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Finger A, Ashash U, Goldenberg D, Raviv Z. Lessons learnt on infectious bronchitis virus lineage GI-23 1. Avian Pathol 2024:1-13. [PMID: 39190026 DOI: 10.1080/03079457.2024.2398030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
Abstract
Infectious bronchitis virus (IBV) is the first coronavirus discovered in the world in the early 1930s and despite decades of extensive immunoprophylaxis efforts, it remains a major health concern to poultry producers worldwide. Rapid evolution due to large poultry population sizes coupled with high mutation and recombination events and the reliance of the antiviral immune response on specific antibodies against the epitopes of the S1 glycoprotein, render the control of IBV extremely challenging. The numerous and rapidly evolving genetic and antigenic IBV types are currently classified based on the whole S1 gene sequence, into 36 lineages clustered in eight genotypes. Most lineages (29) are grouped in genotype I (GI). "Variant 2" (Israel/Variant 2/1998) is the prototype strain of lineage GI-23 and, since this lineage emerged during the mid-1990s in the Middle East, it has evolved into numerous genetically related strains and disseminated to five continents. The hallmarks of IBV Variant 2-like strain infections are high virulence and remarkable nephrotropism and nephropathogenicity; however, the molecular mechanisms of these traits remain to be elucidated. Limited protection from previously utilized vaccine strains and accumulated losses to poultry producers have urged the development and implementation of homologous Variant 2-like vaccine strains. The latest avian coronavirus biology with specific emphasis on the cumulative knowledge about IBV "Variant 2" and emergence of related strains, characteristics and control are reviewed.
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Affiliation(s)
- Avner Finger
- Phibro Animal Health Corporation, Airport City, Israel
| | - Udi Ashash
- Phibro Animal Health Corporation, Airport City, Israel
| | | | - Ziv Raviv
- Poultry PathoScience Solutions, Inc., Plantation, FL, USA
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2
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Patarca R, Haseltine WA. Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2. Int J Mol Sci 2024; 25:8012. [PMID: 39125583 PMCID: PMC11311688 DOI: 10.3390/ijms25158012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Revised: 07/13/2024] [Accepted: 07/20/2024] [Indexed: 08/12/2024] Open
Abstract
Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions.
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Affiliation(s)
- Roberto Patarca
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
| | - William A. Haseltine
- ACCESS Health International, 384 West Lane, Ridgefield, CT 06877, USA;
- Feinstein Institutes for Medical Research, 350 Community Dr, Manhasset, NY 11030, USA
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Le HD, Thai TN, Kim JK, Song HS, Her M, Tran XT, Kim JY, Kim HR. An Amplicon-Based Application for the Whole-Genome Sequencing of GI-19 Lineage Infectious Bronchitis Virus Directly from Clinical Samples. Viruses 2024; 16:515. [PMID: 38675858 PMCID: PMC11054852 DOI: 10.3390/v16040515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/15/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Infectious bronchitis virus (IBV) causes a highly contagious respiratory disease in chickens, leading to significant economic losses in the poultry industry worldwide. IBV exhibits a high mutation rate, resulting in the continuous emergence of new variants and strains. A complete genome analysis of IBV is crucial for understanding its characteristics. However, it is challenging to obtain whole-genome sequences from IBV-infected clinical samples due to the low abundance of IBV relative to the host genome. Here, we present a novel approach employing next-generation sequencing (NGS) to directly sequence the complete genome of IBV. Through in silico analysis, six primer pairs were designed to match various genotypes, including the GI-19 lineage of IBV. The primer sets successfully amplified six overlapping fragments by long-range PCR and the size of the amplicons ranged from 3.7 to 6.4 kb, resulting in full coverage of the IBV genome. Furthermore, utilizing Illumina sequencing, we obtained the complete genome sequences of two strains belonging to the GI-19 lineage (QX genotype) from clinical samples, with 100% coverage rates, over 1000 × mean depth coverage, and a high percentage of mapped reads to the reference genomes (96.63% and 97.66%). The reported method significantly improves the whole-genome sequencing of IBVs from clinical samples; thus, it can improve understanding of the epidemiology and evolution of IBVs.
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Affiliation(s)
- Hoang Duc Le
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi 11300, Vietnam;
| | - Tuyet Ngan Thai
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
| | - Jae-Kyeom Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
| | - Hye-Soon Song
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
| | - Moon Her
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
| | - Xuan Thach Tran
- Institute of Biotechnology, Vietnam Academy of Science and Technology, Cau Giay, Hanoi 11300, Vietnam;
| | - Ji-Ye Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
| | - Hye-Ryoung Kim
- Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; (H.D.L.); (T.N.T.); (J.-K.K.); (H.-S.S.); (M.H.)
