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 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 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 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 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 Delmarva (DMV/1639) Infectious Bronchitis Virus (IBV) Variants Isolated in Eastern Canada Show Evidence of Recombination

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1054 ◽  
Author(s):  
Mohamed S. H. Hassan ◽  
Davor Ojkic ◽  
Carla S. Coffin ◽  
Susan C. Cork ◽  
Frank van der Meer ◽  
...  
Keyword(s):  
Infectious Bronchitis Virus ◽  
Genomic Sequence ◽  
Sequence Similarity ◽  
Clinical Samples ◽  
Complete Genomic Sequence ◽  
Eastern Canada ◽  
Diagnostic Laboratory ◽  
Infectious Bronchitis ◽  
Show Evidence ◽  
Complete Genomic

Infectious bronchitis virus (IBV) infection in chickens can lead to an economically important disease, namely, infectious bronchitis (IB). New IBV variants are continuously emerging, which complicates vaccination-based IB control. In this study, five IBVs were isolated from clinical samples submitted to a diagnostic laboratory in Ontario, Canada, and subjected to detailed molecular characterization. Analysis of the spike (S)1 gene showed that these five IBVs were highly related to the Delmarva (DMV/1639) strain (~97.0% nucleotide sequence similarity) that was firstly isolated from an IB outbreak in the Delmarva peninsula, United States of America (USA), in 2011. However, the complete genomic sequence analysis showed a 93.5–93.7% similarity with the Connecticut (Conn) vaccine strain, suggesting that Conn-like viruses contributed to the evolution of the five Canadian IBV/DMV isolates. A SimPlot analysis of the complete genomic sequence showed evidence of recombination for at least three different IBV strains, including a Conn vaccine-like strain, a 4/91 vaccine-like strain, and one strain that is yet-unidentified. The unidentified strain may have contributed the genomic regions of the S, 3, and membrane (M) genes of the five Canadian IBV/DMV isolates. The study outcomes add to the existing knowledge about involvement of recombination in IBV evolution.

scholarly journals Infectious Bronchitis Virus Evolution, Diagnosis and Control

2020 ◽  
Vol 7 (2) ◽  
pp. 79 ◽  
Author(s):  
Matteo Legnardi ◽  
Claudia Maria Tucciarone ◽  
Giovanni Franzo ◽  
Mattia Cecchinato
Keyword(s):  
Infectious Bronchitis Virus ◽  
Immune Escape ◽  
Control Strategies ◽  
Rapid Evolution ◽  
Emerging Diseases ◽  
Economic Losses ◽  
Recombination Rates ◽  
Infectious Bronchitis ◽  
Advantages And Disadvantages ◽  
And Control

RNA viruses are characterized by high mutation and recombination rates, which allow a rapid adaptation to new environments. Most of the emerging diseases and host jumps are therefore sustained by these viruses. Rapid evolution may also hinder the understanding of molecular epidemiology, affect the sensitivity of diagnostic assays, limit the vaccine efficacy and favor episodes of immune escape, thus significantly complicating the control of even well-known pathogens. The history of infectious bronchitis virus (IBV) fits well with the above-mentioned scenario. Despite being known since the 1930s, it still represents one of the main causes of disease and economic losses for the poultry industry. A plethora of strategies have been developed and applied over time, with variable success, to limit its impact. However, they have rarely been evaluated objectively and on an adequate scale. Therefore, the actual advantages and disadvantages of IBV detection and control strategies, as well as their implementation, still largely depend on individual sensibility. The present manuscript aims to review the main features of IBV biology and evolution, focusing on their relevance and potential applications in terms of diagnosis and control.

scholarly journals Greater Protection against Virulent Infectious Bronchitis Virus Challenge Conferred by Recombinant Baculovirus Co-expressing S1 and N Proteins

2018 ◽  
Author(s):  
Yuan Yuan ◽  
Zhi-Peng Zhang ◽  
Yi-Ning He ◽  
Wen-Sheng Fan ◽  
Zhi-Hua Dong ◽  
...  
Keyword(s):  
Specific Antibody ◽  
Infectious Bronchitis Virus ◽  
Subunit Vaccine ◽  
Recombinant Baculovirus ◽  
Recombinant Baculoviruses ◽  
Economic Losses ◽  
Subunit Vaccines ◽  
Infectious Bronchitis ◽  
Antibody Levels ◽  
N Proteins

Avian infectious bronchitis virus (IBV) is the causative agent of infectious bronchitis, which causes considerable economic losses to the poultry industry worldwide. It is imperative to develop safe and efficient candidate vaccines to control IBV infection. In the current study, recombinant baculoviruses co-expressing S1 and N proteins, mono-expressing S1 or N proteins alone of IBV were constructed and prepared into subunit vaccines rHBM-S1-N, rHBM-S1 and rHBM-N. The levels of immune protection of these subunit vaccines were evaluated by inoculating specific pathogen-free (SPF) chickens at 14 days of age, boosting with the same dose 14 days later, and following challenge with a virulent GX-YL5 strain of IBV 14 days post-booster (dpb). The commercial vaccine strain H120 was used as a control. The IBV-specific antibody levels as well as the percentages of CD4+ and CD8+ T lymphocytes were detected within 28 days post-vaccination (dpv). The morbidity, mortality, and re-isolation of virus from the tracheas and kidneys of challenged birds were evaluated at 5 days post-challenge (dpc). The results showed that the IBV-specific antibody levels and the percentages of CD4+ and CD8+ T lymphocyte in rHBM-S1-N group were higher than those of rHBM-S1 and rHBM-N groups, especially the cellular immunity response. At 5 dpc, the mortality, morbidity and virus re-isolation rate of rHBM-S1-N were slightly higher than those of H120 group, but were lower than those of rHBM-S1 group and rHBM-N group. The present study demonstrated that the protection of recombinant baculovirus co-expressing S1 and N proteins was better than that of recombinant baculoviruses mono-expressing S1 or N protein alone. Thus, the recombinant baculovirus co-expressing S1 and N proteins could serve as a potential IBV vaccine and this demonstrates that the bivalent subunit vaccine including the S1 and N proteins might be a strategy for the development of an IBV subunit vaccine.

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