First detection of African swine fever (ASF) virus genotype X and serogroup 7 in symptomatic pigs in the Democratic Republic of Congo

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Abstract

Background

African swine fever (ASF) is a highly contagious and severe hemorrhagic viral disease of domestic pigs. The analysis of variable regions of African swine fever virus (ASFV) genome led to more genotypic and serotypic information about circulating strains. The present study aimed at investigating the genetic diversity of ASFV strains in symptomatic pigs in South Kivu province of the Democratic Republic of Congo (DRC).

Materials and methods

Blood samples collected from 391 ASF symptomatic domestic pigs in 6 of 8 districts in South Kivu were screened for the presence of ASFV, using a VP73 gene-specific polymerase chain reaction (PCR) with the universal primer set PPA1-PPA2. To genotype the strains, we sequenced and compared the nucleotide sequences of PPA-positive samples at three loci: the C-terminus of B646L gene encoding the p72 protein, the E183L gene encoding the p54 protein, and the central hypervariable region (CVR) of the B602L gene encoding the J9L protein. In addition, to serotype and discriminate between closely related strains, the EP402L (CD2v) gene and the intergenic region between the I73R and I329L genes were analyzed.

Results

ASFV was confirmed in 26 of 391 pigs tested. However, only 19 and 15 PPA-positive samples, respectively, were successfully sequenced and phylogenetically analyzed for p72 ( B646L) and p54 ( E183L). All the ASFV studied were of genotype X. The CVR tetrameric repeat clustered the ASFV strains in two subgroups: the Uvira subgroup (10 TRS repeats, AAAABNAABA) and another subgroup from all other strains (8 TRS repeats, AABNAABA). The phylogenetic analysis of the EP402L gene clustered all the strains into CD2v serogroup 7. Analyzing the intergenic region between I73R and I329L genes revealed that the strains were identical but contained a deletion of a 33-nucleotide internal repeat sequence compared to ASFV strain Kenya 1950.

Conclusion

ASFV genotype X and serogroup 7 was identified in the ASF disease outbreaks in South Kivu province of DRC in 2018–2019. This represents the first report of ASFV genotype X in DRC. CVR tetrameric repeat sequences clustered the ASFV strains studied in two subgroups. Our finding emphasizes the need for improved coordination of the control of ASF.

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Most cited references 33

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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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ICTV Virus Taxonomy Profile: Asfarviridae

Covadonga Alonso, Manuel V Borca, Linda Dixon … (2018)

The family Asfarviridae includes the single species African swine fever virus, isolates of which have linear dsDNA genomes of 170-194 kbp. Virions have an internal core, an internal lipid membrane, an icosahedral capsid and an outer lipid envelope. Infection of domestic pigs and wild boar results in an acute haemorrhagic fever with transmission by contact or ingestion, or by ticks of the genus Ornithodoros. Indigenous pigs act as reservoirs in Africa, where infection is endemic, and from where introductions occur periodically to Europe. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Asfarviridae, which is available at www.ictv.global/report/asfarviridae.

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Author and article information

Contributors

Patrick N. Bisimwa: patrick.ntagereka@gmail.com

Juliette R. Ongus: julietteongus@jkuat.ac.ke

Christian K. Tiambo: C.Tiambo@cgiar.org

Eunice M. Machuka: Eunice.machuka@gmail.com

Espoir B. Bisimwa: ebisimwa@yahoo.com

Lucilla Steinaa: l.steinaa@cgiar.org

Roger Pelle:

ORCID: http://orcid.org/0000-0003-1053-085X

r.pelle@cgiar.org

Journal

Journal ID (nlm-ta): Virol J

Journal ID (iso-abbrev): Virol. J

Title: Virology Journal

Publisher: BioMed Central (London )

ISSN (Electronic): 1743-422X

Publication date (Electronic): 3 September 2020

Publication date PMC-release: 3 September 2020

Publication date Collection: 2020

Volume: 17

Electronic Location Identifier: 135

Affiliations

[1 ]Department of Molecular Biology and Biotechnology, Pan African University, Institute of Basic Sciences, Technology and Innovation, Nairobi, Kenya

[2 ]GRID grid.442835.c, ISNI 0000 0004 6019 1275, Department of Animal Science and Production, , Université Evangélique en Afrique, ; Bukavu, Democratic Republic of the Congo

[3 ]GRID grid.411943.a, ISNI 0000 0000 9146 7108, Department of Medical Laboratory Sciences, , Jomo Kenyatta University of Agriculture and Technology, ; Juja, Kenya

[4 ]GRID grid.419369.0, Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, ; Naivasha Road, P.O. Box 30709, Nairobi, 00100 Kenya

[5 ]GRID grid.419369.0, Centre for Tropical Livestock Genetics and Health (CTLGH), , International Livestock Research Institute, ; Nairobi, Kenya

[6 ]GRID grid.419369.0, International Livestock Research Institute, , Animal and Human Health, ; Nairobi, Kenya

Author information

Roger Pelle http://orcid.org/0000-0003-1053-085X

Article

Publisher ID: 1398

DOI: 10.1186/s12985-020-01398-8

PMC ID: 7468181

PubMed ID: 32883295

SO-VID: fa7cb2bb-2215-4bec-9aec-79e6e3799e74

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 : 27 April 2020

Date accepted : 14 August 2020

Funding

Funded by: FundRef http://dx.doi.org/10.13039/100000865, Bill and Melinda Gates Foundation;

Award ID: OPP1075938

Custom metadata

ScienceOpen disciplines: Microbiology & Virology

Keywords: african swine fever virus,domestic pigs,phylogeny,genotype-serogroup,south kivu province,dr congo

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ScienceOpen disciplines: Microbiology & Virology

Keywords: african swine fever virus, domestic pigs, phylogeny, genotype-serogroup, south kivu province, dr congo

First detection of African swine fever (ASF) virus genotype X and serogroup 7 in symptomatic pigs in the Democratic Republic of Congo

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Zika Virus

Most cited references 33

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

Molecular Characterization of African Swine Fever Virus, China, 2018

ICTV Virus Taxonomy Profile: Asfarviridae

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