TABLE 3.
List of primers and probes designed for the detection of JE and Ntaya serocomplexes by dRRT-PCR assay.
| Primer/Probe name | Sequence and labeling (5' → 3')a | Nucleotide positions | Product size | Target genome region |
|---|---|---|---|---|
| Japanese encephalitis serocomplex | ||||
| JE-3533F | TCAGYTGGGCCTTCTGGT | 3,533–3,550b | 65 bp | NS2A |
| JE-3597R | TGGCCGTCCACCTCTTSC | 3,597–3,580b | ||
| JE-FAM-3553 | 6FAM-TGTTYTTGGCCACCCAGGAGGT -BHQ1 | 3,553–3,574b | ||
| Ntaya Serocomplex | ||||
| NT-10510F | GTTGGATGACGGTGCWGYCTG | 10,510–10,530c | 171 bp | 3′ NTR |
| NT-10680R | GCTGCACTGCATGCTARTGGC | 10,680–10,660c | ||
| NT-JOE-10594 | JOE-TACCGWCTCGGAGARCTCCCTGGC-BHQ1 | 10,594–10,617c |
Primers and probes were purchased from Roche Applied Science (Spain).
a
Code for mixed bases positions: R:A/G, Y:C/T, S:G/C, and W:A/T.
b
Nucleotide positions regarding to the WNV L1 Spain/2010/H-1b strain. GenBank accession no. JF719069.
c
Nucleotide positions regarding to the BAGV Spain H/2010 strain. GenBank accession no. HQ644143.