Sequence analysis of the late region of human papillomavirus type 6 genome

Objective: To study variations of genome late region of human papillomavirus type 6 (HPV-6) isolated from Chinese patients with condyloma acuminatum.

Methods: Using overlap PCR design, major capsid protein (L1) and minor capsid protein (L2) genes were separately amplified from clinical samples following HPV type determination, and were further assembled into HPV-6 genome late region sequences after inserting into plasmid and sequencing.

Results: Two sequences (GenBank accession number AY015006, AY015008) of HPV-6 late region were assembled, which are 2,869 bp long covering 35% HPV-6 genome and with complete open reading frames (ORFs) for L1 and L2. Compared with prototype sequence, nine point mutations were found, including four missense mutations, three of which were located in L2 ORF. Phylogenetic analysis indicated that the cloned sequences are classified into HPV-6b.

Conclusions: HPV-6 genome late region, especially in L1 ORF, is very conserved (variation rate < 0.28%). The mutation from A to G at position 7081 in HPV-6 genome and from G to A at 7099 may represent region characteristics. This is the first report that describes sequence variations among genome late region of HPV-6 isolated from Chinese patients.