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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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2
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Zhao D, Sun E, Huang L, Ding L, Zhu Y, Zhang J, Shen D, Zhang X, Zhang Z, Ren T, Wang W, Li F, He X, Bu Z. Highly lethal genotype I and II recombinant African swine fever viruses detected in pigs. Nat Commun 2023; 14:3096. [PMID: 37248233 DOI: 10.1038/s41467-023-38868-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
African swine fever virus (ASFV) poses a great threat to the global pig industry and food security. Currently, 24 ASFV genotypes have been reported but it is unclear whether recombination of different genotype viruses occurs in nature. In this study, we detect three recombinants of genotype I and II ASFVs in pigs in China. These recombinants are genetically similar and classified as genotype I according to their B646L gene, yet 10 discrete fragments accounting for over 56% of their genomes are derived from genotype II virus. Animal studies with one of the recombinant viruses indicate high lethality and transmissibility in pigs, and deletion of the virulence-related genes MGF_505/360 and EP402R derived from virulent genotype II virus highly attenuates its virulence. The live attenuated vaccine derived from genotype II ASFV is not protective against challenge of the recombinant virus. These naturally occurring recombinants of genotype I and II ASFVs have the potential to pose a challenge to the global pig industry.
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Affiliation(s)
- Dongming Zhao
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Encheng Sun
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Lianyu Huang
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Leilei Ding
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Yuanmao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Jiwen Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Dongdong Shen
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xianfeng Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Zhenjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Tao Ren
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Wan Wang
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Fang Li
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Xijun He
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China
| | - Zhigao Bu
- State Key Laboratory for Animal Disease Control and Prevention, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, People's Republic of China.
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, People's Republic of China.
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Mazloum A, van Schalkwyk A, Chernyshev R, Igolkin A, Heath L, Sprygin A. A Guide to Molecular Characterization of Genotype II African Swine Fever Virus: Essential and Alternative Genome Markers. Microorganisms 2023; 11:microorganisms11030642. [PMID: 36985215 PMCID: PMC10056344 DOI: 10.3390/microorganisms11030642] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/25/2023] [Accepted: 03/01/2023] [Indexed: 03/06/2023] Open
Abstract
African swine fever is a contagious viral disease that has been spreading through Europe and Asia since its initial report from Georgia in 2007. Due to the large genome size of the causative agent, the African swine fever virus (ASFV), the molecular epidemiology, and virus evolution are analyzed by employing different markers. Most of these markers originate from single nucleotide polymorphisms or disparities in the copy number of tandem repeat sequences observed during the comparisons of full genome sequences produced from ASFVs isolated during different outbreaks. Therefore, consistent complete genome sequencing and comparative analysis of the sequence data are important to add innovative genomic markers that contribute to the delineation of ASFV phylogeny and molecular epidemiology during active circulation in the field. In this study, the molecular markers currently employed to assess the genotype II ASFVs circulating in Europe and Asia have been outlined. The application of each of these markers to differentiate between ASFVs from related outbreaks is described to implement a guideline to their suitability for analyzing new outbreaks. These markers do not signify the complete repertoire of genomic differences between ASFVs, but will be beneficial when analyzing the first outbreaks in a new region or a large number of samples. Furthermore, new markers must be determined via complete genome sequence analyses for enabling in-depth insights into the molecular epidemiology of ASFV.
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Affiliation(s)
- Ali Mazloum
- Federal Center for Animal Health, 600901 Vladimir, Russia
- Correspondence: (A.M.); (A.S.)
| | - Antoinette van Schalkwyk
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 Old Soutpan Road, Onderstepoort 0110, South Africa
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7535, South Africa
| | | | - Alexey Igolkin
- Federal Center for Animal Health, 600901 Vladimir, Russia
| | - Livio Heath
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 Old Soutpan Road, Onderstepoort 0110, South Africa
| | - Alexander Sprygin
- Federal Center for Animal Health, 600901 Vladimir, Russia
- Correspondence: (A.M.); (A.S.)
