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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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Liu Y, Bahoussi AN, Wang PH, Wu C, Xing L. Complete genome sequences of classical swine fever virus: Phylogenetic and evolutionary analyses. Front Microbiol 2022; 13:1021734. [PMID: 36225377 PMCID: PMC9549409 DOI: 10.3389/fmicb.2022.1021734] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
The classical swine fever virus (CSFV) outbreaks cause colossal losses of pigs and drastic economic impacts. The current phylogenetic CSFV groups were determined mainly based on the partial genome. Herein, 203 complete genomic sequences of CSFVs collected worldwide between 1998 and 2018 available on the GenBank database were retrieved for re-genotyping and recombination analysis. The maximum likelihood phylogenetic tree determined two main groups, GI and GII, with multiple sub-genotypes. The “strain 39” (GenBank ID: AF407339), previously identified as belonging to sub-genotypes 1.1 or 2.2 based on the partial sequences, is found to be genetically distinct and independent, forming a new lineage depicted as GI-2.2b. Ten potential natural recombination events were identified, seven of which were collected in China and found involved in the genetic diversity of CSFVs. Importantly, the vaccine strains and highly virulent strains were all involved in the recombination events, which would induce extra challenges to vaccine development. These findings alarm that attenuated vaccines should be applied with discretion and recommend using subunit vaccines in parallel with other preventive strategies for better management of CSFVs.
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Affiliation(s)
- Yue Liu
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
| | | | - Pei-Hua Wang
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Changxin Wu
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
| | - Li Xing
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
- The Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Shanxi University, Taiyuan, China
- Shanxi Provincial Key Laboratory for Prevention and Treatment of Major Infectious Diseases, Taiyuan, China
- *Correspondence: Li Xing
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Nielsen SS, Alvarez J, Bicout DJ, Calistri P, Canali E, Drewe JA, Garin‐Bastuji B, Gonzales Rojas JL, Schmidt C, Herskin M, Michel V, Padalino B, Pasquali P, Roberts HC, Spoolder H, Stahl K, Velarde A, Winckler C, Blome S, Boklund A, Bøtner A, Dhollander S, Rapagnà C, Van der Stede Y, Miranda Chueca MA. Research priorities to fill knowledge gaps in wild boar management measures that could improve the control of African swine fever in wild boar populations. EFSA J 2021; 19:e06716. [PMID: 34354769 PMCID: PMC8319816 DOI: 10.2903/j.efsa.2021.6716] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The European Commission asked EFSA to provide study designs for the investigation of four research domains (RDs) according to major gaps in knowledge identified by EFSA in a report published in 2019: (RD 1) African swine fever (ASF) epidemiology in wild boar; (RD 2) ASF transmission by vectors; (RD 3) African swine fever virus (ASFV) survival in the environment, and (RD 4) the patterns of seasonality of ASF in wild boar and domestic pigs in the EU. In this Scientific Opinion, the second RD on ASF epidemiology in wild boar is addressed. Twenty-nine research objectives were proposed by the working group and broader ASF expert networks and 23 of these research objectives met a prespecified inclusion criterion. Fourteen of these 23 research objectives met the predefined threshold for selection and so were prioritised based on the following set of criteria: (1) the impact on ASF management; (2) the feasibility or practicality to carry out the study; (3) the potential implementation of study results in practice; (4) a possible short time-frame study (< 1 year); (5) the novelty of the study; and (6) if it was a priority for risk managers. Finally, after further elimination of three of the proposed research objectives due to overlapping scope of studies published during the development of this opinion, 11 research priorities were elaborated into short research proposals, considering the potential impact on ASF management and the period of one year for the research activities.
