Genotyping of Avian infectious bronchitis viruses in Iran (2015-2017) reveals domination of IS-1494 like virus.
Ontology highlight
ABSTRACT:
SUBMITTER: Modiri Hamadan A
PROVIDER: S-EPMC7114540 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The nephropathogenic infectious bronchitis virus (IBV) strain IS-1494 like (variant-2; GI-23) was first isolated in the Middle East (1998). Despite intensive vaccinations, IS-1494 like IBVs are still circulating in Iran (the dominant genotype) and spread to other countries. Here, the full-length genome of this Iranian IS-1494 like IBV was (Mahed) determined to understand its evolutionary relationships. The genome consists of 27,652 nucleotides, with mutations in most of the structural genes. Thirteen open reading frames (ORFs) were predicted in the Mahed isolate (5' UTR-1a-1b-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3' UTR). ORFs 4b, 4c, and 6b, which has rarely been reported, were present in the Mahed genome. According to phylogenetic analysis of the full-length genome, 1a, S2, M, E, N protein, Mahed isolate clustered with the QX type strain. Based on the partial 1b, S1, Mahed clustered with the Q1 strain. The full-length genome of Mahed isolate shared the highest sequence homology with Gray and JMK (90.06-90.07%) and was least related to the Vic-s (86.21%). These data show that evolutionary variation because of recombination in IBV plays a major role in the adaptation and origin of IBV leading to new genetic and types of the virus strain.
| S-EPMC6111945 | biostudies-literature
Project description:BackgroundAvian infectious bronchitis (IB) is a highly contagious viral disease which affects the poultry industry. The virus exists in a wide variety of genotypes, and phylogenetic analysis has been used to classify infectious bronchitis virus (IBV) strains.AimsThe object of the study is a molecular characterization of circulating IBV in Afghanistan as a first study.MethodsThe tracheal tissue specimens from 100 different commercial broiler flocks with respiratory distress in Afghanistan were collected during 2016-2017. After real-time reverse transcriptase-polymerase chain reaction (RRT-PCR), IBV-positive samples were further characterized. A 390 bp hypervariable spike glycoprotein gene segment was amplified using Nested PCR, sequenced, and analyzed.ResultsThe results of real-time RT-PCR showed that 45/100 of the mentioned flocks were IBV positive. Phylogenetic analysis of all positive samples revealed that IBV strains were clustered into two distinct genotypes: LX4 (GI-19) (9/45) and IS-1494 like (GI-23) (34/45). Also, 2 of the 45 samples remained uncharacterized.ConclusionIt is the first study focusing on the molecular epidemiology of IBV in Afghanistan, extending our understanding of IB in the region. These results showed the high rate of IB infection in Afghanistan broiler farms and confirm the continuing monitoring of IBVs to modify the vaccination program.
| S-EPMC6509913 | biostudies-literature
Project description:Infectious bronchitis virus (IBV) is one of the most critical pathogens in the poultry industry, causing serious economic losses in all countries including Iraq. IBV has many genotypes that do not confer any cross-protection. This virus has been genotyped by sequence analysis of the S1 glycoprotein gene. A total of 100 tracheal and kidney tissue specimens from different commercial broiler flocks in the middle and south of Iraq were collected from September 2013 to September 2014. Thirty-two IBV-positive samples were selected from among the total and were further characterized by nested PCR. Phylogenetic analysis revealed that isolates belong to four groups (group I, variant 2 [IS/1494-like]; group II, 793/B-like; group III, QX-like; group IV, DY12-2-like). Sequence analysis revealed nucleotide sequence identities within groups I, II, and III of 99.68 %-100 %, 99.36 %-100 %, and 96.42 %-100 %, respectively. Group I (variant 2) was the dominant IBV genotype. One Chinese-like recombinant virus (DY12-2-like) that had not been reported in the Middle East was detected. In addition, the presence of QX on broiler chicken farms in the area studied was confirmed. This is the first comprehensive study on the genotyping of IBV in Iraq with useful information regarding the molecular epidemiology of IBV. The phylogenetic relationship of the strains with respect to different time sequences and geographical regions displayed complexity and diversity. Further studies are needed and should include the isolation and full-length molecular characterization of IBV in this region.
| S-EPMC7086866 | biostudies-literature
Project description:The aim of this study was to provide information on the molecular characteristic and the phylogenic relationship of infectious bronchitis viruses (IBV) strains in Bushehr province in comparison to other strains reported in the Middle East. Samples were collected from broiler flocks in Bushehr province during 2014 - 2015. These flocks had respiratory problems such as gasping, sneezing and bronchial rales. A number of 135 tracheal swabs were taken from fifteen flocks (nine swabs per flock). Each three swabs collected from each flock were pooled in one tube (finally, we had three tubes for each flock). The samples were subjected to reverse transcription polymerase chain reaction (RT-PCR). The PCR products of positive samples were analyzed by sequencing of a (392 bp) segment of the spike gene and the related results were compared with the other IBV sequences in GenBank database. Samples from twelve farms (80.0%) were found to be positive. The viruses from seven farms (46.6%) were identified as field viruses closely related to variant 2. The viruses from three farms (20.0%) were characterized as Mass type and were related to vaccine strains. Two different IB viruses (variant 2 and Mass) were detected in samples from two farms (13.3%). The variant 2 genotype detected in Bushehr had high similarity to variant 2 reported from the Middle East. These variants displayed homologies ranging from 72.9% to 76.5%, and 78.8% to 80.0% with H120 and 4/91, respectively. It is necessary to design vaccination program of poultry farms using IBV strains circulating in the region.
