TABLE 1.
Sequences of the primers used for the amplification and sequencing of HCV isolates in the C-E1 region and the capture probe used for RNA extraction, deduced from 5′-UTR
| Name | Position (nt)a | Sequenceb |
|---|---|---|
| Capture probe (5′UTR a2)b | (−13)-(−42) | 5′CGAGACCTCCCGGGGCACTCGCAAGCACCC3′ |
| Outer C-E1 forward (493 S-H77) | 493-518 | 5′GCAACAGGGAACCTTCCTGGTTGCTC3′ |
| Outer C-E1 reverse (987 R-H77) | 987-964 | 5′CGTAGGGGACCAGTTCATCATCAT3′ |
| Inner C-E1 forward (502 S-H77) | 502-527 | 5′AACCTTCCTGGTTGCTCTTTCTCTAT3′ |
| Inner C-E1 reverse (975 R-H77) | 975-952 | 5′GTTCATCATCATATCCCATGCCAT3′ |
| Chimer forwardc | 5′AGCGGATAACAATTTCACACAGGAAACCTTCCTGGTTGCTCTTTCTCT3′ | |
| Chimer reversec | 5′CGCCAGGGTTTTCCCAGTCACGACGTTCATCATCATATCCCATGCCAT3′ | |
| 1223 forward sequencing | 5′AGCGGATAACAATTTCACACAGGA3′ | |
| 1224 reverse sequencing | 5′CGCCAGGGTTTTCCCAGTCACGAC3′ |
a
Numbered according to the first nucleotide in the ORF of the HCV reference strain H77 (GenBank accession no. AF009606) (3).
b
The capture probe is identical to the outer reverse primer in the 5′UTR RT-nested PCR.
c
Underlined sequences of Chimer forward and Chimer reverse correspond to those of the commercial sequencing primers 1223 and 1224 (Promega), respectively.