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Yamamoto T, Sawai K, Nishi T, Fukai K, Kato T, Hayama Y, Murato Y, Shimizu Y, Yamaguchi E. Subgrouping and analysis of relationships between classical swine fever virus identified during the 2018-2020 epidemic in Japan by a novel approach using shared genomic variants. Transbound Emerg Dis 2021; 69:1166-1177. [PMID: 33730417 DOI: 10.1111/tbed.14076] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/01/2021] [Accepted: 03/15/2021] [Indexed: 11/29/2022]
Abstract
Classical swine fever (CSF) is a worldwide devastating disease of the pig industry caused by classical swine fever virus (CSFV). In September 2018, an outbreak of CSF occurred in Japan where the disease had been eradicated and was officially designated a CSF-free country since 2015. Following the detection of the first 2018 case on a farm in Gifu Prefecture, the disease spread among both farm pigs and wild boars and still continues. Epigenome analysis using whole-genome information is helpful in identifying the infection route, but the current approaches provide an insufficient resolution. In this study, a novel method of using single-nucleotide variants (SNVs) was employed to identify the associations among 158 isolates (65 from farms and 93 from wild boars). The identified groups of CSFV strains were plotted in different colours on a map, identifying the location where each strain was collected. The lack of an SNV set shared between the index case and the other strains suggested the first infection in Japan during the outbreak occurred in wild boars, not at the index farm. For the Atsumi Peninsula outbreaks, where nine farms were found infected within a 10-km radius area, the farm strains were assembled into three groups, suggesting these outbreaks resulted from at least three different infection events in this area. For the infections in the area around Saitama Prefecture, an area remote from the epicentre, strains from both the farms and wild boars were identified as being in the same group, suggesting they resulted from one viral introduction. Likewise, seven infected farms in Okinawa Prefecture, almost 1,500 km from Gifu Prefecture, were identified as being in a common, but separate group. By demonstrating the variety of transmission routes and possibility of long-distance infection, these results will help improve disease control measures.
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Affiliation(s)
- Takehisa Yamamoto
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Kotaro Sawai
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Tatsuya Nishi
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Katsuhiko Fukai
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Tomoko Kato
- Foot and Mouth Disease Unit, Division of Transboundary Animal Diseases, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira, Japan
| | - Yoko Hayama
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yoshinori Murato
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Yumiko Shimizu
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
| | - Emi Yamaguchi
- Epidemiology Unit, Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture and Food Research Organization, Ibaraki, Japan
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Immunogenicity of E2CD154 Subunit Vaccine Candidate against Classical Swine Fever in Piglets with Different Levels of Maternally Derived Antibodies. Vaccines (Basel) 2020; 9:vaccines9010007. [PMID: 33374172 PMCID: PMC7823626 DOI: 10.3390/vaccines9010007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/18/2022] Open
Abstract
E2CD154 is a novel subunit vaccine candidate against classical swine fever virus (CSFV). It contains the E2 envelope protein from CSFV fused to the porcine CD154 molecule formulated in the oil adjuvant MontanideTM ISA50 V2. Previous works evidenced the safety and immunogenicity of this candidate. Here, two other important parameters related to vaccine efficacy were assessed. First, the existence of high maternally derived antibody (MDA) titers in piglets born to sows vaccinated with E2CD154 was demonstrated. These MDA titers remained above 1:200 during the first seven weeks of life. To assess whether the titers interfere with active vaccination, 79 piglets from sows immunized with either E2CD154 or a modified live vaccine were vaccinated with E2CD154 following a 0–21-day biphasic schedule. Animals immunized at either 15, 21, or 33 days of age responded to vaccination by eliciting protective neutralizing antibody (NAb) titers higher than 1:600, with a geometric mean of 1:4335, one week after the booster. Those protective levels of NAb were sustained up to six months of age. No vaccination-related adverse effects were described. As a conclusion, E2CD154 is able to induce protective NAb in piglets with different MDA levels and at different days of age.
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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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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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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: 5.0] [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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Leslie EEC, Geong M, Abdurrahman M, Ward MP, Toribio JALML. Live pig markets in eastern Indonesia: Trader characteristics, biosecurity and implications for disease spread. Acta Trop 2016; 155:95-103. [PMID: 26739656 DOI: 10.1016/j.actatropica.2015.12.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/30/2022]
Abstract
Classical swine fever has been negatively impacting pig production in Nusa Tenggara Timur province in eastern Indonesia since its introduction in the 1990s, with live market trade contributing to disease spread. To understand market trader knowledge and practices regarding pig management, biosecurity, pig movements and pig health (specifically CSF), a repeated survey was conducted with pig sellers and pig buyers at 9 market sites across West Timor and the islands of Flores and Sumba. A total of 292 sellers and 281 buyers were interviewed in 2009 during two periods (rounds), a high-demand month (September) and a low-demand month (November). Information was collected via questionnaire. The majority of traders were male (sellers: 89%; buyers: 87%) with the highest level of completed education being primary school (sellers: 48%; buyers: 41%). The primary occupation of most respondents was farming: 90% of sellers and 87% of buyers were smallholder pig farmers and tended to sell their own home-raised pigs at market (52%). Pigs were sold for monetary gain either for primary (52%) or extra income (44%). Markets tended to be selected based on a good reputation (62%), a location close to residence (62%) and having the desired pig type (59%). Pig sales through markets were reported to be highest from August to October with 31% of sellers trading pigs at two or more markets. Prices at market were significantly higher on Sumba compared to West Timor and cross-bred pigs were significantly more expensive than indigenous pigs. Understanding of CSF and biosecurity was limited: 85% of sellers and 83% of buyers had no prior knowledge of CSF. Fifty-four percent of sellers reported no use of any biosecurity practices at market. Most respondents (88%) were able to recognise at least one clinical sign of a sick pig. Informal pig movements were also identified: 18% of pig buyers purchased pigs directly from other farmers. This study has provided baseline information on market trader activities at live pig markets in NTT that can contribute to the formation of sustainable strategies for improving pig health. Since NTT is the poorest province in Indonesia and pigs play a vital socioeconomic role in this province, market management and farmer education is needed to improve the pig market chain and contribute to socioeconomic development.
