Genetic profile of African swine fever virus responsible for the 2019 outbreak in northern Malawi

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Abstract

Background

African swine fever (ASF) is an infectious transboundary animal disease which causes high mortality, approaching 100% in domestic pigs and it is currently considered as the most serious constraint to domestic pig industry and food security globally. Despite regular ASF outbreaks within Malawi, few studies have genetically characterized the causative ASF virus (ASFV). This study aimed at genetic characterization of ASFV responsible for the 2019 outbreak in northern Malawi. The disease confirmation was done by polymerase chain reaction (PCR) followed by molecular characterization of the causative ASFV by partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, nucleotide alignment of the intergenic region (IGR) between I73R and I329L genes and translation of the central variable region (CVR) coded by B602L gene.

Results

All thirteen samples collected during this study in Karonga district in September 2019 were ASFV-positive and after partial genome sequencing and phylogenetic reconstruction of the B646L (p72) gene, the viruses clustered into ASFV p72 genotype II. The viruses characterized in this study lacked a GAATATATAG fragment between the I173R and the I329L genes and were classified as IGR I variants. Furthermore, the tetrameric amino acid repeats within the CVR of the B602L gene of the 2019 Malawian ASFV reported in this study had the signature BNDBNDBNAA, 100% similar to ASFV responsible for the 2013 and 2017 ASF outbreaks in Zambia and Tanzania, respectively.

Conclusions

The results of this study confirm an ASF outbreak in Karonga district in northern Malawi in September 2019. The virus was closely related to other p72 genotype II ASFV that caused outbreaks in neighboring eastern and southern African countries, emphasizing the possible regional transboundary transmission of this ASFV genotype. These findings call for a concerted regional and international effort to control the spread of ASF in order to improve nutritional and food security.

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Most cited references 43

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African swine fever

L.K. Dixon, H. Sun, H. Roberts (2019)

The continuing spread of African swine fever (ASF) outside Africa in Europe, the Russian Federation, China and most recently to Mongolia and Vietnam, has heightened awareness of the threat posed by this devastating disease to the global pig industry and food security. In this review we summarise what we know about the African swine fever virus (ASFV), the disease it causes, how it spreads and the current global situation. We discuss current control methods in domestic and wild pigs and prospects for development of vaccines and other tools for control.

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Genotyping field strains of African swine fever virus by partial p72 gene characterisation.

J L Edrich, M-L Penrith, James G Thomson … (2003)

A PCR-based sequencing method was developed which permits detection and characterization of African swine fever virus (ASFV) variants within 5 and 48 h, respectively, of receipt of a clinical specimen. Amplification of a 478 bp fragment corresponding to the C-terminal end of the p72 gene, confirms virus presence with genetic characterization being achieved by nucleotide sequence determination and phylogenetic analysis. The method was applied to 55 viruses including those representative of the major ASF lineages identified previously by restriction fragment length polymorphism (RFLP) analysis. Results confirmed that the p72 genotyping method identifies the same major viral groupings. Characterization of additional viruses of diverse geographical, species and temporal origin using the PCR-based method indicated the presence of ten major ASF genotypes on the African continent, the largest of which comprised a group of genetically homogeneous viruses recovered from outbreaks in Europe, South America, the Caribbean and West Africa (the ESAC-WA genotype). In contrast, viruses from southern and East African countries were heterogeneous, with multiple genotypes being present within individual countries. This study provides a rapid and accurate means of determining the genotype of field and outbreak strains of ASF and is therefore useful for molecular epidemiological clarification of ASF.

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Molecular Characterization of African Swine Fever Virus, China, 2018

Shengqiang Ge, Jinming Li, Xiaoxu Fan … (2018)

On August 3, 2018, an outbreak of African swine fever in pigs was reported in China. We subjected a virus from an African swine fever–positive pig sample to phylogenetic analysis. This analysis showed that the causative strain belonged to the p72 genotype II and CD2v serogroup 8.

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Author and article information

Contributors

G. Misinzo:

ORCID: http://orcid.org/0000-0003-1827-6403

gerald.misinzo@sacids.org

Journal

Journal ID (nlm-ta): BMC Vet Res

Journal ID (iso-abbrev): BMC Vet. Res

Title: BMC Veterinary Research

Publisher: BioMed Central (London )

ISSN (Electronic): 1746-6148

Publication date (Electronic): 28 August 2020

Publication date PMC-release: 28 August 2020

Publication date Collection: 2020

Volume: 16

Electronic Location Identifier: 316

Affiliations

[1 ]GRID grid.11887.37, ISNI 0000 0000 9428 8105, SACIDS Africa Centre of Excellence for Infectious Diseases, SACIDS Foundation for One Health, , Sokoine University of Agriculture, ; Morogoro, Tanzania

[2 ]GRID grid.11887.37, ISNI 0000 0000 9428 8105, Department of Veterinary Microbiology, Parasitology and Biotechnology, , College of Veterinary Medicine and Biomedical Sciences, Sokoine University of Agriculture, ; Morogoro, Tanzania

[3 ]GRID grid.463495.9, Department of Animal Health and Livestock Development, Ministry of Agriculture, Irrigation and Water Development, ; Lilongwe, Malawi

[4 ]GRID grid.10818.30, ISNI 0000 0004 0620 2260, Department of Food Science and Technology, , College of Agriculture, Animal Sciences and Veterinary Medicine, University of Rwanda, ; Busogo, Rwanda

[5 ]Department of Applied Research and Development and Foresight Incubation, National Industrial Research and Development Agency, Kigali, Rwanda

[6 ]GRID grid.5342.0, ISNI 0000 0001 2069 7798, Laboratory of Virology, Faculty of Veterinary Medicine, , Ghent University, ; Merelbeke, Belgium

Author information

G. Misinzo http://orcid.org/0000-0003-1827-6403

Article

Publisher ID: 2536

DOI: 10.1186/s12917-020-02536-8

PMC ID: 7455991

PubMed ID: 32859205

SO-VID: 9f388f9d-7f94-4c4a-bbd6-b4b842bd718b

License:

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

History

Date received : 24 April 2020

Date accepted : 23 August 2020

Funding

Funded by: Regional Scholarship and Innovation Fund (RSIF) of the Partnership for Skills in Applied Sciences, Engineering and Technology (PASET)

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ScienceOpen disciplines: Veterinary medicine

Keywords: african swine fever virus,asfarviridae,domestic pigs,molecular characterization,malawi

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ScienceOpen disciplines: Veterinary medicine

Keywords: african swine fever virus, asfarviridae, domestic pigs, molecular characterization, malawi

Genetic profile of African swine fever virus responsible for the 2019 outbreak in northern Malawi

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Abstract

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Horses and Humans Research Foundation

Most cited references 43

African swine fever

Genotyping field strains of African swine fever virus by partial p72 gene characterisation.

Molecular Characterization of African Swine Fever Virus, China, 2018

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