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 | 8,678 | This study |
| SLE-NS5-F2 | GGTGGTTCGGGAGCCTTT | 8,678 | This study |
| SLE-NS5-R2 | CACGCCTTTTGGCCAACAA | 8,616 | This study |
| SLE-NS5-R3 | CACGCCTTTTGGTCAACAA | 8,616 | This study |
| SLE-NS5-Vic1 | VIC-CAACCTTTTCTTTGAACACC-MGB | 8,656 | This study |
| SLE-NS5-Vic2 | VIC-CAACCTTTTCTTTGAAGACC-MGB | 8,656 | 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 | 8,206 | Fulop et al., 1993 |
| FG2 | GTGTCCCATCCTGCTGTGTCATCAGCATACA | 9,167 | Fulop et al., 1993 |
| Seq-1-F | GGAACTATCATGGAAGTTATGAAG | 8,486 | This study |
| Seq-1-R | TTGCTTTGAATTCTTCTGGGG | 8,782 | This study |
| Seq-2-F | CTGGCTGTGGGACTTCG | 8,715 | This study |
| Seq-2-R | GGTCTGGCTTCTCTGTGAGC | 8,398 | This study |
| Seq-3-F | CCCCAGAAGAATTCAAAGCAAAGG | 8,762 | This study |
| Seq-3-R | GGCTTCTCTGTGAGCTTTCC | 8,393 | This study |
| Seq-4-F | CTGGTTGTGGGACTTTGTTGC | 8,715 | This study |
EEE, Eastern equine encephalitis; SLE, St. Louis encephalitis; GFP, green fluorescent protein; 6-FAM, 6-carboxyfluorescein; BHQ1, black hole quencher; MGB, minor groove binder; TAMRA, 6-carboxy-tetramethyl-rhodamine. 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).