Full Genome Sequence Analysis of a Newly Emerged QX-Like Infectious Bronchitis Virus
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PROVIDER: PRJEB16135 | ENA |
REPOSITORIES: ENA
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Project description:Infectious bronchitis virus (IBV) infection continues to cause economically important diseases in poultry while different geno- and serotypes continue to circulate globally. Two infectious bronchitis viruses (IBV) were isolated from chickens with respiratory disease in Sudan. Sequence analysis of the hypervariable regions of the S1 gene revealed a close relation to the QX-like genotype which has not been detected in Sudan before. Whole genome analysis of IBV/Ck/Sudan/AR251-15/2014 isolate by next generation sequencing revealed a genome size of 27,646 nucleotides harbouring 13 open reading frames: 5'-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'. Highest nucleotide sequence identity of 93% for the whole genome was found with the Chinese IBV strain Ck/CH/LHLJ/140906, the Italian IBV isolate ITA/90254/2005 and the 4/91 vaccine strain. Phylogenetic analysis of the S1 gene revealed that the IBV/Ck/Sudan/AR251-15/2014 isolate clustered together with viruses of the GI-19 lineage. Recombination analysis gave evidence for distinct patterns of origin of RNA in the Sudanese isolate in multiple genes. Several sites of recombination were scattered throughout the genome suggesting that the Sudan-QX-like strain emerged as a unique recombinant from multiple recombination events of parental viruses from 4/91, H120 and ITA/90254/2005 genotypes. The Sudanese QX-like isolate is plausibly genetically different from IBV strains previously reported in Africa and elsewhere.
| S-EPMC7195004 | biostudies-literature
Project description:We investigated genome-wide DNA methylation of newly emerged queens, newly emerged workers, adult nurses, adult foragers and adult reverted nurses using comprehensive high throughput arrays for relative methylation (CHARM) We used custom Nimblegen microarrays We isolated genomic DNA from newly emerged queens, newly emerged workers, adult continuous nurses, adult continuous foragers and adult reverted nurses hybridized to custom-designed Nimblegen microarrays (CHARM arrays). Multiple brains were pooled for each sample and used for the genome-wide DNA methylation analysis.
2012-09-16 | E-GEOD-36650 | biostudies-arrayexpress
Project description:We investigated genome-wide DNA methylation of newly emerged queens, newly emerged workers, adult nurses, adult foragers and adult reverted nurses using comprehensive high throughput arrays for relative methylation (CHARM) We used custom Nimblegen microarrays
2012-09-16 | GSE36650 | GEO
Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of chicken (Gallus gallus) cells infected with Infectious Bronchitis Virus (IBV) strains Beaudette and M41.
2019-06-18 | E-MTAB-7849 | biostudies-arrayexpress
Project description:Infectious bronchitis virus (IBV), is a coronavirus which infects chickens (Gallus gallus), and is one of the foremost causes of economic loss within the poultry industry, affecting the performance of both meat-type and egg-laying birds. The virus replicates not only in the epithelium of upper and lower respiratory tract tissues, but also in many tissues along the alimentary tract and elsewhere e.g. kidney, oviduct and testes. It can be detected in both respiratory and faecal material. There is increasing evidence that IBV can infect species of bird other than the chicken. Interestingly breeds of chicken vary with respect to the severity of infection with IBV, which may be related to the immune response (Cavanagh, 2006). Here we examine differential expression of genes in the trachea of susceptible and resistant birds, in order to identify genes which may be involved in resistance to IBV.
2015-07-31 | E-TABM-1128 | biostudies-arrayexpress
Project description:To minimize the spread of infectious bronchitis virus (IBV), domestic fowl have been extensively vaccinated with the KM91 strain. However, various IBV QX-like virus strains have become increasingly prevalent in Korea. We conducted comparative genomic analyses of seven QX-like viruses: early viruses (n = 2), new cluster 1 (NC1; recombinants of KM91 and the early QX-like viruses, n = 3) and recurrent viruses (n = 2), to understand their genomic backgrounds. The early and NC1 viruses had KM91-like backgrounds, but the recurrent viruses had QX-like genomic backgrounds. The absence of pure QX-like viruses before the appearance of the early viruses suggests that the viruses were introduced from other countries after recombination, but the NC1 viruses originated in Korea. The recent prevalence of recurrent viruses with different genomic backgrounds and spike genes from the early and the NC1 viruses may indicate the repeated introduction of different infectious bronchitis viruses from other countries and their successful evasion of vaccine immunity in the field. Furthermore, a 1ab gene-based phylogenetic analysis revealed three distinct lineages: North America-Europe, China/Taiwan, and China. KM91 and the early and NC1 viruses were included in the North America-Europe lineage, and the recurrent QX-like viruses were included in the China lineage. The phylogenetic positions of KM91-like 1ab and QX-like spike suggest frequent recombination between the North America-Europe and China lineages. Additional studies on the patterns of recombination, including donor-acceptor relationships, geographical sites, and non-poultry hosts, may be valuable for understanding the evolution of IBVs.
