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Shueb M, Prasad SK, Suresh KP, Indrabalan UB, Beelagi MS, Shivamallu C, Silina E, Stupin V, Manturova N, Kollur SP, Shome BR, Achar RR, Patil SS. The first study on analysis of the codon usage bias and evolutionary analysis of the glycoprotein envelope E2 gene of seven Pestiviruses. Vet World 2022; 15:1857-1868. [PMID: 36185504 PMCID: PMC9394142 DOI: 10.14202/vetworld.2022.1857-1868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
Background and Aim: Pestivirus, a genus of the Flaviviridae family, comprises viruses that affect bovines, sheep, and pigs. Symptoms, including hemorrhagic syndromes, abortion, respiratory complications, and deadly mucosal diseases, are produced in infected animals, which cause huge economic losses to the farmers. Bovine viral diarrhea virus-1, bovine viral diarrhea virus-2, classical swine fever virus, border disease virus, Bungowannah, Hobi-like, and atypical porcine pestivirus belonging to the Pestivirus genus were selected for the study. This study aimed to estimate the codon usage bias and the rate of evolution using the glycoprotein E2 gene. Furthermore, codon usage bias analysis was performed using publicly available nucleotide sequences of the E2 gene of all seven Pestiviruses. These nucleotide sequences might elucidate the disease epidemiology and facilitate the development of designing better vaccines. Materials and Methods: Coding sequences of the E2 gene of Pestiviruses A (n = 89), B (n = 60), C (n = 75), D (n = 10), F (n = 07), H (n = 52), and K (n = 85) were included in this study. They were analyzed using different methods to estimate the codon usage bias and evolution. In addition, the maximum likelihood and Bayesian methodologies were employed to analyze a molecular dataset of seven Pestiviruses using a complete E2 gene region. Results: The combined analysis of codon usage bias and evolutionary rate analysis revealed that the Pestiviruses A, B, C, D, F, H, and K have a codon usage bias in which mutation and natural selection have played vital roles. Furthermore, while the effective number of codons values revealed a moderate bias, neutrality plots indicated the natural selection in A, B, F, and HPestiviruses and mutational pressure in C, D, and KPestiviruses. The correspondence analysis revealed that axis-1 significantly contributes to the synonymous codon usage pattern. In this study, the evolutionary rate of PestivirusesB, H, and K was very high. The most recent common ancestors of all Pestivirus lineages are 1997, 1975, 1946, 1990, 2004, 1990, and 1990 for Pestiviruses A, B, C, D, F, H, and K, respectively. This study confirms that both mutational pressure and natural selection have played a significant role in codon usage bias and evolutionary studies. Conclusion: This study provides insight into the codon usage bias and evolutionary lineages of pestiviruses. It is arguably the first report of such kind. The information provided by the study can be further used to elucidate the respective host adaptation strategies of the viruses. In turn, this information helps study the epidemiology and control methods of pestiviruses.
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Affiliation(s)
- Mohammad Shueb
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Shashanka K. Prasad
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | | | - Uma Bharathi Indrabalan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Mallikarjun S. Beelagi
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Chandan Shivamallu
- Department of Biotechnology and Bioinformatics, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, Karnataka, India
| | - Ekaterina Silina
- Department of Surgery, Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Victor Stupin
- Department of Surgery, Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Natalia Manturova
- Department of Surgery, Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | | | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Raghu Ram Achar
- Division of Biochemistry, School of Life Sciences, JSS Academy of Higher Education and Research, Mysuru, India
| | - Sharanagouda S. Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
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Patil SS, Suresh KP, Hemadri D, Hiremath J, Sridevi R, Krishnamoorthy P, Bhatia S, Roy P. Spatial seroprevalence of classical swine fever in India. Trop Anim Health Prod 2021; 53:389. [PMID: 34219195 DOI: 10.1007/s11250-021-02829-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 06/18/2021] [Indexed: 11/27/2022]
Abstract
Classical swine fever (CSF) is a highly contagious dreadful disease of pigs leading to 100% mortality in acute form in susceptible population thereby causing huge economic loss to pig farmers. This study was undertaken to assess the seroprevalence of CSF at national level. A two-stage random sampling methodology was adopted that included 271 villages from 115 districts of India. A total of 5848 pig serum samples from twenty-five states and one Union Territory of India were collected during 2018-2019. A percent positivity of 38.52 was found at national level. Puducherry and Sikkim showed the highest and lowest percent positivity respectively. Pigs from the west zone showed the highest seroprevalence of 55.83% and those from the south zone showed the lowest of 30.25%. Adult pigs in the north and east zones showed highest percent positivity of 81.8, whereas pigs of more than 3 years of age showed highest percent positivity of 54.9, 75 and 62.5 in the north east, west and central zones respectively. Young ones showed percent positivity of 41.5 in the south zone. Higher rainfall (> 3 mm/day) and lower temperature (< 26 °C) favoured the existence of disease in the north east region combined with high density of pig population. Amidst no fool proof alert system, seroprevalence is the best method to assess the status of CSF in herd/population that provides the policymakers to plan for control of disease.
