Phylogenetic analysis of avian infectious bronchitis virus isolates from Morocco: a retrospective study (1983 to 2014).
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ABSTRACT:
SUBMITTER: Fellahi S
PROVIDER: S-EPMC6598899 | biostudies-literature | 2017 Apr
REPOSITORIES: biostudies-literature
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Phylogenetic analysis of avian infectious bronchitis virus isolates from Morocco: a retrospective study (1983 to 2014).
Fellahi Siham S El Harrak Mehdi M Khayi Slimane S Guerin Jean-Luc JL Kuhn Jens H JH El Houadfi Mohammed M Ennaji My Mustapha MM Ducatez Mariette M
Virologica Sinica 20170401 2
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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:The aim of this study was to decipher the molecular epidemiological and antigenic characteristics of infectious bronchitis virus strains (IBVs) isolated in recent years in southwestern China. A total of 24 field strains were isolated from diseased chickens between 2012 and 2016. Phylogenetic analysis based on S1 nucleotide sequences showed that 16 of the 24 isolates were clustered into four distinct genotypes: QX (37.5%), TW (16.7%, TWI and TWII), Mass (8.3%), and J2 (4.2%). The QX genotype was still the prevalent genotype in southwestern China. Recombination analysis of the S1 subunit gene showed that eight of the 24 field strains were recombinant variants that originated from field strains and vaccine strains. A new potential recombination hotspot [ATTTT(T/A)] was identified, implying that recombination events may become more and more common. The antigenicity of ten IBVs, including seven field strains and commonly used vaccine strains, were assayed with a viral cross-neutralization assay in chicken embryonated kidney cells (CEK). The results showed that the ten IBVs could be divided into four serotypes (Massachusetts, 793B, Sczy3, and SCYB). Sczy3 and 793B were the predominant serotypes. Six of the seven field isolates (all except for cK/CH/SCYB/140913) cross-reacted well with anti-sera against other field strains. In conclusion, the genetic and antigenic features of IBVs from southwestern China in recent years have changed when compared to the previous reports. The results could provide a reference for vaccine development and the prevention of infectious bronchitis in southwestern China.
| S-EPMC7106097 | biostudies-literature
Project description:A rapid and sensitive method for the detection and unambiguous typing of infectious bronchitis virus (IBV) is described. RNA was isolated from IBV-infected allantoic fluid and was transcribed into cDNA. This cDNA was amplified by the polymerase chain reaction. The polymerase chain reaction products were subsequently analyzed on an agarose gel. The presence of IBV-specific RNA in the allantoic fluid then allowed the amplification of a 438-bp DNA fragment from the nucleocapsid (N) gene. For the typing of IBV isolates, we used amplified double-stranded DNA as a template in a sequencing reaction. We report 360 bases of the N gene of 18 IBV isolates. The sequence of the N gene was different between serologically indistinguishable IBV strains and may be a valuable tool in epidemiologic studies. A phylogenetic tree that was based on the sequences obtained did not agree with trees that were based on other parts of the sequence, illustrating the high frequency of recombination between IBV strains.
| S-EPMC265000 | biostudies-other
Project description:Infecting large portions of the global poultry populations, the avian infectious bronchitis virus (IBV) remains a major economic burden in North America. With more than 30 serotypes globally distributed, Arkansas, Connecticut, Delaware, Georgia, and Massachusetts are among the most predominant serotypes in the United States. Even though vaccination is widely used, the high mutation rate exhibited by IBV is continuously triggering the emergence of new viral strains and hindering control and prevention measures. For that reason, targeted strategies based on constantly updated information on the IBV circulation are necessary. Here, we sampled IBV-infected farms from one US state and collected and analyzed 65 genetic sequences coming from three different lineages along with the immunization information of each sampled farm. Phylodynamic analyses showed that IBV dispersal velocity was 12.3 km/year. The majority of IBV infections appeared to have derived from the introduction of the Arkansas DPI serotype, and the Arkansas DPI and Georgia 13 were the predominant serotypes. When analyzed against IBV sequences collected across the United States and deposited in the GenBank database, the most likely viral origin of our sequences was from the states of Alabama, Georgia, and Delaware. Information about vaccination showed that the MILDVAC-MASS+ARK vaccine was applied on 26% of the farms. Using a publicly accessible open-source tool for real-time interactive tracking of pathogen spread and evolution, we analyzed the spatiotemporal spread of IBV and developed an online reporting dashboard. Overall, our work demonstrates how the combination of genetic and spatial information could be used to track the spread and evolution of poultry diseases, providing timely information to the industry. Our results could allow producers and veterinarians to monitor in near-real time the current IBV strain circulating, making it more informative, for example, in vaccination-related decisions.