| S-EPMC5653882 | biostudies-literature
Project description:The coronavirus avian Infectious bronchitis virus (IBV) poses economic threats to poultry farms worldwide, affecting the performance of both meat-type and egg-laying birds. To define the evolution of recent IBVs in Iran, a genetic analysis based on hypervariable nucleotide sequences of S1 gene was carried out. Tracheal swab samples were collected from 170 Broiler flocks during 2017. Ten tracheal swabs from each flock pooled. From a total number of 170 flocks tested, 84.71% found to be positive. Phylogenetic tree analysis revealed the presence of D274 as a first time in Iran. IS/1494/06 was showed to be dominant IBV type circulating in broiler farms with a significantly higher prevalence than other four genotypes. Considering fluctuations in QX-type prevalence in recent years, continuous monitoring is necessary to reduce economic consequences in layer and broiler farms. The findings highlight the importance of using modified vaccination strategies that are adapted to the changing disease scenario.
| S-EPMC7112693 | biostudies-literature
Project description:Avian infectious bronchitis virus is one of the most important gammacoronaviruses, which causes a highly contagious disease. In this study, we investigated changes in the proteome of kidney tissue of specific-pathogen-free (SPF) chickens that were infected with an isolate of the nephrotropic variant 2 genotype (IS/1494/06) of avian coronavirus. Twenty 1-day-old SPF White Leghorn chickens were randomly divided into two groups, each comprising 10 chickens, which were kept in separate positive-pressure isolators. Chickens in group A served as a virus-free control group up to the end of the experiment, whereas chickens in group B were inoculated with 0.1 ml of 104.5 EID50 of the IBV/chicken/Iran/UTIVO-C/2014 isolate of IBV, and kidney tissue samples were collected at 2 and 7 days post-inoculation (dpi) from both groups. Sequencing of five protein spots at 2 dpi and 22 spots at 7 dpi that showed differential expression by two-dimensional electrophoresis (2DE) along with fold change greater than 2 was done by MS-MALDI/TOF/TOF. Furthermore, the corresponding protein-protein interaction (PPI) networks at 2 and 7 dpi were identified to develop a detailed understanding of the mechanism of molecular pathogenesis. Topological graph analysis of this undirected PPI network revealed the effect of 10 genes in the 2 dpi PPI network and nine genes in the 7 dpi PPI network during virus pathogenesis. Proteins that were found by 2DE analysis and MS/TOF-TOF mass spectrometry to be down- or upregulated were subjected to PPI network analysis to identify interactions with other cellular components. The results show that cellular metabolism was altered due to viral infection. Additionally, multifunctional heat shock proteins with a significant role in host cell survival may be employed circuitously by the virus to reach its target. The data from this study suggest that the process of pathogenesis that occurs during avian coronavirus infection involves the regulation of vital cellular processes and the gradual disruption of critical cellular functions.
| S-EPMC7574675 | biostudies-literature
Project description:Seventeen isolates of infectious bronchitis virus (IBV) were obtained from various prefectures of Japan during 2008-2019 and genetically analyzed. The IBV isolates were classified into six genetic groups, based on phylogenetic analysis of the S1 gene. The S1 genotypes were distinguishable by a newly developed restriction fragment length polymorphism (RFLP) method using three endonucleases, Hae II, Hpa I, and Fok I. Moreover, the isolates were classified into four genetic groups, based on phylogenetic analysis of the S2 gene. However, novel genetic groups based on a combination of S1 and S2 genotypes, which were undetected previously, were confirmed in this study, indicating that various recombinant IBV strains were prevalent in poultry in Japan.
