TABLE 2.
Details of primers used in this study
| Primer name | Sequence | Specificity | Positionsa |
|---|---|---|---|
| 5′UTR-Ex-400F | CCTTGTGGTACTGCCTGATAG | Generic | 282–299 |
| 5′UTR-In-405F | CCTGATAGGGTGCTTGCGAG | Generic | 295–311 |
| Gg-767-Rex-Core | CAYGTRAGGGTATCGATGAC | Generic | 721–705 |
| G1-667-Rin-Core | GTCABTGGGGCCCCAACTAG | Genotype 1 | 671–655 |
| G4-668-Rin-Core | ATCATTTGGRCCCCAAGAC | Genotype 4 | 671–656 |
| NS5B-Ex-Fwd | TGGGGTTCTCRTATGAYACCCGCTGYTTTG | Generic | 8248–8274 |
| NS5B-Ex-Rev | AATACCTVGTCATAGCCTCCGTGA | Generic | 8637–8617 |
| NS5B-In-Fwd | GAYACCCGCTGYTTTGACTC | Generic | 8262–8278 |
| NS5B-In-Rev | TACCTNGTCATAGCCTCCGTGAAGACTC | Generic | 8635–8611 |
| CoreOS | ACTGCCTGATAGGGTGCTTGCGAG | Generic | 291–311 |
| CoreOAS | ATGTACCCCATGAGGTCGGC | Generic | 748–732 |
| CoreIS | AGGTCTCGTAGACCGTGCATC ATG | Generic | 324–344 |
| CoreIAS | CAYGTRAGGGTATCGATGAC | Generic | 721–705 |
| Pr3 | TATGAYACCCGCTGYTTTGCTC | Generic | 8259–8278 |
| Pr4 | GCNGARTAYCTVGTCATAGCCTC | Generic | 8641–8622 |
| Pr5 | GCTAGTCATAGCCTCCGT | Generic | 8633–8619 |
a
Location numbering is relative to isolate H77 (GenBank accession number AF009606).