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Ruedas-Torres I, Thi to Nga B, Salguero FJ. Pathogenicity and virulence of African swine fever virus. Virulence 2024; 15:2375550. [PMID: 38973077 PMCID: PMC11232652 DOI: 10.1080/21505594.2024.2375550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024] Open
Abstract
African swine fever (ASF) is a devastating disease with a high impact on the pork industry worldwide. ASF virus (ASFV) is a very complex pathogen, the sole member of the family Asfaviridae, which induces a state of immune suppression in the host through infection of myeloid cells and apoptosis of lymphocytes. Moreover, haemorrhages are the other main pathogenic effect of ASFV infection in pigs, related to the infection of endothelial cells, as well as the activation and structural changes of this cell population by proinflammatory cytokine upregulation within bystander monocytes and macrophages. There are still many gaps in the knowledge of the role of proteins produced by the ASFV, which is related to the difficulty in producing a safe and effective vaccine to combat the disease, although few candidates have been approved for use in Southeast Asia in the past couple of years.
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Affiliation(s)
- Ines Ruedas-Torres
- Vaccine Development and Evaluation Centre (VDEC), United Kingdom Health Security Agency, Salisbury, UK
| | - Bui Thi to Nga
- Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Francisco J. Salguero
- Vaccine Development and Evaluation Centre (VDEC), United Kingdom Health Security Agency, Salisbury, UK
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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Liang Y, Kuang Q, Zheng X, Xu Y, Feng Y, Xiang Q, Zhang G, Zhou P. Monoclonal antibody development for early detection of ASFV I73R protein: Identification of a linear antigenic epitope. Virology 2024; 597:110145. [PMID: 38941747 DOI: 10.1016/j.virol.2024.110145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/06/2024] [Accepted: 06/18/2024] [Indexed: 06/30/2024]
Abstract
African swine fever virus (ASFV), which was first identified in northern China in 2018, causes high mortality in pigs. Since the I73R protein in ASFV is abundantly expressed during the early phase of virus replication, it can be used as a target protein for early diagnosis. In this study, the I73R protein of ASFV was expressed, and we successfully prepared a novel monoclonal antibody (mAb), 8G11D7, that recognizes this protein. Through both indirect immunofluorescence and Western blotting assays, we demonstrated that 8G11D7 can detect ASFV strains. By evaluating the binding of the antibody to a series of I73R-truncated peptides, the definitive epitope recognized by the monoclonal antibody 8G11D7 was determined to be 58 DKTNTIYPP 66. Bioinformatic analysis revealed that the antigenic epitope had a high antigenic index and conservatism. This study contributes to a deeper understanding of ASFV protein structure and function, helping establish ASFV-specific detection method.
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Affiliation(s)
- Yifan Liang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, 510000, China
| | - Qiyuan Kuang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China
| | - Xiaoyu Zheng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Yifan Xu
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China
| | - Yongzhi Feng
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China
| | - Qinxin Xiang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; Maoming Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Maoming, 525000, China
| | - Guihong Zhang
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, 510000, China.
| | - Pei Zhou
- Guangdong Provincial Key Laboratory of Zoonosis Prevention and Control, College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, China; African Swine Fever Regional Laboratory of China (Guangzhou), Guangzhou, 510642, China; Key Laboratory of Animal Vaccine Development, Ministry of Agriculture and Rural Affairs, Guangzhou, 510000, China.
