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Borca MV, Ramirez-Medina E, Espinoza N, Rai A, Spinard E, Velazquez-Salinas L, Valladares A, Silva E, Burton L, Meyers A, Clark J, Wu P, Gay CG, Gladue DP. Deletion of the EP402R Gene from the Genome of African Swine Fever Vaccine Strain ASFV-G-∆I177L Provides the Potential Capability of Differentiating between Infected and Vaccinated Animals. Viruses 2024; 16:376. [PMID: 38543742 PMCID: PMC10974803 DOI: 10.3390/v16030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 05/23/2024] Open
Abstract
The African swine fever virus (ASFV) mutant ASFV-G-∆I177L is a safe and efficacious vaccine which induces protection against the challenge of its parental virus, the Georgia 2010 isolate. Although a genetic DIVA (differentiation between infected and vaccinated animals) assay has been developed for this vaccine, still there is not a serological DIVA test for differentiating between animals vaccinated with ASFV-G-∆I177L and those infected with wild-type viruses. In this report, we describe the development of the ASFV-G-∆I177L mutant having deleted the EP402R gene, which encodes for the viral protein responsible for mediating the hemadsorption of swine erythrocytes. The resulting virus, ASFV-G-∆I177L/∆EP402R, does not have a decreased ability to replicates in swine macrophages when compared with the parental ASFV-G-∆I177L. Domestic pigs intramuscularly (IM) inoculated with either 102 or 106 HAD50 of ASFV-G-∆I177L/∆EP402R remained clinically normal, when compared with a group of mock-vaccinated animals, indicating the absence of residual virulence. Interestingly, an infectious virus could not be detected in the blood samples of the ASFV-G-∆I177L/∆EP402R-inoculated animals in either group at any of the time points tested. Furthermore, while all of the mock-inoculated animals presented a quick and lethal clinical form of ASF after the intramuscular inoculation challenge with 102 HAD50 of highly virulent parental field isolate Georgia 2010 (ASFV-G), all of the ASFV-G-∆I177L/∆EP402R-inoculated animals were protected, remaining clinically normal until the end of the observational period. Most of the ASFV-G-∆I177L/∆EP402R-inoculated pigs developed strong virus-specific antibody responses against viral antigens, reaching maximum levels at 28 days post inoculation. Importantly, all of the sera collected at that time point in the ASFV-G-∆I177L/∆EP402R-inoculated pigs did not react in a direct ELISA coated with the recombinant EP402R protein. Conversely, the EP402R protein was readily recognized by the pool of sera from the animals immunized with recombinant live attenuated vaccine candidates ASFV-G-∆I177L, ASFV-G-∆MGF, or ASFV-G-∆9GL/∆UK. Therefore, ASFV-G-∆I177L/∆EP402R is a novel, safe and efficacious candidate with potential to be used as an antigenically DIVA vaccine.
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Affiliation(s)
- Manuel V. Borca
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Elizabeth Ramirez-Medina
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Nallely Espinoza
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Ayushi Rai
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Edward Spinard
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Lauro Velazquez-Salinas
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Alyssa Valladares
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Ediane Silva
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Leeanna Burton
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Amanda Meyers
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Jason Clark
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
| | - Ping Wu
- Plum Island Animal Disease Center, U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Orient, NY 11957, USA;
| | - Cyril G. Gay
- Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA;
| | - Douglas P. Gladue
- Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, U.S. Department of Agriculture, Agricultural Research Service, Orient, NY 11957, USA; (E.R.-M.); (N.E.); (A.R.); (E.S.); (L.V.-S.); (A.V.); (A.M.)
- Foreign Animal Disease Research Unit, U.S. Department of Agriculture, Agricultural Research Service, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA; (E.S.); (L.B.); (J.C.)
