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Glišić D, Milićević V, Krnjaić D, Toplak I, Prodanović R, Gallardo C, Radojičić S. Genetic analysis reveals multiple intergenic region and central variable region in the African swine fever virus variants circulating in Serbia. Vet Res Commun 2023; 47:1925-1936. [PMID: 37256519 DOI: 10.1007/s11259-023-10145-7] [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: 03/24/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
This study provides the first comprehensive report on the molecular characteristics of African swine fever virus (ASFV) variants in Serbia between 2019 and 2022. Since its first observation in July 2019, the disease has been found in wild boar and domestic swine. The study involved the analysis of 95 ASFV-positive samples collected from 12 infected administrative districts in Serbia. Partial four genomic regions were genetically characterized, including B646L, E183L, B602L, and the intergenic region (IGR) between the I73R-I329L genes. The results of the study suggest that multiple ASFV strains belonging to genotype II are circulating in Serbia, as evidenced by the analysis of the IGR between I73R-I329L genes that showed the most differences. Furthermore, the phylogenetic analysis of the B602L gene showed three different clades within the CVR I group of ASFV strains. Regarding the IGR, 98.4% were grouped into IGR II, with only one positive sample grouped into the IGR III group. These findings provide essential insights into the molecular characteristics of ASFV variants in Serbia and contribute to the knowledge of circulating strains of ASFV in Europe. However, further research is necessary to gain a better understanding of ASFV spread and evolution.
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Affiliation(s)
- Dimitrije Glišić
- Department of Virology, Institute of Veterinary Medicine of Serbia, 11000, Belgrade, Serbia.
| | - Vesna Milićević
- Department of Virology, Institute of Veterinary Medicine of Serbia, 11000, Belgrade, Serbia
| | - Dejan Krnjaić
- Department of Microbiology and Immunology, University of Belgrade Faculty of Veterinary Medicine, 11000, Belgrade, Serbia
| | - Ivan Toplak
- Institute of Microbiology and Parasitology, Laboratory for Virology, Veterinary Faculty, 1000, Ljubljana, Slovenia
| | - Radiša Prodanović
- Department of Ruminants and Swine Diseases, University of Belgrade Faculty of Veterinary Medicine, 11000, Belgrade, Serbia
| | - Carmina Gallardo
- European Union Reference Laboratory for ASF (EURL-ASF): Centro de Investigación en Sanidad Animal (CISA-INIA, CSIC), Valdeolmos, Madrid, Spain
| | - Sonja Radojičić
- Department of Infectious Animals Diseases and Diseases of Bees, University of Belgrade Faculty of Veterinary Medicine, 11000, Belgrade, Serbia
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Cho KH, Yoo DS, Hong SK, Kim DY, Jang MK, Kang HE, Kim YH. Genetic Profile of African Swine Fever Viruses Circulating at Pig Farms in South Korea during the Outbreaks between 2022 and April 2023. Viruses 2023; 15:1552. [PMID: 37515238 PMCID: PMC10383346 DOI: 10.3390/v15071552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Fifteen pig farms were affected by African swine fever (ASF) in South Korea during the outbreaks between 2022 and April 2023. The ASF virus (ASFV) genome was directly extracted from the blood and tissue samples of 15 ASFV-positive pig farms to analyze the genetic characteristics. Phylogenetic analysis revealed that the 15 strains belonged to p72 genotype II and CD2v serogroup 8, which were the central variable region (CVR) I variants of the B602L gene. Fourteen strains were intergenic region (IGR) II variants, containing an additional tandem repeat sequence (TRS), between I73L and I329R, with the exception of one strain from an ASFV-infected pig farm reported on 22 January 2023, which was an IGR I variant. In addition, a single-nucleotide polymorphism (SNP) was detected at position 107 from the start of the IGR between A179L and A137R in six isolates. The findings of this study suggest that the sources of the virus at the pig farms from which these variants originated differed from those of other pig farms.
