Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya
8 affiliations
- 1Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.
- 2Virology and Immunology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
- 3ISLAB Laboratory Centre, Kuopio, Finland.
- 4Department of Medical Microbiology and KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya.
- 5Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.
- 6Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.
- 7Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
- 8Lammi Biological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Lammi, Finland.
Abstract
The majority of emerging infectious diseases are zoonotic, having their origin in wildlife before spilling over into the human population. While small mammals are recognized as critical reservoirs for these viruses, their viral diversity remains largely uncharacterized across many African countries. We conducted molecular surveillance of synanthropic rodents and shrews in the Kibera informal settlement in Nairobi and the rural Taita Hills region of Kenya to detect and characterize potential zoonotic viruses. Tissue samples from 228 rodents and shrews were screened for six viral families using PCR assays. Rat hepatitis E virus (HEV) (Rocahepevirus ratti), a rodent-associated virus with potential for human spillover, was identified in Mus musculus and Rattus norvegicus from Kibera. NGS was conducted for the HEV positive samples, and we obtained two near-complete HEV genomes from Rattus norvegicus, which clustered within rodent-associated HEV genotypes in the phylogenetic analysis. The two sequences from the Rattus norvegicus cluster together, indicating a close genetic relationship. Paramyxoviruses belonging to the genera Jeilongvirus and Parahenipavirus were detected both from Taita and Kibera in nine different samples from Rattus norvegicus, Mus minutoides, Crocidura sp and Acomys ignitus. One paramyxovirus positive sample (Acomys ignitus) from Taita was selected for further sequencing with NGS, and a complete genome of a new jeilongvirus was assembled. Phylogenetic analysis of the detected viruses confirmed the close relation to previously known rodent-borne jeilongviruses but also revealed potentially novel jeilong- and parahenipavirus species. Our findings highlight the circulation of potentially zoonotic viruses in both urban and rural small mammals in Kenya. It emphasizes the necessity of continued genomic surveillance of zoonotic viruses to mitigate risks of their spillover into human populations.
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BibTeX
@article{ochola2026hepatitis,
title = {{Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya}},
author = {Griphin Ochola and Emilia Pulkkinen and Joseph G Ogola and Henna Mäkelä and Moses Masika and Hanna Vauhkonen and Teemu Smura and Anne J Jääskeläinen and Omu Anzala and Olli Vapalahti and Alois Wambua Mweu and Kristian M Forbes and Johanna F Lindahl and Juha Laakkonen and Joni Uusitalo and Eda Altan and Essi M Korhonen and Tarja Sironen},
journal = {One health (Amsterdam, Netherlands)},
year = {2026},
month = oct,
doi = {10.1016/j.onehlt.2026.101625},
url = {https://europepmc.org/article/PMC/PMC13717035},
note = {CC BY},
}
RIS
TY - JOUR
TI - Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya
AU - Griphin Ochola
AU - Emilia Pulkkinen
AU - Joseph G Ogola
AU - Henna Mäkelä
AU - Moses Masika
AU - Hanna Vauhkonen
AU - Teemu Smura
AU - Anne J Jääskeläinen
AU - Omu Anzala
AU - Olli Vapalahti
AU - Alois Wambua Mweu
AU - Kristian M Forbes
AU - Johanna F Lindahl
AU - Juha Laakkonen
AU - Joni Uusitalo
AU - Eda Altan
AU - Essi M Korhonen
AU - Tarja Sironen
PY - 2026
DA - 2026/10/17
JO - One health (Amsterdam, Netherlands)
DO - 10.1016/j.onehlt.2026.101625
UR - https://europepmc.org/article/PMC/PMC13717035
AB - The majority of emerging infectious diseases are zoonotic, having their origin in wildlife before spilling over into the human population. While small mammals are recognized as critical reservoirs for these viruses, their viral diversity remains largely uncharacterized across many African countries. We conducted molecular surveillance of synanthropic rodents and shrews in the Kibera informal settlement in Nairobi and the rural Taita Hills region of Kenya to detect and characterize potential zoonotic viruses. Tissue samples from 228 rodents and shrews were screened for six viral families using PCR assays. Rat hepatitis E virus (HEV) (Rocahepevirus ratti), a rodent-associated virus with potential for human spillover, was identified in Mus musculus and Rattus norvegicus from Kibera. NGS was conducted for the HEV positive samples, and we obtained two near-complete HEV genomes from Rattus norvegicus, which clustered within rodent-associated HEV genotypes in the phylogenetic analysis. The two sequences from the Rattus norvegicus cluster together, indicating a close genetic relationship. Paramyxoviruses belonging to the genera Jeilongvirus and Parahenipavirus were detected both from Taita and Kibera in nine different samples from Rattus norvegicus, Mus minutoides, Crocidura sp and Acomys ignitus. One paramyxovirus positive sample (Acomys ignitus) from Taita was selected for further sequencing with NGS, and a complete genome of a new jeilongvirus was assembled. Phylogenetic analysis of the detected viruses confirmed the close relation to previously known rodent-borne jeilongviruses but also revealed potentially novel jeilong- and parahenipavirus species. Our findings highlight the circulation of potentially zoonotic viruses in both urban and rural small mammals in Kenya. It emphasizes the necessity of continued genomic surveillance of zoonotic viruses to mitigate risks of their spillover into human populations.
SN - 2352-7714
ER -