SEQUENCE VARIATIONS AND VIRAL GENOMIC STATE OF HUMAN-PAPILLOMAVIRUS TYPE-16 IN PENILE CARCINOMAS FROM UGANDAN PATIENTS

Sequence variations in the E6/E7 (nt 34-880) and the L-1 (nt 6584-7035 ) ORFs, and in the long control region (LCR) (nt 7289-93) of human pap illomavirus type 16 (HPV-16) were analysed in five penile carcinoma bi opsies obtained from Ugandan patients. Uganda is a country with a high incidence of genital cancers, All five isolates were classified as me mbers of African-1 lineage (Af1) by phylogenetic analysis based on LCR sequences, The E6 gene phylogenetic analysis, however, showed that fo ur isolates fell into a new subclass designated Af1-u, This subclass, characterized by three point mutations located at the 5' end of the E6 gene with resulting changes in amino acids at positions 10 and 14, is distinguishable from the Af1 class by the absence of synonymous mutat ions at nt 286 and 289. The nonsynonymous substitution at nt 335 was p resent in three out of five samples. The E6 Af1 mutation pattern was p resent in only a single Ugandan HPV-16 isolate. Nucleotide sequence an alysis of the E7 and L1 regions did not allow any Af1 subclass identif ication, The physical state of the viral DNA in these samples was char acterized by PCR and Southern blot analysis. Oligonucleotides which en able amplification of the full length E2 region (nt 2734-3872) failed to amplify the target sequence in four out of five samples, suggesting disruption of the E2 ORF and integration of the HPV genome into the h uman DNA, Southern blot analysis confirmed the virus integration statu s, Our results contribute to the characterization of the HPV-16 'Afric an lineages' with the identification of the Af iu subclass; furthermor e, this is also the first report showing that in male genital cancers HPV-16 is integrated into the human genome with disruption of the E2 O RF.