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Affiliation(s)
- Ki-Hyun Cho
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Dae-Sung Yoo
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seong-Keun Hong
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Da-Young Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Min-Kyung Jang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Hae-Eun Kang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
| | - Yeon-Hee Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea
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Gallardo C, Casado N, Soler A, Djadjovski I, Krivko L, Madueño E, Nieto R, Perez C, Simon A, Ivanova E, Donescu D, Milicevik V, Chondrokouki E, Nurmoja I, Frant M, Feliziani F, Václavek P, Pileviciene S, Marisa A. A multi gene-approach genotyping method identifies 24 genetic clusters within the genotype II-European African swine fever viruses circulating from 2007 to 2022. Front Vet Sci 2023; 10:1112850. [PMID: 36761884 PMCID: PMC9905734 DOI: 10.3389/fvets.2023.1112850] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023] Open
Abstract
Introduction African swine fever (ASF) is a contagious viral disease of pigs and wild boar that poses a major threat to the global swine industry. The genotype II African swine fever virus (ASFV) entered the European Union (EU) in 2014 and since then fourteen countries have been affected, Italy and North Macedonia being the last in 2022. While whole genome sequencing remains the gold standard for the identification of new genetic markers, sequencing of multiple loci with significant variations could be used as a rapid and cost-effective alternative to track outbreaks and study disease evolution in endemic areas. Materials and methods To further our understanding of the epidemiology and spread of ASFV in Europe, 382 isolates collected during 2007 to 2022 were sequenced. The study was initially performed by sequencing the central variable region (CVR), the intergenic region (IGR) between the I73R and I329L genes and the O174L and K145R genes. For further discrimination, two new PCRs were designed to amplify the IGR between the 9R and 10R genes of the multigene family 505 (MGF505) and the IGR between the I329L and I215L genes. The sequences obtained were compared with genotype II isolates from Europe and Asia. Results The combination of the results obtained by sequencing these variable regions allowed to differentiate the European II-ASFV genotypes into 24 different groups. In addition, the SNP identified in the IGR I329L-I215L region, not previously described, grouped the viruses from North Macedonia that caused the 2022 outbreaks with viruses from Romania, Bulgaria, Serbia and Greece, differentiating from other genotype II isolates present in Europe and Asia. Furthermore, tandem repeat sequence (TRS) within the 9R-10R genes of the multigene family 505 (MGF505) revealed eight different variants circulating. Discussion These findings describe a new multi-gene approach sequencing method that can be used in routine genotyping to determine the origin of new introductions in ASF-free areas and track infection dynamics in endemic areas.
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Affiliation(s)
- Carmina Gallardo
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain,*Correspondence: Carmina Gallardo ✉
| | - Nadia Casado
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Alejandro Soler
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Igor Djadjovski
- 2Faculty of Veterinary Medicine, University Ss. Cyril and Methodius in Skopje, Skopje, North Macedonia
| | - Laura Krivko
- 3Latvia NRL: Laboratory of Microbiology and Pathology, Institute of Food Safety, Animal Health and Enviroment, BIOR, Riga, Latvia
| | - Encarnación Madueño
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Raquel Nieto
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Covadonga Perez
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Alicia Simon
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
| | - Emiliya Ivanova
- 4Bulgaria NRL: National Diagnostic and Research Veterinary Medical Institute (NDVRI), Sofia, Bulgaria
| | - Daniel Donescu
- 5Romania NRL: Institute for Diagnostic and Animal Health, Bucharest, Romania
| | - Vesna Milicevik
- 6Republic of Serbia NRL: Institute of Veterinary Medicine of Serbia, Belgrade, Serbia
| | - Eleni Chondrokouki