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Chernyshev RS, Igolkin AS, Shotin AR, Zinyakov NG, Kolbin IS, Sadchikova AS, Lavrentiev IA, Gruzdev KN, Mazloum A. Spatio-temporal clustering of African swine fever virus (Asfarviridae: Asfivirus) circulating in the Kaliningrad region based on three genome markers. Vopr Virusol 2024; 69:241-254. [PMID: 38996373 DOI: 10.36233/0507-4088-231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Indexed: 07/14/2024]
Abstract
INTRODUCTION The rapid spread of African swine fever in the Kaliningrad region makes it necessary to use the methods of molecular epidemiology to determine the dynamics and direction of ASF spread in this region of Russia. The aim of the study was to determine single nucleotide polymorphisms within molecular markers K145R, O174L and MGF 505-5R of ASFVs isolated in Kaliningrad region and to study the circulating of the pathogen in European countries by subgenotyping and spatio-temporal clustering analysis. MATERIALS AND METHODS Blood samples from living domestic pigs and organs from dead domestic pigs and wild boars, collected in the Kaliningrad region between 2017 and 2022 were used. Virus isolation was carried out in porcine bone-marrow primary cell culture. Amplicons of genome markers were amplified by PCR with electrophoretic detection and subsequent extraction of fragments from agarose gel. Sequencing was performed using the Sanger method. RESULTS The circulation of two genetic clusters of ASFV isolates on the territory of the Kaliningrad has been established: epidemic (K145R-III, MGF 505-5R-II, O174L-I - 94.3% of the studied isolates) and sporadic (K145R-II, MGF 505-5R-II, O174L-I - 5.7%). CONCLUSION The broaden molecular genetic surveillance of ASFV isolates based on sequencing of genome markers is necessary in the countries of the Eurasian continent to perform a more detailed analysis of ASF spread between countries and within regions.
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Affiliation(s)
| | | | - A R Shotin
- Federal Center for Animal Health (ARRIAH)
| | | | - I S Kolbin
- Federal Center for Animal Health (ARRIAH)
| | | | | | | | - A Mazloum
- Federal Center for Animal Health (ARRIAH)
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Chernyshev R, Igolkin A, van Schalkwyk A, Zinyakov N, Kolbin I, Shotin A, Korennoy F, Sprygin A, Mazloum A. A proposed update of African swine fever virus (genotype II) subgenotyping based on the central variable region (CVR) of Russian isolates. Arch Virol 2024; 169:147. [PMID: 38879716 DOI: 10.1007/s00705-024-06064-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/06/2024] [Indexed: 07/11/2024]
Abstract
African swine fever virus (ASFV) isolates are grouped and tracked through analysis of their central variable region (CVR) sequences. In this study, sequences of 70 ASFV isolates collected from different regions of Russia between 2018 and 2022 were analyzed. The analysis based on the CVR sequences indicated that the isolates belonged to three distinct groups. Group 1 shared 100% sequence identity to the isolate Georgia 2007/1. Group 5 had a C > A single-nucleotide polymorphism (SNP) at position 601, while group 13 is new and unique to the Far East of Russia, with five isolates from the Amur, Khabarovsk, and Primorsky regions. These findings demonstrate a new approach to phylogenomics and cladistics of ASFV isolates within genotype II on the basis of the CVR.
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Affiliation(s)
| | - Alexey Igolkin
- Federal Center for Animal Health, 600901, Vladimir, Russia
| | - Antoinette van Schalkwyk
- Agricultural Research Council-Onderstepoort Veterinary Institute, 100 Old Soutpan Road, 0110, Onderstepoort, South Africa
- Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, 7535, Bellville, South Africa
| | | | - Ivan Kolbin
- Federal Center for Animal Health, 600901, Vladimir, Russia
| | - Andrey Shotin
- Federal Center for Animal Health, 600901, Vladimir, Russia
| | - Fedor Korennoy
- Federal Center for Animal Health, 600901, Vladimir, Russia
| | | | - Ali Mazloum
- Federal Center for Animal Health, 600901, Vladimir, Russia.
