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Ambagala A, Goonewardene K, Lamboo L, Goolia M, Erdelyan C, Fisher M, Handel K, Lung O, Blome S, King J, Forth JH, Calvelage S, Spinard E, Gladue DP, Masembe C, Adedeji AJ, Olubade T, Maurice NA, Ularamu HG, Luka PD. Characterization of a Novel African Swine Fever Virus p72 Genotype II from Nigeria. Viruses 2023; 15:v15040915. [PMID: 37112895 PMCID: PMC10146018 DOI: 10.3390/v15040915] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
African swine fever (ASF) is a high-consequence transboundary hemorrhagic fever of swine. It continues to spread across the globe causing socio-economic issues and threatening food security and biodiversity. In 2020, Nigeria reported a major ASF outbreak, killing close to half a million pigs. Based on the partial sequences of the genes B646L (p72) and E183L (p54), the virus responsible for the outbreak was identified as an African swine fever virus (ASFV) p72 genotype II. Here, we report further characterization of ASFV RV502, one of the isolates obtained during the outbreak. The whole genome sequence of this virus revealed a deletion of 6535 bp between the nucleotide positions 11,760–18,295 of the genome, and an apparent reverse complement duplication of the 5′ end of the genome at the 3′ end. Phylogenetically, ASFV RV502 clustered together with ASFV MAL/19/Karonga and ASFV Tanzania/Rukwa/2017/1 suggesting that the virus responsible for the 2020 outbreak in Nigeria has a South-eastern African origin.
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Affiliation(s)
- Aruna Ambagala
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kalhari Goonewardene
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Lindsey Lamboo
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Melissa Goolia
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Cassidy Erdelyan
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Mathew Fisher
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Katherine Handel
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Oliver Lung
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB R3E 3M4, Canada
| | - Sandra Blome
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Jan Hendrik Forth
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Suedufer 10, 17493 Greifswald, Germany
| | - Edward Spinard
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
| | - Douglas P. Gladue
- Plum Island Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Greenport, NY 11944, USA
| | - Charles Masembe
- College of Natural Resources (CoNAS), Makerere University, Kampala P.O Box 7062, Uganda
| | | | - Toyin Olubade
- National Veterinary Research Institute, Vom 930103, Nigeria
| | | | | | - Pam D. Luka
- National Veterinary Research Institute, Vom 930103, Nigeria
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Penrith ML, Van Heerden J, Heath L, Abworo EO, Bastos ADS. Review of the Pig-Adapted African Swine Fever Viruses in and Outside Africa. Pathogens 2022; 11:pathogens11101190. [PMID: 36297247 PMCID: PMC9609104 DOI: 10.3390/pathogens11101190] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/08/2022] [Accepted: 10/11/2022] [Indexed: 12/04/2022] Open
Abstract
The region in eastern, central and southern Africa (ECSA) where African swine fever (ASF) originated in a sylvatic cycle is home to all the p72 genotypes of ASF virus identified so far. While 20 of the 24 genotypes have been isolated from outbreaks in domestic pigs in the region, only five of the genotypes (I, II, VIII, IX, X) have an extended field presence associated with domestic pigs. Of the genotypes that appear to be strongly adapted to domestic pigs, two have spread beyond the African continent and have been the focus of efforts to develop vaccines against ASF. Most of the experimental ASF vaccines described do not protect against a wider spectrum of viruses and may be less useful in the event of incursions of different strains or where multiple genotypes co-exist. The other three pig-adapted strains that are currently restricted to the ECSA region might spread, and priority should be given to understanding not only the genetic and antigenic characteristics of these viruses but also their history. We review historic and current knowledge of the distribution of these five virus genotypes, and note that as was the case for genotype II, some pig-associated viruses have the propensity for geographical range expansion. These features are valuable for prioritizing vaccine-development efforts to ensure a swift response to virus escape. However, whilst ASF vaccines are critical for high-production systems, global food security relies on parallel efforts to improve biosecurity and pig production in Africa and on continued ASFV surveillance and characterisation in the ECSA region.