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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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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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Nguyen VT, Cho KH, Mai NTA, Park JY, Trinh TBN, Jang MK, Nguyen TTH, Vu XD, Nguyen TL, Nguyen VD, Ambagala A, Kim YJ, Le VP. Multiple variants of African swine fever virus circulating in Vietnam. Arch Virol 2022; 167:1137-1140. [PMID: 35190886 DOI: 10.1007/s00705-022-05363-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/04/2021] [Indexed: 11/29/2022]
Abstract
African swine fever (ASF) is a contagious and deadly viral disease affecting swine of all ages. ASF was first reported in Vietnam in February 2019, and it is now considered endemic in Vietnam. In this study, 122 ASF-positive samples collected from domestic pigs in 28 different provinces of northern, central, and southern Vietnam during outbreaks in 2019-2021 were genetically characterized. The findings confirmed that all ASF virus (ASFV) strains circulating in Vietnam belonged to p72 genotype II, p54 genotype II, CD2v serogroup 8, and CVR gene variant type I. However, further analysis based on the tandem repeat sequences located between I73R and I329L genes revealed that there were three different variants of ASFV, IGR I, II, and III, circulating in the domestic pig population in Vietnam. The IGR II variants were the most prevalent (117/122 strains) and were detected in pigs in all of the provinces tested, followed by IGR III (4/122 strains) and IGR I (1/122 strains). This study confirms for the first time the presence of IGR III variants in Vietnam.
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Affiliation(s)
- Van Tam Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Ki-Hyun Cho
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Nguyen Tuan Anh Mai
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Jee-Yong Park
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Thi Bich Ngoc Trinh
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Min-Kyung Jang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Thi Thu Huyen Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam.,Bac Giang Agriculture and Forestry University, Bac Giang, Vietnam
| | - Xuan Dang Vu
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi Lan Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Van Diep Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Yong-Joo Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea.
| | - Van Phan Le
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam.
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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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Sheng T, Song G, Yue T, Zhang J, Wang W, Yang Z, Lu Q. Whole-genome sequencing and antimicrobial resistance analysis of multidrug-resistant Aeromonas veronii strain JC529 from a common carp. J Glob Antimicrob Resist 2021; 27:118-122. [PMID: 34508865 DOI: 10.1016/j.jgar.2021.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/06/2021] [Accepted: 08/19/2021] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVES Aeromonas veronii can cause infections in humans and a wide variety of aquatic and terrestrial animals as well as causing serious economic losses in aquaculture worldwide. Aeromonas veronii strain JC529 was isolated from an infected common carp in a fish pond in Jilin Province. In this study, we identified the multidrug resistance genes and traced the source of the strain in order to lay the foundation for research on the resistance mechanisms of other Aeromonas isolates. METHODS The isolated strain was sequenced using PacBio RS II and Illumina HiSeq 4000 platforms. Corrected reads were assembled using Celera and Falcon software and genes were predicted using Glimmer software. Seven databases were used for general function annotation. Virulence factors and resistance genes were identified based on the core data set in the VFDB and ARDB databases. Concurrently, 68 publicly available A. veronii genomes (including A. veronii JC529) were compared to reveal the clustering relationship of JC529. RESULTS Aeromonas veronii strain JC529 has a circular chromosome of 4 834 659 bp with a GC content of 59.64%, including 4264 protein-coding genes, 2 prophages, 482 virulence factors and 27 antibiotic resistance genes, indicating that strain JC529 is a multidrug-resistant strain. The phylogenetic tree showed that strains JC529 and NS, PDB, AG5.28.6 and VCK1 appear to be inherited from a common ancestor and affect aquaculture in China and Greece. CONCLUSION Strain JC529 is a multidrug-resistant A. veronii strain and has been inherited from a common ancestor with Greece.
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Affiliation(s)
- Tiange Sheng
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Gege Song
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Taotao Yue
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Junhui Zhang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Wendong Wang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Zhenguo Yang
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China
| | - Qiang Lu
- Key Laboratory of Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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11
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Hakizimana JN, Ntirandekura JB, Yona C, Nyabongo L, Kamwendo G, Chulu JLC, Ntakirutimana D, Kamana O, Nauwynck H, Misinzo G. Complete genome analysis of African swine fever virus responsible for outbreaks in domestic pigs in 2018 in Burundi and 2019 in Malawi. Trop Anim Health Prod 2021; 53:438. [PMID: 34402985 PMCID: PMC8368048 DOI: 10.1007/s11250-021-02877-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/30/2021] [Indexed: 12/31/2022]
Abstract
Several African swine fever (ASF) outbreaks in domestic pigs have been reported in Burundi and Malawi and whole-genome sequences of circulating outbreak viruses in these countries are limited. In the present study, complete genome sequences of ASF viruses (ASFV) that caused the 2018 outbreak in Burundi (BUR/18/Rutana) and the 2019 outbreak in Malawi (MAL/19/Karonga) were produced using Illumina next-generation sequencing (NGS) platform and compared with other previously described ASFV complete genomes. The complete nucleotide sequences of BUR/18/Rutana and MAL/19/Karonga were 176,564 and 183,325 base pairs long with GC content of 38.62 and 38.48%, respectively. The MAL/19/Karonga virus had a total of 186 open reading frames (ORFs) while the BUR/18/Rutana strain had 151 ORFs. After comparative genomic analysis, the MAL/19/Karonga virus showed greater than 99% nucleotide identity with other complete nucleotides sequences of p72 genotype II viruses previously described in Tanzania, Europe and Asia including the Georgia 2007/1 isolate. The Burundian ASFV BUR/18/Rutana exhibited 98.95 to 99.34% nucleotide identity with genotype X ASFV previously described in Kenya and in Democratic Republic of the Congo (DRC). The serotyping results classified the BUR/18/Rutana and MAL/19/Karonga ASFV strains in serogroups 7 and 8, respectively. The results of this study provide insight into the genetic structure and antigenic diversity of ASFV strains circulating in Burundi and Malawi. This is important in order to understand the transmission dynamics and genetic evolution of ASFV in eastern Africa, with an ultimate goal of designing an efficient risk management strategy against ASF transboundary spread.
