Genome Sequencing of Historical Encephalomyocarditis Viruses from South Africa Links the Historical 1993/4 Savanna Elephant (Loxodonta africana) Outbreak to Cryptic Mastomys Rodents
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From 1993 to 1994, 64 free-ranging elephants (Loxodonta africana) succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. Mastomys rodents were implicated as the reservoir host of the Encephalomyocarditis virus (EMCV) based on serology and RT-PCR. However, in the absence of sequence-confirmation of both the virus and the rodent host, definitive links between the elephant outbreak strains and rodent reservoir could not be established. In this study, we generate the first reference genome sequences for three historical EMCVs isolated from two Mastomys rodents and one Mastomys-associated mite, Laelaps muricola, in Gauteng Province, South Africa, in 1961. In addition, near-complete genome sequences were generated for two elephant outbreak virus strains, for which data were previously limited to the P1 and 3D genome regions. The consensus sequence of each virus was determined using a PCR-Sanger sequencing approach. Phylogenetic analysis confirmed the three near-identical (99.95–99.97%) Mastomys-associated viruses to be sister to the two near-identical (99.85%) elephant outbreak strains, differing from each other at 6.4% of sites across the ~7400-nucleotide region characterised. This study demonstrates a link between Mastomys-associated viruses and the historical elephant outbreak strains and implicates Mastomys as reservoirs of EMCV in South Africa.
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Within the genome and 3D phylogenies, the EMCV-3 isolates clustered with EMCV-2 and associated viruses with strong support.
“However, within the genome and 3D phylogenies, these EMCV-3 isolates clustered with EMCV-2 and associated viruses with strong support (Figs 2A and 4B), as previously noted [27,44].”
From Zoological transmission of encephalomyocarditis virus in the United States: Virus evolution, host ecology, and capsid antigenicity derived from an outbreak (2026) · cites this paper as [44]
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“To further phylogenetically characterize various EMCVs (primarily EMCV-1), viruses have recently been grouped into eight lineages (designated A-H) and also subdivided into four major evolutionary clades (I-IV) [44].”
- Authors
- van Meer, V., Pawęska, J. T., Swanepoel, R., Grobbelaar, A., & Bastos, A. D.
- Affiliations
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield 0028, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- University of Pretoria (ZA)
- National Health Laboratory Service (ZA)
- Corresponding author
- Bastos, Armanda D.
- Venue
- Pathogens
- Publisher
- MDPI AG
- Published
- 2024-03-19
- Volume
- 13
- Issue
- 3
- Pages
- 261
- ISSN
- 2076-0817 (ISSN-L)
- PMC
- PMC10974613
- OpenAlex
- W4392959408
- Cited by
- 5
- References
- 68
- Citations by year
- 2026: 2 · 2025: 3
- FWCI
- 1.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Pathogens (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UpSpace Institutional Repository (University of Pretoria) (submittedVersion, cc-by)
- Funders
- Poliomyelitis Research Foundation (PRF) (78566)
- The National Research Foundation (NRF) (78566)
- University of Pretoria (78566)
- UP postgraduate research bursary (78566)
- Topics
- Health Sciences › Medicine › Epidemiology › Virology and Viral Diseases
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Animal Virus Infections Studies
- Health Sciences › Medicine › Infectious Diseases › Viral Infections and Vectors
- Keywords
- encephalomyocarditis virus, savanna elephant, Loxodonta africana, reservoir hosts, zoonotic transmission, phylogenetic analysis, viral genome sequencing, South Africa
- MeSH terms
- Whole Genome Sequencing, Animals, Disease Outbreaks, Disease Reservoirs, Elephants, Encephalomyocarditis virus, Phylogeny, South Africa, Genome, Viral, Cardiovirus Infections, Murinae
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