Table 3. Primers and probes for the 5′UTR and NS5B regions.
| Oligonucleotide | Genomic region | Genotype/subtype | Modification | Sequence 5′→3′ | Positioning* |
| HCV1F | 5′UTR | biotin | CGGGAGAGCCATAGTGGT | 130–147 | |
| NSNOF | NS5B | biotin | ACMAAGCYCAAACTCACTCCAWT | 1597–1621 | |
| HCVRX | 5′UTR | CGCRACCCAACRCTACT | 256–273 | ||
| NSNOR | NS5B | CAYGMGACACGCTGTGA | 1685–1702 | ||
| U11 | 5′UTR | amino-12C | ACCCGGTCGTCCTGGCAATT | 179–198 | |
| U3a | 5′UTR | 3a | amino-12C | ACCCGGTCACCCCAGCGATT | 179–198 |
| U2a/cx | 5′UTR | 2a & 2c | amino-12C | ACCCAGTCTTCCCGGCAATT | 179–198 |
| U2a/cy | 5′UTR | 2a & 2c | amino-12C | ACCCGGTCTTCCCGGCAATT | 179–198 |
| U2bx | 5′UTR | 2b | amino-12C | ACCCAGTCTTTCCGGTAATT | 179–198 |
| U2by | 5′UTR | 2b | amino-12C | ACCCAGTCTTTCCGGCAATT | 179–198 |
| NS1a | NS5B | 1a | amino-12C | GTAGCCAGCCGTGAACCA | 1652–1668 |
| NS1bx | NS5B | 1b | amino-12C | GTAACCAGCAACGAACCA | 1652–1668 |
| NS1by | NS5B | 1b | amino-12C | GTAGCCAGCAATGAACCA | 1652–1668 |
| NS1c | NS5B | 1c | amino-12C | GTAACCGCCCGTGAACCA | 1652–1668 |
| NS2ax | NS5B | 2a | amino-12C | GGCGCCGACAGTGAACCA | 1652–1668 |
| NS2ay | NS5B | 2a | amino-12C | GGCGCCGACGGTAAACCA | 1652–1668 |
| NS2b | NS5B | 2b | amino-12C | GGCGCCCACGGTGAACCA | 1652–1668 |
| NS2c | NS5B | 2c | amino-12C | AGCGCTGACGGTGAACCA | 1652–1668 |
| NS3ax | NS5B | 3a | amino-12C | GACACCAACCGTAAACCA | 1652–1668 |
| NS3ay | NS5B | 3a | amino-12C | GACGCCAACCGTAAACCA | 1652–1668 |
*Reference sequence (GenBank, AF009606). M: A or C; Y: C or T; W: A or T; R: A or G.
5′UTR (untranslated region) specific primers: HCV1F (forward), HCVRX (reverse).
NS5B (nonstructural 5B region) specific primers: NSNOF (forward), NSNOR (reverse).
Modification: Forward primer had 5′ biotin added for streptavidin-R-phycoerythrin (SA-PE) ligation.
Probes had 5′ amino-12C (carbon linker) added for ligation to the microspheres.