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Affiliation(s)
- Edwina E C Leslie
- The University of Sydney Faculty of Veterinary Science, Camden, NSW, Australia.
| | - Maria Geong
- Provincial Animal Health Services, Kupang, Nusa Tenggara Timur, Indonesia
| | | | - Michael P Ward
- The University of Sydney Faculty of Veterinary Science, Camden, NSW, Australia
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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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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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Blome S, Gabriel C, Schmeiser S, Meyer D, Meindl-Böhmer A, Koenen F, Beer M. Efficacy of marker vaccine candidate CP7_E2alf against challenge with classical swine fever virus isolates of different genotypes. Vet Microbiol 2013; 169:8-17. [PMID: 24411658 DOI: 10.1016/j.vetmic.2013.12.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 11/30/2013] [Accepted: 12/02/2013] [Indexed: 10/25/2022]
Abstract
Classical swine fever (CSF) is among the most important viral disease of domestic and feral pigs and has a serious impact on animal health and pig industry. In most countries with industrialized pig production, prophylactic vaccination against CSF is banned, and all efforts are directed towards eradication of the disease, e.g. by culling of infected herds and animal movement restrictions. Nevertheless, emergency vaccination remains an option to minimize the socio-economic impact of outbreaks. For this application, potent vaccines are needed that allow differentiation of infected from vaccinated animals. Among the promising candidates for next generation marker vaccines is the chimeric pestivirus CP7_E2alf. Efficacy studies are usually carried out using highly virulent CSFV strains of genotype 1 that do not mirror the current field situation where strains of genotype 2 predominate. To prove that CP7_E2alf also protects against these strains, efficacy was assessed after single oral vaccination of wild boar and single intramuscular vaccination of domestic pigs using challenge models with recent CSFV strains and the highly virulent strain "Koslov" (genotype 1.1). It could be demonstrated that CP7_E2alf pilot vaccine batches for intramuscular and oral use were able to protect pigs from challenge infection with a highly virulent CSFV. Moreover, solid protection was also achieved in case of challenge infection with recent field strains of genotypes 2.1 and 2.3. Thus, broad applicability under field conditions can be assumed.
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Affiliation(s)
- Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald - Insel Riems, Germany.
| | - Claudia Gabriel
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald - Insel Riems, Germany
| | - Stefanie Schmeiser
- European Union Reference Laboratory for CSF, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany
| | - Denise Meyer
- European Union Reference Laboratory for CSF, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany
| | - Alexandra Meindl-Böhmer
- European Union Reference Laboratory for CSF, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Buenteweg 17, 30559 Hannover, Germany
| | - Frank Koenen
- CODA-CERVA, Groeselenberg 99, 1180 Ukkel, Belgium
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald - Insel Riems, Germany
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Development and validation of a multiplex, real-time RT PCR assay for the simultaneous detection of classical and African swine fever viruses. PLoS One 2013; 8:e71019. [PMID: 23923045 PMCID: PMC3724773 DOI: 10.1371/journal.pone.0071019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 06/28/2013] [Indexed: 11/19/2022] Open
Abstract
A single-step, multiplex, real-time polymerase chain reaction (RT-PCR) was developed for the simultaneous and differential laboratory diagnosis of Classical swine fever virus (CSFV) and African swine fever virus (ASFV) alongside an exogenous internal control RNA (IC-RNA). Combining a single extraction methodology and primer and probe sets for detection of the three target nucleic acids CSFV, ASFV and IC-RNA, had no effect on the analytical sensitivity of the assay and the new triplex RT-PCR was comparable to standard PCR techniques for CSFV and ASFV diagnosis. After optimisation the assay had a detection limit of 5 CSFV genome copies and 22 ASFV genome copies. Analytical specificity of the triplex assay was validated using a panel of viruses representing 9 of the 11 CSFV subgenotypes, at least 8 of the 22 ASFV genotypes as well as non-CSFV pestiviruses. Positive and negative clinical samples from animals infected experimentally, due to field exposure or collected from the UK which is free from both swine diseases, were used to evaluate the diagnostic sensitivity and specificity for detection of both viruses. The diagnostic sensitivity was 100% for both viruses whilst diagnostic specificity estimates were 100% for CSFV detection and 97.3% for ASFV detection. The inclusion of a heterologous internal control allowed identification of false negative results, which occurred at a higher level than expected. The triplex assay described here offers a valuable new tool for the differential detection of the causative viruses of two clinically indistinguishable porcine diseases, whose geographical occurrence is increasingly overlapping.