| S-EPMC8025416 | biostudies-literature
Project description:Avian infectious bronchitis (IB) is caused by avian infectious bronchitis virus (IBV) belonging to Coronaviridae family. The disease is prevalent in all countries with almost 100% incidence rate. Chicken and commercially reared pheasant are the natural host for IBV. Virus causes respiratory diseases, poor weight gain, feed efficiency in broiler, damage to oviduct, and abnormal egg production in mature hens resulting in economic losses. IBV also replicates in tracheal and renal epithelial cells leading to prominent tracheal and kidney lesions. Virus undergoes spontaneous mutation leading to continual emergence of new variants. The effectiveness of immunization program is diminished because of poor cross-protection among the serotypes. Identification of circulating serotypes is important in controlling IBV infection. Toll-like receptor 3 (TLR3) and TLR21 are involved in early recognition of virus resulting in induction of inflammatory cytokines. Both humoral and cellular immune responses are important in the control of infection. Humoral immunity plays an important role in recovery and clearance of viral infection. IBV-specific cytotoxic T lymphocytes induce lysis of IBV-infected cells. Effective diagnostic tools are required at field level to identify different IBV variants. Embryonated chicken eggs are effective model for virus isolation. Identification by other specific methods like virus neutralization (VN), hemagglutination inhibition (HI), enzyme linked immunosorbent assay (ELISA), immunohistochemistry, or nucleic acid analysis or by electron microscopy is also indispensable. VN test in tracheal organ culture is the best method for antigenic typing for surveillance purposes. Continuous epidemiological surveillance, strict biosecurity measures, and vaccine effective against various serotypes are necessary for controlling IB in chickens.
| S-EPMC7120852 | biostudies-literature
Project description:AIM:To characterize the circulating infectious bronchitis virus (IBV) strains in Egypt depending on the sequence of the spike-1 (S1) gene [hypervariable region-3 (HVR-3)] and to study the pathotypic features of these strains. METHODS:In this work, twenty flocks were sampled for IBV detection using RRT-PCR and isolation of IBV in specific pathogen free (SPF) chicks during the period from 2010 to 2015. Partial sequencing and phylogenetic analysis of 400 bp representing the HVR-3 of the S1 gene was conducted. Pathotypic characterization of one selected virus from each group (Egy/Var-I, Egy/Var-II?and classic) was evaluated in one day old SPF chicks. The chicks were divided into 4 groups 10 birds each including the negative control group. Birds were inoculated at one day by intranasal instillation of 10(5)EID50/100 ?L of IBV viruses [IBV-EG/1212B-2012 (Egy/Var-II), IBV/EG/IBV1-2011 (Egy/Var-I) and IBV-EG/11539F-2011 (classic)], while the remaining negative control group was kept uninfected. The birds were observed for clinical signs, gross lesions and virus pathogenicity. The real-time rRT-PCR test was performed for virus detection in the tissues. Histopathological examinations were evaluated in both trachea and kidneys. RESULTS:The results revealed that these viruses were separated into two distinct groups; variant (GI-23) and classic (GI-1), where 16 viruses belonged to a variant group, including 2 subdivisions [Egy/Var-I (6 isolates) and Egy/Var-II (10 isolates)] and 4 viruses clustered to the classic group (Mass-like). IBV isolates in the variant group were grouped with other IBV strains from the Middle East. The variant subgroup (Egy/Var-I) was likely resembling the original Egyptian variant strain (Egypt/Beni-Suif/01) and the Israeli strain (IS/1494/2006). The second subgroup (Egy/Var-II) included the viruses circulating in the Middle East (Ck/EG/BSU-2 and Ck/EG/BSU-3/2011) and the Israeli strain (IS/885/00). The two variant subgroups (Egy/Var-I and Egy/Var-II) found to be highly pathogenic to SPF chicks with mortalities up to 50% than those of the classic group which was of low virulence (10% mortality). Pathogenicity indices were 25 (Egy/Var-II), 24 (Egy/Var-I) and 8 (classic); with clinical scores 3, 2 and 1 respectively. CONCLUSION:These findings indicated that the recent circulating Egyptian IBVs have multiple heterogeneous origins in marked diversifying nature of their spread, with high pathotype in specific pathogen free chicks.
| S-EPMC4981825 | biostudies-literature
Project description:Background and Objectives:Different epidemiological studies have found that backyard chickens are a reservoir for poultry diseases. Most backyard chicken flocks have a poor level of biosecurity, which increases the risk of spread of diseases. In recent years, the number of backyard chickens has been on the rise in Iran. However, the health status of backyard flocks is still poorly documented. Thus, this study aimed at examining the seroprevalence of antibodies against infectious bronchitis virus (IBV) and molecular surveillance and genotyping of IBV among backyard chickens (without vaccination history) in Mazandaran province, North of Iran, 2014. Materials and Methods:A total of 460 blood samples of unvaccinated backyard chickens in the mentioned area were tested for antibodies against IBV using commercial ELISA. Also, cecal tonsils were collected from 75 chickens in the same area. Real time RT-PCR (for detection) and RT-PCR and sequencing spike gene were performed. Results:The seropositivity rate was 54.5%. In addition, we detected 793/B, Variant 2, and QX in the backyard flocks and performed phylogenetic studies on them. The phylogenetic study revealed that the detected genotypes had high homology with IBV strains that were infected broilers, pullets, and layers in Iran. Conclusion:There is a need for continuous monitoring of IBV among avian species to complete the epidemiological map and work on the pathogenesis of Iranian IBV strains in Iranian backyard chickens.
| S-EPMC6004632 | biostudies-literature