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Shi C, Wang Q, Liu Y, Wang S, Zhang Y, Liu C, Hu Y, Zheng D, Sun C, Song F, Yu X, Zhao Y, Bao J, Wang Z. Generation of High-Quality African Swine Fever Virus Complete Genome from Field Samples by Next-Generation Sequencing. Viruses 2024; 16:312. [PMID: 38400087 PMCID: PMC10891787 DOI: 10.3390/v16020312] [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: 12/25/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
African swine fever (ASF) is a lethal contagious viral disease of domestic pigs and wild boars caused by the African swine fever virus (ASFV). The pandemic spread of ASF has caused severe effects on the global pig industry. Whole-genome sequencing provides crucial information for virus strain characterization, epidemiology analysis and vaccine development. Here, we evaluated the performance of next-generation sequencing (NGS) in generating ASFV genome sequences from clinical samples. Thirty-four ASFV-positive field samples including spleen, lymph node, lung, liver and blood with a range of Ct values from 14.73 to 25.95 were sequenced. For different tissue samples collected from the same sick pigs, the proportion of ASFV reads obtained from the spleen samples was 3.69-9.86 times higher than other tissues. For the high-viral-load spleen samples (Ct < 20), a minimum of a 99.8% breadth of ≥10× coverage was revealed for all the samples. For the spleen samples with Ct ≥ 20, 6/12 samples had a minimum of a 99.8% breadth of ≥10× coverage. A high average depth of sequencing coverage was also achieved from the blood samples. According to our results, high-quality ASFV whole-genome sequences could be obtained from the spleen or blood samples with Ct < 20. The high-quality ASFV genome sequence generated in this study was further used for the high-resolution phylogenetic analysis of the ASFV genomes in the early stage of the ASF epidemic in China. Our study demonstrates that NGS may act as a useful tool for efficient ASFV genome characterization, providing valuable information for disease control.
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Affiliation(s)
- Chuan Shi
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 518083, China
| | - Qinghua Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yutian Liu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Shujuan Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yongqiang Zhang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Chunju Liu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yongxin Hu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Dongxia Zheng
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Chengyou Sun
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Fangfang Song
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Xiaojing Yu
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Yunling Zhao
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Jingyue Bao
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
| | - Zhiliang Wang
- China Animal Health and Epidemiology Center, Qingdao 266032, China (Y.L.); (C.L.); (D.Z.); (C.S.)
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Dinhobl M, Spinard E, Tesler N, Birtley H, Signore A, Ambagala A, Masembe C, Borca MV, Gladue DP. Reclassification of ASFV into 7 Biotypes Using Unsupervised Machine Learning. Viruses 2023; 16:67. [PMID: 38257767 PMCID: PMC10819123 DOI: 10.3390/v16010067] [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: 12/05/2023] [Revised: 12/23/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
In 2007, an outbreak of African swine fever (ASF), a deadly disease of domestic swine and wild boar caused by the African swine fever virus (ASFV), occurred in Georgia and has since spread globally. Historically, ASFV was classified into 25 different genotypes. However, a newly proposed system recategorized all ASFV isolates into 6 genotypes exclusively using the predicted protein sequences of p72. However, ASFV has a large genome that encodes between 150-200 genes, and classifications using a single gene are insufficient and misleading, as strains encoding an identical p72 often have significant mutations in other areas of the genome. We present here a new classification of ASFV based on comparisons performed considering the entire encoded proteome. A curated database consisting of the protein sequences predicted to be encoded by 220 reannotated ASFV genomes was analyzed for similarity between homologous protein sequences. Weights were applied to the protein identity matrices and averaged to generate a genome-genome identity matrix that was then analyzed by an unsupervised machine learning algorithm, DBSCAN, to separate the genomes into distinct clusters. We conclude that all available ASFV genomes can be classified into 7 distinct biotypes.
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Affiliation(s)
- Mark Dinhobl
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Edward Spinard
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Nicolas Tesler
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Hillary Birtley
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Anthony Signore
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Aruna Ambagala
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Charles Masembe
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
- Department of Zoology, Entomology and Fisheries Sciences, School of Biosciences, College of Natural Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Manuel V. Borca
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
| | - Douglas P. Gladue
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, Plum Island Animal Disease Center, Orient, NY 11957, USA; (M.D.); (E.S.); (N.T.); (H.B.)
- United States Department of Agriculture, Agricultural Research Service, Foreign Animal Disease Research Unit, National Bio and Agro-Defense Facility, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.S.); (A.A.); (C.M.)
