Biosurveillance of coronaviruses in Rhinolophus bats from South Africa

Rhinolophus bats harbour various alpha- and betacoronaviruses and are believed to be the progenitor host of SARS-CoV and SARS-CoV-2. These bats are widely distributed, with 38 species recognized in Africa. Although coronaviruses have been detected in several species in Africa, there is a lack of surveillance among South African rhinolophids. This study conducted longitudinal nucleic acid surveillance for Rhinolophus spp. coronaviruses from September 2021 to January 2024 in a mixed species cave in Limpopo, South Africa, using a hemi-nested RT-PCR assay. Among the 492 gastrointestinal samples collected, alphacoronavirus RNA was detected in 29.47% of samples, with betacoronavirus RNA identified among 7.11% of samples, with excretion peaks present in spring and summer (September–February). Based on GAMMs, the alphacoronavirus prevalence was strongly affected by season, total rainfall, and bat mass, whereas the betacoronavirus prevalence was influenced by forearm length, although the small sample size limits this finding. Rhinolophus acrotis contributed greatly to the interspecies sharing of alphacoronaviruses, and R. blasii was the primary origin of betacoronavirus interspecies sharing. This study expanded the known coronavirus diversity in African rhinolophids and highlighted the phylogeographic clustering of these viruses. The research emphasizes the need for more longitudinal studies involving African rhinolophids to better understand the ecological and behavioural factors that drive viral shedding for risk assessment and mitigation strategies.