| S-EPMC8129014 | biostudies-literature
Project description:A Chinese isolate of avian infectious bronchitis virus (IBV) designated HH06 was isolated from the kidney tissues of a chicken flock experiencing an outbreak of nephritis. In vivo pathogenicity of the IBV isolate HH06 was determined by inoculating specific pathogen-free (SPF) chickens. The clinical signs and related gross lesions of HH06 infected chickens were similar with those of the field-infected chickens. SPF embryonated eggs were inoculated with virus suspension for serial passage and their genomic RNA was extracted. RT-PCR technique was utilized to amplify the M gene sequence encoding membrane protein of IBV. Recombinant plasmid named T-vector-M was constructed via inserting the M gene into the TA cloning vector, pMD 18-T. The sequenced M gene and its deduced amino acid (aa) sequences were compared with the published sequences of reference strains. The M gene is of 687 bp in length encoding the M protein of 228 amino acids with a predicted molecular weight of 25.4 kDa. The sequences of the M gene and M protein share 83.9-97.9% and 83.6-96.5% homologous identities, respectively, compared with 29 IBV reference strains derived from different regions or countries, which revealed that there are still significant variations between strains. Furthermore, a phylogenetic tree based on these M DNA sequences was generated, and the tree topology suggests that some Chinese IBV strains may have a common ancestor; however, HH06 is a new local IBV isolate that is responsible for the field outbreak of nephritis.
| S-EPMC7089277 | biostudies-literature
Project description:PurposeTissue samples were collected from suspected broiler flocks showing respiratory signs to identify infectious bronchitis virus (IBV), characterize emerging field strains, and study their relationships with the Massachusetts H120 strain, the only IB vaccine used in Tunisia.Samples and methodsSeveral IBV isolates were identified from field samples collected from flocks located in different regions in the northeast of Tunisia. The IBV isolates were characterized and compared to commonly used vaccine strains (including 793B, D274, and H120 types), other reference IBV strains from Europe, and the recently characterized Tunisian field variants TN20/00, TN200/01, and TN335/01. Reverse transcription-polymerase chain reaction and nucleotide sequencing analyses of the hypervariable regions of the S1 gene were carried out.ResultsFour new IBV variants were isolated during the period 2007-10 and were designated TN295/07, TN296/07, TN556/07, and TN557/07. The amino acid sequence data showed 100% similarity between TN295/07 and TN296/07, suggesting that these two isolates are identical and belong to the same genotype. Similar results were demonstrated for TN556/07 and TN557/07. Sequence identity values indicated that TN296/07 and TN556/07 share 55% amino acid homologies between each other, but are very different from the reference IBV serotypes, in particular the H120 strain. It was also shown that they have 50%-77% similarities with the Tunisian virus isolated between 2000 and 2001. Phylogenetic clustering allowed classification of these Tunisian isolates as new genotypes that are closer to TN200/01, TN335/01 Tunisian field variants, and Italy02 variant than MassH120 vaccine strain.ConclusionS1 sequence analyses confirmed the cocirculation of H120 vaccine strain with novel IBV variants isolated from Tunisian field.
| S-EPMC6065601 | biostudies-literature
Project description:Infectious bronchitis virus (IBV) is a positive-sense, single-stranded, enveloped RNA virus responsible for substantial economic losses to the poultry industry worldwide by causing a highly contagious respiratory disease. The virus can spread quickly through contact, contaminated equipment, aerosols, and personal-to-person contact. We highlight the prevalence and geographic distribution of all nine genotypes, as well as the relevant symptoms and economic impact, by extensively analyzing the current literature. Moreover, phylogenetic analysis was performed using Molecular Evolutionary Genetics Analysis (MEGA-6), which provided insights into the global molecular diversity and evolution of IBV strains. This review highlights that IBV genotype I (GI) is prevalent worldwide because sporadic cases have been found on many continents. Conversely, GII was identified as a European strain that subsequently dispersed throughout Europe and South America. GIII and GV are predominant in Australia, with very few reports from Asia. GIV, GVIII, and GIX originate from North America. GIV was found to circulate in Asia, and GVII was identified in Europe and China. Geographically, the GVI-1 lineage is thought to be restricted to Asia. This review highlights that IBV still often arises in commercial chicken flocks despite immunization and biosecurity measures because of the ongoing introduction of novel IBV variants and inadequate cross-protection provided by the presently available vaccines. Consequently, IB consistently jeopardizes the ability of the poultry industry to grow and prosper. Identifying these domains will aid in discerning the pathogenicity and prevalence of IBV genotypes, potentially enhancing disease prevention and management tactics.