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Chen S, Wang T, Luo R, Lu Z, Lan J, Sun Y, Fu Q, Qiu HJ. Genetic Variations of African Swine Fever Virus: Major Challenges and Prospects. Viruses 2024; 16:913. [PMID: 38932205 PMCID: PMC11209373 DOI: 10.3390/v16060913] [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: 05/06/2024] [Revised: 05/26/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
African swine fever (ASF) is a contagious viral disease affecting pigs and wild boars. It typically presents as a hemorrhagic fever but can also manifest in various forms, ranging from acute to asymptomatic. ASF has spread extensively globally, significantly impacting the swine industry. The complex and highly variable character of the ASFV genome makes vaccine development and disease surveillance extremely difficult. The overall trend in ASFV evolution is towards decreased virulence and increased transmissibility. Factors such as gene mutation, viral recombination, and the strain-specificity of virulence-associated genes facilitate viral variations. This review deeply discusses the influence of these factors on viral immune evasion, pathogenicity, and the ensuing complexities encountered in vaccine development, disease detection, and surveillance. The ultimate goal of this review is to thoroughly explore the genetic evolution patterns and variation mechanisms of ASFV, providing a theoretical foundation for advancement in vaccine and diagnostic technologies.
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Affiliation(s)
- Shengmei Chen
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Tao Wang
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Rui Luo
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Zhanhao Lu
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Jing Lan
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
| | - Yuan Sun
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
| | - Qiang Fu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Hua-Ji Qiu
- College of Life Science and Engineering, Foshan University, Foshan 528231, China
- State Key Laboratory for Animal Disease Control and Prevention, National African Swine Fever Para-Reference Laboratory, National High Containment Facilities for Animal Diseases Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin 150069, China
- College of Animal Sciences, Yangtze University, Jingzhou 434023, China
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Ståhl K, Boklund AE, Podgórski T, Vergne T, Abrahantes JC, Cattaneo E, Papanikolaou A, Mur L. Epidemiological analysis of African swine fever in the European Union during 2023. EFSA J 2024; 22:e8809. [PMID: 38756349 PMCID: PMC11096997 DOI: 10.2903/j.efsa.2024.8809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024] Open
Abstract
In 2023, 14 Member States were affected by African swine fever (ASF), including Croatia and Sweden where ASF emerged (wild boar outbreaks only) and Greece where ASF re-emerged after being free since 2021. The number of ASF outbreaks among domestic pigs in the EU was five times higher than in 2022, reaching a similar magnitude to that in 2019. This was predominantly driven by the introduction and subsequent spread of ASF in Croatia and its resurgence in Romania, representing 96% of the EU outbreaks. ASF outbreaks in domestic pigs were clearly seasonal in all countries, with 88% of outbreaks reported between July and October. Most of the ASF outbreaks among domestic pigs were detected through clinical suspicion (94%), followed by tracing from affected establishments (3%), and the weekly testing of at least two dead pigs in establishments (3%). In wild boar, a 10% increase in the number of notified outbreaks was observed in the EU in comparison with 2022, with considerable variations between countries. A winter peak was observed only in Poland, Slovakia and Hungary. The epidemiological situation in wild boar improved in Germany and Hungary, as suggested by the decrease in the number of outbreaks and in the proportions of PCR-positive samples from dead wild boar. Overall, 31% of wild boar carcasses found during passive surveillance tested positive by PCR, representing 69% of the ASF outbreaks in wild boar in the EU. In contrast, 0.4% of hunted wild boar tested positive, representing 31% of the outbreaks. Despite the introduction of ASF into new countries and the increase in the number of outbreaks, the size of restricted zones in the EU remained stable, due to the highly clustered outbreaks in Croatia, and the reduction of restricted zones in Poland, Slovakia and Bulgaria (in domestic pigs), and Hungary (in wild boar).
