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Robert E, Goonewardene K, Lamboo L, Perez O, Goolia M, Lewis C, Erdelyan CNG, Lung O, Handel K, Moffat E, Embury-Hyatt C, Amaya NN, Parra CPC, Rueda DCG, Monroy MAR, Clavijo A, Ambagala A. Molecular and Pathological Characterization of Classical Swine Fever Virus Genotype 2 Strains Responsible for the 2013-2018 Outbreak in Colombia. Viruses 2023; 15:2308. [PMID: 38140549 PMCID: PMC10747092 DOI: 10.3390/v15122308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/07/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Classical swine fever (CSF) is a highly contagious transboundary viral disease of domestic and wild pigs. Despite mass vaccination and continuous eradication programs, CSF remains endemic in Asia, some countries in Europe, the Caribbean and South America. Since June 2013, Northern Colombia has reported 137 CSF outbreaks, mostly in backyard production systems with low vaccination coverage. The purpose of this study was to characterize the virus responsible for the outbreak. Phylogenetic analysis based on the full-length E2 sequence shows that the virus is closely related to CSF virus (CSFV) genotype 2.6 strains circulating in Southeast Asia. The pathotyping experiment suggests that the virus responsible is a moderately virulent strain. The 190 nucleotide stretch of the E2 hypervariable region of these isolates also shows high similarity to the CSFV isolates from Colombia in 2005 and 2006, suggesting a common origin for the CSF outbreaks caused by genotype 2.6 strains. The emergence of genotype 2.6 in Colombia suggests a potential transboundary spread of CSFV from Asia to the Americas, complicating the ongoing CSF eradication efforts in the Americas, and emphasizes the need for continuous surveillance in the region.
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Affiliation(s)
- Erin Robert
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Kalhari Goonewardene
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Lindsey Lamboo
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Orlando Perez
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Melissa Goolia
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Charles Lewis
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Cassidy N. G. Erdelyan
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Oliver Lung
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Katherine Handel
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Estella Moffat
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Carissa Embury-Hyatt
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Nancy Naranjo Amaya
- National Veterinary Laboratory, Instituto Colombiano Agropecurio, Bogota 110911, DC, Colombia; (N.N.A.); (C.P.C.P.); (D.C.G.R.); (M.A.R.M.)
| | - Claudia Patricia Calderón Parra
- National Veterinary Laboratory, Instituto Colombiano Agropecurio, Bogota 110911, DC, Colombia; (N.N.A.); (C.P.C.P.); (D.C.G.R.); (M.A.R.M.)
| | - Diana Cristina Gómez Rueda
- National Veterinary Laboratory, Instituto Colombiano Agropecurio, Bogota 110911, DC, Colombia; (N.N.A.); (C.P.C.P.); (D.C.G.R.); (M.A.R.M.)
| | - Maria Antonia Rincón Monroy
- National Veterinary Laboratory, Instituto Colombiano Agropecurio, Bogota 110911, DC, Colombia; (N.N.A.); (C.P.C.P.); (D.C.G.R.); (M.A.R.M.)
| | - Alfonso Clavijo
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
| | - Aruna Ambagala
- Canadian Food Inspection Agency, National Centre for Foreign Animal Disease, Winnipeg, MB R3E 3R2, Canada; (E.R.); (K.G.); (L.L.); (O.P.); (M.G.); (C.L.); (C.N.G.E.); (O.L.); (K.H.); (E.M.); (C.E.-H.); (A.C.)
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
- Department of Comparative Biology and Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
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Coronado L, Perera CL, Rios L, Frías MT, Pérez LJ. A Critical Review about Different Vaccines against Classical Swine Fever Virus and Their Repercussions in Endemic Regions. Vaccines (Basel) 2021; 9:154. [PMID: 33671909 PMCID: PMC7918945 DOI: 10.3390/vaccines9020154] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/24/2022] Open
Abstract
Classical swine fever (CSF) is, without any doubt, one of the most devasting viral infectious diseases affecting the members of Suidae family, which causes a severe impact on the global economy. The reemergence of CSF virus (CSFV) in several countries in America, Asia, and sporadic outbreaks in Europe, sheds light about the serious concern that a potential global reemergence of this disease represents. The negative aspects related with the application of mass stamping out policies, including elevated costs and ethical issues, point out vaccination as the main control measure against future outbreaks. Hence, it is imperative for the scientific community to continue with the active investigations for more effective vaccines against CSFV. The current review pursues to gather all the available information about the vaccines in use or under developing stages against CSFV. From the perspective concerning the evolutionary viral process, this review also discusses the current problematic in CSF-endemic countries.
