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Background and Methods: To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing. Results: Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified. Conclusions: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.

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Eastern black rhinos (Diceros bicornis michaeli) are a critically endangered species living in diverse habitats across Africa. In Kenya, once threatened with extinction due to massive poaching pressures, increased protection has resulted in losses being less than 1% annually today. Still, some populations have failed to achieve desired population growth targets. At Ol Jogi Wildlife Conservancy, some individuals are experiencing sub-optimal reproduction based on historical calving records and long inter-calving intervals (>3 years). Hormones drive the reproductive process, so non-invasive assessments of endocrine patterns can be useful indicators of individual reproductive health. In this study, we analysed longitudinal fecal progestagen metabolite (fPM) concentrations in all breeding female eastern black rhinos at Ol Jogi (n = 17) and compared the prevalence of irregular estrous cycles (longer or shorter than 20–40 days) and anestrous periods (interluteal period more than twice the length of a normal follicular phase, i.e. > 10 days) between optimal (inter-calving interval < 3 years) and sub-optimal (>3 years) reproducing individuals. Ten rhinos were pregnant during at least part of the study period. A total of 12 complete cycles were observed in seven females with an average length of 36 ± 3 days and equal numbers of regular and irregular cycles. Single anestrous periods averaging 67 ± 13 days were observed in five females. Surprisingly, a majority of cycles in optimal reproducing individuals were categorized as irregular based on fPM profiles. Overall, results suggest that irregular ovarian activity and isolated bouts of anestrus do not have negative impacts on reproductive performance in this subpopulation at Ol Jogi. A high priority is to continue using noninvasive hormone monitoring to evaluate how ecological or other variables influence reproductive success in this and other eastern black rhino subpopulations in Kenya.