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Shi K, Qian X, Shi Y, Wei H, Pan Y, Long F, Zhou Q, Mo S, Hu L, Li Z. A triplex crystal digital PCR for the detection of genotypes I and II African swine fever virus. Front Vet Sci 2024; 11:1351596. [PMID: 38628942 PMCID: PMC11019002 DOI: 10.3389/fvets.2024.1351596] [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: 12/06/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
African swine fever (ASF) is a highly contagious and lethal viral disease that causes severe hemorrhagic fever in pigs. It keeps spreading around the world, posing a severe socioeconomic risk and endangering biodiversity and domestic food security. ASF first outbroke in China in 2018, and has spread to most provinces nationwide. Genotypes I and II ASF virus (ASFV) as the etiological pathogens have been found in China. In this study, three pairs of specific primers and probes targeting the ASFV B646L gene, F1055L gene, and E183L gene were designed to detect universal, genotype I, and genotype II strains, respectively. A triplex crystal digital PCR (cdPCR) was established on the basis of optimizing various reaction conditions. The assay demonstrated remarkably sensitive with low limits of detection (LODs) of 5.120, 4.218, 4.588 copies/reaction for B646L, F1055L, and E183L gene, respectively; excellent repeatability with 1.24-2.01% intra-assay coefficients of variation (CVs) and 1.32-2.53% inter-assay CVs; good specificity for only detection of genotypes I and II ASFV, without cross-reactivity with PCV2, PRV, SIV, PRRSV, PEDV, FMDV, and CSFV. The triplex cdPCR was used to test 1,275 clinical samples from Guangxi province of China, and the positivity rates were 5.05, 3.22, and 1.02% for genotype I, genotype II, and co-infection of genotypes I and II, respectively. These 1,275 clinical samples were also detected using a reported reference triplex real-time quantitative PCR (qPCR), and the agreements of detection results between these two methods were more than 98.98%. In conclusion, the developed triplex cdPCR could be used as a rapid, sensitive, and accurate method to detect and differentiate genotypes I and II strains of ASFV.
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Affiliation(s)
- Kaichuang Shi
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
- College of Animal Science and Technology, Guangxi University, Nanning, China
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Xinxiu Qian
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yuwen Shi
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Haina Wei
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Yi Pan
- School of Basic Medical Sciences, Youjiang Medical University for Nationalities, Baise, China
| | - Feng Long
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Qingan Zhou
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Shenglan Mo
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Liping Hu
- Guangxi Center for Animal Disease Control and Prevention, Nanning, China
| | - Zongqiang Li
- College of Animal Science and Technology, Guangxi University, Nanning, China
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Hiremath J, Hemadri D, Nayakvadi S, Kumar C, Gowda CSS, Sharma D, Ramamoorthy R, Mamatha SS, Patil S, Ranjini RA, Jayamohanan TV, Swapna SA, Gulati BR. Epidemiological investigation of ASF outbreaks in Kerala (India): detection, source tracing and economic implications. Vet Res Commun 2024; 48:827-837. [PMID: 37955753 DOI: 10.1007/s11259-023-10254-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023]
Abstract
This study investigates suspected African swine fever (ASF) outbreaks in two villages of Kannur district in Kerala, India, with the aim of identifying the causative agent and its genotype, the source of infection, and estimating the economic losses due to the outbreaks. Clinically, the disease was acute with high mortality, while gross pathology was characterized by widespread haemorrhages in various organs, especially the spleen, which was dark, enlarged and had friable cut surfaces with diffuse haemorrhages. Notably, histopathological examination revealed multifocal, diffuse haemorrhages in the splenic parenchyma and lymphoid depletion accompanied by lymphoid cell necrosis. The clinico-pathological observations were suggestive of ASF, which was confirmed by PCR. The source of outbreak was identified as swill and it was a likely point source infection as revealed by epidemic curve analysis. The phylogenetic analysis of p72 gene identified the ASFV in the current outbreak as genotype-II and IGR II variant consistent with ASFVs detected in India thus far. However, the sequence analysis of the Central Variable Region (CVR) of the B602L gene showed that the ASFVs circulating in Kerala (South India) formed a separate clade along with those found in Mizoram (North East India), while ASFVs circulating in Arunachal Pradesh and Assam states of India grouped in to different clade. This study represents the first investigation of ASF outbreak in South India, establishing the genetic relatedness of the ASFV circulating in this region with that in other parts of the country. The study also underscores the utility of the CVR of the B602L gene in genetically characterizing highly similar Genotype II ASFVs to understand the spread of ASF within the country.