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Affiliation(s)
- Liani Coronado
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Carmen L. Perera
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Liliam Rios
- Reiman Cancer Research Laboratory, Faculty of Medicine, University of New Brunswick, Saint John, NB E2L 4L5, Canada;
| | - María T. Frías
- National Centre for Animal and Plant Health (CENSA), OIE Collaborating Centre for Disaster Risk Reduction in Animal Health, San José de las Lajas 32700, Cuba; (L.C.); (C.L.P.); (M.T.F.)
| | - Lester J. Pérez
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois at Urbana–Champaign, Champaign, IL 61802, USA
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Pineda P, Deluque A, Peña M, Diaz OL, Allepuz A, Casal J. Descriptive epidemiology of classical swine fever outbreaks in the period 2013-2018 in Colombia. PLoS One 2020; 15:e0234490. [PMID: 32555613 PMCID: PMC7299363 DOI: 10.1371/journal.pone.0234490] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/26/2020] [Indexed: 11/18/2022] Open
Abstract
Classical swine fever (CSF) is an infectious viral disease caused by an RNA virus belonging to the Pestivirus genus. A total of 134 outbreaks of CSF have occurred in the last seven years in the North of Colombia. The objective of this study was the characterization of the herds affected by CSF from 2013 to 2018. Most of the outbreaks (95%) occured in backyard piggeries. The principal causes of transmission of CSF were the introduction of infected pigs (38%), movements of people (37%) and unknown origin (13%). The epidemiological relationships with 15 affected farms explained 31 outbreaks. The overall attack and mortality rates were 39% and 32%, respectively. The main clinical signs were high fever (67%), incoordination of movements (54%), and prostration (52%). Seventy-three percent of the herds had not been vaccinated against CSF and 17% had been only partially vaccinated. A spatio-temporal analysis, using a Poisson regression model, revealed two clusters with high risk; the first and largest one from 2014 to 2016 had a relative risk (RR) of 13.4 and included part of the departments of Atlántico, Bolívar, Cesar, La Guajira, Norte de Santander, Magdalena and Sucre; and the second cluster (RR = 9.6 in 2016) included municipalities in the north of the department of Cordoba.
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Affiliation(s)
- Pilar Pineda
- Department Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Catalunya, Spain
- * E-mail: (PP); (JC)
| | - Adriana Deluque
- Colombian Agriculture and Livestock Institute – ICA, Bogotá, Cundinamarca, Colombia
| | - Mario Peña
- Colombian Agriculture and Livestock Institute – ICA, Bogotá, Cundinamarca, Colombia
| | - Olga Lucia Diaz
- Colombian Agriculture and Livestock Institute – ICA, Bogotá, Cundinamarca, Colombia
| | - Alberto Allepuz
- Department Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Catalunya, Spain
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Catalunya, Spain
| | - Jordi Casal
- Department Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Catalunya, Spain
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Catalunya, Spain
- * E-mail: (PP); (JC)
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Zhou B. Classical Swine Fever in China-An Update Minireview. Front Vet Sci 2019; 6:187. [PMID: 31249837 PMCID: PMC6584753 DOI: 10.3389/fvets.2019.00187] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 05/28/2019] [Indexed: 11/17/2022] Open
Abstract
Classical swine fever (CSF) remains one of the most economically important viral diseases of domestic pigs and wild boar worldwide. The causative agent is CSF virus, it is highly contagious, with high morbidity and mortality rates; as such, it is an OIE-listed disease. Owing to a nationwide policy of vaccinations of pigs, CSF is well-controlled in China, with large-scale outbreaks rarely seen. Sporadic outbreaks are however still reported every year. In order to cope with future crises and to eradicate CSF, China should strengthen and support biosecurity measures such as the timely reporting of suspected disease, technologies for reliable diagnoses, culling infected herds, and tracing possible contacts, as well as continued vaccination and support of research into drug and genetic therapies. This mini-review summarizes the epidemiology of and control strategies for CSF in China.
