Virome Analysis of South American Arthropodophagous Bat Species With Sequence- and Profile-Based Homology Approaches Reveals Hidden RNA Virus Diversity

Bats harbor a remarkable diversity of viruses, yet much of their virome remains unexplored, particularly in South American species. Here, we characterized the RNA virome in fecal samples of three arthropodophagous bat species roosting in Argentina (Eumops bonariensis, Molossus molossus, Tadarida brasiliensis), and evaluated variation in viral communities across habitats and seasons. Metagenomic sequencing generated 161,871,196 high-quality read pairs, which were assembled into 32,816 contigs longer than 500 bp. BLAST-based analyses identified 11,056 viral contigs, but only 4.6% could be assigned to viral orders or families. Sequences classified at basal ranks were further analyzed using profile-based HMMER searches together with viral dark matter analysis. This approach increased the proportion of viral contigs assigned to orders or families to 45.2% and identified 30 viral families overall. Viral community composition showed species-specific patterns, with habitat-associated differences in E. bonariensis, temporal variation in T. brasiliensis, and comparatively low and homogeneous diversity in M. molossus, although these patterns were not statistically significant. Divergent viruses of bunya-, hepe-, stella-, flavi-, rhabdo-, and reo-like lineages were further characterized. Our findings highlight the value of integrating similarity- and profile-based approaches to improve viral taxonomic resolution and reveal the diversity of RNA viruses associated with South American bats.