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Junnu S, Pohuang T. Molecular investigation of S2-3a/3b-E-M-4b/4c-5a/5b-N gene of QX-like and variant genotype infectious bronchitis virus isolated in Thailand reveals a distinct E gene. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 97:105157. [PMID: 34826625 DOI: 10.1016/j.meegid.2021.105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 11/15/2021] [Accepted: 11/21/2021] [Indexed: 06/13/2023]
Abstract
The QX-like infectious bronchitis virus (IBV) and variant genotype have been discovered worldwide including Thailand. In order to know the origin of QX-like and variant genotype IBV in Thailand, the genetic analysis on multiple genes was investigated. Seven IBVs including four QX-like and three variant genotype were randomly selected from IBVs isolated in Thailand during 2008 and 2010. Phylogenetic analysis of the S2-3a/3b-E-M-4b/4c-5a/5b-N gene showed that Thai QX-like and variant genotype IBV were grouped together in a separate branch from other IBV strains. The isolated IBVs shared nucleotide identities of 96-99.9% with each other. They exhibited a high level of similarity (93.8%) with KM91 strain in South Korea. Phylogenetic analysis of the S2 and 3a/3b gene showed a relationship to KM91 strain. The E gene was distinct from other IBV strains. The M, 4a/4b and 5a/5b gene were closely related to Massachusetts type. The N gene was classified into two groups which were a group of unique to Thailand (variant genotype) and a relationship with Massachusetts type (QX-like). Recombination analysis identified the occurrence of recombination events in the genome of viruses. These findings demonstrated that the QX-like IBV and variant genotype isolates in Thailand were the recombinant viruses. Thai QX-like IBV had a genetic relationship with KM91 strain, Massachusetts type and unknown IBV whereas variant genotype had a genetic relationship with Thai QX-like IBV and Connecticut strain.
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Affiliation(s)
- Sucheeva Junnu
- Research Group for Emerging and Re-emerging Infectious Diseases in Animals and Zoonotic Diseases, Khon Kaen University, Khon Kaen 40002, Thailand; Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Tawatchai Pohuang
- Research Group for Emerging and Re-emerging Infectious Diseases in Animals and Zoonotic Diseases, Khon Kaen University, Khon Kaen 40002, Thailand; Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand.
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Zhang X, Guo M, Zhao J, Wu Y. Avian Infectious Bronchitis in China: Epidemiology, Vaccination, and Control. Avian Dis 2021; 65:652-656. [DOI: 10.1637/aviandiseases-21-00098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/05/2022]
Affiliation(s)
- Xiaorong Zhang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Mengjiao Guo
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jia Zhao
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yantao Wu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
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Han Y, Zhang J, Shi H, Zhou L, Chen J, Zhang X, Liu J, Zhang J, Wang X, Ji Z, Jing Z, Cong G, Ma J, Shi D, Li F. Epitope mapping and cellular localization of swine acute diarrhea syndrome coronavirus nucleocapsid protein using a novel monoclonal antibody. Virus Res 2019; 273:197752. [PMID: 31518629 PMCID: PMC7114574 DOI: 10.1016/j.virusres.2019.197752] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/30/2019] [Accepted: 09/09/2019] [Indexed: 12/23/2022]
Abstract
SADS-CoV N-specific monoclonal antibody (mAb) was generated and characterized. N mAb detected SADS-CoV in infected cells. Identified the motif 343DAPVFTPAP351 as the minimal unit of the linear B-cell epitope recognized by mAb 3E9.
A swine acute diarrhea syndrome coronavirus (SADS-CoV) that causes severe diarrhea in suckling piglets was identified in Southern China in 2017. To develop an antigen that is specific, sensitive, and easy to prepare for serological diagnosis, antigenic sites in the SADS-CoV nucleocapsid (N) protein were screened. We generated and characterized an N-reactive monoclonal antibody (mAb) 3E9 from mice immunized with recombinant N protein. Through fine epitope mapping of mAb 3E9 using a panel of eukaryotic-expressed polypeptides with GFP-tags, we identified the motif 343DAPVFTPAP351 as the minimal unit of the linear B-cell epitope recognized by mAb 3E9. Protein sequence alignment indicated that 343DAPVFTPAP351 was highly conserved in different SADS-CoV strains and SADS-related coronaviruses from bat, with one substitution in this motif in HKU2-related bat coronavirus. Using mAb 3E9, we observed that N protein was expressed in the cytoplasm and was in the nucleolus during SADS-CoV replication. N protein was immunoprecipitated from SADS-CoV-infected Vero E6 cells. Taken together, our results indicated that 3E9 mAb could be a useful tool to investigate the structure and function of N protein during viral replication.
