DOI: 10.1016/j.meegid.2020.104433</identifier><identifier>PMID: 32622080</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>Animals ; Chicken ; Chickens ; Coronavirus ; Coronavirus Infections - veterinary ; Egypt ; Evolution, Molecular ; Infectious bronchitis ; Infectious bronchitis virus - classification ; Infectious bronchitis virus - genetics ; Infectious bronchitis virus - isolation &amp; purification ; Mutation ; Phylogeny ; Poultry Diseases - virology ; Recombination ; Recombination, Genetic ; Research Paper ; RNA, Viral - genetics ; Sequence Analysis, RNA ; Spike Glycoprotein, Coronavirus - genetics ; Trachea - virology ; Whole Genome Sequencing - methods</subject><ispartof>Infection, genetics and evolution, 2020-11, Vol.85, p.104433-104433, Article 104433</ispartof><rights>2020 Elsevier B.V.</rights><rights>Copyright © 2020 Elsevier B.V. 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All rights reserved. 2020 Elsevier B.V.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c463t-6c924fb17d040cd07e2926e1f3b9d2ffed8eeffc3da953e5f69f052f9faa9b093</citedby><cites>FETCH-LOGICAL-c463t-6c924fb17d040cd07e2926e1f3b9d2ffed8eeffc3da953e5f69f052f9faa9b093</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27903,27904</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32622080$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Moharam, Ibrahim</creatorcontrib><creatorcontrib>Sultan, Hesham</creatorcontrib><creatorcontrib>Hassan, K.</creatorcontrib><creatorcontrib>Ibrahim, Mahmoud</creatorcontrib><creatorcontrib>Shany, Salama</creatorcontrib><creatorcontrib>Shehata, Awad A.</creatorcontrib><creatorcontrib>Abo-ElKhair, Mohammed</creatorcontrib><creatorcontrib>Pfaff, Florian</creatorcontrib><creatorcontrib>Höper, Dirk</creatorcontrib><creatorcontrib>EL Kady, Magdy</creatorcontrib><creatorcontrib>Beer, Martin</creatorcontrib><creatorcontrib>Harder, Timm</creatorcontrib><creatorcontrib>Hafez, Hafez</creatorcontrib><creatorcontrib>Grund, Christian</creatorcontrib><title>Emerging infectious bronchitis virus (IBV) in Egypt: Evidence for an evolutionary advantage of a new S1 variant with a unique gene 3ab constellation</title><title>Infection, genetics and evolution</title><addtitle>Infect Genet Evol</addtitle><description>•New prototype of emerging IBV variant recognized in Egypt.•New IBV strains form a forth subclade within S-genotype GI-23.•Mutations in the S1protein, including two defined neutralizing sites, point to antigenic variation.•Intra-genotypic recombination is recognized for genes S1, 3ab and E, inter-genotypic recombination for gene 6b (GI-19).•Specific gene 3ab genotype is linked to new IBV emergence of new variants. 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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. 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1567-7257
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source ScienceDirect Freedom Collection
subjects Animals
Chicken
Chickens
Coronavirus
Coronavirus Infections - veterinary
Egypt
Evolution, Molecular
Infectious bronchitis
Infectious bronchitis virus - classification
Infectious bronchitis virus - genetics
Infectious bronchitis virus - isolation & purification
Mutation
Phylogeny
Poultry Diseases - virology
Recombination
Recombination, Genetic
Research Paper
RNA, Viral - genetics
Sequence Analysis, RNA
Spike Glycoprotein, Coronavirus - genetics
Trachea - virology
Whole Genome Sequencing - methods
title 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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