- 7Greece NRL: Greek Ministry of Rural Development and Food FMD, Virological, Rickettsial & Exotic Diseases, Athens, Greece
| | - Imbi Nurmoja
- 8Estonian NRL: National Centre for Laboratory Research and Risk Assessment (LABRIS), Tartu, Estonia
| | - Maciej Frant
- 9Poland NRL: National Veterinary Research Institute, Puławy, Poland
| | - Francesco Feliziani
- 10Italy NRL: Istituto Zooprofilattico Sperimentale (IZS) dell'Umbria e delle Marche, Perugia, Italy
| | - Petr Václavek
- 11Czech Republic NRL: State Veterinary Institute Jihlava, Jihlava, Czechia
| | - Simona Pileviciene
- 12Lithuania NRL: National Food and Veterinary Risk Assessment Institute (NFVRAI), Vilnius, Lithuania
| | - Arias Marisa
- 1European Union Reference Laboratory for ASF (EURL-ASF): Centro De investigación en Sanidad Animal (CISA-INIA, CSIC), Madrid, Spain
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Zhang H, Zhao S, Zhang H, Qin Z, Shan H, Cai X. Vaccines for African swine fever: an update. Front Microbiol 2023; 14:1139494. [PMID: 37180260 PMCID: PMC10173882 DOI: 10.3389/fmicb.2023.1139494] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 04/05/2023] [Indexed: 05/16/2023] Open
Abstract
African swine fever (ASF) is a fatal infectious disease of swine caused by the African swine fever virus (ASFV). Currently, the disease is listed as a legally notifiable disease that must be reported to the World Organization for Animal Health (WOAH). The economic losses to the global pig industry have been insurmountable since the outbreak of ASF. Control and eradication of ASF are very critical during the current pandemic. Vaccination is the optimal strategy to prevent and control the ASF epidemic, but since inactivated ASFV vaccines have poor immune protection and there aren't enough cell lines for efficient in vitro ASFV replication, an ASF vaccine with high immunoprotective potential still remains to be explored. Knowledge of the course of disease evolution, the way of virus transmission, and the breakthrough point of vaccine design will facilitate the development of an ASF vaccine. In this review, the paper aims to highlight the recent advances and breakthroughs in the epidemic and transmission of ASF, virus mutation, and the development of vaccines in recent years, focusing on future directions and trends.
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Affiliation(s)
- Hongliang Zhang
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Saisai Zhao
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
| | - Haojie Zhang
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Zhihua Qin
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Hu Shan
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- *Correspondence: Hu Shan,
| | - Xiulei Cai
- Shandong Collaborative Innovation Center for Development of Veterinary Pharmaceuticals, College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Xiulei Cai,
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Genetic Characterization of African Swine Fever Virus from Pig Farms in South Korea during Outbreaks in 2019-2021. Viruses 2022; 14:v14122621. [PMID: 36560625 PMCID: PMC9784228 DOI: 10.3390/v14122621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
In South Korea, a total of 21 African swine fever (ASF) infected farms were confirmed during 2019-2021. ASF viruses (ASFVs) were isolated from the blood and spleen samples of the 21 affected farms and their genetic characteristics were analyzed. Phylogenetic analysis indicated that the 21 Korean ASFV strains belonged to p72 genotype II and serogroup 8. All isolates were of the intergenic region (IGR) II variant with 10 tandem repeat sequences between I73R and I329L and the central variable region (CVR) 1 variant of the B602L gene. There were no IGR variations between the A179L and A137R and between the MGF 505 9R and10R nor mutations in the O174L, K145R, MGF 505-5R, CP204L, and Bt/Sj regions. The genes of the 21 ASFV strains were identical to those of Georgia 2007/1 and Chinese and Vietnamese strains (Pig/HLJ/2018, China/2018/AnhuiXCGQ, and ASFV_NgheAn_2019); however, X69R of the J268L region of the 18th isolate (Korea/Pig/Goseong/2021) had three nucleotide (CTA) insertions at the 209th position, which led to the addition of one tyrosine (Y) at the C-terminal. This suggests that there are variations among ASFVs circulating in South Korea and the 18th ASFV-infected farm was due to a variant different from those of the other 20 pig farms.