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Affiliation(s)
- Jagadish Hiremath
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Divakar Hemadri
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Shivasharanappa Nayakvadi
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Chethan Kumar
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | | | - Damini Sharma
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Rajendran Ramamoorthy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Suresh Shankanahalli Mamatha
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | - Sharanagouda Patil
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India
| | | | | | - Susan Abraham Swapna
- Department of Animal Husbandry, State Institute for Animal Diseases, Palode, Kerala, India
| | - Baldev Raj Gulati
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics (NIVEDI), Yelahanka, Bengaluru, Karnataka, India.
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Johnston CM, Olesen AS, Lohse L, le Maire Madsen A, Bøtner A, Belsham GJ, Rasmussen TB. A Deep Sequencing Strategy for Investigation of Virus Variants within African Swine Fever Virus-Infected Pigs. Pathogens 2024; 13:154. [PMID: 38392892 PMCID: PMC10893071 DOI: 10.3390/pathogens13020154] [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: 12/14/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
African swine fever virus (ASFV) is the causative agent of African swine fever, an economically important disease of pigs, often with a high case fatality rate. ASFV has demonstrated low genetic diversity among isolates collected within Eurasia. To explore the influence of viral variants on clinical outcomes and infection dynamics in pigs experimentally infected with ASFV, we have designed a deep sequencing strategy. The variant analysis revealed unique SNPs at <10% frequency in several infected pigs as well as some SNPs that were found in more than one pig. In addition, a deletion of 10,487 bp (resulting in the complete loss of 21 genes) was present at a nearly 100% frequency in the ASFV DNA from one pig at position 6362-16849. This deletion was also found to be present at low levels in the virus inoculum and in two other infected pigs. The current methodology can be used for the currently circulating Eurasian ASFVs and also adapted to other ASFV strains and genotypes. Comprehensive deep sequencing is critical for following ASFV molecular evolution, especially for the identification of modifications that affect virus virulence.
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Affiliation(s)
- Camille Melissa Johnston
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Ann Sofie Olesen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Louise Lohse
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
| | - Agnete le Maire Madsen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Øster Farimagsgade 5, DK-1353 København, Denmark
| | - Anette Bøtner
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark; (A.B.); (G.J.B.)
| | - Graham J. Belsham
- Section for Veterinary Clinical Microbiology, Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Denmark; (A.B.); (G.J.B.)
| | - Thomas Bruun Rasmussen
- Section for Veterinary Virology, Department of Virus & Microbiological Special Diagnostics, Statens Serum Institute, Artillerivej 5, DK-2300 Copenhagen, Denmark; (C.M.J.); (A.S.O.); (L.L.); (A.l.M.M.)
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Simbulan AM, Banico EC, Sira EMJS, Odchimar NMO, Orosco FL. Immunoinformatics-guided approach for designing a pan-proteome multi-epitope subunit vaccine against African swine fever virus. Sci Rep 2024; 14:1354. [PMID: 38228670 DOI: 10.1038/s41598-023-51005-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/29/2023] [Indexed: 01/18/2024] Open
Abstract
Despite being identified over a hundred years ago, there is still no commercially available vaccine for the highly contagious and deadly African swine fever virus (ASFV). This study used immunoinformatics for the rapid and inexpensive designing of a safe and effective multi-epitope subunit vaccine for ASFV. A total of 18,858 proteins from 100 well-annotated ASFV proteomes were screened using various computational tools to identify potential epitopes, or peptides capable of triggering an immune response in swine. Proteins from genotypes I and II were prioritized for their involvement in the recent global ASFV outbreaks. The screened epitopes exhibited promising qualities that positioned them as effective components of the ASFV vaccine. They demonstrated antigenicity, immunogenicity, and cytokine-inducing properties indicating their ability to induce potent immune responses. They have strong binding affinities to multiple swine allele receptors suggesting a high likelihood of yielding more amplified responses. Moreover, they were non-allergenic and non-toxic, a crucial prerequisite for ensuring safety and minimizing any potential adverse effects when the vaccine is processed within the host. Integrated with an immunogenic 50S ribosomal protein adjuvant and linkers, the epitopes formed a 364-amino acid multi-epitope subunit vaccine. The ASFV vaccine construct exhibited notable immunogenicity in immune simulation and molecular docking analyses, and stable profiles in secondary and tertiary structure assessments. Moreover, this study designed an optimized codon for efficient translation of the ASFV vaccine construct into the Escherichia coli K-12 expression system using the pET28a(+) vector. Overall, both sequence and structural evaluations suggested the potential of the ASFV vaccine construct as a candidate for controlling and eradicating outbreaks caused by the pathogen.
