Molecular investigation of coronavirus and Leptospira spp. in bats (Chiroptera, Mammalia) from Brazil

The emergence of zoonotic diseases highlights the need for continuous surveillance of wildlife, particularly bats, known as natural reservoirs of several pathogens. This study aimed to investigate the presence of coronaviruses (CoV) and Leptospira spp. in non-hematophagous bats from the northwestern region of São Paulo State, Brazil, between 2019 and 2024. Samples of intestine and kidney from 98 specimens from 18 species belonging to three families (Molossidae, Phyllostomidae, and Vespertilionidae) were collected in 8 municipalities of the Araçatuba Intermediate Geographic Region. Coronaviruses detection was performed by pan-CoV nested RT-PCR, targeting fragments of 602 and 440 bp of the RNA-dependent RNA polymerase (RdRp) gene. Investigation of Leptospira spp. was conducted by real-time PCR, aiming the amplification of a fragment of 331 bp of the 16 S rRNA gene. The analyses yielded no amplification in any of the intestinal and renal samples. Due to geographic bias and the underrepresentation of phyllostomids - a central taxon in CoV epidemiology in Brazil -, the lack of detection reflects sampling limitations rather than the real absence of these pathogens in the local fauna. Continuous surveillance, integrated with comprehensive and standardized sampling in this under-studied region, remains essential for the early detection of emerging zoonotic pathogens and for characterizing local host-pathogen ecology.