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Penrith ML, Van Heerden J, Heath L, Abworo EO, Bastos ADS. Review of the Pig-Adapted African Swine Fever Viruses in and Outside Africa. Pathogens 2022; 11:pathogens11101190. [PMID: 36297247 PMCID: PMC9609104 DOI: 10.3390/pathogens11101190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 12/04/2022] Open
Abstract
The region in eastern, central and southern Africa (ECSA) where African swine fever (ASF) originated in a sylvatic cycle is home to all the p72 genotypes of ASF virus identified so far. While 20 of the 24 genotypes have been isolated from outbreaks in domestic pigs in the region, only five of the genotypes (I, II, VIII, IX, X) have an extended field presence associated with domestic pigs. Of the genotypes that appear to be strongly adapted to domestic pigs, two have spread beyond the African continent and have been the focus of efforts to develop vaccines against ASF. Most of the experimental ASF vaccines described do not protect against a wider spectrum of viruses and may be less useful in the event of incursions of different strains or where multiple genotypes co-exist. The other three pig-adapted strains that are currently restricted to the ECSA region might spread, and priority should be given to understanding not only the genetic and antigenic characteristics of these viruses but also their history. We review historic and current knowledge of the distribution of these five virus genotypes, and note that as was the case for genotype II, some pig-associated viruses have the propensity for geographical range expansion. These features are valuable for prioritizing vaccine-development efforts to ensure a swift response to virus escape. However, whilst ASF vaccines are critical for high-production systems, global food security relies on parallel efforts to improve biosecurity and pig production in Africa and on continued ASFV surveillance and characterisation in the ECSA region.
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Affiliation(s)
- Mary-Louise Penrith
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- Correspondence: or
| | - Juanita Van Heerden
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa
| | - Livio Heath
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa
| | - Edward Okoth Abworo
- Biosciences, Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
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Hien ND, Nguyen LT, Hoang LT, Bich NN, Quyen TM, Isoda N, Sakoda Y. First Report of a Complete Genome Sequence of a Variant African Swine Fever Virus in the Mekong Delta, Vietnam. Pathogens 2022; 11:pathogens11070797. [PMID: 35890041 PMCID: PMC9318516 DOI: 10.3390/pathogens11070797] [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: 06/14/2022] [Revised: 07/04/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
The objective of this study is to report the complete-genome sequence of a field African swine fever (ASF) virus (ASFV), namely ASF/VN/CanTho-OM/2021, which caused a fatal outbreak in domestic pigs in the Mekong Delta. Complete-genome sequencing detected an 18 bp nucleotide deletion in the EP402R gene (encoding for serotype-specific proteins CD2v) of ASF/VN/CanTho-OM/2021, which was determined to belong to genotype 2 and serotype 8. This mutation pattern was confirmed as unique in GenBank; thus, ASF/VN/CanTho-OM/2021 can be considered a novel variant, with a potential change of sero-characteristics within genotype 2. An additional unique mutation of 78 bp nucleotide insertion was also observed in the B475L gene. Additionally, four copies of tandem repeat sequences were found in the intergenic region (IGR) located between I73R and I329L, previously assigned as the IGR III variant. This study is the first to report the complete genome of ASFV in the Mekong Delta, and it highlights the necessity of strengthening molecular surveillance to provide further knowledge on the evolution and incursion of ASFV in the Mekong Delta and Vietnam.
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Affiliation(s)
- Nguyen Duc Hien
- Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho 900000, Vietnam; (L.T.N.); (L.T.H.); (N.N.B.); (T.M.Q.)
- Can Tho Sub-Department of Animal Health, Ministry of Agriculture and Rural Development, 30/4 Street, Ninh Kieu District, Can Tho 900000, Vietnam
- Correspondence: (N.D.H.); (Y.S.); Tel.: +84-292-384-0371 (N.D.H.); +81-011-706-5207 (Y.S.); Fax: +84-292-384-037 (N.D.H.); +81-1-1706-5273 (Y.S.)
| | - Lam Thanh Nguyen
- Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho 900000, Vietnam; (L.T.N.); (L.T.H.); (N.N.B.); (T.M.Q.)
| | - Le Trung Hoang
- Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho 900000, Vietnam; (L.T.N.); (L.T.H.); (N.N.B.); (T.M.Q.)
