Characterization of human papillomavirus type 154 and tissue tropism of gammapapillomaviruses

Abstract

The novel human papillomavirus type 154 (HPV154) was characterized from a wart on the crena ani of a three-year-old boy. It was previously designated as the putative HPV type FADI3 by sequencing of a subgenomic FAP amplicon. We obtained the complete genome by combined methods including rolling circle amplification (RCA), genome walking through an adapted method for detection of integrated papillomavirus sequences by ligation-mediated PCR (DIPS-PCR), long-range PCR, and finally by cloning of four overlapping amplicons. Phylogenetically, the HPV154 genome clustered together with members of the proposed species Gammapapillomavirus 11, and demonstrated the highest identity in L1 to HPV136 (68.6%). The HPV154 was detected in 3% (2/62) of forehead skin swabs from healthy children. In addition, the different detection sites of 62 gammapapillomaviruses were summarized in order to analyze their tissue tropism. Several of these HPV types have been detected from multiple sources such as skin, oral, nasal, and genital sites, suggesting that the gammapapillomaviruses are generalists with a broader tissue tropism than previously appreciated. The study expands current knowledge concerning genetic diversity and tropism among HPV types in the rapidly growing gammapapillomavirus genus.

Figure 1. Methodological strategy and genomic organization for HPV154.

The ORFs are indicated with light blue arrows. The primers used in the DIPS-PCR are represented with half arrows. The inner circle shows the strategies employed, and the outer circle shows the final clones. Putative binding sites for viral proteins and cellular factors are shown as follows: E2 binding site, E2BS (▾); E1 binding site, E1BS (Δ); TATA-box (▪); Polyadenylation signal (•).

Figure 2. Phylogenetic tree for HPV154 and related papillomaviruses.

Ninety one complete genomes were analyzed, including all gammapapillomaviruses as well as related genera but closer than betapapillomaviruses. HPV154 is indicated with an arrow. The tree was obtained by the maximum likelihood approach using RAxML software and rooted with the betapapillomavirus HPV5 and HPV9. Bootstrap support values are indicated in each branch as percentages. Genera are indicated at the rightmost side, while species of γ-PVs are to the right of brackets. The dotted key to the left of γ-PV11* shows species suggested in this work. The bar indicates the number of substitutions per site. * Proposed category and pending approval by ICTV. †Putative novel species. ‡: Uncloned HPV genome (not official type). The following species are represented by the types included in the tree: AsPV1, Apodemus sylvaticus papillomavirus 1; BPV, Bos taurus papillomavirus spp.; ChPV1, Capra hircus papillomavirus 1; CPV, Canis familiaris papillomavirus spp.; DdPV1, Delphinus delphis papillomavirus 1; HPV, Gammapapillomavirus spp.; McPV2, Mastomys coucha Papillomavirus 2; PphPV, Phocoena phocoena papillomavirus spp.; PsPV1, Phocoena spinipinnis Papillomavirus 1; TtPV, Tursiops truncatus Papillomavirus spp.