Unbiased approach for virus detection in skin lesions

PLoS One. 2013 Jun 28;8(6):e65953. doi: 10.1371/journal.pone.0065953. Print 2013.

Abstract

To assess presence of virus DNA in skin lesions, swab samples from 82 squamous cell carcinomas of the skin (SCCs), 60 actinic keratoses (AKs), paraffin-embedded biopsies from 28 SCCs and 72 kerathoacanthomas (KAs) and fresh-frozen biopsies from 92 KAs, 85 SCCs and 92 AKs were analyzed by high throughput sequencing (HTS) using 454 or Ion Torrent technology. We found total of 4,284 viral reads, out of which 4,168 were Human Papillomavirus (HPV)-related, belonging to 15 known (HPV8, HPV12, HPV20, HPV36, HPV38, HPV45, HPV57, HPV59, HPV104, HPV105, HPV107, HPV109, HPV124, HPV138, HPV147), four previously described putative (HPV 915 F 06 007 FD1, FA73, FA101, SE42) and two putatively new HPV types (SE46, SE47). SE42 was cloned, sequenced, designated as HPV155 and found to have 76% similarity to the most closely related known HPV type. In conclusion, an unbiased approach for viral DNA detection in skin tumors has found that, although some new putative HPVs were found, known HPV types constituted most of the viral DNA.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alphapapillomavirus / genetics*
  • Alphapapillomavirus / isolation & purification
  • Carcinoma, Squamous Cell / virology*
  • DNA, Viral / genetics
  • DNA, Viral / isolation & purification
  • Genome, Viral
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Keratoacanthoma / virology*
  • Keratosis, Actinic / virology*
  • Molecular Typing
  • Sensitivity and Specificity
  • Sequence Analysis, DNA
  • Skin Neoplasms / virology*

Substances

  • DNA, Viral

Grant support

The work was supported by the Swedish Cancer Society (110569), the Swedish Research Council (3468) and the Swedish government strategic program on Biomarkers in Cancer Research (BioCARE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.