Complete genome and phylogenetic characterization of a novel papillomavirus from Cuniculus paca in the Brazilian Amazon.

Wild rodents remain underrepresented in papillomavirus genomics, limiting current understanding of host range, tissue tropism, and evolutionary diversity. Here, we report the first papillomavirus identified in the spotted lowland paca, Cuniculus paca, from the Brazilian Amazon, provisionally designated Cuniculus paca papillomavirus 1 (CpPV1). Histopathological examination supported the diagnosis of a virally induced squamous papilloma. Broad-range L1 PCR (FAP59/64), rolling-circle amplification, and Illumina MiSeq sequencing enabled recovery of a complete circular genome of 8,803 bp containing the canonical early (E6, E7, E1, and E2) and late (L2 and L1) open reading frames, together with a typical long control region. Pairwise comparison of the complete L1 gene showed 63.10% nucleotide identity to Erethizon dorsatum papillomavirus 2 (EdPV2), well below the threshold used for papillomavirus type demarcation. Maximum-likelihood phylogenetic analysis recovered CpPV1 as a distinct lineage sister to EdPV2 within a broader, non-monophyletic rodent papillomavirus assemblage. This finding expands the known diversity of Papillomaviridae in Neotropical rodents and provides new insight into papillomavirus evolution in an under-sampled host group.