Exploring viral diversity and host reservoirs: a metagenomic study of zoonotic and pandemic-potential viruses in Vietnam

Abstract

Emerging viral diseases with pandemic potential are frequently of zoonotic origin, highlighting the critical need for proactive surveillance of animal hosts and reservoirs. This study aims to characterise the viral diversity and host range of mammalian viruses in Vietnam using a metagenomic approach, with a focus on zoonotic transmission, novel virus discovery, and pandemic preparedness.

A total of 2,100 faecal samples were collected between 2012 and 2016 from enteric patients, individuals with high occupational contact with animals, and a diverse range of farmed and wild animals, including bats, pigs, and rodents. Samples were subjected to metagenomic sequencing, followed by bioinformatic analyses including metagenomic assembly, genomic annotation, phylogenetic reconstruction, and taxonomic classification.

Seventeen viral families were identified and investigated, revealing substantial viral diversity. Viral species generally clustered strongly by their isolation host. Rotavirus A, a zoonotic virus, was highly prevalent in enteric patients, with evidence of recombination events involving swine-origin segments detected in the human population. Diverse CRESS-DNA viruses were identified in humans, bats, rodents and swine, including 30 novel viral genera falling outside of current ICTV families. Insights were gained into potential host reservoirs, with several novel species of smacoviruses and cycloviruses observed in swine and bats, respectively. For the remaining families, evidence of recent zoonotic events were limited. Phylogenetic clustering by host demonstrates the host specificity of these viral species.

This work uncovers a wealth of viral diversity and demonstrates the challenges of real-time zoonotic surveillance, constrained by sampling structure, sequencing methodologies, and the limitations of current genomic databases. While the shared viruses identified in this study represent only a fraction of the broader viral diversity present in these ecosystems, the findings show a critical need for systematic viral surveillance across human and animal populations. They highlight the importance of developing targeted sampling strategies to detect zoonotic spill over events and enhancing genomic databases to improve viral discovery and classification. These results provide a foundation for the refinement of surveillance systems and support the integration of metagenomics into public health frameworks to anticipate and mitigate emerging viral threats more effectively.