scholarly journals Presence of Infectious Bronchitis Virus Strain CK/CH/LDL/97I in the Middle East

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Mustafa Ababneh ◽  
Abd Elhafeed Dalab ◽  
Saad Alsaad ◽  
Mohammad Al-Zghoul
Keyword(s):  
Middle East ◽  
Infectious Bronchitis Virus ◽  
Hypervariable Region ◽  
Disease Outbreaks ◽  
Nucleotide Identity ◽  
Economic Losses ◽  
Strain Identification ◽  
S1 Gene ◽  
Infectious Bronchitis ◽  
First Time

Infectious bronchitis virus (IBV) is a very dynamic and evolving virus, causing major economic losses to the global poultry industry. In early 2011, respiratory disease outbreaks were investigated in Iraq, Jordan, and Saudi Arabia. Five IBV isolates (JOA2, JOA4, Saudi-1, Saudi-2, and Iraqi IBV) were detected by diagnostic-nested nucleocapsid RT-PCR. Strain identification was characterised by sequencing and phylogenetic analysis of the amplified hypervariable region of the spike 1 (S1) gene. These five IBV isolates were found to be of the IBV strain CK/CH/LDL/97I. Nucleotide identity between these five IBV isolates ranged from 96.9% to 99.7%, and between these isolates and the CK/CH/LDL/97I strain in the range of 96.6–99.1%. The sequenced fragment of the S1 gene of the CK/CH/LDL/97I strain had less than 80% nucleotide identity to the IBV vaccine strains commonly used in the Middle East (M41 and H120). The presence of these CK/CH/LDL/97I-like strains may account for vaccination failure against IBV, since all IBV isolates were from vaccinated chickens. In this paper, we documented for the first time the presence of IBV strain CK/CH/LDL/97I in the Middle East. This strain is known to have originated in China and Taiwan.

scholarly journals Cocirculation of Four Infectious Bronchitis Virus Lineages in Broiler Chickens in the Eastern Region of Saudi Arabia from 2012 to 2014

2020 ◽  
Vol 2020 ◽  
pp. 1-10 ◽  
Author(s):  
Abdullah I. A. Al-Mubarak ◽  
Anwar A. G. Al-Kubati
Keyword(s):  
Saudi Arabia ◽  
Middle East ◽  
Infectious Bronchitis Virus ◽  
Broiler Chickens ◽  
Direct Sequencing ◽  
Hypervariable Region ◽  
Economic Losses ◽  
Eastern Region ◽  
Infectious Bronchitis ◽  
First Time

Avian infectious bronchitis virus (IBV) is an evolving and dynamic virus that causes major economic losses for the poultry industry worldwide. Continuous evolution and emergence of new variants of this virus are the major challenges for controlling the disease with routine vaccination. Successful vaccination usually requires the use of a homologous vaccine, which in turn necessitates continuous investigation of the circulating strains. Herein, we performed a reverse transcriptase-polymerase chain reaction- (RT-PCR-) based investigation in broiler chicken flocks of the Eastern Region of Saudi Arabia. IBV was detected in 36.5% of the tested flocks (42 out of 115) from January 2012 to March 2014. Direct sequencing of hypervariable region-3 (HVR-3) of the Spike (S)-1 gene was performed, followed by phylogenetic analysis to determine the circulating IBV genotypes. Four lineages appear to coexist in this region, including the GI-13 or 4/91 IBV (31%), GI-16 or CK/CH/LDL/97I IBV (28.6%), GI-1 or Mass IBV (19%), and GI-23 or Middle East IBV (21.4%). The latter lineage include two subgroups: IS/720/99 IBV (16.7%) and IS/Variant2/98 IBV (4.7%). Some of the detections made in the 4/91 and Mass lineages are expected to belong to the vaccine strains. Lineages without a homologous vaccine in use (CK/CH/LDL/97I and Middle East) represent 50% of the isolates recovered in this study. Based on identity with the vaccine sequences, field observations, and frequent detection, these two lineages appear to be out of coverage of the IBV vaccines used in Saudi Arabia. This is the first time to identify Middle East lineage (IS/720/99 IBV and IS/Variant2/98 IBV) in the Eastern Region of Saudi Arabia.

