Figure A2.

Multiple alignment of Raw E7 DNA sequences. Multiple sequence alignments of HPV E7 sequences from tumor biopsies KTS1–9 are shown. The reference sequence is E7 from KTS6, identical to worldwide strain that has 100% identity to more than 50 reported sequences (representative sequence: GenBank K02718; Seedorf et al., 1985). E7 KTS1 is a novel sequence showing a single nt difference to East Asian (AF534061) and Thai (FJ610150) strains. KTS2 represents another worldwide strain (AY686582). E7 KTS3 is a novel sequence showing a single nt difference to the worldwide strain (AY686582). E7 KTS4, KTS5, and KTS8 sequences represent Asian strains (AF534061). E7 KTS7 sequence represents East Asian strain (AF486333). E7 KTS9 sequence represents East Asian strain (AF486332). Positions 31–57 encode HLA-A02 T cell epitope YMLDLQPET. Codon 85–87 encodes amino acid variability (N or S), while all other variable positions, shown as shaded, represent silent mutations. Unresolved nucleotides in KTS1 and KTS4 are represented by ambiguity code “n”. In summary, the HPV E7 sequence variability in the cohort is relatively high, representing multiple HPV-16 species. At the protein level, on the contrary, the sequence is extremely well conserved indicating high stability of the protein product.