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Liu Y, Bahoussi AN, Wang PH, Wu C, Xing L. Complete genome sequences of classical swine fever virus: Phylogenetic and evolutionary analyses. Front Microbiol 2022; 13:1021734. [PMID: 36225377 PMCID: PMC9549409 DOI: 10.3389/fmicb.2022.1021734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
The classical swine fever virus (CSFV) outbreaks cause colossal losses of pigs and drastic economic impacts. The current phylogenetic CSFV groups were determined mainly based on the partial genome. Herein, 203 complete genomic sequences of CSFVs collected worldwide between 1998 and 2018 available on the GenBank database were retrieved for re-genotyping and recombination analysis. The maximum likelihood phylogenetic tree determined two main groups, GI and GII, with multiple sub-genotypes. The “strain 39” (GenBank ID: AF407339), previously identified as belonging to sub-genotypes 1.1 or 2.2 based on the partial sequences, is found to be genetically distinct and independent, forming a new lineage depicted as GI-2.2b. Ten potential natural recombination events were identified, seven of which were collected in China and found involved in the genetic diversity of CSFVs. Importantly, the vaccine strains and highly virulent strains were all involved in the recombination events, which would induce extra challenges to vaccine development. These findings alarm that attenuated vaccines should be applied with discretion and recommend using subunit vaccines in parallel with other preventive strategies for better management of CSFVs.
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Affiliation(s)
- Yue Liu
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
| | | | - Pei-Hua Wang
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Changxin Wu
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- *Correspondence: Li Xing
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Malik YS, Bhat S, Kumar ORV, Yadav AK, Sircar S, Ansari MI, Sarma DK, Rajkhowa TK, Ghosh S, Dhama K. Classical Swine Fever Virus Biology, Clinicopathology, Diagnosis, Vaccines and a Meta-Analysis of Prevalence: A Review from the Indian Perspective. Pathogens 2020; 9:pathogens9060500. [PMID: 32580503 PMCID: PMC7350356 DOI: 10.3390/pathogens9060500] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/21/2020] [Accepted: 06/21/2020] [Indexed: 12/19/2022] Open
Abstract
Classical swine fever (CSF) is an economically significant, multi-systemic, highly contagious viral disease of swine world over. The disease is notifiable to the World Organization for Animal Health (OIE) due to its enormous consequences on porcine health and the pig industry. In India, the pig population is 9.06 million and contributes around 1.7% of the total livestock population. The pig industry is not well organized and is mostly concentrated in the eastern and northeastern states of the country (~40% of the country’s population). Since the first suspected CSF outbreak in India during 1944, a large number of outbreaks have been reported across the country, and CSF has acquired an endemic status. As of date, there is a scarcity of comprehensive information on CSF from India. Therefore, in this review, we undertook a systematic review to compile and evaluate the prevalence and genetic diversity of the CSF virus situation in the porcine population from India, targeting particular virus genes sequence analysis, published reports on prevalence, pathology, and updates on indigenous diagnostics and vaccines. The CSF virus (CSFV) is genetically diverse, and at least three phylogenetic groups are circulating throughout the world. In India, though genotype 1.1 predominates, recently published reports point toward increasing evidence of co-circulation of sub-genotype 2.2 followed by 2.1. Sequence identities and phylogenetic analysis of Indian CSFV reveal high genetic divergence among circulating strains. In the meta-analysis random-effects model, the estimated overall CSF prevalence was 35.4%, encompassing data from both antigen and antibody tests, and region-wise sub-group analysis indicated variable incidence from 25% in the southern to nearly 40% in the central zone, eastern, and northeastern regions. A country-wide immunization approach, along with other control measures, has been implemented to reduce the disease incidence and eliminate the virus in time to come.
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Affiliation(s)
- Yashpal Singh Malik
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243001, India; (S.B.); (S.S.); (M.I.A.)
