Summary of HPV isolates and sequenced complete genomes.

aNumber of HPV isolates characterized by sequencing the URR ± E6 region;bNumber of isolate genomes sequenced;cNumber of nucleotide sequences within the genome based on one genome size for each HPV type calculated from the global sequence alignments (see Materials and Methods). Minimum and maximum lengths of sequenced genomes for each type are shown and represent the presence of insertion and deletions (indels);dTotal number and percentage of variable nucleotide positions based on one genome size for each HPV type as described above. Nucleotide variations include single nucleotide polymorphisms (SNPs) and indels, which are considered equivalent to one variation per indel independent of indel size;eMaximum number of encoded amino acids (not including overlapping ORFs) based on one genome size for each type as described above. Cumulative number of amino acids are taken from 7 ORFs (E6, E7, E1, E2, E5, L2 and L1), E4 is not counted separately nor are other overlapping ORFs;fTotal number and percentage of variable amino acids based on the total number of amino acid positions derived from the established genome size for each HPV type.