scholarly journals Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples

2020 ◽  
pp. 104063872091010
Author(s):  
Salman L. Butt ◽  
Eric C. Erwood ◽  
Jian Zhang ◽  
Holly S. Sellers ◽  
Kelsey Young ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Amplicon Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Strain Identification ◽  
Accurate Identification ◽  
Oral Swab ◽  
Spike Gene ◽  
Infectious Bronchitis ◽  
Sequencing Library

Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. Although serotyping requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV, and it is inefficient at detecting multiple viruses in a single sample. We describe herein a MinION-based, amplicon-based sequencing (AmpSeq) method that genetically categorized IBV from clinical samples, including samples with multiple IBVs. Total RNA was extracted from 15 tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer’s instructions into a 1D MinION sequencing library, and then sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in 3 of 5 samples containing 2 IBV lineages. Additionally, 1 sample contained 3 IBV lineages, and AmpSeq accurately detected 2 of the 3 lineages. Strain identification, including detection of different IBVs from the same lineage, was also possible with this AmpSeq method. Our results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples.

scholarly journals GENETIC CHARACTERIZATION OF AVIAN INFECTIOUS BRONCHITIS VIRUS ISOLATES RECOVERED IN CIS COUNTRIES IN 2015–2017

2018 ◽  
pp. 30-39 ◽  
Author(s):  
L. O. Scherbakova ◽  
S. N. Kolosov ◽  
Z. B. Nikonova ◽  
N. G. Zinyakov ◽  
Ye. V. Ovchinnikova ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Hypervariable Region ◽  
Economic Losses ◽  
Avian Infectious Bronchitis Virus ◽  
Genetic Lineages ◽  
Infectious Bronchitis ◽  
Poultry Farms ◽  
Cis Countries ◽  
In Cis ◽  
Virus Isolates

Avian infectious bronchitis virus is a cause of major economic losses in poultry industry. However, control of the virus is very complicated due to its high variability. The mutation frequency in the hypervariable region of the S1 gene of the virus isolated from the vaccinated birds annually amounts to 1.5%. Long-term observations of the circulation of IBV isolates detected in a number of poultry farms demonstrated that the virus genetic lineages circulating on the poultry farms could eventually change. This stipulates the need for the continuous monitoring of the virus isolates for the prevention schedule optimization. The paper demonstrates test results of 840 biological samples collected from chickens on the poultry farms in Russia and some CIS countries in 2015–2017. From 311 positive samples 147 IBV isolates were recovered, the majority of which belonged to eight genetic lines of GI genotype: GI-1, GI-12, GI-13, GI-14, GI-16, GI-19, GI-22, GI-23. Moreover, recombinant isolates were detected as well as variant isolates that belonged to none of the known genotypes.

scholarly journals Typing of Field Isolates of Infectious Bronchitis Virus Based on the Sequence of the Hypervariable Region in the S1 Gene

2003 ◽  
Vol 15 (4) ◽  
pp. 344-348 ◽  
Author(s):  
Chang-Won Lee ◽  
Deborah A. Hilt ◽  
Mark W. Jackwood
Keyword(s):  
Phylogenetic Analysis ◽  
Infectious Bronchitis Virus ◽  
Direct Sequencing ◽  
Hypervariable Region ◽  
The United States ◽  
Rt Pcr ◽  
Universal Primer ◽  
S1 Gene ◽  
Infectious Bronchitis ◽  
Field Isolates

A universal primer set was developed that amplifies a region covering hypervariable region (HVR) 1 and HVR 2 in the S1 gene of the infectious bronchitis virus (IBV). The universality of this primer set was confirmed by testing the reference strains of different serotypes or variants of the IBV present in the United States. An approximately 450-bp region containing HVR 1 and HVR 2 of 7 untyped field isolates obtained in 1999 and 2000 was amplified. Direct sequencing followed by phylogenetic analysis on that region allowed us to type those field isolates that were not typable by reverse transcriptase–polymerase chain reaction (RT-PCR) and restriction fragment length polymorphism (RFLP). Furthermore, it was found that typing by phylogenetic analysis of that region correlates with virus neutralization results. Together with RT-PCR and RFLP, this method will serve as a fast typing method for IBV diagnosis.