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Affiliation(s)
- Mary-Louise Penrith
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, Pretoria 0110, South Africa
- Correspondence: or
| | - Juanita Van Heerden
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa
| | - Livio Heath
- Transboundary Animal Diseases, Onderstepoort Veterinary Research, Agricultural Research Council, Pretoria 0110, South Africa
| | - Edward Okoth Abworo
- Biosciences, Animal and Human Health Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Armanda D. S. Bastos
- Department of Zoology and Entomology, Faculty of Natural and Agricultural Sciences, University of Pretoria, Pretoria 0028, South Africa
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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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Wu Y, Yang Y, Ru Y, Qin X, Li M, Zhang Z, Zhang R, Li Y, Zhang Z, Li Y. The Development of a Real-Time Recombinase-Aid Amplification Assay for Rapid Detection of African Swine Fever Virus. Front Microbiol 2022; 13:846770. [PMID: 35369479 PMCID: PMC8969597 DOI: 10.3389/fmicb.2022.846770] [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] [Received: 12/31/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF), caused by the African swine fever virus (ASFV), is an acute, deadly, infectious disease of domestic pigs and wild boars and has a tremendous negative socioeconomic impact on the swine industry. ASF is a notifiable disease to the World Organization for Animal Health (OIE). Currently, no effective vaccine or treatment against ASF is available. Early detection and rapid diagnosis are potentially significant to control ASF spread with the emerging ASFV mutant strains and non-classical symptoms. In this study, we developed a real-time recombinase-aid amplification (RAA) assay to detect the ASFV genome rapidly. Thirty samples were detected using commercial lysis buffer for DNA extraction and equipped with a portable testing instrument. The results showed that the sensitivity of RAA was 103 copies per reaction at 95% probability in 9 min at 39°C. The method was universally specific for three strains of ASFV, and there was no cross-reaction with other pathogens, including foot-and-mouth disease virus (FMDV), classical swine fever virus (CSFV), porcine reproductive and respiratory syndrome virus (PRRSV), porcine circovirus 2 (PCV2), pseudorabies virus (PRV), and porcine parvovirus (PPV). The coefficient of variation (C.V) of repetitive experiments was 0%, and the coincidence rate was 100% compared to the real-time qPCR. 123 field samples were detected by the real-time RAA assay, and the results showed that the clinical coincidence rate of the real-time RAA assay was 98% compared to the real-time qPCR assay. The advantages of this method were as follows: the extraction of DNA can be performed on site, the DNA template is directly used, a small battery-powered instrument is easily available, and the on-site diagnostic process is finished within an hour. These suggest that this assay could be used to detect different genotypes of ASFV and play a vital role in the control of ASF.
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Affiliation(s)
- Yongshu Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Yang Yang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaodong Qin
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Miaomiao Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Zhixiong Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Rui Zhang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Yijing Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Zhidong Zhang
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
| | - Yanmin Li
- College of Animal Science and Veterinary Medicine, Southwest Minzu University, Chengdu, China
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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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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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Hakizimana JN, Yona C, Kamana O, Nauwynck H, Misinzo G. African Swine Fever Virus Circulation between Tanzania and Neighboring Countries: A Systematic Review and Meta-Analysis. Viruses 2021; 13:v13020306. [PMID: 33672090 PMCID: PMC7919636 DOI: 10.3390/v13020306] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
For over 100 years after the description of the first case of African swine fever (ASF) in Kenya, ASF virus (ASFV) cross-border spread in eastern and southern Africa has not been fully investigated. In this manuscript, we reviewed systematically the available literature on molecular epidemiology of ASF in Tanzania and its eight neighboring countries in order to establish the transmission dynamics of ASFV between these countries. Data were retrieved from World Animal Health Information System (WAHIS), Google Scholar, PubMed, Scopus, and CrossRef databases, using the recommendations of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and reviewed to document ASF outbreaks and ASFV genotypes distribution. Using phylogeographic approach applied to ASFV p72 sequence dataset, the evolutionary history and the dispersal pattern of the ASFV strains were assessed. From 2005 to 2019, a total of 1588 ASF outbreaks affecting 341,742 cases that led to 302,739 domestic pig deaths were reported. The case fatality rates (CFR) varied from 15.41% to 98.95% with an overall CFR of 88.58%. Fifteen different p72 ASFV genotypes were reported and the time to the most recent common ancestor (TMRCA) for ASFV strains dated back to 1652.233 (1626.473, 1667.735) with an evolutionary rate of 4.805 × 10−5 (2.5857 × 10−5, 9.7789 × 10−5). Phylogeographic dispersal analysis revealed several transboundary spread events of ASFV strains between these countries. These results suggest persistent circulation of ASFV in these countries and advocate for more research to improve our understanding of the transmission dynamics of the virus and for a regional approach to mitigate the spread of ASFV.