- Can Tho Sub-Department of Animal Health, Ministry of Agriculture and Rural Development, 30/4 Street, Ninh Kieu District, Can Tho 900000, Vietnam
| | - Nguyen Ngoc Bich
- Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho 900000, Vietnam; (L.T.N.); (L.T.H.); (N.N.B.); (T.M.Q.)
| | - To My Quyen
- Department of Veterinary Medicine, College of Agriculture, Can Tho University, Campus II, 3/2 Street, Ninh Kieu District, Can Tho 900000, Vietnam; (L.T.N.); (L.T.H.); (N.N.B.); (T.M.Q.)
| | - Norikazu Isoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan;
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, North 18, West 9, Kita-ku, Sapporo 060-0818, Hokkaido, Japan;
- Correspondence: (N.D.H.); (Y.S.); Tel.: +84-292-384-0371 (N.D.H.); +81-011-706-5207 (Y.S.); Fax: +84-292-384-037 (N.D.H.); +81-1-1706-5273 (Y.S.)
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Shi K, Liu H, Yin Y, Si H, Long F, Feng S. Molecular Characterization of African Swine Fever Virus From 2019-2020 Outbreaks in Guangxi Province, Southern China. Front Vet Sci 2022; 9:912224. [PMID: 35782548 PMCID: PMC9240437 DOI: 10.3389/fvets.2022.912224] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
African swine fever virus (ASFV) causes contagious hemorrhagic disease of pigs with high morbidity and mortality. To identify the molecular characteristics of ASFV strains circulating in Guangxi province, southern China, a total of 336 tissue samples collected from 336 domestic pigs that died as a result of severe hemorrhagic disease during 2019–2020 were tested for ASFV. Furthermore, 66 ASFV strains were genetically characterized by sequence analysis of the C-terminal region of B646L (p72) gene, the complete E183L (p54) gene, the variable region of EP402R (CD2v) gene, the central variable region (CVR) of B602L gene, the full MGF505-2R gene, and the tandem repeat sequence (TRS) within intergenic region (IGR) between the I73R and I329L (I73R/I329L) genes. Phylogenetic analysis revealed that the ASFV strains from Guangxi province belonged to genotypes I and II based on the B646L (p72) and E183L (p54) genes, and there were eight different tetrameric TRS variants based on the CVR of B602L gene. Phylogenetic analysis of the EP402R (CD2v) gene revealed that these ASFV strains belonged to serogroups 4 and 8. Eight of the 66 strains belonged to genotype I and serogroup 4, and showed deletion of whole MGF505-2R gene. The sequence analysis of the IGR between the I73R/I329L genes showed that IGR II and III variants were co-circulating in Guangxi province. The results indicated that ASFV strains circulating in Guangxi province during 2019–2020 outbreaks showed high genetic diversity, of which genotypes I and II, as well as serogroups 4 and 8, were simultaneously circulating in Guangxi province, and there existed wild-type and naturally gene-deleted strains in the field. This is the first detailed report on the molecular characterization of the ASFV strains circulating in southern China, and serogroup 4 in China.
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Affiliation(s)
- Kaichuang Shi
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
- College of Animal Science and Technology, Guangxi University, Nanning, China
- *Correspondence: Kaichuang Shi
| | - Huixin Liu
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yanwen Yin
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Hongbin Si
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Hongbin Si
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Shuping Feng
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
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Cho KH, Kim HJ, Jang MK, Ryu JH, Yoo D, Kang HE, Park JY. Detection of African Swine Fever at an Abattoir in South Korea, 2020. Vet Sci 2022; 9:vetsci9040150. [PMID: 35448648 PMCID: PMC9028545 DOI: 10.3390/vetsci9040150] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023] Open
Abstract
In October 2020, a suspect case of African swine fever (ASF) was detected at an abattoir located in the north-central border region of South Korea. The farm of origin was traced and confirmed positive for ASF. This recurrence was following a period of absence of outbreaks in domestic pigs after the first incursion in 2019, during which a total of 14 domestic pig farms were confirmed between September and October 2019. In 2020, a total of two farms were confirmed, and the molecular characterization of key regions of the genome showed that the two isolates from 2020 were identical with the previous isolates from South Korea in 2019. The continued spread and circulation of ASF in the wild boar population represents an increased risk of spill-over outbreaks in domestic pigs, and, therefore, additional control measures should be implemented for farms in these regions, including a heightened level of surveillance. This was the case for the index farm, which was required to send pigs only to the designated abattoir at which the suspect case was quickly detected. The improvement of biosecurity in pig farms, particularly at the wild boar-domestic pig interface, will be key to the successful control of ASF in the region.