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Affiliation(s)
- Sharanagouda S Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India.
| | | | - Divakar Hemadri
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Jagadish Hiremath
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Rajangam Sridevi
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Paramanadham Krishnamoorthy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
| | - Sandeep Bhatia
- ICAR-National Institute of High Security Animal Diseases, Bhopal, MP, India
| | - Parimal Roy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, India
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Patil SS, Indrabalan UB, Suresh KP, Shome BR. Analysis of codon usage bias of classical swine fever virus. Vet World 2021; 14:1450-1458. [PMID: 34316191 PMCID: PMC8304411 DOI: 10.14202/vetworld.2021.1450-1458] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/21/2021] [Indexed: 11/22/2022] Open
Abstract
Background and Aim: Classical swine fever (CSF), caused by CSF virus (CSFV), is a highly contagious disease in pigs causing 100% mortality in susceptible adult pigs and piglets. High mortality rate in pigs causes huge economic loss to pig farmers. CSFV has a positive-sense RNA genome of 12.3 kb in length flanked by untranslated regions at 5’ and 3’ end. The genome codes for a large polyprotein of 3900 amino acids coding for 11 viral proteins. The 1300 codons in the polyprotein are coded by different combinations of three nucleotides which help the infectious agent to evolve itself and adapt to the host environment. This study performed and employed various methods/techniques to estimate the changes occurring in the process of CSFV evolution by analyzing the codon usage pattern. Materials and Methods: The evolution of viruses is widely studied by analyzing their nucleotides and coding regions/codons using various methods. A total of 115 complete coding regions of CSFVs including one complete genome from our laboratory (MH734359) were included in this study and analysis was carried out using various methods in estimating codon usage bias and evolution. This study elaborates on the factors that influence the codon usage pattern. Results: The effective number of codons (ENC) and relative synonymous codon usage showed the presence of codon usage bias. The mononucleotide (A) has a higher frequency compared to the other mononucleotides (G, C, and T). The dinucleotides CG and CC are underrepresented and overrepresented. The codons CGT was underrepresented and AGG was overrepresented. The codon adaptation index value of 0.71 was obtained indicating that there is a similarity in the codon usage bias. The principal component analysis, ENC-plot, Neutrality plot, and Parity Rule 2 plot produced in this article indicate that the CSFV is influenced by the codon usage bias. The mutational pressure and natural selection are the important factors that influence the codon usage bias. Conclusion: The study provides useful information on the codon usage analysis of CSFV and may be utilized to understand the host adaptation to virus environment and its evolution. Further, such findings help in new gene discovery, design of primers/probes, design of transgenes, determination of the origin of species, prediction of gene expression level, and gene function of CSFV. To the best of our knowledge, this is the first study on codon usage bias involving such a large number of complete CSFVs including one sequence of CSFV from India.
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Affiliation(s)
- Sharanagouda S Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Uma Bharathi Indrabalan
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | | | - Bibek Ranjan Shome
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
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Investigation of congenital tremor associated with Classical swine fever virus genotype 2.2 in an organized pig farm in north-eastern India. Virusdisease 2021; 32:173-182. [PMID: 33748346 PMCID: PMC7965332 DOI: 10.1007/s13337-021-00678-3] [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: 12/22/2020] [Accepted: 03/02/2021] [Indexed: 12/04/2022] Open
Abstract
The present study describes an outbreak of Classical swine fever (CSF) in an organized pig farm followed by an episode of CSF virus (CSFV) associated congenital tremors in piglets. The outbreak was recorded in a newly procured herd of Hampshire pigs housed adjacent to the existing pigs of the farm. The recorded CSF outbreak caused a mortality of 100% in the newly procured and 54.28% in the existing herd. As the disease subsides, the clinically recovered boars were served naturally with Tamworth gilts. Though, the sows farrowed on usual gestation period, litters born to each sow showed congenital tremors and eventually died within 24 h of birth. Necropsy analysis of affected piglets was indicative of CSFV infection and was further confirmed using RT-PCR signifying a transplacental infection. The CSFV strains from the initial outbreak and post outbreak episode of congenital tremors were successfully isolated in PK-15 cells and detected in indirect FAT and RT-PCR. Phylogenetic analysis based on E2 gene and 5′NTR of CSFV grouped the isolates within the genotype 2.2 and revealed close resemblance with previously reported Indian isolates of CSFV genotype 2.2 origin. To the best of our knowledge, this is the first report of CSFV induced congenital form reported from India under natural conditions.
