Gut Virome of Tibetan Pigs Reveals the Diversity, Composition, and Distribution of Potential Novel Viruses/Variants.

As a local breed adapted to the extreme environment of the Tibetan Plateau, Tibetan pigs have not yet been systematically characterized in terms of their gut viral communities. In this study, we applied viral metagenomics to sequence fecal samples from 191 Tibetan pigs (including both healthy and diarrheal individuals) across four farms in Nyingchi, Tibet, aiming to reveal the diversity, composition, and distribution of gut viral communities in Tibetan pigs living at high altitudes. A total of nearly 120 million high-quality viral sequence reads were obtained, which were annotated into 16 viral families. The viral community was predominantly dominated by Microviridae, but its composition varied across different farms and health statuses. Phylogenetic analysis identified numerous virus sequences associated with pigs, including RNA viruses (such as Astroviridae (n = 7), Caliciviridae (n = 6), Picornaviridae (n = 15), etc.) and DNA viruses (such as Circoviridae (n = 3), Genomoviridae (n = 4), Smacoviridae (n = 41), Parvoviridae (n = 11), etc.). Notably, the study found multiple viral sequences exhibiting genetic differences from known strains, suggesting the potential presence of novel viruses or variants. For instance, a papain-like protease (PLP) insertion sequence, identified to have high sequence identity with Torovirus (ToV), was found in six Enterovirus G (EV-G) strains, indicating a cross-family genetic recombination event. This study systematically outlines the viral metagenomic profile of gut viral communities in Tibetan pigs at high altitudes, revealing their unique viral diversity and complex community structure. The results suggest that the gut viral community of Tibetan pigs consists of host-associated viruses, bacteriophages, and potentially viruses originating from the environment or diet, with its composition influenced by farming conditions and host health status. These findings provide an important data foundation for understanding the interactions between viruses, hosts, and the environment in unique ecological settings and offer new insights into the health management and virology research of Tibetan pigs.