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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, P.O. Box 3019 Morogoro, Tanzania;
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019 Morogoro, Tanzania
- Correspondence: (J.N.H.); (G.M.)
| | - Clara Yona
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, P.O. Box 3019 Morogoro, Tanzania;
- Department of Biosciences, Solomon Mahlangu College of Science and Education, Sokoine University of Agriculture, P.O. Box 3019 Morogoro, Tanzania
| | - Olivier Kamana
- Department of Applied Research and Development and Foresight Incubation, National Industrial Research and Development Agency, P.O. 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, P.O. Box 3019 Morogoro, Tanzania;
- Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, P.O. Box 3019 Morogoro, Tanzania
- Correspondence: (J.N.H.); (G.M.)
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Hakizimana JN, Nyabongo L, Ntirandekura JB, Yona C, Ntakirutimana D, Kamana O, Nauwynck H, Misinzo G. Genetic Analysis of African Swine Fever Virus From the 2018 Outbreak in South-Eastern Burundi. Front Vet Sci 2020; 7:578474. [PMID: 33251264 PMCID: PMC7674587 DOI: 10.3389/fvets.2020.578474] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/01/2020] [Indexed: 11/24/2022] Open
Abstract
African swine fever (ASF) is a contagious viral disease that causes high mortality, approaching 100%, in domestic pigs and wild boars. The disease has neither a cure nor a vaccine, and it is caused by an ASF virus (ASFV), the only member of the family Asfarviridae, genus Asfivirus, and the only known DNA arbovirus. Twenty-four genotypes of ASFV have been described to date, and all of them have been described in Africa. ASF is endemic in Burundi, and several outbreaks have been reported in the country; the disease continues to economically impact on small-scale farmers. This study aimed at genetic characterization of ASFV that caused an ASF outbreak in the Rutana region, Burundi, in the year 2018. Tissue samples from domestic pigs that died as a result of a severe hemorrhagic disease were collected in order to confirm the disease using polymerase chain reaction (PCR) and to conduct partial genome sequencing. Nucleotide sequences were obtained for the B646L (p72) gene, the intergenic fragment between the I73R and I329L genes, and the central variable region (CVR) of the B602L gene. Phylogenetic analysis of the Burundian 2018 ASFV grouped the virus within B646L (p72) genotype X and clustered together with those reported during the 1984 and 1990 outbreaks in Burundi with high nucleotide identity to some ASFV strains previously reported in neighboring East African countries, indicating a regional distribution of this ASFV genotype. Analysis of the intergenic fragment between I73R and I329L genes showed that the Burundian 2018 ASFV described in this study lacked a 32–base pair (bp) fragment present in the reference genotype X strain, Kenya 1950. In addition, the strain described in this study had the signature AAABNAABA at the CVR (B602L) gene and showed 100% amino acid sequence identity to viruses responsible for recent ASF outbreaks in the region. The virus described in this study showed high genetic similarities with ASFV strains previously described in domestic pigs, wild suids, and soft ticks in East African countries, indicating a possible common wild source and continuous circulation in domestic pigs in the region.
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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, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Lionel Nyabongo
- National Veterinary Laboratory of Burundi, Bujumbura, Burundi
| | - Jean B Ntirandekura
- Department of Animal Health and Productions, University of Burundi, Bujumbura, Burundi
| | - Clara Yona
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Biosciences, Solomon Mahlangu College of Science and Education, Sokoine University of Agriculture, Morogoro, Tanzania
| | | | - Olivier Kamana
- Department of Food Science and Technology, College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, Busogo, Rwanda.,Department of Applied Research and Development and Foresight Incubation, National Industrial Research and Development Agency, Kigali, Rwanda
| | - Hans Nauwynck
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Gerald Misinzo
- SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania.,Department of Veterinary Microbiology, Parasitology and Biotechnology, College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, Morogoro, Tanzania
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