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Barman NN, Patil SS, Kurli R, Deka P, Bora DP, Deka G, Ranjitha KM, Shivaranjini C, Roy P, Suresh KP. Meta-analysis of the prevalence of livestock diseases in North Eastern Region of India. Vet World 2020; 13:80-91. [PMID: 32158155 PMCID: PMC7020116 DOI: 10.14202/vetworld.2020.80-91] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/22/2019] [Indexed: 11/16/2022] Open
Abstract
Aim: The study aimed to determine the overall prevalence of livestock diseases in North Eastern Region (NER) of India, through a systematic review and meta-analysis of published data. Materials and Methods: The articles used for the study were retrieved from PubMed, J-Gate Plus, Indian Journals, and Google scholar, R open-source scripting software 3.4.3. Metafor, Meta. The Chi-square test was conducted to assess for the heterogeneity, forest plot (confidence interval [CI] plot) is a method utilized to present the results of meta-analysis, displaying effect estimate and their CIs for each study were used for searching and retrieval of livestock diseases prevalence data in India using a search strategy combining keywords and related database-specific subject terms from 2008 to 2017 in English only. Results: The prevalence of various livestock diseases are foot-and-mouth disease (21%), bluetongue (28%), brucellosis in bovine (17%), brucellosis in caprine (2%), brucellosis in porcine (18%), brucellosis in sheep and goat (3%), babesiosis (6%), theileriosis (26%), porcine reproductive and respiratory syndrome (1%), porcine cysticercosis (6%), classical swine fever (31%), Porcine circovirus (43%), and Peste des petits ruminants (15%). This information helps policymakers to take appropriate measures to reduce the disease burden. Conclusion: This study indicates that the overall prevalence of various livestock diseases in NER of India.
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Affiliation(s)
- Nagendra Nath Barman
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agriculture University, Guwahati, Assam, India
| | - Sharanagouda S Patil
- Department of Virology, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Rashmi Kurli
- Department of Spatial Epidemiology, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Pankaj Deka
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agriculture University, Guwahati, Assam, India
| | - Durlav Prasad Bora
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agriculture University, Guwahati, Assam, India
| | - Giti Deka
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agriculture University, Guwahati, Assam, India
| | - Kempanahalli M Ranjitha
- Department of Virology, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Channappagowda Shivaranjini
- Department of Virology, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Parimal Roy
- Director, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Kuralayanapalya P Suresh
- Department of Spatial Epidemiology, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
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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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PATIL SS, SURESH KP, SAHA SNEHA, HAMSAPRIYA S, BARMAN NN, ROY PARIMAL. Import risk model: A quantitative risk assessment of classical swine fever virus (CSFV) introduction into Arunachal Pradesh via importation of pigs from bordering countries. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v88i10.84144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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8
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Chakraborty AK, Mukherjee P, Karam A, Das S, Barkalita L, Puro K, Sanjukta R, Ghatak S, Sakuntala I, Laha RG, Borah P, Ngachan SV, Sharma I, Sen A. Evidence of BVDV in Pigs from North Eastern Part of India- Genetic Profiling and Characterisation. Open Virol J 2018; 12:110-120. [PMID: 30288199 PMCID: PMC6142659 DOI: 10.2174/1874357901812010110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Revised: 07/06/2018] [Accepted: 07/16/2018] [Indexed: 01/27/2023] Open
Abstract
Introduction: The work has been attempted to detect and genetically characterise the nature of Bovine Viral Diarrhea Virus (BVDV) isolates from the porcine population of the north east. Methods and Material: The samples have been collected over a two year period and are from areas where there is a mixed and integrated rearing of livestock in close proximity. The isolates were identified, cloned and sequenced using BVD specific genomic primers for two important domains viz., E-2 and 5’ UTR. Results: Porcine BVD Sequences were analysed phylogenetically. Divergence in 3 sequences is noted in the 5’ UTR region that are forming a clear outlier group while E-2 sequences are coming close to BVDV group but forming a separate cluster.
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Affiliation(s)
- Amit Kr Chakraborty
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India.,Department of Microbiology, Assam University, Silchar - 788011, India
| | - Priyanka Mukherjee
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India.,Department of Microbiology, Assam University, Silchar - 788011, India
| | - Amarjit Karam
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Samir Das
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Luit Barkalita
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam, India
| | - Kekungo Puro
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Rajkumari Sanjukta
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Ingudam Sakuntala
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Ram Gopal Laha
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Prabodh Borah
- Department of Biotechnology, C.V.Sc, AAU, Khanapara, Assam, India
| | - S V Ngachan
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
| | - Indu Sharma
- Department of Microbiology, Assam University, Silchar - 788011, India
| | - Arnab Sen
- Division of Animal Health, ICAR Research Complex for NEH, Barapani - 793103, India
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CHOORI P, PATIL SS, RATNAMMA D, APRAJAPATI, MUKARTAL SY, REDDY GBMANJUNATHA, SURESH KP, HEMADRI D, RAHMAN H. Seroprevalence of Classical Swine Fever in pigs of Karnataka and comparative diagnostic evaluation of antigen ELISA and reverse transcriptase -PCR. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2018. [DOI: 10.56093/ijans.v87i12.79743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Classical swine fever is highly contagious viral disease of swine causing huge economic losses to pig farmersand pig industry. The study was conducted in Karnataka to understand the current scenario of CSF in the state andto evaluate efficiency of diagnostic tests (antigen ELISA and RT-PCR) in detecting the disease. Serum sampleswere collected from 270 pigs from 13 districts of the state and were tested for the presence of CSF antibodies.Whole blood samples (151) from 14 outbreaks of CSF were collected for the comparative diagnosis of the diseaseusing Antigen ELISA and reverse transcriptase (RT)-PCR. A seroprevalence of 28.5% (77/270) was found in theserum samples collected form the whole Karnataka. The southern Karnataka had higher seroprevalence (47%) incomparison to northern Karnataka region where seroprevalence was 17%. It confirms endemicity of the disease insouthern region. Of 151 blood samples collected for comparative diagnosis, 61 samples were positive for CSF byRT-PCR and 39 by antigen ELISA, indicating the superiority of RT-PCR over antigen ELISA to detect CSFVinfection in earliest stages of infection.
