One Health surveillance of bat virome in mainland Southeast Asia and adjacent regions

Bats are critical viral reservoirs that harbor viromes with high cross-species transmission risks, yet their virome diversity in the Indochina Peninsula remains underexplored. Here, we characterized the bat viromes from 659 samples (197 individuals, 16 species) from Yunnan province and Guangxi Zhuang autonomous region of China, and from Cambodia using next-generation sequencing (NGS). RNA sequencing, viral classification, phylogenetic analyses, and deep-learning-based host adaptability analysis were performed to reveal the viral composition and cross-species transmission risks. We identified 137 viral strains, including 40 novel species spanning 27 families. Viral richness was highest in Rhinolophidae bats (13 viral families found) along China's southwestern border, where Middle Eastern respiratory syndrome (MERS)-like coronavirus (CoV) was found. Cambodian bat viruses were evolutionarily more distant from those of known viruses. A porcine epidemic diarrhea virus (PEDV)-related CoV was found in Cambodia, showing 90.36% genome homology with PEDV CV777 and exhibiting recombinant features between Suidae-adapted ORF1ab and Chiroptera-adapted Spike genes, suggesting that bats are the evolutionary source of PEDV. These findings illuminate the undercharacterized bat viral diversity in biogeographic transition zones and highlight the Indochina Peninsula as a hotspot for CoV recombination. We advocate for enhanced One Health-aligned surveillance targeting viral recombination hotspots and human–bat interfaces in this ecologically critical region. • Bat viromes in southern China and Cambodia show strong species-driven differences, with Cambodian bats harboring highly divergent viruses that reveal vast unexplored diversity. • A porcine epidemic diarrhea virus (PEDV)-related coronavirus in Cambodian bats has a potential recombinant event, indicating bats as a potential PEDV origin. • The Indochina Peninsula emerges as a hotspot for coronavirus recombination, underscoring the need for expanded “One Health” surveillance.