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Affiliation(s)
- Alea Maurice Simbulan
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Edward C Banico
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Ella Mae Joy S Sira
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Nyzar Mabeth O Odchimar
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines
| | - Fredmoore L Orosco
- Department of Science and Technology, Virology and Vaccine Research and Development Program, Industrial Technology Development Institute, Bicutan, 1634, Taguig, Metro Manila, Philippines.
- Department of Science and Technology, S&T Fellows Program, Bicutan, 1634, Taguig, Metro Manila, Philippines.
- Department of Biology, University of the Philippines Manila, 1000, Manila, Philippines.
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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, Hong SK, Kim DY, Jang MK, Kim JH, Lee H, Kim EM, Park JH, Suh TY, Choi JG, Yoo DS, Kang HE, Kim YH. Pathogenicity and Pathological Characteristics of African Swine Fever Virus Strains from Pig Farms in South Korea from 2022 to January 2023. Pathogens 2023; 12:1158. [PMID: 37764966 PMCID: PMC10534632 DOI: 10.3390/pathogens12091158] [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: 08/10/2023] [Revised: 09/06/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Since the first African swine fever (ASF) outbreak occurred at a pig farm in South Korea in September 2019, as of 31 January 2023, 31 ASF cases have occurred at pig farms, while 2799 ASF virus (ASFV)-infected wild boars have been identified. The circulation of ASFV in wild boar populations poses a high risk of spillover to pig farms in the country. However, information on the changes in the pathogenicity of Korean ASFV strains from wild boars is not available. Investigating the pathogenicity of ASFV strains from pig farms is the only way to predict their alterations. In a previous study, no changes in the pathogenicity of ASFV strains circulating during 2019-2021 were identified through animal experiments. In this study, we chose two ASFV strains with potentially reduced pathogenicity among ten viruses obtained from pig premises from 2022 to January 2023 and estimated their pathogenicities and pathological characteristics. All the inoculated pigs died 8-10 days post-inoculation after showing pyrexia, depression, anorexia, and recumbency together with the common pathological lesions of enlarged hemorrhagic lymph nodes and splenomegaly with infarction. These results support that the pathogenicity among ASFV isolates in South Korea still remained unchanged during the study period.
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Affiliation(s)
- Ki-Hyun Cho
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Seong-Keun Hong
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Da-Young Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Min-Kyung Jang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Jong-Ho Kim
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (J.-H.K.); (H.L.); (E.-M.K.)
| | - Hyunkyoung Lee
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (J.-H.K.); (H.L.); (E.-M.K.)
| | - Eun-Mi Kim
- Animal Disease Diagnostic Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (J.-H.K.); (H.L.); (E.-M.K.)
| | - Ji-Hoon Park
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Tae-Young Suh
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Jun-Gu Choi
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Dae-Sung Yoo
- College of Veterinary Medicine, Chonnam National University, Gwangju 61186, Republic of Korea;
| | - Hae-Eun Kang
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
| | - Yeon-Hee Kim
- Foreign Animal Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Republic of Korea; (K.-H.C.); (S.-K.H.); (D.-Y.K.); (M.-K.J.); (J.-H.P.); (T.-Y.S.); (J.-G.C.); (H.-E.K.)
