A novel papillomavirus identified through viromic analysis of stranded Yangtze finless porpoises (Neophocaena asiaeorientalis asiaeorientalis).

The Yangtze finless porpoise (Neophocaena asiaeorientalis asiaeorientalis) is a critically endangered freshwater cetacean that is endemic to China. In this study, we conducted viromic analysis on swab and tissue samples from three stranded individuals collected in 2024, using high-throughput meta-transcriptomic sequencing. A diverse range of viral sequences was identified, including a large proportion of unclassified viruses, bacteriophage-related viruses, and vertebrate-associated viruses. Notably, we assembled the complete genome sequence of a novel papillomavirus, designated Neophocaena asiaeorientalis papillomavirus isolate WH240216 (NasiPV-WH240216), which shares 82.2% overall nucleotide sequence identity and 87.5% L1 gene identity with Phocoena spinipinnis papillomavirus 1 (PsPV1). The genome is 8,010 bp in length and exhibits the typical genome organization and conserved protein motifs of a papillomavirus. Phylogenetic analysis placed this virus within the genus Omikronpapillomavirus, and its sequence divergence met the ICTV criteria for a novel papillomavirus type. These findings expand our knowledge of the diversity of papillomaviruses in cetaceans and provide important insights into the evolution and potential pathogenicity of marine mammal papillomaviruses.