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Affiliation(s)
- Ki-Hyun Cho
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Korea; (K.-H.C.); (M.-K.J.); (J.-H.R.); (H.-E.K.)
| | - Hyun-Joo Kim
- National Institute of Health, Osong Health Technology Administration Complex, 187, Osongsaengmyeong 2-ro, Osong-eup, Heungduk-gu, Cheongju 28159, Korea;
| | - Min-Kyung Jang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Korea; (K.-H.C.); (M.-K.J.); (J.-H.R.); (H.-E.K.)
| | - Ji-Hyoung Ryu
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Korea; (K.-H.C.); (M.-K.J.); (J.-H.R.); (H.-E.K.)
| | - Daesung Yoo
- Department of Public Health, Graduate School, Korea University, 75 Goryeodae-ro, Seongbuk-gu, Seoul 02841, Korea;
| | - Hae-Eun Kang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Korea; (K.-H.C.); (M.-K.J.); (J.-H.R.); (H.-E.K.)
| | - Jee-Yong Park
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, 177 Hyeoksin 8-ro, Gimcheon 39660, Korea; (K.-H.C.); (M.-K.J.); (J.-H.R.); (H.-E.K.)
- Correspondence: ; Tel.: +82-54-912-0858
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A systematic review of genotypes and serogroups of African swine fever virus. Virus Genes 2022; 58:77-87. [PMID: 35061204 PMCID: PMC8778497 DOI: 10.1007/s11262-021-01879-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 11/20/2021] [Indexed: 11/04/2022]
Abstract
African swine fever virus (ASFV) is the causative agent of African swine fever (ASF). The virus causes an acute highly hemorrhagic disease in domestic pigs, with high mortality. Although the overall genome mutation rate of ASFV, a large DNA virus, is relatively low, ASFV exhibits genetic and antigenic diversity. ASFV can be classified into 24 genotypes on the basis of the B646L gene. Cross-protected ASFV strains can be divided into eight serogroups on the basis of antibody-mediated hemadsorption inhibition. Here, we review research progress on ASFV genotyping and serogrouping, and explain how this information assists in the rapid identification of virus origin during ASF outbreaks and will aid in the development of ASF vaccines.
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11
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Zhu Z, Ge S, Cai Z, Wu Y, Lu C, Zhang Z, Fu P, Mao L, Wu X, Peng Y. Systematic identification and characterization of repeat sequences in African swine fever virus genomes. Vet Res 2022; 53:101. [PMID: 36461107 PMCID: PMC9717548 DOI: 10.1186/s13567-022-01119-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/19/2022] [Indexed: 12/03/2022] Open
Abstract
African swine fever virus (ASFV) is a large DNA virus that infects domestic pigs with high morbidity and mortality rates. Repeat sequences, which are DNA sequence elements that are repeated more than twice in the genome, play an important role in the ASFV genome. The majority of repeat sequences, however, have not been identified and characterized in a systematic manner. In this study, three types of repeat sequences, including microsatellites, minisatellites and short interspersed nuclear elements (SINEs), were identified in the ASFV genome, and their distribution, structure, function, and evolutionary history were investigated. Most repeat sequences were observed in noncoding regions and at the 5' end of the genome. Noncoding repeat sequences tended to form enhancers, whereas coding repeat sequences had a lower ratio of alpha-helix and beta-sheet and a higher ratio of loop structure and surface amino acids than nonrepeat sequences. In addition, the repeat sequences tended to encode penetrating and antimicrobial peptides. Further analysis of the evolution of repeat sequences revealed that the pan-repeat sequences presented an open state, showing the diversity of repeat sequences. Finally, CpG islands were observed to be negatively correlated with repeat sequence occurrences, suggesting that they may affect the generation of repeat sequences. Overall, this study emphasizes the importance of repeat sequences in ASFVs, and these results can aid in understanding the virus's function and evolution.