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Affiliation(s)
- Yuru Han
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jiyu Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Hongyan Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Ling Zhou
- College of Animal Science, South China Agricultural University, Tianhe District, Wushan Road 483, Guangzhou, 510642, China
| | - Jianfei Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Xin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jianbo Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jialin Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Xiaobo Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Zhaoyang Ji
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Zhaoyang Jing
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Guangyi Cong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China
| | - Jingyun Ma
- College of Animal Science, South China Agricultural University, Tianhe District, Wushan Road 483, Guangzhou, 510642, China.
| | - Da Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China.
| | - Feng Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Xiangfang District, Haping Road 678, Harbin, 150069, China.
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Zhou H, Zhang M, Tian X, Shao H, Qian K, Ye J, Qin A. Identification of a novel recombinant virulent avian infectious bronchitis virus. Vet Microbiol 2017; 199:120-127. [PMID: 28110778 PMCID: PMC7117249 DOI: 10.1016/j.vetmic.2016.12.038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 12/30/2016] [Accepted: 12/31/2016] [Indexed: 11/15/2022]
Abstract
A novel IBV variant CK/CH/2010/JT-1 was identified. A novel genotypic cluster IBV has emerged in China. Isolate CK/CH/2010/JT-1 originated from homologous RNA recombination. Isolate CK/CH/2010/JT-1 is highly virulent.
The emergence of new infectious bronchitis virus (IBV) variants is often disastrous in the poultry industry. In this study, an IBV, CK/CH/2010/JT-1, was isolated from an H120- and 4/91-IBV-vaccinated flock in China. Antisera against vaccine strains H120 and 4/91 could not provide effective protection against CK/CH/2010/JT-1 in virus neutralization assays. CK/CH/2010/JT-1 could cause 43.75% mortality with respiratory and severe renal lesions in inoculated chickens. Phylogenetic analysis of the S1 gene showed that CK/CH/2010/JT-1 and 31 other isolates could be grouped as a new genotypic cluster. Recombination analysis revealed that three recombination events could be found in the genome of CK/CH/2010/JT-1 at positions 24709-365, 17160-19811 and 21136-21770. Whole-genome sequence analysis showed that CK/CH/2010/JT-1 originated from multiple template switches among QX-like, CK/CH/LSC/99I-, tl/CH/LDT3/03- and 4/91-type IBVs. All of these data demonstrated that CK/CH/2010/JT-1 is a new recombinant genotype IBV with high virulence. Our findings suggest that the surveillance of new genotype strains of IBV is very important for developing more effective anti-IBV strategies.
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Affiliation(s)
- Haisheng Zhou
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
| | - Meihong Zhang
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
| | - Xue Tian
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China.
| | - Hongxia Shao
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China; Jiangsu Key Lab of Zoonosis, Yangzhou 225009, PR China.
| | - Kun Qian
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China; Jiangsu Key Lab of Zoonosis, Yangzhou 225009, PR China.
| | - Jianqiang Ye
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China; Jiangsu Key Lab of Zoonosis, Yangzhou 225009, PR China.
| | - Aijian Qin
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, No. 12 East Wenhui Road, Yangzhou, Jiangsu 225009, PR China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou 225009, PR China; Jiangsu Key Lab of Zoonosis, Yangzhou 225009, PR China.