- Correspondence: (Y.S.M.); (K.D.); Tel.: +91-58-1230-2777 (Y.S.M. & K.D.); Fax: +91-58-1230-1757 (Y.S.M. & K.D.)
| | - Sudipta Bhat
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243001, India; (S.B.); (S.S.); (M.I.A.)
| | - O. R. Vinodh Kumar
- Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India;
| | - Ajay Kumar Yadav
- Animal Health, ICAR-National Research Centre on Pig (ICAR-NRCP), Guwahati, Assam 781015, India;
| | - Shubhankar Sircar
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243001, India; (S.B.); (S.S.); (M.I.A.)
| | - Mohd Ikram Ansari
- Division of Biological Standardization, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243001, India; (S.B.); (S.S.); (M.I.A.)
| | - Dilip Kumar Sarma
- Department of Veterinary Microbiology, Assam Agricultural University, Khanapara, Guwahati 781022, India;
| | - Tridib Kumar Rajkhowa
- College of Veterinary Sciences & Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram 796001, India;
| | - Souvik Ghosh
- Department of Biomedical Sciences, One Health Center for Zoonoses and Tropical Veterinary Medicine, Basseterre, St. Kitts PO Box 334, West Indies;
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, Uttar Pradesh 243122, India
- Correspondence: (Y.S.M.); (K.D.); Tel.: +91-58-1230-2777 (Y.S.M. & K.D.); Fax: +91-58-1230-1757 (Y.S.M. & K.D.)
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Tomar S, Mahajan S, Kumar R. Advances in structure-assisted antiviral discovery for animal viral diseases. GENOMICS AND BIOTECHNOLOGICAL ADVANCES IN VETERINARY, POULTRY, AND FISHERIES 2020. [PMCID: PMC7149589 DOI: 10.1016/b978-0-12-816352-8.00019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Genome Sequence of Classical Swine Fever Virus NIVEDI-165, Subtype 1.1, a Field Virus Strain Isolated from the Southern Part of India. Microbiol Resour Announc 2019; 8:8/21/e00295-19. [PMID: 31123014 PMCID: PMC6533384 DOI: 10.1128/mra.00295-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The whole-genome sequence of an Indian field isolate of classical swine fever virus, NIVEDI-165, was found to be subtype 1.1, and it showed 89 to 99% amino acid identity and 84 to 99% nucleotide identity with four and five Indian classical swine fever virus (CSFV) isolates, respectively. To the best of our knowledge, this is the first report on a full-genome sequence of CSFV from South India.
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Classical swine fever in India: current status and future perspective. Trop Anim Health Prod 2018; 50:1181-1191. [DOI: 10.1007/s11250-018-1608-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 04/23/2018] [Indexed: 10/17/2022]
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Singh VK, Rajak KK. Phylogenetic analysis of Classical swine fever virus from archival formalin fixed clinical tissues reveals vietnamese origin of the isolates. Virusdisease 2017; 28:121-125. [PMID: 28466064 DOI: 10.1007/s13337-017-0364-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/02/2017] [Indexed: 10/20/2022] Open
Abstract
Detection of Classical swine fever virus (CSFV) nucleic acid in archival formalin fixed tissue samples and their use for phylogenetic analysis was investigated. Ten samples were examined for the presence of CSFV nucleic acid by reverse transcriptase polymerase chain reaction (RT-PCR) amplification of 5'UTR and E2 gene. RT-PCR was found positive for 5'UTR fragment in eight samples while only one tissue samples showed amplification for E2 gene target fragment. For molecular epidemiology of the disease, 5'UTR PCR product of sample from Darbhanga (Bihar), was cloned and sequenced. The sequence was compared with the sequences available in database. The phylogenetic analysis reveals that the isolate belongs to subgroup 2.2 sharing 98.7% nucleotide identities with Vietnamese isolate (CaTh05-1, AB252170), indicating towards the possible origin of genogroup 2.2 CSFV isolates involved in the outbreak from Vietnam. From the study, it can be concluded that the tissue samples collected and stored in buffer formalin for years can be used to detect CSFV nucleic acid. Results are also suggestive of that the 5'UTR region of genome is more suitable target for RT-PCR based detection of CSFV in archival formalin fixed specimens. The study also indicates the potential of archival formalin fixed tissues for molecular epidemiology and genotyping of the CSF virus.
