Table 1.
Polymerase Chain Reaction Primers Used for Detection and Sequencing of Culex Flavivirus from RNA of Culex Mosquito Pools
| Primer namea | Sequence (5′ to 3′) | |
|---|---|---|
| Diagnostic PCR for detection of CxFVb | ||
| External 1-step RT-PCR | FU2 | GCTGATGACACCGCCGGCTGGGACAC |
| cFD3 | AGCATGTCTTCCGTGGTCATCCA | |
| Internal PCR | CxFV_9131F | TTGTGGTTCTTGCTGGACCAAGTG |
| CxFV_9337R | ATTCTCCCAACCTGGTTCTTCCCA | |
| PCRs for sequencing of CxFV NS5 gene segment for phylogenetic analysisb | ||
| External 1-step RT-PCR | CxFV_8880F | GGAGAAGAAGCCGTCCTCTTTCGG |
| CxFV_10814R | AGACGTGAACAAAAGCTTGCCCAC | |
| Internal PCR 1 | CxFV_8880F | GGAGAAGAAGCCGTCCTCTTTCGG |
| CxFV_9538R | CTCGGTCGGTTGCAAGTTCTTG | |
| Internal PCR 2 | CxFV_9516F | CCACACCAGTCTAAGGTACATC |
| CxFV_10188R | GTTGTTCTCTACGAGTCGCGTG | |
| Internal PCR 3 | CxFV_10182F | CAACCGACGRCGTGTTCTGGTG |
| CxFV_10814R | AGACGTGAACAAAAGCTTGCCCAC | |
a
Primer names indicate the nucleotide coordinate of the 3′ base of the primer with respect to the CxFV reference sequence (GenBank accession number NC_008604) and the forward (F) or reverse (R) direction. Primers FU2 and cFD3 are from Kuno et al. (1998).
b
CxFV, Culex flavivirus; NS5, nonstructural protein 5; RT-PCR, reverse-transcription polymerase chain reaction.