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Characterization of Two Monoclonal Antibodies That Recognize Linker Region and Carboxyl Terminal Domain of Coronavirus Nucleocapsid Protein. PLoS One 2016; 11:e0163920. [PMID: 27689694 PMCID: PMC5045181 DOI: 10.1371/journal.pone.0163920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/17/2016] [Indexed: 12/27/2022] Open
Abstract
The transmissible gastroenteritis virus (TGEV) nucleocapsid (N) protein plays important roles in the replication and translation of viral RNA. The present study provides the first description of two monoclonal antibodies (mAbs) (5E8 and 3D7) directed against the TGEV N protein linker region (LKR) and carboxyl terminal domain (CTD). The mAbs 5E8 and 3D7 reacted with native N protein in western blotting and immunofluorescence assay (IFA). Two linear epitopes, 189SVEQAVLAALKKLG202 and 246VTRFYGARSSSA257, located in the LKR and CTD of TGEV N protein, respectively, were identified after truncating the protein and applying a peptide scanning technique. Using mAb 5E8, we observed that the N protein was expressed in the cytoplasm during TGEV replication and that the protein could be immunoprecipitated from TGEV-infected PK-15 cells. The mAb 5E8 can be applied for different approaches to diagnosis of TGEV infection. In addition, the antibodies represent useful tools for investigating the antigenic properties of the N protein.
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Distribution of infectious bronchitis virus strains in different organs and evidence of vertical transmission in natural infection. Arch Virol 2016; 161:3355-3363. [PMID: 27586414 PMCID: PMC7087270 DOI: 10.1007/s00705-016-3030-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 08/22/2016] [Indexed: 01/12/2023]
Abstract
On the basis of partial sequencing of the infectious bronchitis virus (IBV) S1 gene, this study investigated the molecular diversity of the virus in two life periods of a batch of breeding hens at the field level. The chicks were vaccinated against IBV on the second day of life with the vaccine Ma5, but at the age of 18 days, they exhibited clinical signs and macroscopic lesions compatible with avian infectious bronchitis (IB). In the clinical disease stage, the Ma5 vaccine strain was detected in the trachea, lungs, and small intestine of the chicks, while IBV variants were detected in the bursa of Fabricius and kidneys. Subsequently, new samples were collected from the same batch at the end of the production cycle. In this phase, the Ma5 vaccine strain was detected in the kidneys, small intestine, and oviduct of the hens. However, a previously unidentified IBV variant was found in the cecal tonsils. Additionally, a fragment of viral RNA with that was completely identical to the corresponding region of the Ma5 vaccine was detected in the allantoic fluid of viable embryos from the hens under study after 18 days of incubation. These findings suggest that, in addition to the Ma5 vaccine, other strains of IBV variants can coexist, seeming to establish a chronic infection in the chickens, and that they can potentially be transmitted vertically. These results may assist in immunoprophylaxis control programs against IBV.
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Huang SW, Chiang YC, Chin CY, Tang PC, Liu PC, Wang CY. The phylogenetic and recombinational analysis of beak and feather disease virus Taiwan isolates. Arch Virol 2016; 161:2969-88. [DOI: 10.1007/s00705-016-2963-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 06/29/2016] [Indexed: 11/28/2022]
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Genome sequence and origin analyses of the recombinant novel IBV virulent isolate SAIBK2. Virus Genes 2016; 52:509-20. [PMID: 27108998 PMCID: PMC7088859 DOI: 10.1007/s11262-016-1337-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 04/05/2016] [Indexed: 01/16/2023]
Abstract
Recombination between infectious bronchitis viruses (IBVs), together with point mutations, insertions, and deletions, is thought to be responsible for the emergence of new IBV variants. SAIBK2 is a nephropathogenic strain isolated from layer flocks vaccinated with live attenuated H120 vaccine in Sichuan province, China in 2011. SAIBK2 causes severe kidney lesions and results in 50 % mortality in 30-day-old specific-pathogen-free chickens (with a dose of 105 EID50/0.1 mL SAIBK2 per chicken). The complete genome of SAIBK2 consists of 27669 nucleotides, excluding the poly-A tail at the 3′ end. SAIBK2 has the highest identity to YX10 in terms of complete genome. Phylogenetic analysis of complete sequence showed that SAIBK2 belongs to the most dominant genotype in China. Comparison and recombination analyses with other IBV strains revealed that SAIBK2 may originate from recombination events among a YX10-, a YN-, and a Mass-like strain. Furthermore, whole gene 5 and parts of nsp 3, nsp 4, nsp 16, and N genes are involved in the recombination events, and the uptake of these regions from YN and Mass strains by SAIBK2 may increase its replication efficiency and be responsible for its increased virulence in specific-pathogen-free chickens.
