Differences in Oropharyngeal Viromes Between Surviving and Deceased Malayan Pangolins in a Rescue Context

Pangolins are heavily affected by illegal wildlife trade, but little is known about their viromes during rescue and recovery or their association with survival. Here, oropharyngeal swabs from rescued Malayan pangolins (Manis javanica) were examined by metatranscriptomic sequencing and compared between surviving (S1-S4) and deceased (D1-D4) individuals. Major organs from deceased pangolins were further examined histologically. The oropharyngeal virome was dominated by bacteriophages and arthropod- or environment-associated viral signals, but viral communities differed between outcome groups. Deceased pangolins showed higher alpha diversity than surviving pangolins, and beta-diversity analysis showed significant separation between groups. Phylogenetic analyses identified pestivirus-like, gammaretrovirus-like and picorna-like sequences that were detected mainly in deceased individuals, whereas Iflavirus- and Ghabrivirales-related sequences were most consistent with dietary or environmental exposure. Histopathology revealed multi-organ lesions in deceased pangolins, including interstitial lung injury, renal tubular degeneration and necrosis, hepatocellular steatosis and necrosis, tracheal mucosal injury, intestinal lesions and focal myocardial damage. These findings demonstrate heterogeneous oropharyngeal viral communities among rescued pangolins and reveal differences in viral community diversity and composition between surviving and deceased individuals. Given the small sample size and unequal sampling times between groups, these findings should be considered preliminary and exploratory and should not be interpreted as evidence of a causal relationship between viral signals and mortality. The study highlights the value of virome-based surveillance and careful discrimination between host-associated and exogenous viral signals in wildlife rescue settings.