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Affiliation(s)
- Bin Zhou
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
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Garrido Haro AD, Barrera Valle M, Acosta A, J Flores F. Phylodynamics of classical swine fever virus with emphasis on Ecuadorian strains. Transbound Emerg Dis 2018; 65:782-790. [PMID: 29322688 DOI: 10.1111/tbed.12803] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Indexed: 11/26/2022]
Abstract
Classic swine fever virus (CSFV) is a Pestivirus from the Flaviviridae family that affects pigs worldwide and is endemic in several Latin American countries. However, there are still some countries in the region, including Ecuador, for which CSFV molecular information is lacking. To better understand the epidemiology of CSFV in the Americas, sequences from CSFVs from Ecuador were generated and a phylodynamic analysis of the virus was performed. Sequences for the full-length glycoprotein E2 gene of twenty field isolates were obtained and, along with sequences from strains previously described in the Americas and from the most representative strains worldwide, were used to analyse the phylodynamics of the virus. Bayesian methods were used to test several molecular clock and demographic models. A calibrated ultrametric tree and a Bayesian skyline were constructed, and codons associated with positive selection involving immune scape were detected. The best model according to Bayes factors was the strict molecular clock and Bayesian skyline model, which shows that CSFV has an evolution rate of 3.2 × 10-4 substitutions per site per year. The model estimates the origin of CSFV in the mid-1500s. There is a strong spatial structure for CSFV in the Americas, indicating that the virus is moving mainly through neighbouring countries. The genetic diversity of CSFV has increased constantly since its appearance, with a slight decrease in mid-twentieth century, which coincides, with eradication campaigns in North America. Even though there is no evidence of strong directional evolution of the E2 gene in CSFV, codons 713, 761, 762 and 975 appear to be selected positively and could be related to virulence or pathogenesis. These results reveal how CSFV has spread and evolved since it first appeared in the Americas and provide important information for attaining the goal of eradication of this virus in Latin America.
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Affiliation(s)
- A D Garrido Haro
- Ecuadorian Agency for Quality Assurance in Agriculture, Tumbaco, Ecuador
| | - M Barrera Valle
- Facultad de Ciencias Veterinarias, Universidad Técnica de Manabí, Portoviejo, Ecuador
| | - A Acosta
- Ecuadorian Agency for Quality Assurance in Agriculture, Tumbaco, Ecuador
| | - F J Flores
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad Tecnológica Equinoccial, Quito, Ecuador.,Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas ESPE, Sangolquí, Ecuador
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Gong W, Lu Z, Zhang L, Xie X, Jiang D, Jia J, Guo H, Shi J, Tu C. In vitro adaptation and genome analysis of a sub-subgenotype 2.1c isolate of classical swine fever virus. Virus Genes 2016; 52:651-9. [PMID: 27155669 DOI: 10.1007/s11262-016-1350-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 04/26/2016] [Indexed: 11/25/2022]
Abstract
Classical swine fever (CSF) still causes substantial economic losses in the pig industry in China. This study reports the isolation and characterization of a field CSF virus named GD53/2011 from pig kidney tissue collected during a CSF outbreak in Guangdong province, China. Phylogenetic analysis based on the full-length E2 gene sequence revealed that this isolate belongs to CSFV sub-subgenotype 2.1c. To further understand the replication characteristics, GD53/2011 was subsequently adapted in PK-15 cells, and its full-length genome was sequenced. After adaptation in PK-15 cells, the titer of GD53/2011 was significantly increased from 10(3.39) TCID50/ml at passage 6 (F6) to 10(8.50) TCID50/ml at passage 46 (F46) with the peak titer obtained at 48 h post-inoculation. Sequence comparison revealed that the E(rns) gene at passages 6, 15, and 25 of GD53/2011 was identical to that in the original tissue, but one amino acid substitution (S476R) was detected at passages 35 and 46. Furthermore, E2 gene sequences at passages 6, 15, 25, 35, and 46 was found identical to that in the original tissue, indicating that the E2 gene was stable during CSF virus adaptation in PK-15 cells. Full-length protein sequence comparison of GD53/2011 with other 2.1 sub-subgenotype isolates showed that Core and NS5A, rather than E2, are more genetically variable. Taken together, a field CSFV strain GD53/2011 was isolated, fully sequenced, and adapted to high growth titer in PK-15 cells, which might be suitable for future studies on CSFV infection, replication, and vaccine development.
