Complete genome sequences of two avian infectious bronchitis viruses isolated in Egypt: Evidence for genetic drift and genetic recombination in the circulating viruses

Abozeid, Hassanein H.; Paldurai, Anandan; Khattar, Sunil K.; Afifi, Manal A.; El‐Kady, Magdy F.; El‐Deeb, Ayman H.; Samal, Siba K.

doi:10.1016/j.meegid.2017.05.006

Cited by 41 publications

(44 citation statements)

References 35 publications

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“…For nearly 20 years, the strains of GI-23 have been geographically limited to Middle East countries, but have recently spread to some European countries (Valastro et al, 2016;Lisowska et al, 2017;Fischer et al, 2019). In Egypt, GI-23 lineage has become the most prevalent lineage in the field as the majority of circulating IBV variant strains reported in chickens belong to this lineage as stated in many studies (Awad et al, 2014;Valastro et al, 2016;Zanaty et al, 2016;Abdel-Sabour et al, 2017;Abozeid et al, 2017;Naguib et al, 2017), Which is consistent with the results obtained in this study.…”

Section: Distance and Phylogenetic Analysis Of Full-length S1 Genesupporting

confidence: 91%

Molecular Characterization and Phylogenetic Analysis of Full-length S1 Gene of GI-16 and GI-23 Infectious Bronchitis Virus in Qena, Egypt.

Sabra¹,

Abdellatif²,

Ahmed³

et al. 2020

jwpr

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Infectious Bronchitis Virus (IBV) is a highly evolving virus that affects respiratory, urinary and reproductive systems. This virus is recognized as an important pathogen due to the continuous genesis of new variants that threaten the poultry industry worldwide. The aim of this study was to characterize emerging IBV variants originated from field outbreaks in Qena province, Egypt, and to study their genetic relationships with global strains. From September 2017 to January 2019, 52 field samples were collected from broiler flocks suspected of being infected with IBV. The collected samples were inoculated into embryonated chicken eggs via allantoic route for virus isolation. The IBV presence was confirmed using real-time reverse transcriptase PCR (rRT-PCR) assay targeting nucleocapsid (N) gene and finally, nine samples were selected from 29 positive samples with rRT-PCR for further genetic characterization through full-length spike (S1) gene sequencing. Phylogenetic analyses indicated that one isolate (IBV/CK/EG/QENA-4/2017) clustered within genotype I lineage 16 (GI-16). On the other hand, the remaining eight isolates (2017-2018) belonged to genotype I lineage 23 (GI-23) and clustered separately in monophyletic clade. The isolates in this study were found to share only 74.6-82.1% amino acid identity with the commonly used vaccine strains in Egypt. In conclusion, findings of this study provide informative data on circulating IBVs in the study area and highlight the importance of adopting a convenient vaccination strategy that can be more efficient for controlling the emergence of new IBV variants.

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Section: Distance and Phylogenetic Analysis Of Full-length S1 Genesupporting

confidence: 91%

Molecular Characterization and Phylogenetic Analysis of Full-length S1 Gene of GI-16 and GI-23 Infectious Bronchitis Virus in Qena, Egypt.

Sabra¹,

Abdellatif²,

Ahmed³

et al. 2020

jwpr

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“…To our knowledge this is the first study, which investigated the full genome of Canadian IBV isolates. Although, IBV strains circulating in other countries have been characterized and changes in the IBV genome due to mutations and recombination have been shown [40,[55][56][57][58][59], our whole genome sequencing data shows that mutations are more common than the recombination and genes other than S1 have been affected by mutations. These changes in the genome of these two IBV isolates reflected in the differences in the pathogenicity although host response characterized by macrophage recruitment into the respiratory tract were similar.…”