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13
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Bru G, Martínez-Candela M, Romero P, Navarro A, Martínez-Murcia A. Internal Validation of the ASFV MONODOSE dtec-qPCR Kit for African Swine Fever Virus Detection under the UNE-EN ISO/IEC 17025:2005 Criteria. Vet Sci 2023; 10:564. [PMID: 37756086 PMCID: PMC10535882 DOI: 10.3390/vetsci10090564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/17/2023] [Accepted: 09/06/2023] [Indexed: 09/28/2023] Open
Abstract
African swine fever virus is considered an emerging virus that causes African swine fever, a disease characterised by high mortality and elevated transmission rates and that, as it is for most other viral diseases, cannot be treated with specific drugs. Effective and reliable detection of the virus is relevant to prevent uncontrolled contagion among boar populations and to reduce economic losses. Moreover, animal health laboratories are demanding standardisation, optimisation and quality assurance of the available diagnostic assays. In the present study, the ASFV MONODOSE dtec-qPCR kit was validated following the UNE-EN ISO/IEC 17025:2005 guidelines. Analytical validation terms include in silico and in vitro specificity, sensitivity, efficiency and reliability (repeatability/reproducibility). Diagnostic validation of the method was assessed through the analysis of a total of 181 porcine samples originating from six different matrix types doped with African swine fever virus DNA received from the European reference laboratory for African Swine Fever (INIA-CISA, Madrid, Spain): whole blood, blood serum, kidney, heart, liver and tonsil. Results agreed with those obtained from a reference detection method also based on real-time PCR, endorsed by WOAH, but the ASFV MONODOSE dtec-qPCR kit incorporates some technical innovations and improvements which may benefit end-users. This kit, available worldwide with full analytical and diagnostic validation, can recognise all known ASFV genotypes and brings additional benefits to the current qPCR technology.
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Affiliation(s)
- Gema Bru
- Genetic PCR Solutions™, 03300 Orihuela, Spain
| | | | | | | | - Antonio Martínez-Murcia
- Genetic PCR Solutions™, 03300 Orihuela, Spain
- Department of Microbiology, University Miguel Hernández, 03312 Orihuela, Spain
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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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15
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Vilem A, Nurmoja I, Tummeleht L, Viltrop A. Differentiation of African Swine Fever Virus Strains Isolated in Estonia by Multiple Genetic Markers. Pathogens 2023; 12:pathogens12050720. [PMID: 37242390 DOI: 10.3390/pathogens12050720] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/08/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
The African swine fever virus (ASFV) was first detected in Estonia, in September 2014. In the subsequent three years, the virus spread explosively all over the country. Only one county, the island of Hiiumaa, remained free of the disease. Due to the drastic decrease in the wild boar population in the period of 2015-2018, the number of ASFV-positive cases among wild boar decreased substantially. From the beginning of 2019 to the autumn of 2020, no ASFV-positive wild boar or domestic pigs were detected in Estonia. A new occurrence of ASFV was detected in August 2020, and by the end of 2022, ASFV had been confirmed in seven counties in Estonia. Investigations into proven molecular markers, such as IGR I73R/I329L, MGF505-5R, K145R, O174L, and B602L, were performed with the aim of clarifying whether these cases of ASFV were new entries or remnants of previous epidemics. The sequences from the period of 2014-2022 were compared to the Georgia 2007/1 reference sequence and the variant strains present in Europe. The results indicated that not all the molecular markers of the virus successfully used in other geographical regions were suitable for tracing the spread of ASFV in Estonia. Only the B602L-gene analysis enabled us to place the ASFV isolates spreading in 2020-2022 into two epidemiologically different clusters.
