TABLE 2.
Comparison of the ORF sequence of S52 with the ORFs of other genotype 3a isolates
| Genomic region | Comparison of the ORF sequence at the nucleotide levela |
Comparison of the ORF sequence at the amino acid levela |
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Nucleotide positionb | GenBank accession number (isolate name) |
Amino acid positionb | GenBank accession no. (isolate name) |
|||||||||||
|
D17763 (NZL1) |
D28917 (HCV-K3a/650) |
DQ437509 (452) |
D17763 (NZL1) |
D28917 (HCV-K3a/650) |
DQ437509 (452) |
|||||||||
| No. | % | No. | % | No. | % | No. | % | No. | % | No. | % | |||
| Core | 340-912 | 11 | 1.9 | 31 | 5.4 | 14 | 2.4 | 1-191 | 1 | 0.5 | 9 | 4.7 | 1 | 0.5 |
| E1 | 913-1488 | 27 | 4.7 | 34 | 5.9 | 36 | 6.3 | 192-383 | 6 | 3.1 | 12 | 6.3 | 11 | 5.7 |
| E2 | 1489-2595 | 94 | 8.5 | 108 | 9.8 | 118 | 10.7 | 384-752 | 39 | 10.6 | 42 | 11.4 | 44 | 11.9 |
| HVR1 | 1489-1569 | 25 | 30.9 | 24 | 29.6 | 21 | 25.9 | 384-410 | 17 | 63.0 | 11 | 40.7 | 12 | 44.4 |
| p7 | 2596-2784 | 10 | 5.3 | 13 | 6.9 | 12 | 6.3 | 753-815 | 3 | 4.8 | 3 | 4.8 | 5 | 7.9 |
| NS2 | 2785-3435 | 39 | 6.0 | 45 | 6.9 | 36 | 5.5 | 816-1032 | 8 | 3.7 | 17 | 7.8 | 8 | 3.7 |
| NS3 | 3436-5328 | 80 | 4.2 | 112 | 5.9 | 105 | 5.5 | 1033-1663 | 17 | 2.7 | 24 | 3.8 | 20 | 3.2 |
| NS4A | 5329-5490 | 10 | 6.2 | 11 | 6.8 | 11 | 6.8 | 1664-1717 | 2 | 3.7 | 3 | 5.6 | 2 | 3.7 |
| NS4B | 5491-6273 | 32 | 4.1 | 52 | 6.6 | 53 | 6.8 | 1718-1978 | 6 | 2.3 | 12 | 4.6 | 5 | 1.9 |
| NS5A | 6274-7629 | 71 | 5.2 | 85 | 6.3 | 104 | 7.7 | 1979-2430 | 21 | 4.6 | 27 | 6.0 | 27 | 6.0 |
| NS5B | 7630-9402 | 59 | 3.3 | 95 | 5.4 | 87 | 4.9 | 2431-3021 | 6 | 1.0 | 27 | 4.6 | 17 | 2.9 |
| ORF | 340-9402 | 433 | 4.8 | 586 | 6.5 | 576 | 6.4 | 1-3021 | 109 | 3.6 | 176 | 5.8 | 140 | 4.6 |
The S52 consensus sequence and published sequences with complete ORFs of other genotype 3a isolates were compared. The other genotype 3a isolates are indicated as follows: the GenBank accession number is shown first and the isolate name is shown in parentheses. The number and percentage (related to respective genome region) of positions with sequence variation between the S52 consensus sequence and the published sequences with complete ORFs of other genotype 3a isolates are shown. At nt 5358, 3/6 S52 clones had T, and the other 3 had C, while all other genotype 3a isolates had either T or C. Thus, this position was not considered to be different.
The nucleotide and amino acid positions refer to pS52.