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Kabuuka T, Mulindwa H, Bastos ADS, van Heerden J, Heath L, Fasina FO. Retrospective Multi-Locus Sequence Analysis of African Swine Fever Viruses by "PACT" Confirms Co-Circulation of Multiple Outbreak Strains in Uganda. Animals (Basel) 2023; 14:71. [PMID: 38200802 PMCID: PMC10777903 DOI: 10.3390/ani14010071] [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: 11/30/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
African swine fever (ASF) is a haemorrhagic fever of swine that severely constrains pig production, globally. In Uganda, at least 388 outbreaks of ASF were documented from 2001 to 2012. We undertook a retrospective serological and molecular survey of ASF virus (ASFV) using banked samples collected from seven districts (Pallisa, Lira, Abim, Nebbi, Kabarole, Kibaale, and Mukono) of Uganda. Six assays (ELISA for antibody detection, diagnostic p72 gene PCR and genomic amplification, and sequencing of four gene regions (p72 [P], p54 [A], CVR of the 9RL-ORF [C], and TK [T]), hereinafter referred to as P-A-C-T (PACT)) were evaluated. Antibodies to ASFV were detected in the Abim district (6/25; 24.0%), and the remainder of the serum samples were negative (187/193; 96.9%). For the tissue samples, ASFV detection by assay was 8.47% for P, 6.78% for A, 8.47% for C, and 16.95% for T. The diagnostic PCR (p72 gene) detected seven positive animals from four districts, whereas the TK assay detected ten positives from all seven districts. In addition to the superior detection capability of TK, two virus variants were discernible, whereas CVR recovered three variants, and p72 and p54 sequencing each identified a single variant belonging to genotype IX. Our results indicate that dependence on serology alone underestimates ASF positivity in any infected region, that multi-locus sequence analysis provides better estimates of outbreak strain diversity, and that the TK assay is superior to the WOAH-prescribed conventional p72 diagnostic PCR, and warrants further investigation.
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Affiliation(s)
- Tonny Kabuuka
- Infectious Animal Diseases Laboratory, National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research Organisation (NARO), Totoro 21403, Uganda;
- Department of Production Animal Studies (DPAS), Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Henry Mulindwa
- Infectious Animal Diseases Laboratory, National Livestock Resources Research Institute (NaLIRRI), National Agricultural Research Organisation (NARO), Totoro 21403, Uganda;
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Hatfield 0028, South Africa;
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
| | - Juanita van Heerden
- Transboundary Animal Diseases Programme, Agricultural Research Centre-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa; (J.v.H.); (L.H.)
| | - Livio Heath
- Transboundary Animal Diseases Programme, Agricultural Research Centre-Onderstepoort Veterinary Institute, Onderstepoort 0110, South Africa; (J.v.H.); (L.H.)
| | - Folorunso O. Fasina
- Department of Production Animal Studies (DPAS), Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort 0110, South Africa
- Food and Agriculture Organization of the United Nations (FAO), I-00100 Rome, Italy
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Spinard E, Dinhobl M, Tesler N, Birtley H, Signore AV, Ambagala A, Masembe C, Borca MV, Gladue DP. A Re-Evaluation of African Swine Fever Genotypes Based on p72 Sequences Reveals the Existence of Only Six Distinct p72 Groups. Viruses 2023; 15:2246. [PMID: 38005923 PMCID: PMC10675559 DOI: 10.3390/v15112246] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/07/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The African swine fever virus (ASFV) is currently causing a world-wide pandemic of a highly lethal disease in domestic swine and wild boar. Currently, recombinant ASF live-attenuated vaccines based on a genotype II virus strain are commercially available in Vietnam. With 25 reported ASFV genotypes in the literature, it is important to understand the molecular basis and usefulness of ASFV genotyping, as well as the true significance of genotypes in the epidemiology, transmission, evolution, control, and prevention of ASFV. Historically, genotyping of ASFV was used for the epidemiological tracking of the disease and was based on the analysis of small fragments that represent less than 1% of the viral genome. The predominant method for genotyping ASFV relies on the sequencing of a fragment within the gene encoding the structural p72 protein. Genotype assignment has been accomplished through automated phylogenetic trees or by comparing the target sequence to the most closely related genotyped p72 gene. To evaluate its appropriateness for the classification of genotypes by p72, we reanalyzed all available genomic data for ASFV. We conclude that the majority of p72-based genotypes, when initially created, were neither identified under any specific methodological criteria nor correctly compared with the already existing ASFV genotypes. Based on our analysis of the p72 protein sequences, we propose that the current twenty-five genotypes, created exclusively based on the p72 sequence, should be reduced to only six genotypes. To help differentiate between the new and old genotype classification systems, we propose that Arabic numerals (1, 2, 8, 9, 15, and 23) be used instead of the previously used Roman numerals. Furthermore, we discuss the usefulness of genotyping ASFV isolates based only on the p72 gene sequence.