| S-EPMC10875066 | biostudies-literature
Project description:Recombination in the family Coronaviridae has been well documented and is thought to be a contributing factor in the emergence and evolution of different coronaviral genotypes as well as different species of coronavirus. However, there are limited data available on the frequency and extent of recombination in coronaviruses in nature and particularly for the avian gamma-coronaviruses where only recently the emergence of a turkey coronavirus has been attributed solely to recombination. In this study, the full-length genomes of eight avian gamma-coronavirus infectious bronchitis virus (IBV) isolates were sequenced and along with other full-length IBV genomes available from GenBank were analyzed for recombination. Evidence of recombination was found in every sequence analyzed and was distributed throughout the entire genome. Areas that have the highest occurrence of recombination are located in regions of the genome that code for nonstructural proteins 2, 3 and 16, and the structural spike glycoprotein. The extent of the recombination observed, suggests that this may be one of the principal mechanisms for generating genetic and antigenic diversity within IBV. These data indicate that reticulate evolutionary change due to recombination in IBV, likely plays a major role in the origin and adaptation of the virus leading to new genetic types and strains of the virus.
| S-EPMC3187689 | biostudies-literature
Project description:BACKGROUND:The nephropathogenic avian infectious bronchitis (IB) caused unprecedented economic losses to the commercial chicken industry of China in 2008-2009. To investigate the prevalence of nephropathogenic IB in China, eighty IBV isolates from different provinces during 2008-2009 were identified by dwarf embryo test and RT-PCR. RESULTS:The strains were mostly isolated in winter and spring with a wide age range of IB outbreaks, from 4 to 69 days. By the virus recovery trials, 70/80 of the strains resulted in the deaths or distresses of birds from nephritis. To learn more about the molecular evolutionary characteristics of the circulating field strains, the coding region of major spike 1 (S1) protein gene of these strains was RT-PCR amplified and sequenced. Compared to the published representative strains, nucleotides and amino acids sequence analysis indicated that the S1 genes of these strains and the reference strains displayed homologies ranging from 75.1% to 99.8% and from 73.1% to 99.8% respectively. S1 protein of the major pandemic strains contained 540 or 542 amino acids with the cleavage site of HRRRR or RRFRR. Phylogenetic analysis revealed that recent field isolates of IBV in China were mostly belonged to A2-branch (QXIBV-branch) and HN08-branch, only one isolate was belonged to Gray-branch and M41-branch respectively. Most of the 80 strains showed evolutionarily distant from vaccine strains. CONCLUSIONS:The results of this study suggested that nephropathogenic IBVs were mainly A2-like strains in China during 2008-2009.
| S-EPMC3094301 | biostudies-literature
Project description:Background:Infectious bronchitis virus (IBV) is the etiological agent of an acute and highly contagious disease. Infectious bronchitis (IB) affects chicken of all ages and poses major economic loses to the poultry industry worldwide. The continuous evolution of the spike protein (S1) of IBV is responsible for the prevalence of many serotypes/genotypes around the world. Multiple lineages of IBV strains have been detected in chicken flocks in India since 2003. Aims:To detect IBV genotypes prevalent in India. Methods:Organ samples from 20 IBV-positive flocks with variable clinical signs were used for the amplification of the S1 gene of IBV by reverse transcriptase-polymerase chain reaction (RT-PCR). Results:Positive PCR amplicons were sequenced. Sequence analysis showed that 14 field isolates belonged to the GI-1 genetic lineage (Mass 41 serotype), two field isolates belonged to the GI-13 (UK 4/91 variant IBV strain), one field isolate grouped with GIII, GV, and GVI genetic lineage and three belonged to a variant genotype unique to India (GI-24). Phylogenetic analysis also showed a similar type of grouping within the field isolates. Among the fourteen GI-1 isolates, 12 were isolated between 2003 and 2006 and only two were isolated between 2009 and 2011. The two field isolates belonging to GI-13 were isolated in 2007, another one belonging to GIII, GV, and GVI was isolated in 2010 and three field isolates were not close to any reference IBV sequences isolated in 2006 (IND-TN-168-06), 2010 (IND-TN-280-10) and 2011 (IND-TN-290-11). Conclusion:A unique variant of IBV is emerging in India (GI-24). Our findings will have important implications for future vaccine intervention.
| S-EPMC7183371 | biostudies-literature