Gut Virome Diversity and Health Status in Rescued Pangolins: Metaviromics Reveals Parvovirus as a Key Virus Associated with Disease

Abstract

BackgroundPangolins are critically endangered mammals that suffer from high rates of gastrointestinal disease during captivity, yet the role of the gut virome in their health remains unexplored. This study presents the first comprehensive characterization of the gut DNA virome in Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins across different health states. ResultsMetaviromic sequencing of 16 fecal samples from healthy, diarrheal, pneumonic, free-ranging, and deceased pangolins generated 7.2-11.8 Gb clean data per sample. A total of 12 viral phyla, 26 families, 219 genera, and 1,132 species were identified. Caudovirales phages (Siphoviridae, Myoviridae, and Podoviridae) dominated the gut virome of healthy individuals, with phage content exceeding 90% in most healthy samples. However, diseased and deceased individuals exhibited a significant reduction in phage proportion (94.5% vs. 53.3%, P = 0.02), accompanied by a dramatic increase in eukaryotic viruses--particularly Parvoviridae, which accounted for 66% of the virome in deceased Malayan pangolins. Iridoviridae (38%) and Polydnaviridae (34%) dominated in deceased Chinese pangolins. SIMPER analysis identified Parvoviridae as the primary contributor to virome dissimilarity between healthy and diseased Malayan pangolins, whereas Iridoviridae and Polydnaviridae were the key contributors for Chinese pangolins. LEfSe analysis revealed 12 biomarker viruses in free-ranging pangolins (predominantly Staphylococcus and Escherichia phages), six in healthy Chinese pangolins (predominantly Streptococcus phages and Lactobacillus viruses), and six in deceased Malayan pangolins (predominantly vertebrate viruses). KEGG functional annotation revealed that genes related to DNA replication, repair, and recombination were the most abundant, suggesting frequent genomic recombination within the pangolin gut virome. ConclusionsThe gut virome of pangolins is closely associated with health status. Disease induces a shift from a phage-dominated to a eukaryotic virus-dominated virome, with Parvoviridae and Iridoviridae emerging as candidate pathogenic viruses in Malayan and Chinese pangolins, respectively. These findings provide molecular evidence for virome monitoring in pangolin conservation and highlight the need for targeted surveillance of ImportancePangolins are the most trafficked mammals in the world, and all eight species are critically endangered. During rescue and captive care, these animals suffer from high rates of gastrointestinal disease, yet the role of viruses in their gut health has never been studied. This research provides the first comprehensive map of the gut virus community in pangolins, revealing that healthy individuals carry a virus community dominated by beneficial bacterial viruses called phages, while sick and dying animals show a dramatic shift toward disease-causing viruses. Notably, parvoviruses emerge as potential pathogens in Malayan pangolins, while iridoviruses dominate in deceased Chinese pangolins. These findings offer a new tool for monitoring pangolin health in rescue centers: by tracking the balance between beneficial phages and harmful viruses, veterinarians may be able to detect illness earlier and improve survival rates. The study also highlights the importance of environmental exposure for maintaining a healthy gut virus community, supporting the creation of semi-natural enclosures for rescued pangolins. Beyond conservation, this work contributes to our understanding of how viruses move between wildlife and humans, which is critical for preventing future disease outbreaks.