TABLE 1.

Variation of HPV58 genome regions and ORFs^e

ORF or region	Maximum nucleotide pairwise difference (%)	Length of nucleotide sequence alignment (bp)	No. of variable nucleotide positionsa	% of variable nucleotide positions	No. of variable nucleotide changes at each codon positionb			Maximum amino acid pairwise difference (%)	Length of amino acid alignment	No. of variable amino acid positionsc	% of variable amino acid positions	Ratio of nonsynonymous to synonymous changes
					1st	2nd	3rd
E6	1.8	447	16	3.6	8	1	7	4.0	148	8	5.4	1.33
E7	3.4	294	20	6.8	7	6	7	7.1	97	12	12.4	1.71
E1	1.3	1,932	89	4.6	35	17	37	2.0	645	46	7.1	1.12
E2	1.3	1,074	53	4.9	11	9	33	2.2	357	27	7.6	1.13
E4	2.2	273	19	7.0	5	10	4	5.6	90	17	18.9	17.00
NCR1	3.2	62	4	6.5
E5	3.5	228	19	8.3	8	0	11	4.0	75	5	6.7	0.36
NCR2	5.8	122	18	14.8
L2	2.5	1,419	103	7.3	24	25	53	3.4	472	52	11.0	1.24
L1	2.2	1,572	94	6.0	17	15	62	3.6	523	35	6.7	0.67
LCR	3.6	849	92	10.8
CG/8 ORFsd	1.7	7,834	500	6.4	115	83	214	2.2	2,407	202	8.4	1.08

^aEach insert or deletion event was counted as one variation.

^bThe first, second, and third nucleotide positions in a codon.

^cAmino acid changes (nonsynonymous changes). Each insert or deletion event was counted as one variation.

^dEach nucleotide position is counted once based on 90 complete genome alignments.

^eCG, complete genome; NCR1, noncoding region 1 between the E2 and E5 ORFs; NCR2, noncoding region 2 between the E5 and L2 ORFs; LCR, long control region.