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Affiliation(s)
- Wenjie Gong
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, 66506, USA
| | - Zongji Lu
- College of Life Science, Foshan University, Foshan, Guangdong, 528231, China
| | - Li Zhang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130122, China
| | - Xiaoming Xie
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130122, China
| | - Daliang Jiang
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Junjie Jia
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Huancheng Guo
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China
| | - Jishu Shi
- Department of Anatomy and Physiology, College of Veterinary Medicine, Kansas State University, Manhattan, 66506, USA.
| | - Changchun Tu
- Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, 130122, China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China.
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Complete genome sequence of a novel sub-subgenotype 2.1g isolate of classical swine fever virus from China. Arch Virol 2016; 161:2613-7. [PMID: 27318930 DOI: 10.1007/s00705-016-2932-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 06/11/2016] [Indexed: 11/26/2022]
Abstract
Current subgenotype 2.1 isolates of classical swine fever virus (CSFV) play a dominant role in CSF outbreaks in China, and a novel sub-subgenotype 2.1g of CSFV was recently identified, but the complete genome sequence of this new sub-subgenotype has not been reported. In this study, complete genome of 2.1g isolate GD19/2011 collected from Guangdong province of China in 2011 was sequenced. It was found to be 12,298 nucleotides (nt) in length, including a 375-nt 5'UTR, a 11,697-nt opening reading frame (ORF), and a 227-nt 3'UTR. GD19/2011 shared 91.0-93.7 % and 95.6-97.5 % nt and amino acid sequence identity, respectively, with other subgenotype 2.1 isolates. The topology of a phylogenetic tree constructed based on complete genome sequences of GD19/2011 and other CSFV isolates was identical to that obtained with full-length E2 gene sequences, but it was significantly different from those obtained with the 5'UTR and core sequences. Serial passages of GD9/2011 in PK-15 cells generated a highly cell-adapted virus stock with an infectious titer of 10(7.8) TCID50/ml at the 12(th) passage in which two amino acid substitutions, S476R and N2494S, were observed in comparison with the complete polyprotein sequence of the original isolate from kidney tissue, GD19/2011. This is the first report of the complete genome sequence of a 2.1g isolate, and the GD19/2011 isolate will be useful for further analysis of the evolution and virulence of CSFV isolates.
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Genetic diversity of subgenotype 2.1 isolates of classical swine fever virus. INFECTION GENETICS AND EVOLUTION 2016; 41:218-226. [PMID: 27085291 DOI: 10.1016/j.meegid.2016.04.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 02/28/2016] [Accepted: 04/04/2016] [Indexed: 11/21/2022]
Abstract
As the causative agent of classical swine fever, the economically devastating swine disease worldwide, classical swine fever virus (CSFV) is currently classified into the 11 subgenotypes, of which subgenotype 2.1 is distributed worldwide and showing more genetic diversity than other subgenotypes. Prior to this report, subgenotype 2.1 was divided into three sub-subgenotypes (2.1a-2.1c). To further analyze the genetic diversity of CSFV isolates in China, 39 CSFV isolates collected between 2004 and 2012 in two Chinese provinces Guangxi and Guangdong were sequenced and subjected to phylogenetic analysis together with reference sequences retrieved from GenBank. Phylogenetic analyses based on the 190-nt and/or 1119-nt full length E2 gene fragments showed that current CSFV subgenotype 2.1 virus isolates in the world could be divided into 10 sub-subgenotypes (2.1a-2.1j) and the 39 isolates collected in this study were grouped into 7 of them (2.1a-2.1c and 2.1g-2.1j). Among the 10 sub-subgenotypes, 2.1d-2.1j were newly identified. Sub-subgenotype 2.1d isolates were circulated only in India, however the rest 9 sub-subgenotypes were from China with some of them closely related to isolates from European and neighboring Asian countries. According to the temporal and spatial distribution of CSFV subgenotype 2.1 isolates, the newly classified 10 sub-subgenotypes were further categorized into three groups: dominant sub-subgenotype, minor sub-subgenotype and silent sub-subgenotype, and each sub-subgenotype can be found only in certain geographical areas. Taken together, this study reveals the complex genetic diversity of CSFV subgenotype 2.1 and improves our understanding about the epidemiological trends of CSFV subgenotype 2.1 in the world, particularly in China.
