title: Unbiased approach for virus detection in skin lesions.
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.
authors.affiliation: Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
authors.forename: Davit
authors.initials: D
authors.lastname: Bzhalava
authors.forename: Hanna
authors.initials: H
authors.lastname: Johansson
authors.forename: Johanna
authors.initials: J
authors.lastname: Ekström
authors.forename: Helena
authors.initials: H
authors.lastname: Faust
authors.forename: Birgitta
authors.initials: B
authors.lastname: Möller
authors.forename: Carina
authors.initials: C
authors.lastname: Eklund
authors.forename: Peter
authors.initials: P
authors.lastname: Nordin
authors.forename: Bo
authors.initials: B
authors.lastname: Stenquist
authors.forename: John
authors.initials: J
authors.lastname: Paoli
authors.forename: Bengt
authors.initials: B
authors.lastname: Persson
authors.forename: Ola
authors.initials: O
authors.lastname: Forslund
authors.forename: Joakim
authors.initials: J
authors.lastname: Dillner
mesh_terms: D052685:Alphapapillomavirus / Q000235:genetics* / Q000302:isolation & purification; D002294:Carcinoma, Squamous Cell / Q000821:virology*; D004279:DNA, Viral / Q000235:genetics / Q000302:isolation & purification; D016679:Genome, Viral; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007636:Keratoacanthoma / Q000821:virology*; D055623:Keratosis, Actinic / Q000821:virology*; D058889:Molecular Typing; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D012878:Skin Neoplasms / Q000821:virology*
chemical_list: D004279:DNA, Viral