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Zhao Y, Zhang H, Zhao J, Zhong Q, Jin JH, Zhang GZ. Evolution of infectious bronchitis virus in China over the past two decades. J Gen Virol 2016; 97:1566-1574. [PMID: 27008625 PMCID: PMC7079583 DOI: 10.1099/jgv.0.000464] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Avian infectious bronchitis is a highly contagious disease caused by infectious bronchitis virus (IBV) that affects poultry production worldwide. The absence of vaccine cross-protection and the frequent emergence of new variant strains complicate control of IBV. Here we designed a study to measure the evolution dynamics of IBV strains in China. One hundered and seven complete sequences and 1022 S1-region sequences of Chinese IBVs isolated between 1994 and 2014 were analysed by using MEGA 5.0 software and the Bayesian analysis sampling trees (BEAST) method, and selection pressure on different proteins was assessed. The phylogenetic dissimilarity of different gene trees in the data set indicated possible recombination. Fourteen isolates were identified as recombinants, possibly generated from vaccines of the Massachusetts serotype in recombination with circulating viruses. The earliest IBV in China was found to have existed in the early 1900s, and continues to evolve at a rate of approximately 10-5 substitutions per site per year. We found that purifying selection was the main evolutionary pressure in the protein-coding regions, while the S1 gene bears the greatest positive selection pressure. The proportion of QX-like genotype strains increased over time. These results indicate that the genotypes of Chinese IBVs have undergone a remarkable transition during the past 20 years.
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Affiliation(s)
- Ye Zhao
- Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Hui Zhang
- National Clinical Research Center of Digestive Diseases and Beijing Friendship Hospital, Capital Medical University, Beijing 100050, PR China.,Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jing Zhao
- Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Qi Zhong
- Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Ji-Hui Jin
- Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Guo-Zhong Zhang
- Key Laboratory of Animal Epidemiology and Zoonoses, Ministry of Agriculture, College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
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Molecular detection and Smoothing spline clustering of the IBV strains detected in China during 2011-2012. Virus Res 2015; 211:145-50. [PMID: 26494165 DOI: 10.1016/j.virusres.2015.10.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 09/22/2015] [Accepted: 10/13/2015] [Indexed: 11/23/2022]
Abstract
Infectious bronchitis virus (IBV) is a highly variable virus with a large number of genotypes. During 2011-2012, nineteen wild IBV strains were isolated in China. Sequence analysis showed that these isolates were divided into five sub-clusters: A2-like, CKCHLDL08I-like, SAIBK-like, KM91-like and TW97/4-like. Phylogenetic analysis based on the 1118 sequences available on line suggested that all IBVs were classified into six clusters. The prevalent strains including all the isolates were in cluster VI with a 0.194-0.259 genetic distance to Mass type vaccines. In addition, we introduced the smoothing spline clustering (SSC) method to estimate the highly variable sites for some sub-clusters. The results showed that highly variable sites range from sub-clusters, the N-terminal sequences of 4/91-like, TW97/4-like and Arkansas-like are more variable than other sub-clusters. This is the first time that the SSC method has been used for the evolution study of IBV.
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Dhama K, Singh SD, Barathidasan R, Desingu PA, Chakraborty S, Tiwari R, Kumar MA. Emergence of Avian Infectious Bronchitis Virus and its variants need better diagnosis, prevention and control strategies: a global perspective. Pak J Biol Sci 2015; 17:751-67. [PMID: 26035949 DOI: 10.3923/pjbs.2014.751.767] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Growth in poultry sector is being challenged due to increased incidence and re-emergence of diseases caused due to evolution of several viral pathogens and use of live vaccines. Piles of economic losses are encountered due to these diseases. Avian Infectious Bronchitis (IB), caused by Corona virus, is OIE-listed disease and characterized by respiratory, renal and urogenital involvements, causing high mortality. Economic losses are encountered due to loss of productive performance of both egg and meat-type chickens. Variant viruses evolve due to spontaneous mutations and recombinations, causing disease in vaccinated flocks of all ages. Serotyping and genotyping are the common methods of classification of IBV strains. The virus has 4 clusters, grouped into 7 serotypes and the most important strains are Massachusetts, Connecticut, Arkansas, Gray, Holte and Florida along with numerous others, distributed round the globe. Several conventional and molecular diagnostic methods have been described for the diagnosis of IB in chickens. 'All-in/all-out' operations of rearing along with good biosafety measures forms the basis of prevention, whereas vaccination forms the backbone of IB control programme. Both live and inactivated (oil emulsified) conventional vaccines are available. The new generation vaccines (recombinant and vector-based) developed against locally prevailing IBV strains may be more helpful and avoid the reversion of virulence in live vaccine viruses. The present review deals with all these perspectives of this important emerging poultry pathogen.