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14
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Postel A, Schmeiser S, Bernau J, Meindl-Boehmer A, Pridotkas G, Dirbakova Z, Mojzis M, Becher P. Improved strategy for phylogenetic analysis of classical swine fever virus based on full-length E2 encoding sequences. Vet Res 2012; 43:50. [PMID: 22676246 PMCID: PMC3403906 DOI: 10.1186/1297-9716-43-50] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 06/07/2012] [Indexed: 01/21/2023] Open
Abstract
Molecular epidemiology has proven to be an essential tool in the control of classical swine fever (CSF) and its use has significantly increased during the past two decades. Phylogenetic analysis is a prerequisite for virus tracing and thus allows implementing more effective control measures. So far, fragments of the 5´NTR (150 nucleotides, nt) and the E2 gene (190 nt) have frequently been used for phylogenetic analyses. The short sequence lengths represent a limiting factor for differentiation of closely related isolates and also for confidence levels of proposed CSFV groups and subgroups. In this study, we used a set of 33 CSFV isolates in order to determine the nucleotide sequences of a 3508-3510 nt region within the 5´ terminal third of the viral genome. Including 22 additional sequences from GenBank database different regions of the genome, comprising the formerly used short 5´NTR and E2 fragments as well as the genomic regions encoding the individual viral proteins Npro, C, Erns, E1, and E2, were compared with respect to variability and suitability for phylogenetic analysis. Full-length E2 encoding sequences (1119 nt) proved to be most suitable for reliable and statistically significant phylogeny and analyses revealed results as good as obtained with the much longer entire 5´NTR-E2 sequences. This strategy is therefore recommended by the EU and OIE Reference Laboratory for CSF as it provides a solid and improved basis for CSFV molecular epidemiology. Finally, the power of this method is illustrated by the phylogenetic analysis of closely related CSFV isolates from a recent outbreak in Lithuania.
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Affiliation(s)
- Alexander Postel
- EU and OIE Reference Laboratory for Classical Swine Fever, Institute of Virology, Department of Infectious Diseases, University of Veterinary Medicine, Hannover, Germany.
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Leifer I, Hoeper D, Blome S, Beer M, Ruggli N. Clustering of classical swine fever virus isolates by codon pair bias. BMC Res Notes 2011; 4:521. [PMID: 22126254 PMCID: PMC3341591 DOI: 10.1186/1756-0500-4-521] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Accepted: 11/29/2011] [Indexed: 11/29/2022] Open
Abstract
Background The genetic code consists of non-random usage of synonymous codons for the same amino acids, termed codon bias or codon usage. Codon juxtaposition is also non-random, referred to as codon context bias or codon pair bias. The codon and codon pair bias vary among different organisms, as well as with viruses. Reasons for these differences are not completely understood. For classical swine fever virus (CSFV), it was suggested that the synonymous codon usage does not significantly influence virulence, but the relationship between variations in codon pair usage and CSFV virulence is unknown. Virulence can be related to the fitness of a virus: Differences in codon pair usage influence genome translation efficiency, which may in turn relate to the fitness of a virus. Accordingly, the potential of the codon pair bias for clustering CSFV isolates into classes of different virulence was investigated. Results The complete genomic sequences encoding the viral polyprotein of 52 different CSFV isolates were analyzed. This included 49 sequences from the GenBank database (NCBI) and three newly sequenced genomes. The codon usage did not differ among isolates of different virulence or genotype. In contrast, a clustering of isolates based on their codon pair bias was observed, clearly discriminating highly virulent isolates and vaccine strains on one side from moderately virulent strains on the other side. However, phylogenetic trees based on the codon pair bias and on the primary nucleotide sequence resulted in a very similar genotype distribution. Conclusion Clustering of CSFV genomes based on their codon pair bias correlate with the genotype rather than with the virulence of the isolates.
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Affiliation(s)
- Immanuel Leifer
- Institute of Virology and Immunoprophylaxis (IVI), Sensemattstrasse 293, CH-3147 Mittelhäusern, Switzerland.
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