Animal markets are associated with elevated viral diversity and virus–host connectivity across wildlife–farm interfaces

Animal markets represent important interfaces among wildlife, farmed animals, and humans, yet their role in shaping viral diversity, community structure, and cross-host viral sharing remains incompletely understood. We performed metatranscriptomic analysis of 279 samples collected across wild, farm, and market-associated settings in Guangdong Province, China, with the animal-derived samples encompassing 15 host orders. We identified 106 vertebrate-associated viral lineages represented by 259 viral strains, including 19 putative novel viruses representing 13 putative viral lineages. Viral diversity and viral community composition differed significantly among ecological settings, with market-associated samples generally showing higher viral richness and distinct virome structures than wild and farm samples. The higher viral richness observed in market-associated samples remained evident in sensitivity analyses addressing pooled sampling, host composition, and unequal sampling effort. Viral sharing was observed across wild, farm, and market-associated settings, with market-associated host groups showing particularly extensive virus–host connectivity. Network analyses further indicated greater viral connectivity in market-associated settings, with host groups showing higher degree and betweenness centrality and more extensive virus–host associations. In addition, 38 viral sequences representing 13 viral lineages had documented pathogenic relevance based on reported disease associations in humans or other vertebrate hosts. Zoonotic relevance varied among viral lineages and depended on lineage-, subtype-, or genotype-specific evidence, highlighting the importance of distinguishing disease-associated viruses from those with demonstrated zoonotic potential. Animal markets were associated with greater viral diversity, distinct viral community composition, and broader patterns of viral sharing and connectivity, supporting their role as ecological interfaces linking wildlife and farm systems. However, shared detections do not establish the direction or frequency of viral movement, and temporal heterogeneity remains an important consideration. These findings highlight the value of integrated One Health surveillance across wildlife trade and agricultural systems, together with lineage-specific assessment of viruses with potential human-health relevance.