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Development of a new LAMP assay for the detection of CSFV strains from Cuba: a proof-of-concept study. Arch Virol 2015; 160:1435-48. [PMID: 25877822 DOI: 10.1007/s00705-015-2407-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 03/22/2015] [Indexed: 10/23/2022]
Abstract
Classical swine fever (CSF) is a devastating animal disease of great economic impact worldwide. In many countries, CSF has been endemic for decades, and vaccination of domestic pigs is one of the measures to control the disease. Consequently, differentiating infected from vaccinated animals by antibody ELISA screening is not applicable. In some countries, such as Cuba, lack of molecular techniques for sensitive, rapid and reliable detection of virus genomes is a critical point. To overcome this problem, an easy-to-use one-tube assay based on the loop-mediated isothermal amplification (LAMP) principle has been developed for detection of the genome of CSF virus (CSFV) of endemic Cuban genotype 1.4 isolates. The assay reliably detected recent isolates from three different regions of Cuba with an analytical sensitivity 10-100 times lower than that of quantitative reverse transcription RT-qPCR. Diagnostic test sensitivity was examined using reference sera from two groups of pigs experimentally infected with Cuban virulent strain CSF0705 "Margarita" and the recent field isolate CSF1058 "Pinar del Rio". Differences in pathogenicity of the two viruses were reflected in the clinical course of disease as well as in virus loads of blood samples. Low viral RNA loads in samples from pigs infected with the field isolate caused serious detection problems in RT-LAMP as well as in RT-qPCR. Thus, it will be necessary in future research to focus on targeted sampling of diseased animals and to restrict diagnosis to the herd level in order to establish LAMP as an efficient tool for diagnosing CSF under field conditions.
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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: 1.3] [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: 1.0] [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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12
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Porcine bocaviruses: genetic analysis and prevalence in Chinese swine population. Epidemiol Infect 2011; 139:1581-6. [DOI: 10.1017/s0950268811000847] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
SUMMARYIn members of theBocavirusgenus, that contain three open reading frames (ORFs) of the Parvovirinae subfamily, porcine bocaviruses (PoBoVs) exhibit the most genetic diversity. Based on the ORF2-encoded viral protein (VP1) classification, the six reported porcine bocaviruses were grouped into four species: PoBoV1 (porcine boca-like virus or PBoLV), PoBoV2 (porcine parvovirus 4 or PPV4), PoBoV3 (PBoV1/PBoV2) and PoBoV4 (6V/7V), with PoBoV3 and PoBoV4 each having two genotype viruses. All four PoBoV species were detected in the 166 samples collected in 2010 from swine herds located in ten provinces of China. The detection rates for PoBoV1-4 were 28·9%, 6·6%, 19·3% and 39·7%, respectively. The co-infection combinations involving these six porcine bocaviruses in the collected samples were very complex. Furthermore, mixed infections with viruses from other families (porcine reproductive and respiratory syndrome virus, classic swine fever virus and porcine circovirus type 2) were also detected.
