Seroevidence of Zoonotic Viruses in Rodents and Humans in Kibera Informal Settlement, Nairobi, Kenya

Frequent and intense human-bat interactions occur in buildings of rural Kenya

Simultaneous use of domestic spaces by humans and wildlife is little understood, despite global ubiquity, and can create an interface for human exposure to wildlife pathogens. Bats are a pervasive synanthropic taxon and are associated with several pathogens that can spill over and cause disease in humans. Urbanization has destroyed much natural bat habitat and, in response, many species increasingly use buildings as roosts. The purpose of this study was to characterize human interactions with bats in shared buildings to assess potential for human exposure to and spillover of bat-borne pathogens. We surveyed 102 people living and working in buildings used as bat roosts in Taita-Taveta county, Kenya between 2021 and 2023. We characterized and quantified the duration, intensity, and frequency of human-bat interactions occurring in this common domestic setting. Survey respondents reported living with bats in buildings year-round, with cohabitation occurring consistently for at least 10 years in 38% of cases. Human contact with bats occurred primarily through direct and indirect routes, including exposure to excrement (90% of respondents), and direct touching of bats (39% of respondents). Indirect contacts most often occurred daily, and direct contacts most often occurred yearly. Domestic animal consumption of bats was also reported (16% of respondents). We demonstrate that shared building use by bats and humans in rural Kenya leads to prolonged, frequent, and sometimes intense interactions between bats and humans, consistent with interfaces that can facilitate exposure to bat pathogens and subsequent spillover. Identifying and understanding the settings and practices that may lead to zoonotic pathogen spillover is of great global importance for developing countermeasures, and this study establishes bat roosts in buildings as such a setting.

Divergent Hantavirus in Somali Shrews (Crocidura somalica) in the Semi-Arid North Rift, Kenya

Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93-97% nucleotide and 96-99% amino acid identities among each other, as well as 74-76% nucleotide and 79-83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.

Effects of habitat management on rodent diversity, abundance, and virus infection dynamics

As anthropogenic factors continue to degrade natural areas, habitat management is needed to restore and maintain biodiversity. However, the impacts of different habitat management regimes on ecosystems have largely focused on vegetation analyses, with limited evaluation of downstream effects on wildlife. We compared the effects of grassland management regimes (prescribed burning, cutting/haying, or no active management) on rodent communities and the viruses they hosted. Rodents were trapped in 13 existing grassland sites in Northwest Arkansas, USA during 2020 and 2021. Rodent blood samples were screened for antibodies against three common rodent-borne virus groups: orthohantaviruses, arenaviruses, and orthopoxviruses. We captured 616 rodents across 5953 trap nights. Burned and unmanaged sites had similarly high abundance and diversity, but burned sites had a higher proportion of grassland species than unmanaged sites; cut sites had the highest proportion of grassland species but the lowest rodent abundance and diversity. A total of 38 rodents were seropositive for one of the three virus groups (34 orthohantavirus, three arenavirus, and one orthopoxvirus). Thirty-six seropositive individuals were found in burned sites, and two orthohantavirus-seropositive individuals were found in cut sites. Cotton rats and prairie voles, two grassland species, accounted for 97% of the rodents seropositive for orthohantavirus. Our study indicates that prescribed burns lead to a diverse and abundant community of grassland rodent species compared with other management regimes; as keystone taxa, these results also have important implications for many other species in food webs. Higher prevalence of antibodies against rodent-borne viruses in burned prairies shows an unexpected consequence likely resulting from robust host population densities supported by the increased habitat quality of these sites. Ultimately, these results provide empirical evidence that can inform grassland restoration and ongoing management strategies.