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Abolnik C. Genomic and single nucleotide polymorphism analysis of infectious bronchitis coronavirus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 32:416-24. [PMID: 25843648 PMCID: PMC7106318 DOI: 10.1016/j.meegid.2015.03.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/13/2015] [Accepted: 03/26/2015] [Indexed: 01/03/2023]
Abstract
Infectious bronchitis virus (IBV) is a Gammacoronavirus that causes a highly contagious respiratory disease in chickens. A QX-like strain was analysed by high-throughput Illumina sequencing and genetic variation across the entire viral genome was explored at the sub-consensus level by single nucleotide polymorphism (SNP) analysis. Thirteen open reading frames (ORFs) in the order 5'-UTR-1a-1ab-S-3a-3b-E-M-4b-4c-5a-5b-N-6b-3'UTR were predicted. The relative frequencies of missense: silent SNPs were calculated to obtain a comparative measure of variability in specific genes. The most variable ORFs in descending order were E, 3b, 5'UTR, N, 1a, S, 1ab, M, 4c, 5a, 6b. The E and 3b protein products play key roles in coronavirus virulence, and RNA folding demonstrated that the mutations in the 5'UTR did not alter the predicted secondary structure. The frequency of SNPs in the Spike (S) protein ORF of 0.67% was below the genomic average of 0.76%. Only three SNPS were identified in the S1 subunit, none of which were located in hypervariable region (HVR) 1 or HVR2. The S2 subunit was considerably more variable containing 87% of the polymorphisms detected across the entire S protein. The S2 subunit also contained a previously unreported multi-A insertion site and a stretch of four consecutive mutated amino acids, which mapped to the stalk region of the spike protein. Template-based protein structure modelling produced the first theoretical model of the IBV spike monomer. Given the lack of diversity observed at the sub-consensus level, the tenet that the HVRs in the S1 subunit are very tolerant of amino acid changes produced by genetic drift is questioned.
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Affiliation(s)
- Celia Abolnik
- Poultry Section, Department of Production Animal Studies, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa.
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Abdel-Moneim AS, Giesow K, Keil GM. High-level protein expression following single and dual gene cloning of infectious bronchitis virus N and S genes using baculovirus systems. Viral Immunol 2014; 27:75-81. [PMID: 24605790 DOI: 10.1089/vim.2013.0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Baculovirus is an efficient system for the gene expression that can be used for gene transfer to both insect and different vertebrate hosts. The nucleocapsid gene (N) of the infectious bronchitis virus was cloned in a baculovirus expression system for insect cell expression. Dual expression vectors containing IBV N and spike (S) proteins of the avian infectious bronchitis virus were engineered under the control of human and murine cytomegalovirus immediate-early enhancer/promoter elements in combination with the baculoviral polyhedrin and p10 promoters for simultaneous expression in both vertebrate and insect cells. Transduction of the N gene in the insect Sf9 cells revealed a high level of protein expression. The expressed protein, used in ELISA, effectively detected chicken anti-IBV antibodies with high specificity. Transduction of mammalian and avian cells with BacMam viruses revealed that dual expression cassettes yielded high levels of protein from both transcription units.
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Molecular characterization of major structural protein genes of avian coronavirus infectious bronchitis virus isolates in southern china. Viruses 2013; 5:3007-20. [PMID: 24304696 PMCID: PMC3967158 DOI: 10.3390/v5123007] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Revised: 11/09/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022] Open
Abstract
To gain comprehensive genetic information of circulating avian coronavirus infectious bronchitis virus (IBV) isolates in China, analysis of the phylogenetic tree, entropy of the amino acid sequences, and the positive selection as well as computational recombinations of S1, M and N genes of 23 IBV isolates was conducted in the present study. The phylogenetic trees based on the S1, M and N genes exhibited considerably different topology and the CK/CH/LSC/99I-type isolates were the predominant IBVs based on the phylogenetic analysis of S1 gene. Results of entropy of amino acid sequences revealed that the S1 gene had the largest variation; the M gene had less variation than the N gene. Positive selections were detected in not only S1 but also M and N gene proteins. In addition, five S1 gene recombinants between vaccine strain 4/91 and CK/CH/LSC/99I-type field isolate were confirmed. In conclusion, multiple IBV genotypes co-circulated; genetic diversity and positive selections existed in S1, M and N genes; 4/91 vaccine recombinants emerged in China. Our results show that field IBVs in China are continuing to evolve and vaccine strains may have an important role in the appearance of new IBV strains via recombination. In addition, the present study indicates that IBV evolution is driven by both generations of genetic diversity and selection.