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Affiliation(s)
- Zhaozhong Zhu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Shengqiang Ge
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Zena Cai
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Yifan Wu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Congyu Lu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Zheng Zhang
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Ping Fu
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Longfei Mao
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
| | - Xiaodong Wu
- grid.414245.20000 0004 6063 681XChina Animal Health and Epidemiology Center, Qingdao, 266032 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Animal Biosafety Risk Prevention and Control (South), Ministry of Agriculture and Rural Affairs, Qingdao, China
| | - Yousong Peng
- grid.67293.39Bioinformatics Center, College of Biology, Hunan Provincial Key Laboratory of Medical Virology, Hunan University, Changsha, 410082 China
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12
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Cho KH, Kim HJ, Kim DY, Yoo D, Nah JJ, Kim YJ, Kang HE. Surveillance of ASF-infected pig farms from September to October 2019 in South Korea. J Vet Sci 2021; 22:e26. [PMID: 33774941 PMCID: PMC8007448 DOI: 10.4142/jvs.2021.22.e26] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 11/22/2022] Open
Abstract
Fourteen African swine fever (ASF) outbreaks occurred in the pig farms in the northwestern region of South Korea, near the border with North Korea, from September 16, 2019 to October 9, 2019. Active and passive surveillance on the ASF-infected farms indicated that the infection was limited only to pigsties where the infected pigs were detected on the farm for the first time before further transmission to other pigsties and farms. This early detection could be one of the pivotal factors for the prompt eradication of ASF in domestic pig farms within 1 month in the northwestern region of South Korea.
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Affiliation(s)
- Ki Hyun Cho
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hyun Joo Kim
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Da Young Kim
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Daesung Yoo
- Department of Public Health, Graduate School, Korea University, Seoul 02841, Korea
| | - Jin Ju Nah
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Yong Joo Kim
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea
| | - Hae Eun Kang
- Animal and Plant Quarantine Agency, Gimcheon 39660, Korea.
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13
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Kim SH, Lee SI, Jeong HG, Yoo J, Jeong H, Choi Y, Son K, Jheong WH. Rapid emergence of African swine fever virus variants with different numbers of a tandem repeat sequence in South Korea. Transbound Emerg Dis 2020; 68:1726-1730. [PMID: 33012101 PMCID: PMC8359160 DOI: 10.1111/tbed.13867] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/02/2020] [Accepted: 09/26/2020] [Indexed: 11/29/2022]
Abstract
African swine fever virus variants with different numbers of a 10‐bp tandem repeat were isolated in South Korea soon after being identified in wild boar. The short emergence periods and sympatric distributions within a narrow geographical region suggest that the variants were sporadically generated in the pre‐existing viral population.
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Affiliation(s)
- Seon-Hee Kim
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
| | - Song-I Lee
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
| | - Hyun-Gi Jeong
- Nakdong River Environment Research Center, National Institute of Environmental Research, Daegu, South Korea
| | - Jongchan Yoo
- Nakdong River Basin Environment Office, Ministry of Environment, Changwon, South Korea
| | - Hyesung Jeong
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
| | - Yongjun Choi
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
| | - Kidong Son
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
| | - Weon-Hwa Jheong
- Biosafety Research Team, Environmental Health Research Department, National Institute of Environmental Research, Incheon, South Korea
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14
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Isolation and Genetic Characterization of African Swine Fever Virus from Domestic Pig Farms in South Korea, 2019. Viruses 2020; 12:v12111237. [PMID: 33143155 PMCID: PMC7693868 DOI: 10.3390/v12111237] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/28/2020] [Accepted: 10/28/2020] [Indexed: 11/18/2022] Open
Abstract
On 17 September 2019, the first outbreak of African swine fever in a pig farm was confirmed in South Korea. By 9 October, 14 outbreaks of ASF in domestic pigs had been diagnosed in 4 cities/counties. We isolated viruses from all infected farms and performed genetic characterization. The phylogenetic analysis showed that all of fourteen ASFV isolates in South Korea belong to genotype II and serogroup 8. Additionally, all isolates had an intergenic region (IGR) II variant with additional tandem repeat sequences (TRSs) between the I73R and I329L genes and showed characteristics of central variable region (CVR) 1 of the B602L gene and IGR 1 of MGF 505 9R/10R genes. These are identical to the genetic characteristics of some European isolates and Chinese isolates.
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