Human papillomavirus type 197 is commonly present in skin tumors

Non-melanoma skin cancers commonly contain Human Papillomavirus (HPV), but the types found have varied depending on the polymerase chain reaction (PCR) primer systems used. Whole genome amplified DNA (not amplified by any specific PCR primers) from 91 skin lesions [41 squamous cell skin carcinomas (SCCs), 8 keratoacanthomas, 22 actinic keratoses, 3 basal cell carcinomas and 17 SCCs in situ] were sequenced. All samples were sequenced both at 160 Mb and 1.8 Gb sequencing depth per sample. The sequences from 10 different HPVs in 47/91 specimens were found. Sequences represented four established HPV types (HPV types 16, 22, 120, 124), two previously known putative types (present in GenBank) and four previously unknown HPV sequences (new putative types). The most commonly detected virus was cloned, sequenced and designated as HPV197. Type-specific real-time PCR detected HPV197 in 34/91 specimens. For comparison, a pool of the same samples after general primer PCR amplification was also sequenced. This revealed 40 different HPVs, but only two HPV types were detected both with sequencing without prior PCR and with sequencing PCR amplicons, suggesting that sequencing without prior PCR gives a more unbiased representation of the HPVs present. In summary, it was found that HPV can be sequenced from most skin disease specimens and HPV197 appeared to be the most commonly present virus. What's new? Some skin cancers such as squamous cell carcinomas occur more often in immune compromised individuals, pointing to an infectious agent as cause. In an unbiased approach the authors used next-generation sequencing to examine 91 non-melanoma skin cancer lesions. Most skin lesions contained Human Papilloma Virus (HPV). The authors cloned and sequenced a new type, HPV type 197, present in 34 of the 91 skin lesions. HPV197 has only 75% similarity with the most closely related known HPV (HPV178), suggesting a possible new agent involved in the carcinogenesis of non-melanoma skin lesions