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Brandão PE. The evolution of codon usage in structural and non-structural viral genes: the case of Avian coronavirus and its natural host Gallus gallus. Virus Res 2013; 178:264-71. [PMID: 24091362 PMCID: PMC7114390 DOI: 10.1016/j.virusres.2013.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 09/13/2013] [Accepted: 09/20/2013] [Indexed: 12/28/2022]
Abstract
Avian coronavirus codon usage is closer to chicken for non-structural proteins. Spike glycoprotein gene shares less preferred codons with chicken. Avian coronavirus balances replication and immune camouflage for its codon usage.
To assess the codon evolution in virus–host systems, Avian coronavirus and its natural host Gallus gallus were used as a model. Codon usage (CU) was measured for the viral spike (S), nucleocapsid (N), nonstructural protein 2 (NSP2) and papain-like protease (PLpro) genes from a diverse set of A. coronavirus lineages and for G. gallus genes (lung surfactant protein A, intestinal cholecystokinin, oviduct ovomucin alpha subunit, kidney vitamin D receptor and the ubiquitary beta-actin) for different A. coronavirus replicating sites. Relative synonymous codon usage (RSCU) trees accommodating all virus and host genes in a single topology showed a higher proximity of A. coronavirus CU to the respiratory tract for all genes. The codon adaptation index (CAI) showed a lower adaptation of S to G. gallus compared to NSP2, PLpro and N. The effective number of codons (Nc) and GC3% revealed that natural selection and genetic drift are the evolutionary forces driving the codon usage evolution of both A. coronavirus and G. gallus regardless of the gene being considered. The spike gene showed only one 100% conserved amino acid position coded by an A. coronavirus preferred codon, a significantly low number when compared to the three other genes (p < 0.0001). Virus CU evolves independently for each gene in a manner predicted by the protein function, with a balance between natural selection and mutation pressure, giving further molecular basis for the viruses’ ability to exploit the host's cellular environment in a concerted virus–host molecular evolution.
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Affiliation(s)
- Paulo Eduardo Brandão
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine, University of São Paulo, Brazil.
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Chen GQ, Zhuang QY, Wang KC, Liu S, Shao JZ, Jiang WM, Hou GY, Li JP, Yu JM, Li YP, Chen JM. Identification and survey of a novel avian coronavirus in ducks. PLoS One 2013; 8:e72918. [PMID: 24023656 PMCID: PMC3758261 DOI: 10.1371/journal.pone.0072918] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 07/16/2013] [Indexed: 01/08/2023] Open
Abstract
The rapid discovery of novel viruses using next generation sequencing (NGS) technologies including DNA-Seq and RNA-Seq, has greatly expanded our understanding of viral diversity in recent years. The timely identification of novel viruses using NGS technologies is also important for us to control emerging infectious diseases caused by novel viruses. In this study, we identified a novel duck coronavirus (CoV), distinct with chicken infectious bronchitis virus (IBV), using RNA-Seq. The novel duck-specific CoV was a potential novel species within the genus Gammacoronavirus, as indicated by sequences of three regions in the viral 1b gene. We also performed a survey of CoVs in domestic fowls in China using reverse-transcription polymerase chain reaction (RT-PCR), targeting the viral nucleocapsid (N) gene. A total of 102 CoV positives were identified through the survey. Phylogenetic analysis of the viral N sequences suggested that CoVs in domestic fowls have diverged into several region-specific or host-specific clades or subclades in the world, and IBVs can infect ducks, geese and pigeons, although they mainly circulate in chickens. Moreover, this study provided novel data supporting the notion that some host-specific CoVs other than IBVs circulate in ducks, geese and pigeons, and indicated that the novel duck-specific CoV identified through RNA-Seq in this study is genetically closer to some CoVs circulating in wild water fowls. Taken together, this study shed new insight into the diversity, distribution, evolution and control of avian CoVs.