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10
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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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Patil SS, Suresh KP, Saha S, Prajapati A, Hemadri D, Roy P. Meta-analysis of classical swine fever prevalence in pigs in India: A 5-year study. Vet World 2018; 11:297-303. [PMID: 29657420 PMCID: PMC5891843 DOI: 10.14202/vetworld.2018.297-303] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 01/18/2018] [Indexed: 11/24/2022] Open
Abstract
Aim: The aim of the study was to determine the overall prevalence of classical swine fever (CSF) in pigs in India, through a systematic review and meta-analysis of published data. Materials and Methods: Consortium for e-Resources in Agriculture, India, Google Scholar, PubMed, annual reports of All India Coordinated Research Project on Animal Disease Monitoring and Surveillance, and All India Animal Disease database of NIVEDI (NADRES) were used for searching and retrieval of CSF prevalence data (seroprevalence, virus antigen, and virus nucleic acid detection) in India using a search strategy combining keywords and related database-specific subject terms from January 2011 to December 2015 in English only. Results: A total of 22 data reports containing 6,158 samples size from 18 states of India were used for the quantitative synthesis, and overall 37% (95% confidence interval [CI]=0.24, 0.51) CSF prevalence in India was estimated. The data were classified into 4 different geographical zones of the country: 20% (95% CI=0.05, 0.55), 31% (95% CI=0.18, 0.47), 55% (95% CI=0.32, 0.76), and 34% (95% CI=0.14, 0.62). CSF prevalence was estimated in northern, eastern, western, and southern regions, respectively. Conclusion: This study indicates that overall prevalence of CSF in India is much lower than individual published reports.
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Affiliation(s)
- S S Patil
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
| | - K P Suresh
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
| | - S Saha
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
| | - A Prajapati
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
| | - D Hemadri
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
| | - P Roy
- Indian Council of Agricultural Research - National Institute of Veterinary Epidemiology and Disease Informatics (ICAR-NIVEDI), PBNO-6450, Yelahanka, Bengaluru, Karnataka, India
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Khatoon E, Barman NN, Deka M, Rajbongshi G, Baruah K, Deka N, Bora DP, Kumar S. Molecular characterization of classical swine fever virus isolates from India during 2012-14. Acta Trop 2017; 170:184-189. [PMID: 28279702 DOI: 10.1016/j.actatropica.2017.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 10/20/2022]
Abstract
Classical swine fever is a highly contagious and economically important viral disease of pigs. Outbreaks of classical swine fever virus (CSFV) were recorded in different places in the Kamrup district of Assam in India between the years 2012 and 2014. The nucleotide sequences of the 10 CSFV isolates were analyzed based on the partial nucleotide sequences of the E2, 5'NTR and NS5B genes. Phylogenetic analysis indicated the dominance of subgroup 2.2 along with 2.1 strains in the northeast part of India. Variation in the nucleotide sequences of E2, 5'NTR and 3'NS5B genes of CSFV allows tracking changes in the virus population over time. The study will provide epidemiological information useful for assessing CSFV circulating genogroups in India.
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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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Classical Swine Fever-An Updated Review. Viruses 2017; 9:v9040086. [PMID: 28430168 PMCID: PMC5408692 DOI: 10.3390/v9040086] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/11/2017] [Accepted: 04/13/2017] [Indexed: 01/03/2023] Open
Abstract
Classical swine fever (CSF) remains one of the most important transboundary viral diseases of swine worldwide. The causative agent is CSF virus, a small, enveloped RNA virus of the genus Pestivirus. Based on partial sequences, three genotypes can be distinguished that do not, however, directly correlate with virulence. Depending on both virus and host factors, a wide range of clinical syndromes can be observed and thus, laboratory confirmation is mandatory. To this means, both direct and indirect methods are utilized with an increasing degree of commercialization. Both infections in domestic pigs and wild boar are of great relevance; and wild boars are a reservoir host transmitting the virus sporadically also to pig farms. Control strategies for epidemic outbreaks in free countries are mainly based on classical intervention measures; i.e., quarantine and strict culling of affected herds. In these countries, vaccination is only an emergency option. However, live vaccines are used for controlling the disease in endemically infected regions in Asia, Eastern Europe, the Americas, and some African countries. Here, we will provide a concise, updated review on virus properties, clinical signs and pathology, epidemiology, pathogenesis and immune responses, diagnosis and vaccination possibilities.
