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.
Department of Laboratory Medicine, Karolinska Institutet, Stockholm, SE-141 86, Sweden.
L Sara
LS
Arroyo Mühr
Emilie
E
Hultin
Davit
D
Bzhalava
Carina
C
Eklund
Camilla
C
Lagheden
Johanna
J
Ekström
Hanna
H
Johansson
Ola
O
Forslund
Joakim
J
Dillner
D002280:Basal Cell Carcinoma / Q000235:genetics / Q000821:virology; D002294:Carcinoma, Squamous Cell / Q000235:genetics / Q000821:virology; D003001:Cloning, Molecular; D004279:DNA, Viral / Q000235:genetics; D006801:Humans; D007636:Keratoacanthoma / Q000235:genetics / Q000821:virology; D055623:Keratosis, Actinic / Q000235:genetics / Q000821:virology; D008969:Molecular Sequence Data; D027383:Papillomaviridae / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D012878:Skin Neoplasms / Q000235:genetics / Q000473:pathology / Q000821:virology*
D004279:DNA, Viral
HPV197; cutaneous lesions; human papillomavirus; metagenomic sequencing; novel types