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Affiliation(s)
- Jean N Hakizimana
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3019, Morogoro, Tanzania
| | - Jean B Ntirandekura
- Department of Animal Health and Productions, University of Burundi, PO Box 1550, Bujumbura, Burundi
| | - Clara Yona
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.,Department of Biosciences, Solomon Mahlangu College of Science and Education, Sokoine University of Agriculture, PO Box 3038, Morogoro, Tanzania
| | - Lionel Nyabongo
- National Veterinary Laboratory of Burundi, PO Box 227, Bujumbura, Burundi
| | - Gladson Kamwendo
- Department of Animal Health and Livestock Development, Ministry of Agriculture, Irrigation and Water Development, PO Box 2096, Lilongwe, Malawi
| | - Julius L C Chulu
- Department of Animal Health and Livestock Development, Ministry of Agriculture, Irrigation and Water Development, PO Box 2096, Lilongwe, Malawi
| | | | - Olivier Kamana
- Department of Applied Research and Development and Foresight Incubation, National Industrial Research and Development Agency, PO Box 273, Kigali, Rwanda
| | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania. .,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, PO Box 3019, Morogoro, Tanzania.
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12
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Complete Genome Sequence of African Swine Fever Virus Isolated from a Domestic Pig in Timor-Leste, 2019. Microbiol Resour Announc 2021; 10:e0026321. [PMID: 34197195 PMCID: PMC8248885 DOI: 10.1128/mra.00263-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the complete genome sequence of the African swine fever virus (ASFV) isolate ASFV/Timor-Leste/2019/1, isolated from a domestic pig during the first outbreak of ASF in Timor-Leste in 2019. Using target enrichment short-read Illumina data combined with long-read Oxford Nanopore data, we assembled a full-length genome sequence of 192,237 bp.
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Mai NTA, Vu XD, Nguyen TTH, Nguyen VT, Trinh TBN, Kim YJ, Kim HJ, Cho KH, Nguyen TL, Bui TTN, Jeong DG, Yoon SW, Truong T, Ambagala A, Song D, Le VP. Molecular profile of African swine fever virus (ASFV) circulating in Vietnam during 2019-2020 outbreaks. Arch Virol 2021; 166:885-890. [PMID: 33454861 DOI: 10.1007/s00705-020-04936-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/09/2020] [Indexed: 10/22/2022]
Abstract
African swine fever (ASF) is a highly infectious disease of pigs caused by African swine fever virus (ASFV). In order to identify potential genetic variations among ASFV strains circulating in Vietnam, 26 ASFV isolates from organs and blood samples collected from domestic pigs from 23 different provinces of northern, central and southern Vietnam during 2019-2020 ASF outbreaks were genetically characterized. Nucleotide sequences were determined for a portion of the B646L (p72) gene, the complete E183L (p54) gene, the variable region of EP402R (CD2v), the central variable region (CVR) of pB602L, and a tandem repeat sequence (TRS) between the I73R and I329L genes. Analysis of the partial B646L (p72) and EP402R (CD2v) gene sequences and the full-length E183L (p54) gene sequence showed that all 26 ASFV isolates belonged to genotype II and serotype VIII and that they were identical to the strain Georgia/2007/1 and all ASFV strains sequenced in China. The TRS between the I73R and I329L genes contained a 10-nucleotide insertion that was observed in the Chinese ASFV strain CN201801 isolated from domestic pigs in 2018, but not in the Georgia/2007/1 and China/Jilin/2018/boar strains isolated from wild boar in China. This is the first intra-epidemic genome analysis reported for the ASFV strains circulating in Vietnam.
