Molecular-based detection Of Coronaviridae and Paramyxoviridae in Fecal samples of Bats inhabiting the Gcwihaba caves, Northwestern Botswana

Abstract

Bats have been associated with emerging and re-emerging viral diseases of public health concern, including the most recent pandemic, COVID-19, caused by a coronavirus named Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A number of zoonotic viruses have been detected in bats globally, including countries bordering Botswana, such as South Africa, Zimbabwe, and Zambia. Given the potential public health risk of these viruses, the current study sought to detect the presence of members of the Coronaviridae (CoV) and Paramyxoviridae(PMV) in bats fecal samples. A total of 173 fecal samples we collected non-invasively from insectivorous bats that inhabit the Gcwihaba caves. Detection was done using heminested-RT PCR to determine the presence of viral RNA from the two virus families in the fecal samples. From the sample batches assessed, 2.31% (4/173) and 30.41% (52/173) tested positive for CoV and PMV RNA, respectively. On further assessment of sequences with phylogenetic analysis and pair-wise identity, the CoV positives were identified to belong to the Betacoronavirus (subgenus: Merbecovirus), and PMV positives belonged to the Jeilongvirus-related viruses, with some being putative jeilongviruses. These findings, provide vital information on the genus of bat-associated viruses in Botswana, specifically the viruses in circulation within the Gcwihaba cave bats. The detection of these viruses and their excretion into the environment has a possible public implication, as the presence of viruses within the bat population of Gcwihaba may pose a health risk to those who visit the caves for tourism. Furthermore, there is a possibility that related viruses may be in circulation in other bats of Botswana, warranting the necessity for further surveillance of these viruses within the country, particularly where the human-bat interaction interface is higher, such as public buildings and homes.