TABLE 2.
Details of primers and probes used in the study
| Primer or probe | Sequence (5′-3′)a | Application | Position on genomeb | Reference |
|---|---|---|---|---|
| Primers | ||||
| JW12 | ATGTAACACC(C/T)CTACAATTG | cDNA synthesis, PCR, hnPCR | 55-74 | 9 |
| JW6 (DPL) | CAATTCGCACACATTTTGTG | PCR | 660-641 | |
| JW6 (E) | CAGTTGGCACACATCTTGTG | PCR | 660-641 | |
| JW6 (M) | CAGTTAGCGCACATCTTATG | PCR | 660-641 | |
| JW10 (DLE2) | GTCATCAAAGTGTG(A/G)TGCTC | hnPCR | 636-617 | |
| JW10 (ME1) | GTCATCAATGTGTG(A/G)TGTTC | hnPCR | 636-617 | |
| JW10 (P) | GTCATTAGAGTATGGTGTTC | hnPCR | 636-617 | |
| 001lys | ACGCTTAACGAMAAA | cDNA synthesis, PCR | 1-15 | 20 |
| 550B | GTRCTCCARTTAGCRCACAT | PCR, hnPCR | 647-666 | 20 |
| 541lys | CACMGSNAAYTAYAARACNAA | hnPCR | 541-561 | This study |
| 18S rRNA for | CGCCGCTAGAGGTGAAATTC | Real-time PCR internal control | 18S rRNA | 23 |
| 18S rRNA rev | CGAACC TCCGACTTTCGTTCT | Real-time PCR internal control | ||
| Probes | ||||
| 620lyssa | FAM-CATCACACCTTGATGACAACTCACAA-BHQ-1 | Real-time PCR | 620-645 | This study |
| 18S probe | FAM-CCGGCGCAAGACGGACCAGA-BHQ-1 | Real-time PCR | 18S rRNA | 23 |
a
FAM, 6-carboxyfluorescein; BHQ-1, Black Hole Quencher 1.
b
Nucleotide positions are numbered according to the Pasteur virus sequence (GenBank accession number M13215).