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Affiliation(s)
- Edward Spinard
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Mark Dinhobl
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Nicolas Tesler
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Hillary Birtley
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN 37830, USA
| | - Anthony V. Signore
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Aruna Ambagala
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Charles Masembe
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
- College of Natural Resources (CoNAS), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Manuel V. Borca
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
| | - Douglas P. Gladue
- Plum Island Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture, Foreign Animal Disease Research Unit, Orient, NY 11957, USA; (E.S.); (M.D.); (N.T.); (H.B.)
- National Bio and Agro-Defense Facility, Agricultural Research Service, U.S. Department of Agriculture, Manhattan, KS 66502, USA
- Center of Excellence for African Swine Fever Genomics, Guilford, CT 06437, USA; (A.V.S.); (A.A.); (C.M.)
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Okwasiimire R, Kayaga EB, Ekakoro JE, Ndoboli D, Schumann K, Faburay B, Nassali A, Hauser C, Ochoa K, Wampande EM, Havas KA. Spatiotemporal description of African swine fever virus nucleic acid and antibodies detected in pigs sampled at abattoirs in the greater Kampala metropolitan area, Uganda from May 2021 through June 2022. Porcine Health Manag 2023; 9:51. [PMID: 37919811 PMCID: PMC10623799 DOI: 10.1186/s40813-023-00345-7] [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: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023] Open
Abstract
BACKGROUND African swine fever virus (ASFV) infections in Africa cause hemorrhagic disease in domestic pigs and is maintained by a sylvatic cycle in warthogs. It is endemic in Uganda, leading to significant economic losses. Previous studies performed in rural areas and in Kampala had differing diagnostic results. The purpose of this study was to provide a robust spatial, temporal, and diagnostic summary of pigs slaughtered in the greater Kampala metropolitan area over the course of one year. This study characterized 1208 to 1323 serum, blood, and tissue samples collected from pigs at six abattoirs in the greater Kampala metropolitan area of Uganda monthly from May 2021 through June 2022. Validated and standardized serologic and molecular diagnostics were used. RESULTS Only 0.15% of pigs had detectable antibodies against ASFV, suggesting low survival rates or pre-clinical diagnosis. Yet, 59.5% of pigs were positive for ASFV DNA. Blood had the lowest detection rate (15.3%) while tonsil and lymph nodes had the highest (38% and 37.5%, respectively), spleen samples (31.5%) were in between. Agreement between sample types was fair to moderate overall. A significant seasonality of ASFV infections emerged with infections found predominately in the dry seasons. Spatial assessments revealed that the greater Kampala metropolitan area abattoirs have a catchment area that overlaps with Uganda's most pig dense regions. CONCLUSIONS Pigs at greater Kampala metropolitan area abattoirs can be sentinels for acute disease throughout the pig dense region of Uganda, particularly in the dry seasons. The high prevalence detected suggests that pigs are sold in response to local reports of ASFV infections (panic sales). Serological surveillance is not useful, as very few pigs seroconverted in this study prior to slaughter. In contrast, tissue samples of pigs can be used to detect disease using qPCR methods.
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Affiliation(s)
- Rodney Okwasiimire
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda
| | - Edrine B Kayaga
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda
| | - John E Ekakoro
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853-6401, USA
| | - Dickson Ndoboli
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda
| | - Kate Schumann
- Foreign Animal Disease Diagnostic Laboratory, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, National Veterinary Services Laboratories, Greenport, NY, USA
| | - Bonto Faburay
- Foreign Animal Disease Diagnostic Laboratory, Veterinary Services, Animal and Plant Health Inspection Services, United States Department of Agriculture, National Veterinary Services Laboratories, Greenport, NY, USA
| | - Aisha Nassali
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda
| | - Cole Hauser
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853-6401, USA
| | - Krista Ochoa
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853-6401, USA
| | - Eddie M Wampande
- Central Diagnostic Laboratory, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P.O.Box 7062, Kampala, Uganda
| | - Karyn A Havas
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853-6401, USA.
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