Deep sequencing extends the diversity of human papillomaviruses in human skin

Abstract

Most viruses in human skin are known to be human papillomaviruses (HPVs). Previous sequencing of skin samples has identified 273 different cutaneous HPV types, including 47 previously unknown types. In the present study, we wished to extend prior studies using deeper sequencing. This deeper sequencing without prior PCR of a pool of 142 whole genome amplified skin lesions identified 23 known HPV types, 3 novel putative HPV types and 4 non-HPV viruses. The complete sequence was obtained for one of the known putative types and almost the complete sequence was obtained for one of the novel putative types. In addition, sequencing of amplimers from HPV consensus PCR of 326 skin lesions detected 385 different HPV types, including 226 previously unknown putative types. In conclusion, metagenomic deep sequencing of human skin samples identified no less than 396 different HPV types in human skin, out of which 229 putative HPV types were previously unknown.

Figure 1. Coverage plot of the putative HPV type SE46 genome.

Coverage is represented as percentages (maximum coverage/coverage at a particular position), comparing different sequencing methods with each other. Grey, green and red histograms correspond to genome coverage from the Roche 454GSFLX, Ion Torrent PGM and Illumina MiSeq platform, respectively. The data from GSFLX and PGM platforms are previously published. Light blue lines represent putative open reading frames of SE46. The plot was generated using Circos visualization tool.

Figure 2. Bayesian phylogenetic tree based on the L1 part of the complete 164 established HPV types (+ bovine papillomavirus type 3 and type 5) and 160 putative novel HPV types (SE-types) that were >400 bp or contained >200 bp of the 3′-end of the amplimer.

SE-types discovered using 454GSFLX and using Illumina MiSeq are presented in blue and red colors, respectively.