Genetic characterization of influenza viruses in bat populations in selected caves in Kapchorwa District

Abstract

Bats are well-established reservoirs for a wide range of zoonotic viruses, including those with pandemic potential. Despite their significance as reservoirs for zoonotic viruses, the potential role of Ugandan bats in influenza virus transmission remains poorly characterized. Their ecological diversity and frequent interactions with human environments underscore the need for targeted surveillance in selected caves in Kapchorwa district. This study investigated the diversity of bat species, the detection, and genetic characteristics of influenza viruses in bat populations inhabiting selected caves in Kapchorwa district in 2022. Bats were captured using mist traps by trained field personnel and subsequently released after sampling. Using sterile swabs, oral and rectal swabs were collected from each captured bat for laboratory analysis. Bat species, sex, reproductive status, age class, and morphometric evaluation were conducted. Specimens were obtained and transported to the laboratory for further investigations. Molecular analysis was performed on all samples, and sequencing was conducted on the presumptive positive ones to genetically characterize the influenza viruses. In the selected caves in Kapchorwa district, six bat species were captured inhabiting caves in 2022, with Rhinolophus spp. being the most frequently sampled, followed by Myonycteris angolensis and Hipposideros ruber. Less frequently captured species included Nycteris thebaica, Coleura afra, and Miniopterus fraterculus. Influenza A viruses were detected in 0.59% (n=3/512) samples analyzed. The positive samples were all obtained from rectal swabs collected in 2022. Influenza detections were in Hipposideros ruber (n=2) and Rhinolophus eloquens/ fumigatus species complex (n=1), confirming that these species are potential reservoirs of influenza viruses. Molecular characterization of the positive samples showed strong alignments with the PB1 gene of the H18N11 influenza virus, confirming the presence of this distinct bat-specific virus lineage in those selected caves in Kapchorwa district. The high sequence identity and low E-values across all samples provide robust evidence of the genetic relationship between these local strains and previously identified H18N11 viruses from other regions. Although the influenza virus was found in only three (3) bats, which lowers the immediate risk to humans, it is important to monitor influenza strains circulating in bats for any changes that might make it more dangerous. We recommend protecting bat habitats, keeping track of bat-borne viruses regularly, and studying how these viruses interact with bats to better understand and prevent future health risks and outbreaks.