TABLE 1.
Primers used in this study
| Primer | Sequence (5′–3′) | Usage |
|---|---|---|
| 3Dpol-F1 | TTTCATCGTCGGCACTCACTC | Sequencing of the full-length 3Dpol-encoding gene |
| 3Dpol-F2 | TGCGCTGATTGACTTCGAGAAC | |
| 3Dpol-R | GGAATGTGGAAGCGGGAAAAG | |
| D5N-mu-F | CGAGGGATTGGTTGTTAACACCAGAGATGTGGG | Production of the D5N mutant |
| D5N-mu-R | CTCCACATCTCTGGTGTTAACAACCAATCCCTCG | |
| A38V-mu-F | GAATTTGGGCCTGCTGTCTTGTCCAACAAGGAC | Production of the A38V mutant |
| A38V-mu-R | GTCCTTGTTGGACAAGACAGCAGGCCCAAATTC | |
| M194I-mu-F | CACATTCTTTACACCAGGATTATGATTGGCAGATTTTGGC | Production of the M194I mutant |
| M194I-mu-R | GCACAAAATCTGCCAATCATAATCCTGGTGTAAAGAATGTG | |
| M296V-mu-F | CATTGTTGTTGAGGGCGGGGTGCCGTCTGGCTGTTCCGC | Production of the M296V mutant |
| M296V-mu-R | GCGGAACAGCCAGACGGCACCCCGCCCTCAACAACAATG | |
| Real-time-F | AATGCACTCAAACAACGGAC | Quantitative real-time PCR for detecting RNA synthesis |
| Real-time-R | GCAGTGGTTAGCATCAAAGG | |
| Di-Fitness-F1 | TTTCATCGTCGGCACTCACTC | Amplification of 3D for the direct fitness assay |
| Di-Fitness-F2 | TGCGCTGATTGACTTCGAGAAC | |
| Indi-Fitness-F | CGCGCAAGAGACAGCAGATGG | Amplification of 3A to 3D for the indirect fitness assay |
| Indi-Fitness-R | GGAATGTGGAAGCGGGAAAAG | |
| Mu-frequency-F | TGTCCAACCTTCCTCCGCTTC | Amplification of VP3 for the mutation frequency assay |