TABLE 1.
Primer and probe sequences used to detect HAV and RVFV and primers for HAV genotyping
| Purpose | 5′→3′ primer or probe sequencea | Accession no. | nt positionb | Gene |
|---|---|---|---|---|
| HAV detection | TCACCGCCGTTTGCCTAG | EU131373.1 | 68-85 | 5′ UTRc |
| GGGAGAGCCCTGGAAGAAA | 242-224 | |||
| FAM-CCTGAACCTGCAGGAATTAA- MGB-NFQ | 169-150 | |||
| HAV genotyping | CTATTCAGATTGCAAATTAYAAT | EU131373.1 | 2396-2418 | VP1/2A |
| AAYTTCATYATTTCATGCTCCT | 3289-3268 | |||
| RVFV detection | AAAGGAACAATGGACTCTGGTCA | EF467178.1 | 1164-1186 | G2 |
| CACTTCTTACTACCATGTCCTCCAAT | 1258-1233 | |||
| FAM-AAAGCTTTGATATCTCTCAGTGCCCCAA-TAMRA | 1204-1231 |
a
FAM, 6-carboxyfluorescein; MGB-NFQ, molecular-groove binding nonfluorescence quencher; TAMRA, 6-carboxytetramethylrhodamine.
b
Nucleotide (nt) position of the binding site.
c
UTR, untranslated region.