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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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Abstract
Classical swine fever is a highly contagious disease that affects domestic and wild pigs worldwide. The causative agent of the disease is Classical swine fever virus (CSFV), which belongs to the genus Pestivirus within the family Flaviviridae. On the genome level, CSFV can be divided into three genotypes with three to four sub-genotypes. Those genotypes can be assigned to distinct geographical regions. Knowledge about CSFV diversity and distribution is important for the understanding of disease dynamics and evolution, and can thus help to design optimized control strategies. For this reason, the geographical pattern of CSFV diversity and distribution are outlined in the presented review. Moreover, current knowledge with regard to genetic virulence markers or determinants and the role of the quasispecies composition is discussed.
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Bhaskar N, Ravishankar C, Rajasekhar R, Sumod K, Sumithra TG, John K, Mini M, Ravindran R, Shaji S, Aishwarya J. Molecular typing and phylogenetic analysis of classical swine fever virus isolates from Kerala, India. Virusdisease 2015; 26:260-6. [PMID: 26645036 PMCID: PMC4663717 DOI: 10.1007/s13337-015-0271-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022] Open
Abstract
Classical swine fever (CSF) is an economically important disease of pigs caused by CSF virus (CSFV) belonging to the genus Pestivirus within the family Flaviviridae. The disease is endemic in many countries including India. A comprehensive study was carried out to assess the type of CSFV circulating in the South Indian state of Kerala. During the period 2013-2014, clinical samples were collected from 19 suspected CSF outbreaks of domestic pigs in different districts of Kerala. The samples were tested using nested reverse transcription PCR (RT-PCR) targeting the E2 gene and RT-PCR for 5'UTR of the virus. Partial 5' UTR and E2 gene regions of six CSFV isolates were sequenced. Phylogenetic analysis revealed that all the CSFV isolates belonged to subgroup 2.2. The isolates showed close resemblance to the other CSFV isolates circulating in India. It was also observed that the CSFV viruses from Kannur district were distinct from those circulating in the other districts as evidenced by their divergence from other Kerala isolates in the phylogenetic tree. Close relationship was seen to the CSFV isolates from South East Asian countries.
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Affiliation(s)
- Nimisha Bhaskar
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - Chintu Ravishankar
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - R. Rajasekhar
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - K. Sumod
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - T. G. Sumithra
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, Kerala 680651 India
| | - Koshy John
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - M. Mini
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, Kerala 680651 India
| | - Reghu Ravindran
- />Department of Veterinary Parasitology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - Shiju Shaji
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
| | - J. Aishwarya
- />Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Pookode, Lakkidi P.O., Wayanad, Kerala 673576 India
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Genetic clustering of recent classical swine fever virus isolates from Karnataka, India revealed the emergence of subtype 2.2 replacing subtype 1.1. Virusdisease 2015; 26:170-9. [PMID: 26396984 DOI: 10.1007/s13337-015-0273-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/03/2015] [Indexed: 02/02/2023] Open
Abstract
The phylogenetic analysis of 11 CSFV isolates from Karnataka, India obtained during the year 2012-13 was undertaken to obtain the most reliable genetic typing of the CSFV isolates based on E2, NS5B and 5'UTR genomic regions. The study indicated that all the 11 CSFV isolates belonged to subgroup 2.2. The most reliable classification was obtained with sequence data from the NS5B region which separated all the isolates based on the history of outbreak and geographic origin. Analysis of full length E2 amino acid sequences revealed different genetic makeup of Indian 2.2 isolates compared to 2.2 isolates from different countries. The group 2.2 viruses are gradually spreading as confirmed by frequent detection/ isolation of group 2.2 viruses in the recent years and replacing the subgroup 1.1 viruses, which were hitherto predominantly involved in CSF outbreaks in India.