scholarly journals Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples

2019 ◽  
Author(s):  
Salman L. Butt ◽  
Eric C. Erwood ◽  
Jian Zhang ◽  
Holly S. Sellers ◽  
Kelsey Young ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Amplicon Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Strain Identification ◽  
Accurate Identification ◽  
Spike Gene ◽  
Infectious Bronchitis ◽  
Sequencing Library ◽  
Different Strains

AbstractInfectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of infectious bronchitis is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (IBV), which has led to the emergence of several serotypes that lack complete serologic cross-protection. While serotyping by definition requires immunologic characterization, genotyping is an efficient means to identify IBVs detected in samples. Sanger sequencing of the S1 subunit of the spike gene is currently used to genotype IBV; however, the universal S1 PCR was created to work from cultured IBV and it is inefficient at detecting mixed isolates. This paper describes a MinION-based AmpSeq method that genetically typed IBV from clinical samples, including samples with multiple isolates. Total RNA was extracted from fifteen tracheal scrapings and choanal cleft swab samples, randomly reverse transcribed, and PCR amplified using modified S1-targeted primers. Amplicons were barcoded to allow for pooling of samples, processed per manufacturer’s instructions into a 1D MinION sequencing library, and sequenced on the MinION. The AmpSeq method detected IBV in 13 of 14 IBV-positive samples. AmpSeq accurately detected and genotyped both IBV lineages in three of five samples containing two IBV lineages. Additionally, one sample contained three IBV lineages, and AmpSeq accurately detected two of the three. Strain identification, including detection of different strains from the same lineage, was also possible with this AmpSeq method. The results demonstrate the feasibility of using MinION-based AmpSeq for rapid and accurate identification and lineage typing of IBV from oral swab samples.

scholarly journals Design and Characterization of a DNA Vaccine Based on Spike with Consensus Nucleotide Sequence against Infectious Bronchitis Virus

Vaccines ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 50
Author(s):  
Lei Zuo ◽  
Wenjun Yan ◽  
Zhou Song ◽  
Hao Li ◽  
Xin Xie ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Dna Vaccine ◽  
Infectious Bronchitis Virus ◽  
Neutralizing Antibody ◽  
Economic Losses ◽  
Post Translational Modification ◽  
Virus Shedding ◽  
Infectious Bronchitis ◽  
Specific Pathogen ◽  
Cellular Immune

Avian coronavirus infectious bronchitis virus (IBV) causes severe economic losses in the poultry industry, but its control is hampered by the continuous emergence of new genotypes and the lack of cross-protection among different IBV genotypes. We designed a new immunogen based on a spike with the consensus nucleotide sequence (S_con) that may overcome the extraordinary genetic diversity of IBV. S_con was cloned into a pVAX1 vector to form a new IBV DNA vaccine, pV-S_con. pV-S_con could be correctly expressed in HD11 cells with corresponding post-translational modification, and induced a neutralizing antibody response to the Vero-cell-adapted IBV strain Beaudette (p65) in mice. To further evaluate its immunogenicity, specific-pathogen-free (SPF) chickens were immunized with the pV-S_con plasmid and compared with the control pVAX1 vector and the H120 vaccine. Detection of IBV-specific antibodies and cell cytokines (IL-4 and IFN-γ) indicated that vaccination with pV-S_con efficiently induced both humoral and cellular immune responses. After challenge with the heterologous strain M41, virus shedding and virus loading in tissues was significantly reduced both by pV-S_con and its homologous vaccine H120. Thus, pV-S_con is a promising vaccine candidate for IBV, and the consensus approach is an appealing method for vaccine design in viruses with high variability.

scholarly journals Evolutionary implications of genetic variations in the S1 gene of infectious bronchitis virus

1994 ◽  
Vol 34 (3) ◽  
pp. 327-338 ◽  
Author(s):  
Wang Li ◽  
Dave Junker ◽  
Lisa Hock ◽  
Elham Ebiary ◽  
Ellen W. Collisson
Keyword(s):  
Infectious Bronchitis Virus ◽  
Genetic Variations ◽  
S1 Gene ◽  
Infectious Bronchitis
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