{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Department of Virology, Medicum, University of Helsinki, Helsinki, Finland.",
    "Virology and Immunology, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.",
    "ISLAB Laboratory Centre, Kuopio, Finland.",
    "Department of Medical Microbiology and KAVI Institute of Clinical Research, University of Nairobi, Nairobi, Kenya.",
    "Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.",
    "Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA.",
    "Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.",
    "Lammi Biological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Lammi, Finland."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 18,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "Griphin Ochola"
    },
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Emilia Pulkkinen"
    },
    {
      "affs": [
        3
      ],
      "name": "Joseph G Ogola"
    },
    {
      "affs": [
        0
      ],
      "name": "Henna Mäkelä"
    },
    {
      "affs": [
        3
      ],
      "name": "Moses Masika"
    },
    {
      "affs": [
        0
      ],
      "name": "Hanna Vauhkonen"
    },
    {
      "affs": [
        0
      ],
      "name": "Teemu Smura"
    },
    {
      "affs": [
        1
      ],
      "name": "Anne J Jääskeläinen"
    },
    {
      "affs": [
        3
      ],
      "name": "Omu Anzala"
    },
    {
      "affs": [
        0,
        1,
        4
      ],
      "name": "Olli Vapalahti"
    },
    {
      "affs": [
        5
      ],
      "name": "Alois Wambua Mweu"
    },
    {
      "affs": [
        5
      ],
      "name": "Kristian M Forbes"
    },
    {
      "affs": [
        6
      ],
      "name": "Johanna F Lindahl"
    },
    {
      "affs": [
        4
      ],
      "name": "Juha Laakkonen"
    },
    {
      "affs": [
        7
      ],
      "name": "Joni Uusitalo"
    },
    {
      "affs": [
        0
      ],
      "name": "Eda Altan",
      "orcid": "0000-0001-7903-6986"
    },
    {
      "affs": [
        0
      ],
      "name": "Essi M Korhonen"
    },
    {
      "affs": [
        0,
        4
      ],
      "name": "Tarja Sironen",
      "orcid": "0000-0002-2344-2755"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/5140gh64bnm98.bib",
  "cited_by": 0,
  "doi": "10.1016/j.onehlt.2026.101625",
  "fulltext_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717035/?tool=EBI",
  "id": "5140gh64bnm98",
  "issns": [
    "2352-7714"
  ],
  "landing_url": "https://europepmc.org/article/PMC/PMC13717035",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "heading",
      "Research Paper"
    ],
    [
      "openalex",
      "2739|Zoonotic diseases and public health"
    ]
  ],
  "openalex": "W7222785668",
  "pdf_url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13717035/pdf/?tool=EBI",
  "pmcid": "PMC13717035",
  "pmid": "42959492",
  "published": "2026-10-17",
  "publisher": "Elsevier",
  "ris": "https://research.draconitic.com/paper/5140gh64bnm98.ris",
  "sources": [
    {
      "first_seen": "2026-10-31T00:20:38Z",
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      "url": "https://europepmc.org/article/PMC/PMC13717035"
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    {
      "first_seen": "2026-11-01T00:20:50Z",
      "native_id": "MED:42959492",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42959492"
    },
    {
      "first_seen": "2026-11-02T12:21:25Z",
      "native_id": "PMC13717035",
      "source": "pmc",
      "url": "https://doi.org/10.1016/j.onehlt.2026.101625"
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  "subjects": [
    {
      "field": "medicine",
      "origin": "openalex:2739|Zoonotic diseases and public health",
      "subfield": "epidemiology-public-health"
    }
  ],
  "title": "Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya",
  "title_text": "Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya",
  "type": "peer-reviewed",
  "updated_at": "2026-11-02T12:21:25Z",
  "url": "https://research.draconitic.com/paper/5140gh64bnm98",
  "venue": "One health (Amsterdam, Netherlands)",
  "versions": []
}