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13
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Luo TR, Liao SH, Wu XS, Feng L, Yuan ZX, Li H, Liang JJ, Meng XM, Zhang HY. Phylogenetic analysis of the E2 gene of classical swine fever virus from the Guangxi Province of southern China. Virus Genes 2011; 42:347-54. [DOI: 10.1007/s11262-011-0578-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 01/19/2011] [Indexed: 10/18/2022]
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14
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Leifer I, Hoffmann B, Höper D, Bruun Rasmussen T, Blome S, Strebelow G, Höreth-Böntgen D, Staubach C, Beer M. Molecular epidemiology of current classical swine fever virus isolates of wild boar in Germany. J Gen Virol 2010; 91:2687-97. [PMID: 20660149 DOI: 10.1099/vir.0.023200-0] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Classical swine fever (CSF) has caused significant economic losses in industrialized pig production, and is still present in some European countries. Recent CSF outbreaks in Europe were mainly associated with strains of genogroup 2 (subgroup 2.3). Although there are extensive datasets regarding 2.3 strains, there is very little information available on longer fragments or whole classical swine fever virus (CSFV) genomes. Furthermore, there are no detailed analyses of the molecular epidemiology of CSFV wild boar isolates available. Nevertheless, complete genome sequences are supportive in phylogenetic analyses, especially in affected wild boar populations. Here, German CSFV strains of subgroup 2.3 were fully sequenced using two different approaches: (i) a universal panel of CSFV primers that were developed to amplify the complete genome in overlapping fragments for chain-terminator sequencing; and (ii) generation of a single full-length amplicon of the CSFV genome obtained by long-range RT-PCR for deep sequencing with next-generation sequencing technology. In total, five different strains of CSFV subgroup 2.3 were completely sequenced using these newly developed protocols. The approach was used to study virus spread and evolutionary history in German wild boar. For the first time, the results of our study clearly argue for the possibility of a long-term persistence of genotype 2.3 CSFV strains in affected regions at an almost undetectable level, even after long-term oral vaccination campaigns with intensive monitoring. Hence, regional persistence in wild boar populations has to be taken into account as an important factor in the continual outbreaks in affected areas.
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Affiliation(s)
- Immanuel Leifer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, D-17493 Greifswald-Insel Riems, Germany
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15
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Araínga M, Hisanaga T, Hills K, Handel K, Rivera H, Pasick J. Phylogenetic analysis of classical swine fever virus isolates from Peru. Transbound Emerg Dis 2010; 57:262-70. [PMID: 20545910 DOI: 10.1111/j.1865-1682.2010.01144.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Classical swine fever (CSF) is considered to be endemic in Peru with outbreaks reported to the World Organization for Animal Health as recently as 2008 and 2009. Nevertheless, little is known regarding the genetic subgroup(s) of CSF virus that are circulating in Peru or their relationship to recent CSF viruses that have been isolated from neighbouring South American countries or other parts of the world. In this study, we molecularly characterize CSF viruses that were isolated from domestic pigs from different regions of Peru from the middle of 2007 to early 2008. All virus isolates were found to belong to genetic subgroup 1.1, consistent with the subgroup of viruses that have been identified from other South American countries. Although the Peruvian isolates are most closely related to viruses from Colombia and Brazil, they form a monophyletic clade, which suggests they have a distinct evolutionary history.
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Affiliation(s)
- M Araínga
- Universidad Nacional Mayor de San Marcos, Lima, Perú
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Blome S, Grotha I, Moennig V, Greiser-Wilke I. Classical swine fever virus in South-Eastern Europe--retrospective analysis of the disease situation and molecular epidemiology. Vet Microbiol 2010; 146:276-84. [PMID: 20541876 DOI: 10.1016/j.vetmic.2010.05.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 05/14/2010] [Accepted: 05/21/2010] [Indexed: 10/19/2022]
Abstract
Classical swine fever (CSF) is among the most important diseases of domestic pigs and causes great socio-economic losses. Therefore, control of CSF is given high priority within the European Union, including financial support of concerted control actions in candidate and in potential candidate countries. Unfortunately, from some of these countries information on the CSF situation and related data is very limited. This study was undertaken to gather all available information on the domestic pig population and husbandry, and of the CSF situation in domestic pigs and wild boar in South-Eastern European countries that have recently joined or are applying to join the European Union. A characteristic feature of pig production in Eastern Europe is that most of them are in backyard holdings. Although mandatory vaccination is carried out in most of these countries, sporadic CSF outbreaks still occur. Little is still known about the CSF situation in wild boar. In addition, molecular epidemiology of 97 CSF virus isolates available from these countries, from outbreaks that occurred between 1994 and 2007, was performed. Most of the isolates were from Romania and Bulgaria. Genetic typing showed that almost all isolates (with exception of Croatian and of the Macedonian isolates) belonged to genotype 2.3. On the basis of these sequences, and additional sequences from outbreaks in Eastern and Western European countries taken from the database held at the European Union Reference Laboratory (EURL), two clusters could be distinguished within subtype 2.3. They were tentatively named 2.3.1 and 2.3.2.