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Affiliation(s)
- Nguyen Tuan Anh Mai
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Xuan Dang Vu
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi Thu Huyen Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Van Tam Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi Bich Ngoc Trinh
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Yong Joo Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Hyun-Joo Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Ki-Hyun Cho
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon, South Korea
| | - Thi Lan Nguyen
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Thi To Nga Bui
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Dae Gwin Jeong
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Sun-Woo Yoon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Thang Truong
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Daesub Song
- College of Pharmacy, Korea University, Sejong, South Korea
| | - Van Phan Le
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam.
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14
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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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15
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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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The Spillover of African Swine Fever in Western Poland Revealed Its Estimated Origin on the Basis of O174L, K145R, MGF 505-5R and IGR I73R/I329L Genomic Sequences. Viruses 2020; 12:v12101094. [PMID: 32992547 PMCID: PMC7601147 DOI: 10.3390/v12101094] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023] Open
Abstract
The African swine fever epidemic occurred in Poland at the beginning of 2014 and, up to date, the disease has been spreading mainly in the eastern part of the country. Unexpectedly, in November 2019 an infected wild boar case was confirmed in Lubuskie voivodship in western Poland. During the following weeks, several dozen African swine fever virus (ASFV)-positive animals were notified in the neighboring area, causing severe concern regarding further spread of the disease to the mostly pig-dense region in Poland, namely, Wielkopolskie voivodship. Moreover, almost a year after, several infected wild boar cases were confirmed for the first time in Germany, just beyond the Polish border, sending out a shock wave through the global pig market. The whole genome sequence of ASFV, isolated from the first case of ASF in western Poland, and three selected viruses from other affected areas, revealed the tandem repeat and single nucleotide polymorphism (SNP) variations in reference to the Georgia 2007/1 strain. These data, supported by the conventional sequencing of selected genomic regions from a total of 154 virus samples isolated between 2017 and 2020 in Poland, shed a new light on pathogen epidemiology. The sequence variations within the O174L gene detected in this study showed that cases identified in western Poland might be originating from the so-called southern Warsaw cluster. Moreover, the viruses originating from the northern Warsaw cluster do not possess single nucleotide polymorphism (SNP) mutations within the K145R and MGF 505-5R genes, which are specific to all of the other Polish ASFV strains. These results led to a conclusion of their distinct origin. Supporting these results, the nucleotide sequencing of I73R/I329L intergenic region revealed its new, previously undescribed variant, called IGR IV, with an additional three tandem repeats of 10 nucleotides in comparison to the reference sequence of the Georgia 2007/1 strain.
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17
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Meekins DA, Trujillo JD, Gaudreault NN, Morozov I, Pérez-Núñez D, Revilla Y, Richt JA. Long amplicon sequencing for improved genetic characterization of African swine fever virus. J Virol Methods 2020; 285:113946. [PMID: 32758620 DOI: 10.1016/j.jviromet.2020.113946] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 11/26/2022]
Abstract
African Swine Fever Virus (ASFV) causes a transmissible and fatal disease in pigs that is currently devastating global swine production. Efficient and economical collection of genetic data from ASFV field isolates is essential for bio-surveillance, to limit and control its spread, and to better understand ASF disease ecology. Standard genotyping and subtyping of ASFV field isolates is currently limited to a few variable regions within the ASFV genome. However, more extensive sequencing is necessary to better understand ASFV molecular evolution and identify regions relevant to genetic diversity. In this study, we developed a method for rapid and efficient next generation sequencing of approximately 40% of the ASFV genome using long PCR amplification of six different genomic regions. The amplified regions contain all segments currently used for genotyping and additional genes predicted to contribute to ASFV diversity. The primers used for amplification are broadly compatible with published ASFV genomes, permitting their use on relevant ASFV isolates. This methodology provides the enhanced depth of coverage of amplicon-based sequencing while mitigating complications associated with ASFV whole-genome sequencing. Implementation of this methodology could substantially increase the scale of ASFV genetic data collection, which is necessary to effectively monitor and combat this critical agricultural disease.
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Affiliation(s)
- David A Meekins
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Jessie D Trujillo
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Natasha N Gaudreault
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Igor Morozov
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA
| | - Daniel Pérez-Núñez
- CBMSO-CSIC-UAM, C/Nicolás Cabrera 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Yolanda Revilla
- CBMSO-CSIC-UAM, C/Nicolás Cabrera 1, Campus de Cantoblanco, 28049, Madrid, Spain
| | - Juergen A Richt
- Center of Excellence for Emerging and Zoonotic Animal Diseases, Department of Diagnostic Medicine & Pathobiology, College of Veterinary Medicine, Kansas State University, Manhattan, KS, USA.
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