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Affiliation(s)
- Gui-Qian Chen
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Qing-Ye Zhuang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Kai-Cheng Wang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Shuo Liu
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jian-Zhong Shao
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Wen-Ming Jiang
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Guang-Yu Hou
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jin-Ping Li
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Jian-Min Yu
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
| | - Yi-Ping Li
- Institute of Cell Biology and Genetics, College of Life Sciences, Zhejiang University, Hangzhou, China
- * E-mail: (JMC); (YPL)
| | - Ji-Ming Chen
- The Laboratory of Avian Disease Surveillance, China Animal Health and Epidemiology Center, Qingdao, China
- * E-mail: (JMC); (YPL)
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Acevedo AM, Perera CL, Vega A, Ríos L, Coronado L, Relova D, Frías MT, Ganges L, Núñez JI, Pérez LJ. A duplex SYBR Green I-based real-time RT-PCR assay for the simultaneous detection and differentiation of Massachusetts and non-Massachusetts serotypes of infectious bronchitis virus. Mol Cell Probes 2013; 27:184-92. [PMID: 23810983 DOI: 10.1016/j.mcp.2013.06.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 05/13/2013] [Accepted: 06/17/2013] [Indexed: 12/22/2022]
Abstract
Infectious bronchitis is a highly contagious viral disease of poultry caused by infectious bronchitis virus (IBV) and is considered one of the most economically important viral diseases of chickens. Control of IBV has been attempted using live attenuated and inactivated vaccines. Live attenuated vaccines of the Massachusetts (Mass.) serotype are the most commonly used for this purpose. Due to the continuous emergence of new variants of the infectious bronchitis virus, the identification of the type of IBV causing an outbreak in commercial poultry is important in the selection of the appropriate vaccine(s) capable of inducing a protective immune response. The present work was aimed at developing and evaluating a duplex SYBR Green I-based real-time RT-PCR (rRT-PCR) assay for the simultaneous detection and differentiation of Mass. and non-Mass. serotypes of IBV. The duplex rRT-PCR yielded curves of amplification with two specific melting curves (Tm1 = 83 °C ± 0.5 °C and Tm2 = 87 °C ± 0.5 °C) and only one specific melting peak (Tm = 87 °C ± 0.5 °C) when the IBV Mass. serotype and IBV non-Mass. serotype strains were evaluated, respectively. The detection limit of the assay was 8.2 gene copies/μL based on in vitro transcribed RNA and 0.1 EID50/mL. The assay was able to detect all the IBV strains assessed and discriminated well among the IBV Mass. and the IBV non-Mass. serotypes strains. In addition, amplification curves were not obtained with any of the other viruses tested. From the 300 field samples tested, the duplex rRT-PCR yielded a total of 80 samples that were positive for IBV (26.67%), 73 samples identified as the IBV Mass. serotype and seven samples as identified as the IBV non-Mass. serotype. A comparison of the performance of test as assessed with field samples revealed that the duplex rRT-PCR detected a higher number of IBV-positive samples than when conventional RT-PCR or virus isolation tests were used. The duplex rRT-PCR presented here is a useful tool for the rapid identification of outbreaks and for surveillance programmes during IB-suspected cases, particularly in countries with a vaccination control programme.
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Affiliation(s)
- Ana M Acevedo
- Centro Nacional de Sanidad Agropecuaria (CENSA), OIE Collaborating Centre for Diagnosis and Risk Analysis of The Caribean Region, Carretera de Jamaica, San José de las Lajas, La Habana 32700, Cuba
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Chen IJ, Yuann JMP, Chang YM, Lin SY, Zhao J, Perlman S, Shen YY, Huang TH, Hou MH. Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1054-62. [PMID: 23501675 PMCID: PMC3774783 DOI: 10.1016/j.bbapap.2013.03.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 02/06/2013] [Accepted: 03/05/2013] [Indexed: 02/04/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.
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Affiliation(s)
- I-Jung Chen
- Department of Life Science, National Chung Hsing University, Taichung, Taiwan
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