Table 1.
Primer and probe sequences for the DENV–YFV assay
| Name | Sequence (5′ → 3′) | Concentration (nM)* | Location† |
|---|---|---|---|
| DENV primers and probe | |||
| DENV-1, 2, 3 forward | AGATYTCTGATGAAYAACCAACG | 300 | 87–109 |
| DENV-4 forward | GGAAGCTTGCTTAACACAGTTCT | 300 | 34–56 |
| DENV-1, 3 reverse | GAATCTCTTCGCCAACTGTGA | 300 | 174–194 |
| DENV-2 reverse | TGCAGCATTCCAAGTGAGAATCT | 300 | 190–212 |
| DENV-4 reverse | GAGAATCTCTTCACCAACCCTTG | 300 | 169–191 |
| DENV probe‡ | CAATATGCTGAAACGCGHGAGAAACCG | 300 | 134–160 |
| RNase P primers and probe | |||
| RNase P forward | AGATTTGGACCTGCGAGCG | 50 | NA |
| RNase P reverse | GAGCGGCTGTCTCCACAAGT | 50 | NA |
| RNase P probe‡ | TTCTGACCTGAAGGCTCTGCGCG | 50 | NA |
| YFV primers and probe | |||
| YFV forward | AGGTGCATTGGTCTGCAAAT | 300 | 13–32 |
| YFV reverse | TCTCTGCTAATCGCTCAACG | 300 | 77–96 |
| YFV reverse G → T | TCTCTGCTAATCGCTCAAAG | 300 | 77–96 |
| YFV probe‡ | GTTGCTAGGCAATAAACACATTTGGA | 200 | 36–61 |
DENV = dengue virus; YFV = yellow fever virus.
* Concentration of each oligonucleotide in the final reaction mixture is provided.
† Genomic locations for viral primers and probes are provided based on the following reference sequences: DENV-1 US/Hawaii/1944 (GenBank: EU848545.1), DENV-2 New Guinea C Strain (GenBank: AF038403.1), DENV-4 strain H-241 (GenBank: AY947539.1), and YFV Asibi strain, complete genome (Genbank: KF769016.1). For sequences present in multiple serotypes, locations are shown for DENV-1.
‡
5′ fluor and 3′ quencher pairs were the following: DENV, FAM and BHQ-1; RNase P, Cal Fluor 560 and BHQ-1; YFV, Quasar 670 and BHQ-2.