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Choori P, Patil SS, Rathnamma D, Sharada R, Chandranaik BM, Isloor S, Reddy GBM, Geetha S, Rahman H. Prevalence of classical swine fever in Karnataka, India. Vet World 2015; 8:541-4. [PMID: 27047131 PMCID: PMC4774808 DOI: 10.14202/vetworld.2015.541-544] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 03/06/2015] [Accepted: 03/14/2015] [Indexed: 11/16/2022] Open
Abstract
Aim: The present study was conducted to know the current scenario of classical swine fever (CSF) in Bengaluru Urban, Bengaluru Rural, Chikkaballapur, Madikeri, Mandya, Bagalkot, Gadag, Yadgir, Koppal, and Bidar districts of Karnataka with the using of both antigen and antibody ELISA. Materials and Methods: We collected 218 sera and 121 blood samples from pigs from 10 different districts of Karnataka. Screening of sera for CSF IgG antibody and whole blood for CSF virus antigen were carried out using the CSF virus (CSFV) antibody and antigen ELISA kits, respectively. Results: The mean seroprevalence was 41% (89/218) and prevalence of CSFV antigen in blood samples was 32% (39/121) for the 10 districts of Karnataka. Seroprevalence of 61%, 29%, 20%, and 21%; and antigen prevalence of 40%, 50%, 13%, and 12% were recorded for Bangalore, Mysore, Belgaum, and Gulbarga divisions of Karnataka, respectively. Conclusions: The study revealed an alarmingly high prevalence of CSF, both for the antigen (32%) and antibody (41%) in Karnataka. Southern Karnataka has the highest seroprevalence (61% in Bangalore and 29% in Mysore divisions), which confirms the endemicity of the disease in that region. This could be attributed to the intensive pig farming practices in the region as compared to Northern Karnataka (Seroprevalence of 20% in Belgaum and 21% in Gulbarga divisions), where the commercial pig farming is still in infantile stages.
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Affiliation(s)
- Prakash Choori
- Department of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bengaluru, Karnataka, India
| | - S S Patil
- Department of Virology, National Institute of Veterinary Epidemiology and Disease Informatics (Formerly PD_ADMAS), Hebbal, Bengaluru, Karnataka, India
| | - D Rathnamma
- Department of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bengaluru, Karnataka, India
| | - R Sharada
- Department of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bengaluru, Karnataka, India
| | - B M Chandranaik
- Department of Microbiology, Institute of Animal Health and Veterinary Biologicals, Hebbal, Bengaluru, Karnataka, India
| | - S Isloor
- Department of Veterinary Microbiology, Veterinary College, KVAFSU, Hebbal, Bengaluru, Karnataka, India
| | - G B Manjunath Reddy
- Department of Virology, National Institute of Veterinary Epidemiology and Disease Informatics (Formerly PD_ADMAS), Hebbal, Bengaluru, Karnataka, India
| | - S Geetha
- Department of Virology, National Institute of Veterinary Epidemiology and Disease Informatics (Formerly PD_ADMAS), Hebbal, Bengaluru, Karnataka, India
| | - H Rahman
- Department of Virology, National Institute of Veterinary Epidemiology and Disease Informatics (Formerly PD_ADMAS), Hebbal, Bengaluru, Karnataka, India
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Abstract
Classical swine fever (CSF) is one of the most devastating epizootic diseases of pigs, causing high morbidity and mortality worldwide. The diversity of clinical signs and similarity in disease manifestations to other diseases make CSF difficult to diagnose with certainty. The disease is further complicated by the presence of a number of different strains belonging to three phylogenetic groups. Advanced diagnostic techniques allow detection of antigens or antibodies in clinical samples, leading to implementation of proper and effective control programs. Polymerase chain reaction (PCR)-based methods, including portable real-time PCR, provide diagnosis in a few hours with precision and accuracy, even at the point of care. The disease is controlled by following a stamping out policy in countries where vaccination is not practiced, whereas immunization with live attenuated vaccines containing the 'C' strain is effectively used to control the disease in endemic countries. To overcome the problem of differentiation of infected from vaccinated animals, different types of marker vaccines, with variable degrees of efficacy, along with companion diagnostic assays have been developed and may be useful in controlling and even eradicating the disease in the foreseeable future. The present review aims to provide an overview and status of CSF as a whole with special reference to swine husbandry in India.
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Kwon T, Yoon SH, Kim KW, Caetano-Anolles K, Cho S, Kim H. Time-calibrated phylogenomics of the classical swine fever viruses: genome-wide bayesian coalescent approach. PLoS One 2015; 10:e0121578. [PMID: 25815768 PMCID: PMC4376735 DOI: 10.1371/journal.pone.0121578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 02/13/2015] [Indexed: 01/03/2023] Open
Abstract
The phylogeny of classical swine fever virus (CSFV), the causative agent of classical swine fever (CSF), has been investigated extensively. However, no evolutionary research has been performed using the whole CSFV genome. In this study, we used 37 published genome sequences to investigate the time-calibrated phylogenomics of CSFV. In phylogenomic trees based on Bayesian inference (BI) and Maximum likelihood (ML), the 37 isolates were categorized into five genetic types (1.1, 1.2, 2.1, 2.3, and 3.4). Subgenotype 1.1 is divided into 3 groups and 1 unclassified isolate, 2.1 into 4 groups, 2.3 into 2 groups and 1 unclassified isolate, and subgenotype 1.2 and 3.4 consisted of one isolate each. We did not observe an apparent temporal or geographical relationship between isolates. Of the 14 genomic regions, NS4B showed the most powerful phylogenetic signal. Results of this evolutionary study using Bayesian coalescent approach indicate that CSFV has evolved at a rate of 13×.010-4 substitutions per site per year. The most recent common ancestor of CSFV appeared 2770.2 years ago, which was about 8000 years after pig domestication. The effective population size of CSFV underwent a slow increase until the 1950s, after which it has remained constant.
