TABLE 2.
Primers used for amplification and sequencing of VEEV subtype IC strains
| Primer namea | Sequence (5′-3′)b | Predicted melting temp (°C) |
|---|---|---|
| 5′ Xba (+) | GTGCCAAGCTTCTAGAAATTTAATACGACTC | 73.9 |
| ACTATAATGGGCGGCGCATGAGAGAAG | ||
| V-478 (+) | GGCAAGTCGCTGTTTACC | 60.9 |
| V-796 (−) | TTCTCGTGGTAGATGGTCGAGC | 67.5 |
| V-952 (+) | ATGCTGCTACGATGCACCG | 67.3 |
| V-1245 (−) | GCCTCTCATCTTCTTGATC | 56.3 |
| V-1526 (+) | CGATGAGGCTAAGGAAGTGCG | 67.9 |
| V-1714 (−) | GAAAGCACAGCGTAAGAGC | 60.3 |
| V-2010 (+) | AAAACTGTCAAGCCCAGCGAGCAC | 73.0 |
| V-2193 (−) | TGGTTGGTACTTGGTAAGGAG | 60.4 |
| V-2519 (+) | CCTGAAAGTGCATTTTAACC | 58.7 |
| V-3130 (+) | CCACTGAACAATGGAACAC | 58.9 |
| V-3419 (+) | GCGCAATTATGATCCGCG | 67.4 |
| V-3800 (+) | CGTCAGCATAGGTTATGGTTAC | 59.9 |
| V-4039 (−) | CCCTCGCACCACATGATATG | 66.3 |
| V-4669 (+) | AGGCGGCCAAGGATATAG | 61.5 |
| V-4738 (−) | TCACCGAGGATATACATGC | 58.4 |
| V-4883 (−) | GAGGCTTTTAGGCGTTGTAC | 60.3 |
| V-5065 (+) | AGAACCAATCCACAGAGGGGAC | 67.4 |
| V-5251 (−) | AGGAATGGACCAGGATGAGCTGG | 71.3 |
| V-5649 (+) | GAGGAGTTTGAGGCGTTC | 59.9 |
| V-6208 (+) | GCAGCTTTCCAAAGAAAC | 57.5 |
| V-6894 (+) | GAGCTGTTGACGCTGATTGA | 64.2 |
| V-6972 (−) | GGATTTCATCATGGCTCC | 60.4 |
| V-7514 (+) | ACYCTCTACGGCTRACCTRA | 59.2–61.6 |
| V-7651 (−) | CATCGCCAGAAAAGGGTCG | 67.8 |
| V-7886 (+) | AACAAGAAACCAGGCAAGAG | 60.8 |
| V-8659 (+) | AATTGAGGCAGTGAAGAGCGAC | 66.6 |
| V-8953 (−) | CTGCCTACAGGATTAAAT | 51.4 |
| V-9747 (+) | CGTGCCTAACTCCTTACC | 57.2 |
| V-9847 (−) | TGTTCCATAGGTGATCCAAGGAC | 65.9 |
| V-10247A (+) | TACCCNTTYATGTGGGG | 59.7–60.8 |
| V-10566 (+) | TTCCTGAGTATGGGGCAG | 61.2 |
| V-10664 (−) | TCGCTCCTGCTTTGGGTCTCTG | 71.8 |
| V-10830 (+) | CATTAGCCTTTGACATTCCC | 60.9 |
| T25V-Mlu (−) | TTACGAATTCACGCGTTTTTTTTTTTTTTTTTTTTTTTTTV | 50.4–51.4 |
a
Each numbers represents the 5′ genomic sequence position to which the primer anneals; the RNA strand orientation of each primer is given in parentheses.
b
R = A or G; Y = C or T; V = A, C, or G; N = A, C, G, or T.