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Affiliation(s)
- Sandra Blome
- Friedrich-Loeffler-Institute, Institute of Diagnostic Virology, Suedufer 10, 17493 Greifswald-Isle of Riems, Germany
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Genetic typing of recent classical swine fever isolates from India. Vet Microbiol 2009; 141:367-73. [PMID: 19836905 DOI: 10.1016/j.vetmic.2009.09.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 09/07/2009] [Accepted: 09/22/2009] [Indexed: 11/24/2022]
Abstract
Seventeen classical swine fever virus (CSFV) isolates recovered during the period of 3 years (2006-2008) from India were subjected to nucleotide sequencing in the 5' untranslated region (UTR). For genetic typing, 150 nucleotides within this region were used. For better epizootiological understanding, 39 nucleotide sequences of the above region, including 13 Indian CSFV sequences, available either in the Genbank or published literature were also included in the study. Based on the phylogenetic analysis, the Indian isolates could be grouped in to two subgroups, viz., 1.1 and 2.2. The study also revealed predominance of subgroup 1.1 and involvement of viruses of more than one subgroup in an outbreak.
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18
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European Food Safety Authority (EFSA). Animal health safety of fresh meat derived from pigs vaccinated against Classic Swine Fever. EFSA J 2009. [DOI: 10.2903/j.efsa.2009.933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Huang YL, Pang VF, Pan CH, Chen TH, Jong MH, Huang TS, Jeng CR. Development of a reverse transcription multiplex real-time PCR for the detection and genotyping of classical swine fever virus. J Virol Methods 2009; 160:111-8. [PMID: 19414034 PMCID: PMC7112934 DOI: 10.1016/j.jviromet.2009.04.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Revised: 04/22/2009] [Accepted: 04/27/2009] [Indexed: 11/30/2022]
Abstract
A reverse transcription multiplex real-time PCR (RT-MRT-PCR) was developed for rapid detection and genotyping of classical swine fever virus (CSFV). The universal primers and specific TaqMan probes for each of the three genotypes, genotypes 1, 2, and 3, were designed within the 3′-UTR of the CSFV. Non-CSFV swine virus and clinical samples from specific pathogen-free (SPF) pigs were both demonstrated to be CSFV-negative by RT-MRT-PCR. The diagnostic sensitivity of RT-MRT-PCR was determined to be 1 viral copy/μl for each genotype of standard plasmid. For the analytical sensitivity experiment, 100 samples of 14 CSFV genotype 1 strains and 86 samples from CSFV outbreak farms were all detected as CSFV-positive by RT-MRT-PCR, and the genotype results were consistent with the results of sequencing from a previous study. The intra-assay and inter-assay variations of RT-MRT-PCR were below 3% in all experiments. The sensitivity of RT-MRT-PCR was the same as the reverse transcription nested PCR (RT-nPCR) and higher than reverse transcription PCR (RT-PCR) and viral isolation from clinical samples. This assay was used further to evaluate the duration of viremia of wild-type CSFV in vaccinated exposed pigs. The results indicated that pigs vaccinated with the E2 subunit vaccine had longer viremia than pigs given the C-strain vaccine, which is compatible with the findings of previous studies. Thus, the new RT-MRT-PCR is a rapid, reproducible, sensitive, and specific genotyping tool for CSFV detection.
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Affiliation(s)
- Yu-Liang Huang
- Animal Health Research Institute, Council of Agriculture, Taipei County, Taiwan
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Le Dimna M, Vrancken R, Koenen F, Bougeard S, Mesplède A, Hutet E, Kuntz-Simon G, Le Potier MF. Validation of two commercial real-time RT-PCR kits for rapid and specific diagnosis of classical swine fever virus. J Virol Methods 2008; 147:136-42. [PMID: 17913249 DOI: 10.1016/j.jviromet.2007.08.013] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 08/03/2007] [Accepted: 08/22/2007] [Indexed: 11/30/2022]
Abstract
Two real-time RT-PCR kits, developed by LSI (TaqVet CSF) and ADIAGENE (Adiavet CSF), obtained an agreement to be commercialised in France, subject to conditions, defined by the French Classical Swine Fever (CSF) National Reference Laboratory. The producers were asked to introduce an internal control to check the RNA extraction efficacy. The different criteria assessed were sensitivity, "pestivirus specificity", reproducibility and ease of handling, using 189 different samples. These samples were either CSFV inactivated strains or blood/serum/organs collected from CSFV experimentally infected pigs or naturally infected wild boars. The reproducibility of the assays was confirmed by the analysis of a batch-to-batch panel control that was used for inter-laboratory tests involving nine laboratories. The two kits were also tested for the use in mass diagnostics and the results proved the kits to be suited using pools of blood, serum and tonsils. Moreover, a field evaluation, carried out on spleen samples collected from the CSF surveillance of wild boars in an area known to be infected and from domestic pigs at a slaughterhouse, confirmed the high sensitivity and specificity of the two kits. This step-by-step evaluation procedure confirmed that the two commercial CSF real-time RT-PCR kits have a higher predictive value than the current diagnostic standard, Virus Isolation.