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Affiliation(s)
- Taehyung Kwon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sook Hee Yoon
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Kyu-Won Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 151-747, Republic of Korea
| | - Kelsey Caetano-Anolles
- Department of Animal Sciences, University of Illinois, Urbana, IL, 61801, United States of America
| | - Seoae Cho
- C&K Genomics Inc. 514 Main Bldg., Seoul National University Research Park, San 4-2 Boncheon-dong, Gwanak-gu, Seoul, 151-919, Republic of Korea
| | - Heebal Kim
- Department of Agricultural Biotechnology and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
- * E-mail:
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Malswamkima D, Rajkhowa TK, Chandra R, Dutta TK. Pathology and molecular diagnosis of classical swine fever in Mizoram. Vet World 2015; 8:76-81. [PMID: 27047001 PMCID: PMC4777816 DOI: 10.14202/vetworld.2015.76-81] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/05/2014] [Accepted: 12/14/2014] [Indexed: 11/16/2022] Open
Abstract
AIM Clinical histopathological and molecular diagnosis of classical swine fever disease in pigs of Mizoram. MATERIALS AND METHODS Totally, 31 clinically suspected pigs from 6 districts of Mizoram were examined, and clinical symptoms were recorded. Detailed post mortem examination of all the 31 dead animals was conducted, and gross changes were recorded. Tissue samples were collected for histopathological examination and molecular diagnosis. The collected tissues (tonsil, lymph nodes, spleen) were also processed for RNA extraction. Reverse transcription polymerase chain reaction (RT-PCR) was performed to detect the specific gene fragments of classical swine fever virus (CSFV). RESULTS Clinical examination of all the 31 suspected pigs revealed typical clinical signs of CSF. All the animals also showed typical gross and microscopic lesions of CSF. RT-PCR on tissue samples amplified the 421bp, 449bp and 735bp region of 5´NCR, non-structural protein 5B and E(rns) gene regions of CSFV, respectively. Nested PCR for internal region of E2 gene also amplified the expected product of 271bp using PCR product of whole E2 region as template DNA. CONCLUSION CSF is highly endemic disease in Mizoram. The viral strains circulating in this region are highly virulent. The disease can be diagnosed specifically using RT-PCR.
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Affiliation(s)
- David Malswamkima
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - T K Rajkhowa
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Rajesh Chandra
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - T K Dutta
- Department of Veterinary Pathology, College of Veterinary Sciences and Animal Husbandry, Central Agricultural University, Selesih, Aizawl, Mizoram, India
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Roychoudhury P, Sarma DK, Rajkhowa S, Munir M, Kuchipudi SV. Predominance of genotype 1.1 and emergence of genotype 2.2 classical swine fever viruses in north-eastern region of India. Transbound Emerg Dis 2014; 61 Suppl 1:69-77. [PMID: 25135466 DOI: 10.1111/tbed.12263] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF) is a highly contagious and the most important disease of pigs worldwide.CSF is enzootic in pig herds in India and continues to cause huge economic losses to pig farmers. Nearly 40% of the total pig population of India is present in the north-eastern (NE) states where pig husbandry plays an important role in the socio-economic development. Pigs reared in the backyards are the only source of livelihood for a majority of poor tribal population in the region. Hardly any CSF vaccination is currently being undertaken in the unorganized pig farming in the NE region due to economic reasons and vaccine unavailability. A thorough understanding of the current epidemiological status of CSF is essential for the effective control of the disease in the NE region. Hence, we carried out molecular characterization of CSFV isolates from field outbreaks during 2011-2012 in the entire north-eastern region of India to establish the genetic groups of prevalent CSF viruses in the region. A total of 17 CSFV isolates obtained from different parts of the NE region were characterized by comparing the sequences of three partial genomic regions of the virus, that is 150 nt of 5' UTR, 190 nt of E2 and 409 nt of NS5B. Of the 17 CSFV isolates, 15 isolates belonged to 1.1 (88.2%) and two isolates (11.8%) belonged to 2.2 subgenogroup. The genogroup 2.2 CSFV were associated with outbreaks in Arunachal Pradesh that shares international borders with Bhutan, Myanmar and China. Genogroup 2.2 CSFV isolated in the present study shared high level of sequence similarity with 2.2 viruses form China, raising the possibility of virus incursion from this region. In summary, we found a continued predominance of 1.1 subgroup and an emergence of 2.2 subgroup CSFV in NE region of India.
