Bat viruses in Indochina Peninsula reveal viral diversity, PEDV origins, and spillover risks

Bats, critical reservoirs of viruses with significant cross-species spillover risks, have long been understudied in the Indochina Peninsula. A study led by researchers from Beijing University of Chemical Technology, the Academy of Military Medical Sciences, and their partners has unveiled the region's bat virome diversity, offering key insights into the origins of porcine epidemic diarrhea virus (PEDV) and critical surveillance priorities.

From 2020 to 2024, the team analyzed 659 samples from 197 bats across 16 species using next-generation sequencing (NGS). They identified 137 viral strains across 27 families, including 40 novel species. Rhinolophidae bats from China's Yunnan and Guangxi Zhuang Autonomous Region provinces exhibited the highest viral diversity, with 13 viral families and MERS-like coronaviruses. In contrast, Cambodian bats harbored viruses that were evolutionarily distant from known strains.

A notable discovery was a PEDV-related virus in Cambodian Chaerephon plicatus bats. This virus (CB_Mo.plicatus_PEDV-like_1) shared 90.36% genome homology with the PEDV CV777 strain and displayed a recombinant structure, combining suid-adapted ORF1ab and bat-adapted Spike genes. This finding further strengthens the evidence of bats as the potential evolutionary source of PEDV. Recombination analysis of 18 sequences revealed mosaicism in 16, with five regions showing no breakpoints (BFRs), emphasizing the frequency of viral genetic exchange.

Deep learning models further highlighted host adaptation risks. The ORF1ab of the PEDV-related virus showed a preference for suids (pigs), while its Spike gene favored bats, raising concerns about potential spillover if mutations occur.

Our findings underscore critical surveillance gaps. The unique ecology of the Indochina Peninsula drives viral diversity and recombination. We call for enhanced cross-border 'One Health' initiatives targeting bat-human interfaces and recombination hotspots to prevent future zoonotic outbreaks."

Yigang Tong, corresponding author