Section: Discussionmentioning

confidence: 86%

Comparative features of infections of two Massachusetts (Mass) infectious bronchitis virus (IBV) variants isolated from Western Canadian layer flocks

et al. 2018

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BackgroundInfectious bronchitis virus (IBV) is one of the leading causes of mortality and morbidity in chickens. There are numerous serotypes and variants, which do not confer cross protection resulting in failure of currently used IBV vaccines. Although variant IBV isolates with major genetic differences have been subjected to comparative studies, it is unknown whether minor genetic differences in IBV variants within a serotype are different in terms of pathogenesis and eliciting host responses. Two Massachusetts (Mass) variant IBV isolates recovered from commercial layer flocks in the Western Canadian provinces of Alberta (AB) and Saskatchewan (SK) were compared genetically and evaluated for their pathogenicity, tissue distribution and ability to recruit and replicate in macrophages.ResultsAlthough whole genome sequencing of these two Mass IBV isolates showed low similarity with the M41 vaccinal strain, they had an identical nucleotide sequence at open reading frames (ORFs) 3a, 3b, envelop (E), matrix (M), 5a and 5b. The rest of the ORFs of these 2 IBV isolates showed 99.9% nucleotide similarity. However, upon experimental infection, we found that the IBV isolate originating from AB was different to the one that originated in SK due to higher tracheal lesion scores and lower lung viral replication and lower genome loads in cecal tonsils. Nevertheless, both IBV isolates elicited host responses characterized by significant macrophage recruitment to the respiratory tract and there was evidence that both IBV isolates replicated within tracheal and lung macrophages.ConclusionsOverall, this study shows that Mass variant IBV isolates, although possessing minor genetic variations, can lead to significant differences in pathogenicity in young chickens. Further studies are required to investigate the pathogenicity of these two Mass variant IBV isolates in laying hens.Electronic supplementary materialThe online version of this article (10.1186/s12917-018-1720-9) contains supplementary material, which is available to authorized users.

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“…4). Isolate IBV/KFS/2017/4 was closely related to the Egyptian strain IBV/Ck/EG/ CU/4/2014 which has shown evidence for recombination from the Italian strain (90254/2005), 4/91 and H120 vaccinal strains (Abozeid et al, 2017).…”

Section: Discussionmentioning

confidence: 96%

Molecular and Histopathological Investigation of Avian Infectious Bronchitis Virus in the Delta of Egypt between 2016 and 2017

Magouz

Abdo

Abdelsabour

et al. 2018

PVJ

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Infectious bronchitis virus (IBV) is a highly contagious viral disease of Family Coronaviridae. The current study reports the molecular and histopathological investigation of IBV strains emerged in outbreaks in the Nile Delta of Egypt. Tissue specimens from thirty-six chicken flocks were subjected to virus isolation, histopathology and PCR. Twenty-three isolates were confirmed as IBVs based on the amplification of the highly conserved nucleocapsid (N) gene. Further characterization of five selected isolates was done by amplification of the (S1) glycoprotein gene. Phylogenetic analysis revealed that the isolated strains were clustered into three distinct groups within the variant II clade. Alignment of S1gene amino acid sequences showed significant amino acid substitutions in relation to the currently used vaccinal strains which displays that new IBV variants which are evolutionarily distant from vaccinal strains are still emerging within the Egyptian chicken flocks and are mostly associated with acute tubular nephrosis syndrome.

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Complete genome sequences of two avian infectious bronchitis viruses isolated in Egypt: Evidence for genetic drift and genetic recombination in the circulating viruses

Cited by 41 publications

References 35 publications

Molecular Characterization and Phylogenetic Analysis of Full-length S1 Gene of GI-16 and GI-23 Infectious Bronchitis Virus in Qena, Egypt.

Molecular Characterization and Phylogenetic Analysis of Full-length S1 Gene of GI-16 and GI-23 Infectious Bronchitis Virus in Qena, Egypt.

Comparative features of infections of two Massachusetts (Mass) infectious bronchitis virus (IBV) variants isolated from Western Canadian layer flocks

Molecular and Histopathological Investigation of Avian Infectious Bronchitis Virus in the Delta of Egypt between 2016 and 2017

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