Genomic diversity of human papillomavirus (HPV) genotype 38

Human papillomavirus (HPV) genotype HPV 38 is a HPV genotype associated with skin cancer and is classified taxonomically in the beta-PV genus-species 2. At least six genomic variants of HPV 38, including prototype isolate and its subtype FA125, have been characterized so far. In order to investigate further the genomic diversity of HPV 38, a total of 39 HPV 38 positive samples obtained from hairs plucked from pubic, scrotal, perianal or eyebrow regions from 31 immunocompetent healthy male individuals were analyzed. The characterization of genomic variants was based on analysis of L1, E6, and E7 genomic regions. Sequence analysis revealed the presence of a single genomic variant in 35 samples and the presence of at least two different HPV 38 genomic sequences in four samples. A total of nine, nine, and five L1, E6, and E7 genomic variants were identified among 35 isolates, respectively. After combining nucleotide variations in all three genomic regions for a particular isolate, 13 different variants were identified, of which 6 and 7 corresponded to HPV 38 and FA125, respectively. In addition to 5 genomic variants identified previously (prototype isolate, subtype FA125, putative subtype AF091444, isolates U21875 and AF091443), 12 novel genomic variants were characterized. A sixth genomic variant described previously (L38917) was found to be identical with prototype HPV 38 isolate. Taking into account the results of this and previous studies, at least seventeen HPV 38 genomic variants exist today, 12 of which are described for the first time in this study.