| S-EPMC7087172 | biostudies-literature
Project description:Infectious bronchitis is a highly contagious respiratory disease of poultry caused by the coronavius infectious bronchitis virus (IBV). Until recently is was thought that coronavirus virions were composed of the structural proteins nucleocapsid, envelope, spike and membrane proteins, but investigations of TGEV and SARS-CoV have shown the proteome of coronavirus virions also includes viral non-structural and group specific proteins as well as host cell proteins. To study the proteome of IBV virions, virus was grown in embryonated chicken eggs and purified by sucrose gradient ultracentrifugation. Purified virus was analysed using sensitive gel-free proteomic techniques to determine the proteome of IBV. Analysis of three preparations of purified IBV yielded a list of 39 proteins commonly associated with the IBV virion. Three of these proteins were the viral structural proteins spike, membrane and nucleocapsid, but none of the viral non-strucutral or groups specific proteins could be identified. The other 35 proteins commonly associated to the IBV virion were all found to be host cell proteins. These proteins were classified into 12 categories using pantherdb (pantherdb.org). These proteins were involved in a diverse range of functions such as cytoskeletal proteins, nucleic acid binding proteins and chaperone proteins. Some of these proteins were unique to this study, whilst others were found to be orthologous to proteins identified in the SARS-CoV protein, and indeed some were also identified in association with virions from a number of other RNA and DNA viruses.
2016-02-15 | PXD002936 | Pride
Project description:Avian infectious bronchitis is a serious and highly contagious disease caused by infectious bronchitis virus (IBV). We isolated a highly virulent IBV strain (CK/CH/JS/TAHY) from kidneys of diseased chickens. Phylogenetic analysis based on the S1 gene revealed that CK/CH/JS/TAHY clustered with the QX-like type. The S1 gene has 1,620 nucleotides and encoded a polypeptide of 540 amino acids with typical coronavirus cleavage recognition sites of HRRR. About 1-day-old specific pathogen-free White Leghorn chickens inoculated with CK/CH/JS/TAHY at 105.5 EID50 exhibited clinical signs including coughing, sneezing, nasal discharge, and tracheal vocalization accompanied by depression with 84% mortality and 100% morbidity. The kidneys of dead birds were swollen and pale and exhibited severe urate deposition. Histopathological examination revealed kidney hemorrhages, multifocal necrosis of the renal tubules and trachea with cilia loss, sloughing of epithelial cells, and edema of the lamina propria. IBV-specific antibodies appeared at 10 D post-infection. Chickens vaccinated with a CK/CH/JS/TAHY oil-emulsion vaccine showed 26.7% morbidity and 3% mortality indicating a protective effect. In conclusion, the IBV strain is a virulent avian IBV and that exhibited severe pathogenicity in chickens and is a vaccine candidate to prevent infection by Chinese QX-like nephropathogenic IBV strains.
| S-EPMC7111634 | biostudies-literature
Project description:Infectious bronchitis, an acute and highly contagious disease that affects chickens, is caused by the infectious bronchitis virus (IBV). The antigenic variant QX-like IBV was first reported in China in 1996 and is now endemic in many countries. Our previous study reported the first detection and isolation of QX-like IBVs in Japan and that they were genetically related to the recently detected strains in China and South Korea. The pathogenicity of 2 Japanese QX-like IBV strains (JP/ZK-B7/2020 and JP/ZK-B22/2020) was evaluated by inoculating specific pathogen-free (SPF) chickens with 102 to 106 median embryo infectious dose. Both strains caused clinical signs of respiratory symptoms, gross tracheal lesions, and moderate-to-severe suppression of tracheal ciliostasis. To evaluate the efficacy of commercial IBV live vaccines against the JP/ZK-B7/2020 strain, vaccinated SPF chickens were challenged with the JP/ZK-B7/2020 strain at 104 EID50 (median embryo infectious dose). Only the JP-Ⅲ vaccine provided high levels of protection (reduced suppression of tracheal ciliostasis and reduced viral loads in organs), whereas the Mass vaccine showed little protective effect. Virus neutralization test results and comparisons between IBV genotypes based on the S1 gene suggested that QX-like and JP-III genotypes were closely related. These results suggest that the JP-III IBV vaccine, which has relatively high S1 gene homology with QX-like IBVs, is effective against Japanese QX-like IBV strain.
| S-EPMC10064428 | biostudies-literature
Project description:Infectious bronchitis (IB) is an acute, highly contagious disease, which causes economic losses to the poultry industry worldwide. To control the disease, biosecurity and vaccination are required. In the current research, we rapidly attenuated a QX-like IBV field strain ZYY-2014 using passage in embryos at limiting dilution and tested the safety and efficacy of the attenuated Chinese QX-like IBV strain ZYYR-2014 in 1-day-old specific-pathogen-free (SPF) chickens through spray route. Our result revealed that the attenuated strain presented a decreased pathogenicity in 1-day-old chickens. The strain ZYY-2014 inoculated birds presented typical IBV clinical signs with a mortality of 43%, while the attenuated strain ZYYR-2014 inoculated birds remained healthy. The strain ZYYR-2014 also presented stronger antibody responses and lower viral loads in tracheas, lungs and kidneys. When vaccinated through spray route into 1-day-old SPF chickens, our data suggest a potential of the attenuated ZYYR-2014 strain as a vaccine candidate applied in hatchery, which can contribute in preventing the QX-like IBV infections. Furthermore, attenuation by passage at limiting dilution could be applied for rapid vaccine development against emerging strains.
| S-EPMC7173324 | biostudies-literature