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Affiliation(s)
- P Roychoudhury
- Department of Microbiology, College of Veterinary Science, Assam Agricultural University, Guwahati, Assam, India
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Rajkhowa TK, Hauhnar L, Lalrohlua I, Mohanarao G J. Emergence of 2.1. subgenotype of classical swine fever virus in pig population of India in 2011. Vet Q 2014; 34:224-8. [PMID: 25365116 DOI: 10.1080/01652176.2014.973122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND Limited studies are available on molecular epidemiology of classical swine fever virus (CSFV) in India and are restricted to domestic pigs. These studies show the presence of 1.1. genotype. HYPOTHESIS/OBJECTIVES The aim of the present study was to subgenotype four CSFV isolates, two each from the outbreaks of CSF in wild (Sus scrofa) and domestic pigs of Mizoram state, India, in 2011. ANIMALS AND METHODS CSFV isolates were subjected to nucleotide sequencing in E2 and NS5B genomic regions. Phylogenetic analysis of the isolates in both genomic regions was carried out with 39 Indian isolates (4 isolates from the present study of Mizoram state and 35 isolates from the other states of India) and 57 reference sequences retrieved from the GenBank database. Two of the 39 isolates from India were collected from wild boar and were subgenotyped as 2.1. Out of 37 isolates from domestic pigs, only two were subgenotyped as 2.1. RESULTS The analysis revealed the emergence of 2.1. subgenotype of CSFV in both wild and domestic pigs in India. CONCLUSIONS AND CLINICAL IMPORTANCE The isolates from domestic pigs of Mizoram state (CSF/MZ/KOL/73 and CSF/MZ/AIZ/115) were grouped in genotype 1 and subgenotype 1.1., thus confirming that the source of CSF outbreaks in domesticated pigs in Mizoram was not from wild pigs. The current study forms an essential step for better understanding of the epidemiology of 2.1 subgroup as well as the movement and spread of the disease in India.
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Affiliation(s)
- T K Rajkhowa
- a Department of Veterinary Pathology , College of Veterinary Sciences & Animal Husbandry, Central Agricultural University , Selesih , Aizawl , Mizoram , India
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Whole-genome sequence of a classical Swine Fever virus isolated from the uttarakhand state of India. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00371-14. [PMID: 24812219 PMCID: PMC4014687 DOI: 10.1128/genomea.00371-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We report the first complete genome sequence of a classical swine fever (CSF) virus of subgenotype 2.2. The virus (CSFV/IND/UK/LAL-290) was isolated from the Uttarakhand state of India from a backyard pig suspected of having CSF. This genome sequence will give useful insight for future molecular epidemiological studies and the development of an effective vaccine in India.
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Ahuja A, Sen A, Yogisharadhya R, Rajak KK, Shivachandra SB. Prokaryotic expression and purification of highly soluble partial glycoprotein erns of Indian strain of classical Swine Fever virus. INDIAN JOURNAL OF VIROLOGY : AN OFFICIAL ORGAN OF INDIAN VIROLOGICAL SOCIETY 2012; 23:397-401. [PMID: 24293833 DOI: 10.1007/s13337-012-0110-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 08/29/2012] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF) or hog cholera, caused by a positive stranded RNA virus belonging to the genus Pestivirus of the Flaviviridae family, is highly contagious and fatal disease of pigs. We report the novel design of construct for production of highly soluble glycoprotein Erns fragment using prokaryotic expression system. A truncated fragment of the Erns gene (coding for aa 109-170) denoted as 'Erns-Ag' was subcloned and expressed as hexa-histidine tag fusion on both terminus of protein in Escherichia coli. The highly soluble recombinant Erns-Ag protein with purity >95 % was purified by one step Ni-NTA affinity chromatography under native condition. Anti Erns-Ag polyclonal antibodies raised in guinea pig was found to react with CSFV antigen in infected MDCK cell line during immunoperoxidase test. The described methodology of producing a highly soluble recombinant protein with native conformation would likely to assist in development of differential diagnostic test as well as its application in raising hyperimmune sera for detection of CSFV antigen either in tissue materials or infected cell lines.
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Affiliation(s)
- A Ahuja
- Division of Virology, Indian Veterinary Research Institute (IVRI), Regional Campus, Mukteswar, 263138 Nainital, Uttarakhand India
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Sun SQ, Yin SH, Guo HC, Jin Y, Shang YJ, Liu XT. Genetic typing of classical swine fever virus isolates from China. Transbound Emerg Dis 2012; 60:370-5. [PMID: 22672483 DOI: 10.1111/j.1865-1682.2012.01346.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The E2 genes of 73 classical swine fever virus (CSFV) originated from CSF suspected cases in different regions of China were genetically characterized and compared with reference CSF viruses. All Chinese viruses that characterized were segregated into two major groups and subdivided into four subgroups. Most of isolates (61.6%) belonged to group 2 and were further divided into three subgroups: subgroup 2.1, 2.2 and 2.3. Subgroup 2.1 was the largest subgroup which contained 46.6% of isolates, while subgroup 2.3 was the smallest subgroup which contained only one isolate (1.4%). The remaining 38.4% of isolates were classified into subgroup 1.1 within group 1. However, no group 3 and subgroups 1.2 and 1.3 viruses were found in this study. This study has provided epidemiological information useful for assessing the virus origin and establishing a national prevention and control strategy against the disease.
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Affiliation(s)
- S-Q Sun
- State Key Laboratory of Veterinary Etiological Biology, National Foot and Mouth Disease Reference Laboratory, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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