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.

Typhoid fever is caused by the bacteria Salmonella enterica subspecies enterica serovar Typhi ( S . Typhi) and remains a significant health problem in many developing countries. The lack of adequate diagnostic capabilities in these poor resource settings have contributed greatly in making typhoid fever endemic in these regions. Reliable and inexpensive diagnostic tests are needed to improve the management of this disease burden. This study evaluated the ability of staA, viaB and sopE genes to detect Salmonella spp. Conventional polymerase chain reaction (PCR) amplification of staA , viaB and sopE genes of Salmonella was used to detect and differentiate between the three most prevalent Salmonella spp. in Kenya ( S . Typhi, S. Typhimurium and S. Enteritidis). The staA primers (StaA-Forward / StaA-Reverse) and viaB primers (vi-Forward / vi-Reverse) were found to be specific only for the different strains of S . Typhi, producing PCR products of 585 bp and 540 bp respectively. No amplification was observed with S. Typhimurium, S. Enteritidis, E . coli and S . boydii bacterial strains. The sopE primers (SopE-Forward / SopE-Reverse) was demonstrated to be specific for all Salmonella spp. producing a 465 bp PCR product with no amplification observed with the E . coli and S . boydii bacterial strains. Conventional PCR using these staA and viaB primers for detection of S . Typhi shows great potential for diagnosis of typhoid fever however, further studies need to be carried out with actual food samples and human samples (blood, stool or saliva) to determine the effectiveness of this method in the detection of common Salmonella spp. in Kenya. Author summary: Typhoid fever is a severe disease caused by the bacteria Salmonella Typhi ( S . Typhi) and is a significant health problem in many developing countries. The lack of adequate diagnostic capabilities in poor resource settings common in most public health facilities in Kenya and Africa in general, hinder prompt diagnosis of typhoid fever. Currently, the available diagnostic tests are often expensive and more so not readily available in most resource poor endemic areas. This has often led to misdiagnosis of the disease, thereby delaying appropriate treatment and making typhoid fever widespread in most resource poor areas. This study examines the ability of three different genes to detect and differentiate between the three most prevalent Salmonella strains in Kenya using a readily available and widely used genetic test known as conventional polymerase chain reaction (PCR). This research found that staA and viaB genes were specific only for S . Typhi, while the sopE gene was specific for all Salmonella strains. Consequently, conventional PCR using these staA and viaB genes for detection of S . Typhi shows great potential to be used as a readily available diagnostic tool to detect the presence of the S . Typhi organism in individuals or foods sample in Kenya.