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Nath B, Morla S, Kumar S. Reverse Genetics and Its Usage in the Development of Vaccine Against Poultry Diseases. Methods Mol Biol 2022; 2411:77-92. [PMID: 34816399 DOI: 10.1007/978-1-0716-1888-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Vaccines are the most effective and economic way of combating poultry viruses. However, the use of traditional live-attenuated poultry vaccines has problems such as antigenic differences with the currently circulating strains of viruses and the risk of reversion to virulence. In veterinary medicine, reverse genetics is applied to solve these problems by developing genotype-matched vaccines, better attenuated and effective live vaccines, broad-spectrum vaccine vectors, bivalent vaccines, and genetically tagged recombinant vaccines that facilitate the serological differentiation of vaccinated animals from infected animals. In this chapter, we discuss reverse genetics as a tool for the development of recombinant vaccines against economically devastating poultry viruses.
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Affiliation(s)
- Barnali Nath
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sudhir Morla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India
| | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, India.
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Van Borm S, Steensels M, Mathijs E, Vandenbussche F, van den Berg T, Lambrecht B. Metagenomic sequencing determines complete infectious bronchitis virus (avian Gammacoronavirus) vaccine strain genomes and associated viromes in chicken clinical samples. Virus Genes 2021; 57:529-540. [PMID: 34626348 PMCID: PMC8501334 DOI: 10.1007/s11262-021-01872-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022]
Abstract
Infectious bronchitis virus (IBV, genus Gammacoronavirus) causes an economically important and highly contagious disease in chicken. Random primed RNA sequencing was applied to two IBV positive clinical samples and one in ovo-passaged virus. The virome of a cloacal swab pool was dominated by IBV (82% of viral reads) allowing de novo assembly of a GI-13 lineage complete genome with 99.95% nucleotide identity to vaccine strain 793B. In addition, substantial read counts (16% of viral reads) allowed the assembly of a near-complete chicken astrovirus genome, while lower read counts identified the presence of chicken calicivirus and avian leucosis virus. Viral reads in a respiratory/intestinal tissue pool were distributed between IBV (22.53%), Sicinivirus (Picornaviridae, 24%), and avian leucosis virus (37.04%). A complete IBV genome with 99.95% nucleotide identity to vaccine strain H120 (lineage GI-1), as well as a near-complete avian leucosis virus genome and a partial Sicinivirus genome were assembled from the tissue sample data. Lower read counts identified chicken calicivirus, Avibirnavirus (infectious bursal disease virus, assembling to 98.85% of segment A and 69.66% of segment B closely related to D3976/1 from Germany, 2017) and avian orthoreovirus, while three avian orthoavulavirus 1 reads confirmed prior real-time RT-PCR result. IBV sequence variation analysis identified both fixed and minor frequency variations in the tissue sample compared to its in ovo-passaged virus. Metagenomic methods allow the determination of complete coronavirus genomes from clinical chicken samples while providing additional insights in RNA virus sequence diversity and coinfecting viruses potentially contributing to pathogenicity.
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Affiliation(s)
- Steven Van Borm
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium.
| | - Mieke Steensels
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
| | - Elisabeth Mathijs
- Department of Animal Infectious Diseases, Sciensano, Brussels, Belgium
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Abozeid HH, Naguib MM. Infectious Bronchitis Virus in Egypt: Genetic Diversity and Vaccination Strategies. Vet Sci 2020; 7:vetsci7040204. [PMID: 33348570 PMCID: PMC7766096 DOI: 10.3390/vetsci7040204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Infectious bronchitis virus (IBV) is a highly evolving avian pathogen that has increasingly imposed a negative impact on poultry industry worldwide. In the last 20 years, IBV has been continuously circulating among chicken flocks in Egypt causing huge economic losses to poultry production. Multiple IBV genotypes, namely, GI-1, GI-13, GI-16, and GI-23 have been reported in Egypt possessing different genetic and pathogenic features. Different vaccine programs are being used to control the spread of the disease in Egypt. However, the virus continues to spread and evolve where multiple IBV variants and several recombination evidence have been described. In this review, we highlight the current knowledge concerning IBV circulation, genesis, and vaccination strategies in Egypt. In addition, we analyze representative Egyptian IBV strains from an evolutionary perspective based on available data of their S1 gene. We also provide insight into the importance of surveillance programs and share our perspectives for better control of IBV circulating in Egypt.
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Affiliation(s)
- Hassanein H. Abozeid
- Department of Poultry Diseases, Faculty of Veterinary Medicine, Cairo University, Giza 12211, Egypt;
| | - Mahmoud M. Naguib
- Reference Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Agriculture Research Center, Giza 12618, Egypt
- Zoonosis Science Center, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 21 Uppsala, Sweden
- Correspondence:
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