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Affiliation(s)
- Annika Vilem
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
- The National Centre for Laboratory Research and Risk Assessment, LABRIS, 51006 Tartu, Estonia
| | - Imbi Nurmoja
- The National Centre for Laboratory Research and Risk Assessment, LABRIS, 51006 Tartu, Estonia
| | - Lea Tummeleht
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
| | - Arvo Viltrop
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, 51006 Tartu, Estonia
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16
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Ståhl K, Boklund A, Podgórski T, Vergne T, Abrahantes JC, Papanikolaou A, Zancanaro G, Mur L. Epidemiological analysis of African swine fever in the European Union during 2022. EFSA J 2023; 21:e08016. [PMID: 37223755 PMCID: PMC10201408 DOI: 10.2903/j.efsa.2023.8016] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
This report presents the epidemiological analysis of African swine fever (ASF) during 2022 based on the surveillance and pig population data submitted by the European Union (EU) affected countries and one neighbouring country. Coinciding with regulatory changes and an important decrease in ASF outbreaks in 2022 in the EU, the number of domestic pig samples tested as part of active surveillance decreased by 80%, while the number of samples from passive surveillance almost doubled compared with 2021. Most outbreaks among domestic pigs in the EU were detected by testing clinical suspicions (93% of outbreaks), followed by tracing activities (5%) and weekly testing of the first two dead pigs per establishment (2%). Although most of the wild boar samples came from hunted animals, the probability of detecting PCR-positive animals was much higher in wild boar found dead. The ASF outbreaks among domestic pigs in the EU decreased by 79% while a decrease of 40% in the wild boar cases was observed in comparison with 2021. This was strongly marked in Romania, Poland and Bulgaria, with a reduction of 50-80% compared with 2021. In many countries, an important decrease in the number of pig establishments was observed, especially of small establishments with fewer than 100 pigs. The regional between farm incidence and proportion of pigs lost due to ASF in the EU was in general very low (average of 1%) apart from some regions in Romania. The impact of ASF on wild boar populations was variable, with a decline in wild boar abundance observed in certain countries versus a stable or even increased population after ASF introduction. This supports the negative relationship observed in this report between the proportion of the country with restricted zones due to ASF in wild boar and wild boar hunting bags.
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17
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Hakizimana JN, Yona C, Makange MR, Kasisi EA, Netherton CL, Nauwynck H, Misinzo G. Complete genome analysis of African swine fever virus genotypes II, IX and XV from domestic pigs in Tanzania. Sci Rep 2023; 13:5318. [PMID: 37002287 PMCID: PMC10066019 DOI: 10.1038/s41598-023-32625-1] [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: 01/23/2023] [Accepted: 03/30/2023] [Indexed: 04/03/2023] Open
Abstract
African swine fever (ASF) caused by ASF virus (ASFV) is an infectious transboundary animal disease notifiable to the World Organization for Animal Health causing high mortality in domestic pigs and wild boars threatening the global domestic pig industry. To date, twenty-four ASFV genotypes have been described and currently genotypes II, IX, X, XV and XVI are known to be circulating in Tanzania. Despite the endemic status of ASF in Tanzania, only one complete genome of ASFV from the country has been described. This study describes the first complete genome sequence of ASFV genotype XV. In addition, the first Tanzanian complete genome of ASFV genotype IX and three ASFV strains belonging to genotype II collected during ASF outbreaks in domestic pigs in Tanzania were determined in this study using Illumina sequencing and comparative genomics analysis. The generated ASFV complete genome sequences ranged from 171,004 to 184,521 base pairs in length with an average GC content of 38.53% and encoded 152 to 187 open reading frames. The results of this study provide insights into the genomic structure of ASFV and can be used to monitor changes within the ASFV genome and improve our understanding of ASF transmission dynamics.
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Affiliation(s)
- Jean N Hakizimana
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Clara Yona
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
- Department of Biosciences, Solomon Mahlangu College of Natural and Applied Sciences, Sokoine University of Agriculture, PO Box 3038, Morogoro, Tanzania
| | - Mariam R Makange
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Ester A Kasisi
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania
| | - Christopher L Netherton
- African Swine Fever Vaccinology Group, The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, Surrey, UK
| | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - Gerald Misinzo
- OR Tambo Africa Research Chair for Viral Epidemics, SACIDS Foundation for One Health, Sokoine University of Agriculture, PO Box 3297, Morogoro, Tanzania.
- 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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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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