TABLE 2.
Primers for DNA template synthesis and sequencing
| Namea | Sequence (5′→3′) | Genomic positionb |
|---|---|---|
| FU1 (F) | TACAACATGATGGGAAAGAGAGAGAA | 8993 |
| FU1PMc (F) | TACAACATGATGGGVAARAGWGARAA | 8993 |
| cFD3 (R) | AGCATGTCTTCCGTGGTCATCCA | 10077 |
| cFD3PMd (R) | ARCATGTCTTCYGTBGTCATCCA | 10077 |
| FU2 (F) | GCTGATGACACCGCCGGCTGGGACAC | 9233 |
| cFD2 (R) | GTGTCCCAGCCGGCGGTGTCATCAGC | 9258 |
| FU3 (F) | AGCGGAGATGATTGTGTGGT | 9629 |
| FU3PMe (F) | AGYGGAGAYGAYTGYGTNGT | 9629 |
| cFD4 (R) | ACCACACAATCATCTCCGCT | 9648 |
| cFD4PMf (R) | ATNACRCARTCRTCTCCRCT | 9648 |
| FG1g (F) | TCAAGGAACTCCACACATGAGATGTACT | 8270 |
| G4 (R) | CCAGATGTTCTTWGCCCAYTCTGC | 10261i |
| VD8h (R) | GGGTCTCCTCTAACCTCTAG | 10728 |
a
F, forward primer; R, reverse primer.
b
Except for primer G4, numbers are genomic positions of YF virus (GenBank accession no. K02749) to which the first bases (5′ end) of primers correspond.
c
Degenerate primer at the position of FU1.
d
Degenerate primer at the position of cFD3.
e
Degenerate primer at the position of FU3.
f
Degenerate primer at the position of cFD4.
g
Source, Fulop et al. (14).
h
Source, Pierre and Deubel (33).
i
Genomic position of tick-borne encephalitis virus (strain 263) (GenBank accession no. U-27491) to which the first base (5′ end) of the primer corresponds.