Table 2. Primers and probes used to test specimens from ill travelers returning to Canada for viral RNA*.
| Primer and probe | Sequence, 5′→ 3′ | Concentration, nmol/L | Reference |
|---|---|---|---|
| Pandengue-MS2 | (23,24) | ||
| Den Eili fwd primer | GGACTAGAGGTTAGAGGAGACCCC | 500 | |
| Den Eili rev primer | GAGACAGCAGGATCTCTGGTC | 500 | |
| Den Eili probe | FAM-AGCATATTGACGCTGGGA-MGB-BHQ1 | 125 | |
| MS2-TM2 fwd primer | TGCTCGCGGATACCCG | 500 | |
| MS2-TM2 rev primer | AACTTGCGTTCTCGAGCGAT | 500 | |
| MS2-TM2 probe |
Quasar670-ACCTCGGGTTTCCGTCTTGCTCGT-BHQ1 |
125 |
|
| Dengue virus serotyping | (25) | ||
| DENV-1 fwd primer | CAAAAGGAAGTCGTGCAATA | 500 | |
| DENV-1 rev primer | CTGAGTGAATTCTCTCTACTGAACC | 500 | |
| DENV-1 probe | FAM-CATGTGGTTGGGAGCACGC-BHQ1 | 125 | |
| DENV-2 fwd primer | CAGGTTATGGCACTGTCACGAT | 500 | |
| DENV-2 rev primre | CCATCTGCAGCAACACCATCTC | 500 | |
| DENV-2 probe | HEX-CTCTCCGAGAACAGGCCTCGACTTCAA-BHQ-1 | 125 | |
| DENV-3 fwd primer | GGACTGGACACACGCACTCA | 500 | |
| DENV-3 rev primer | CATGTCTCTACCTTCTCGACTTGTCT | 500 | |
| DENV-3 probe | FAM-ACCTGGATGTCGGCTGAAGGAGCTTG-BHQ1 | 125 | |
| DENV-4 fwd primer | TTGTCCTAATGATGCTGGTCG | 500 | |
| DENV-4 rev primer | TCCACCTGAGACTCCTTCCA | 500 | |
| DENV-4 probe |
HEX-TTCCTACTCCTACGCATCGCATTCCG-BHQ1 |
125 |
|
| Panflavivirus | (26) | ||
| Flavi all S (sense) | TACAACATgATggggAARAgAgARAA | 500 | |
| Flavi all AS2 (antisense) | gTgTCCCAgCCNgCKgTgTCATCWgC | 500 | |
| DENV-4F | TACAACATgATgggRAAACgTgAGAA | 500 | |
| Flavi all probe 1 | FAM-AARggHAgYMgNgCCA+TH+T+g+g+T-BBQ† | 100 | |
| Flavi probe 3a | FAM-CCgTgCCATATggTATATgTggCTgggAgC-BBQ† | 100 | |
| Flavi probe 3b |
FAM-TTTCTggAATTTgAAgCCCTgggTTT-BBQc |
100 |
|
| Hepatitis A virus | (27); vital SOP‡ | ||
| HAV 68 | TCACCGCCGTTTGCC | 500 | |
| HAV240 | GGAGAGCCCTGGAAGAAAG | 500 | |
| HAV150 probe |
FAM-CCTGAACCTGCAGGAATTAA-MGB-NFQ |
125 |
|
| Chikungunya virus | (28) | ||
| ChikF10378–10398 | GCATCAGCTAAGCTCCGGGTC | 500 | |
| ChikR 10487–10508¶ | GGTGTCCAGGCTGAAGACATTG | 500 | |
| Chik Pongsiri | HEX-ATGCAAACGGCGACCATGCCGTCA-VIC | 125 |
*The primers and probes were used with the Applied Biosystems 7500 Fast Real-Time PCR System (Thermo Fisher Scientific, Waltham, MA, USA). fwd, forward; rev, reverse; SOP, standard operating procedure. †Locked nucleic acid bases. ‡Vital Standard Operating Procedure modified from Costafreda et al. (27). ¶ChikR10487-10508 reverse complement used from published sequence.