Genomic characterization of Erethizon dorsatum papillomavirus 2, a new papillomavirus species marked by its exceptional genome size

Co-infection of distinct papillomavirus types in a captive North American porcupine

“…In the case of EdPV-2, this region is exceptionally large, although its precise function remains to be elucidated. We have previously published a detailed overview of the known regulatory motives in the genome of EdPV-2 [ 9 ]. Nearly all of these motives are identical to the ones found in the genome presented here, with only minor differences in the E2 DNA-binding motif ( GR A N A LKC W R H R ) and the L2 arginine/lysine-rich region ( KRRRRRR vs KRRRRRRR ).…”

“…However, in several cases, divergent viruses from separate clades have been identified in the same host species, hinting at the occurrence of ancient host-jumping events [ 7 , 8 ]. An example of this are Erethizon dorsatum papillomavirus 1 and 2 (EdPV-1/-2), which were both discovered in North American porcupines [ 9 – 11 ]. While EdPV-2 clusters directly adjacent to the rodent-borne papillomaviruses of the genus Pipapillomavirus , albeit potentially as a separate genus, EdPV-1 is the sole member of the distantly related genus Sigmapapillomavirus , clustering next to the nupapillomavirus human papillomavirus 41.…”

PVAmpliconFinder: a workflow for the identification of human papillomaviruses from high-throughput amplicon sequencing

“…This is what is suspected to happen for the classification by EPA of the Erethizon dorsatum sequences identified in our experiment. They are inferred to be close to EdPV2 (MH376689), a recently referenced but unclassified Erethizon dorsatum PV [22], presenting large differences from other known PVs on its L1 gene, and thought to represent a new genus in the family Papillomaviridae. Although this led to an incomplete classification, these sequences may represent new species or virus features.…”

“…Finally, RaxML-EPA found homology with EdPV2 (MH376689), an unclassified Erethizon dorsatum PV species (Table 2; Supplementary Table S6). EdPV2 was proposed to represent a new genus in the family Papillomaviridae [22]. From these results, this 352 bp sequence may represent a novel PV type, although it remains to be fully characterized.…”

“…BlastN could not classify 0.008% of the sequences, due to a best subject sequence associated with an e-value under the threshold defined as 1e-1 ( Supplementary Table S3). RaxML-EPA also classified 0.8% of the sequences as "Unclassified" because those sequences presented homology to a newly described Erethizon dorsatum PV (EdPV2; MH376689), not yet classified by the ICTV, and potentially the first representative genome of a new PV genus [22]. Interestingly, the 46 reads that were unclassified by BlastN (due to the e-value threshold) were classified as Taupapillomavirus by RaxML-EPA, with homology to Felis catus PV type 4 and 5 ( Supplementary Table S4).…”