Table 1.
Primers and probes used in real-time RT-PCR assays for SLEV and EEEV and for internal control detection and for PCR and sequencing of the NS5 region of genomes of SLEV strains
| Name of primer or probe | Sequence (5′→3′) | Nucleotide start | Reference |
|---|---|---|---|
| EEE-E1-F | ACACTAAATTCACCCTAGTTCGAT | 11 376 | This study |
| EEE-E1-R | GTGTATAAAATTACTTAGGAGCAGCATTATG | 11 522 | This study |
| EEE-E1-Fam | 6-FAM-CGAGCTATGGTGACGGTGGTGCA-BHQ1 | 11 407 | This study |
| SLE-NS5-F1 | GGTGGTTCGGGAGCCCTT | 8678 | This study |
| SLE-NS5-F2 | GGTGGTTCGGGAGCCTTT | 8678 | This study |
| SLE-NS5-R2 | CACGCCTTTTGGCCAACAA | 8616 | This study |
| SLE-NS5-R3 | CACGCCTTTTGGTCAACAA | 8616 | This study |
| SLE-NS5-Vic1 | VIC-CAACCTTTTCTTTGAACACC-MGB | 8656 | This study |
| SLE-NS5-Vic2 | VIC-CAACCTTTTCTTTGAAGACC-MGB | 8656 | This study |
| GFP forward primer | CACCCTCTCCACTGACAGAAAAT | 549 | Tavakoli et al. (2007) |
| GFP reverse primer | TTTCACTGGAGTTGTCCCAATTC | 470 | Tavakoli et al. (2007) |
| GFP probe | 6-FAM-TGTGCCCATTAACATCACCATCTAATTCAACA- TAMRA | 525 | Tavakoli et al. (2007) |
| FG1 | TCAAGGAACTCCACACATGAGATGTACT | 8206 | Fulop et al. (1993) |
| FG2 | GTGTCCCATCCTGCTGTGTCATCAGCATACA | 9167 | Fulop et al. (1993) |
| Seq-1-F | GGAACTATCATGGAAGTTATGAAG | 8486 | This study |
| Seq-1-R | TTGCTTTGAATTCTTCTGGGG | 8782 | This study |
| Seq-2-F | CTGGCTGTGGGACTTCG | 8715 | This study |
| Seq-2-R | GGTCTGGCTTCTCTGTGAGC | 8398 | This study |
| Seq-3-F | CCCCAGAAGAATTCAAAGCAAAGG | 8762 | This study |
| Seq-3-R | GGCTTCTCTGTGAGCTTTCC | 8393 | This study |
| Seq-4-F | CTGGTTGTGGGACTTTGTTGC | 8715 | This study |
EEE = eastern equine encephalitis; SLE = St. Louis encephalitis. EEEV sequence is from GenBank accession EF568607 (EEEV strain NJ/60). SLEV sequence is from GenBank accession EF158050 (SLEV MSI-7). Nucleotide numbers are given based on the genome of MSI-7, but not all primers perfectly match this strain. GFP sequence is from GenBank accession EU341596 (cloning vector pGFPm-T).