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Affiliation(s)
- M Le Dimna
- Agence Française de Sécurité Sanitaire des Aliments, Unité de Virologie Immunologie Porcines, BP53, F-22440 Ploufragan, France
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Cha SH, Choi EJ, Park JH, Yoon SR, Kwon JH, Yoon KJ, Song JY. Phylogenetic characterization of classical swine fever viruses isolated in Korea between 1988 and 2003. Virus Res 2007; 126:256-61. [PMID: 17328983 DOI: 10.1016/j.virusres.2007.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 01/23/2007] [Accepted: 01/24/2007] [Indexed: 11/25/2022]
Abstract
Twenty-four isolates of classical swine fever (CSF) virus which were obtained from CSF outbreaks during 1988 and 2003 in the Republic of Korea were genetically characterized for partial E2 gene (190 nucleotides) and compared with CSF viruses reported by other countries. Phylogenetic analyses classified Korean field isolates between1988 and 1999 into subgroup 3.2, forming an independent clade distinct from CSF viruses identified in other countries. In contrast, the viruses isolated during 2002-2003 CSF epidemics were classified into a different subgroup (2.1). The 2.1 viruses showed a close genetic relationship (92.1-100% nucleotide similarity) with CSF viruses reported from China and Taiwan in 1998-2001. As no evidence of CSF virus infection was detected in the wild boar (Sus scrofa coreanus) population that inhabits Korea, the results of molecular characterization strongly suggest that CSF epidemic outbreaks in Korean swine populations during 2002-2003 were attributed to the introduction of a new strain or strains, likely from neighboring countries.
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Affiliation(s)
- Sang-Ho Cha
- Virology Division, National Veterinary Research and Quarantine Service, 480, Anyang 6-dong, Anyang, Gyeonggido, Republic of Korea
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Dreier S, Zimmermann B, Moennig V, Greiser-Wilke I. A sequence database allowing automated genotyping of Classical swine fever virus isolates. J Virol Methods 2006; 140:95-9. [PMID: 17187869 DOI: 10.1016/j.jviromet.2006.11.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2006] [Revised: 10/25/2006] [Accepted: 11/07/2006] [Indexed: 11/25/2022]
Abstract
Classical swine fever (CSF) is a highly contagious viral disease of pigs. According to the OIE classification of diseases it is classified as a notifiable (previously List A) disease, thus having the potential for causing severe socio-economic problems and affecting severely the international trade of pigs and pig products. Effective control measures are compulsory, and to expose weaknesses a reliable tracing of the spread of the virus is necessary. Genetic typing has proved to be the method of choice. However, genotyping involves the use of multiple software applications, which is laborious and complex. The implementation of a sequence database, which is accessible by the World Wide Web with the option to type automatically new CSF virus isolates once the sequence is available is described. The sequence to be typed is tested for correct orientation and, if necessary, adjusted to the right length. The alignment and the neighbor-joining phylogenetic analysis with a standard set of sequences can then be calculated. The results are displayed as a graph. As an example, the determination is shown of the genetic subgroup of the isolate obtained from the outbreaks registered in Russia, in 2005. After registration (Irene.greiser-wilke@tiho-hannover.de) the database including the module for genotyping are accessible under http://viro08.tiho-hannover.de/eg/eurl_virus_db.htm.
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Affiliation(s)
- Sabrina Dreier
- Institute of Virology, Department of Infectious Diseases, EU Reference Laboratory for Classical Swine Fever, University of Veterinary Medicine, Buenteweg 17, 30559 Hannover, Germany
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