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Affiliation(s)
- Vinod Kumar Singh
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, UKD 263138 India.,Department of Veterinary Microbiology, College of Veterinary Science and Animal Husbandry, DUVASU, Mathura, UP 281001 India
| | - Kaushal Kishore Rajak
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, UKD 263138 India
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Changing pattern of classical swine fever virus genogroup from classical 1.1 to emerging 2.2 in India. Virusdisease 2017; 28:174-181. [PMID: 28770243 DOI: 10.1007/s13337-017-0368-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/18/2017] [Indexed: 11/27/2022] Open
Abstract
Classical swine fever (CSF) is one of the most important viral diseases of pigs with high economic impact. The causative agent, Classical swine fever virus (CSFV) is a member of genus Pestivirus in family Flaviviredae and is structurally and antigenically related to other members of the genus. The identification of virus strains and genotypes can conveniently be used to trace the origin and patterns of virus spread, which contribut substantially in control strategies. In the present study, we have partially sequenced and analysed the 5' untranslated region (UTR) and E2 regions of CSFV clinical samples (n = 24) from various parts of the country. Among the samples, the sequence alignment of 5'UTR and E2 regions revealed 96.7-100 and 94.7-100% identities at the nucleotide level, respectively. The samples under study showed the close resemblance to the other CSFV isolates reported in India. In phylogenetic analysis, all the field samples were clustered in subgroup 2.2. Thus the study presents a further phylogenetic evidence for the emergence of subgroup 2.2 CSFV replacing the predominant subgroup 1.1 viruses in India. As the information regarding the molecular epidemiology the CSFV in india is very little, generation of such epidemiological data is warranted to help in comprehensing the nationwide disease control program to sustain the growth of pig industry in India.
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Kumar R, Rajak KK, Chandra T, Muthuchelvan D, Saxena A, Chaudhary D, Kumar A, Pandey AB. Sequence-based comparative study of classical swine fever virus genogroup 2.2 isolate with pestivirus reference strains. Vet World 2016; 8:1059-62. [PMID: 27047198 PMCID: PMC4774772 DOI: 10.14202/vetworld.2015.1059-1062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/31/2015] [Accepted: 08/08/2015] [Indexed: 12/03/2022] Open
Abstract
Aim: This study was undertaken with the aim to compare and establish the genetic relatedness between classical swine fever virus (CSFV) genogroup 2.2 isolate and pestivirus reference strains. Materials and Methods: The available complete genome sequences of CSFV/IND/UK/LAL-290 strain and other pestivirus reference strains were retrieved from GenBank. The complete genome sequence, complete open reading frame, 5’ and 3’ non-coding region (NCR) sequences were analyzed and compared with reference pestiviruses strains. Clustal W model in MegAlign program of Lasergene 6.0 software was used for analysis of genetic heterogeneity. Phylogenetic analysis was carried out using MEGA 6.06 software package. Results: The complete genome sequence alignment of CSFV/IND/UK/LAL-290 isolate and reference pestivirus strains showed 58.9-72% identities at the nucleotide level and 50.3-76.9% at amino acid level. Sequence homology of 5’ and 3’ NCRs was found to be 64.1-82.3% and 22.9-71.4%, respectively. In phylogenetic analysis, overall tree topology was found similar irrespective of sequences used in this study; however, whole genome phylogeny of pestivirus formed two main clusters, which further distinguished into the monophyletic clade of each pestivirus species. CSFV/IND/UK/LAL-290 isolate placed with the CSFV Eystrup strain in the same clade with close proximity to border disease virus and Aydin strains. Conclusion: CSFV/IND/UK/LAL-290 exhibited the analogous genomic organization to those of all reference pestivirus strains. Based on sequence identity and phylogenetic analysis, the isolate showed close homology to Aydin/04-TR virus and distantly related to Bungowannah virus.
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Affiliation(s)
- Ravi Kumar
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India; Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Kaushal Kishor Rajak
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
| | - Tribhuwan Chandra
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Dhanavelu Muthuchelvan
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
| | - Arpit Saxena
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
| | - Dheeraj Chaudhary
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
| | - Ajay Kumar
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
| | - Awadh Bihari Pandey
- Division of Virology, Indian Veterinary Research Institute, Mukteswar, Nainital, Uttarakhand, India
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Homologous recombination in pestiviruses: Identification of three putative novel events between different subtypes/genogroups. INFECTION GENETICS AND EVOLUTION 2015; 30:219-224. [DOI: 10.1016/j.meegid.2014.12.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 12/17/2014] [Accepted: 12/26/2014] [Indexed: 11/20/2022]
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Complete genome sequence of an Indian field isolate of classical Swine Fever virus belonging to subgenotype 1.1. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00886-14. [PMID: 25278522 PMCID: PMC4183866 DOI: 10.1128/genomea.00886-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the complete genome sequence of an Indian field isolate of classical swine fever virus (CSFV) belonging to predominant subgenotype 1.1 prevalent in India. This report will help in understanding the molecular diversity of CSFV strains circulating worldwide and to select and develop a suitable vaccine candidate for classical swine fever (CSF) control in India.
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