Viral metagenomics of synanthropic urban bats: a surveillance strategy for uncovering potentially zoonotic viruses

Zoonotic spillover events are increasing in frequency, highlighting the urgent need for integrated surveillance systems capable of detecting emerging viruses at the human–animal–environment interface. Bats are natural reservoirs for diverse zoonotic viruses, including coronaviruses, filoviruses, and paramyxoviruses. Here, we present a surveillance framework that leverages Brazil’s rabies passive surveillance program to detect bat-borne viruses using metagenomic sequencing. We developed an algorithm to select representative samples from 2,422 bats collected across São Paulo state between October 2023 and February 2024. Paired lung and intestine samples from 150 specimens underwent RNA extraction and nanopore sequencing. A custom bioinformatics pipeline enabled the detection of 66 viral contigs from nine zoonotic-relevant families, including Arenaviridae, Coronaviridae, Filoviridae, and Paramyxoviridae. Notably, we report the first detection of a filovirus in bats in the Americas and characterize the presence of multiple potentially public health–relevant viruses in close contact with humans. These findings reveal previously undetected viral diversity in Brazilian bats and demonstrate how existing animal surveillance initiatives can be leveraged to monitor broader pathogen threats. Our approach provides a scalable, cost-effective model for operationalizing surveillance towards a One Health approach, with potential applications in epidemic and pandemic prevention, particularly in low- and middle-income countries.