Host specificity and geographic dispersion shape virome diversity in
Rhinolophus bats
Abstract
Rhinolophus bats have been identified as natural reservoirs for viruses
with global health implications, including severe acute respiratory
syndrome–related coronaviruses (SARSr-CoV) and swine acute diarrhea
syndrome-related coronavirus (SADSr-CoV). In this study, we
characterized the individual viromes of 603 bats to systematically
investigate the diversity, abundance, and geographic distribution of
viral communities within R. affinis, R. sinicus, and 11 related bat
species. The massive metatranscriptomic data revealed substantial viral
genome resources of 133 vertebrate-infecting viral clusters, which
contain occasional cross-species transmission across mammalian orders
and specially across bat families. Notably, those viruses included nine
clusters closely related to human and/or livestock pathogens, such as
SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct
features of viral diversity between and within bat colonies, which
appear to be influenced by the distinct host population genetics of R.
affinis and R. sinicus species. The comparison of SARSr-CoVs further
showed varied impact of host specificity along genome-wide
diversification and modular viral evolution among Rhinolophus species.
Overall, the findings point to a complex interaction between host
genetic diversity, and the way viruses spread and structure within
natural populations, calling for continued surveillance efforts to
understand factors driving viral transmission and emergence in human
populations. These results present the underestimated spillover risk of
bat viruses, highlighting the importance of enhancing preparedness and
surveillance for emerging zoonotic viruses.