Table 2.
Position wise conservation of nucleotides in primers and probes among the analysed sequences of DENV-1
| Position | Primers | Probes# | ||||||
|---|---|---|---|---|---|---|---|---|
| D1Fa | D1Rb | Asianc | AMAFd | |||||
| Nucleotide | Number of sequences conserved (%)# | Nucleotide | Number of sequences conserved (%) | Nucleotide | Number of sequences conserved (%)* | Nucleotide | Number of sequences conserved (%)* | |
| 1 | G | 1633 (99.9) | G | 1630 (99.7) | T | 1242 (100) | A | 212 (66.2) |
| 2 | A | 1632 (99.9) | C | 1632 (99.9) | T | 1242 (100) | A | 200 (62.5) |
| 3 | A | 1630 (99.7) | T | 1622 (99.3) | T | 1241 (99.9) | T | 320 (100) |
| 4 | C | 1630 (99.7) | G | 1632 (99.9) | C | 1200 (96.6) | T | 306 (95.6) |
| 5 | A | 1633 (99.9) | T | 1634 (100) | G | 1234 (99.3) | T | 319 (99.7) |
| 6 | G | 1634 (100) | T | 1633 (99.9) | A | 1242 (100) | C | 311 (97.1) |
| 7 | A | 1634 (100) | A | 1634 (100) | C | 1242 (100) | A | 227 (70.9) |
| 8 | T (Y)* | 1580 (96.7) | T | 1607 (98.3) | C | 1237 (99.6) | A | 319 (99.7) |
| 9 | G | 1634 (100) | C (Y)* | 1403 (85.9) | C | 1242 (100) | C | 311 (97.1) |
| 10 | C | 1629 (99.6) | A | 1634 (100) | A | 1240 (99.8) | C | 307 (95.9) |
| 11 | A (R)* | 1549 (94.8) | A (R)* | 1363 (83.4) | A | 1240 (99.8) | C | 320 (100) |
| 12 | C | 1632 (99.9) | T | 1632 (99.9) | G | 1241 (99.9) | A | 320 (100) |
| 13 | C | 1632 (99.9) | C | 1634 (100) | A | 1242 (100) | A | 320 (100) |
| 14 | A | 1634 (100) | T | 1634 (100) | T | 1242 (100) | G | 320 (100) |
| 15 | T | 1634 (100) | C | 1599 (97.8) | G | 1242 (100) | A | 320 (100) |
| 16 | G | 1634 (100) | C | 1631 (99.8) | A | 1234 (99.3) | T | 320 (100) |
| 17 | C | 1613 (98.7) | C | 1632 (99.9) | A | 1166 (99.9) | G | 320 (100) |
| 18 | A | 1634 (100) | A | 1615 (98.8) | A | 1242 (100) | A | 320 (100) |
| 19 | A | 1634 (100) | T | 1632 (99.9) | A | 1231 (99.1) | G | 320 (100) |
| 20 | G | 1634 (100) | T | 1634 (100) | A | 1231 (99.1) | A | 320 (100) |
| 21 | A | 1633 (99.9) | C | 1630 (99.7) | G | 1242 (100) | A | 320 (100) |
| 22 | T | 1634 (100) | G | 1242 (100) | A | 320 (100) | ||
| 23 | G | 1632 (99.9) | A | 1238 (99.7) | G | 320 (100) | ||
| 24 | G | 1237 (99.6) | G | 320 (100) | ||||
| 25 | T | 1231 (99.1) | A | 312 (97.5) | ||||
| 26 | A | 1164 (93.7) | G | 320 (100) | ||||
| 27 | A | 1238 (99.7) | T | 320 (100) | ||||
| 28 | C | 1240 (99.8) | G | 320 (100) | ||||
| 29 | A | 314 (98.1) | ||||||
| 30 | C | 320 (100) | ||||||
#
The total number of DENV-1 sequences used for primer designing was 1634. The total number of sequences used for designing probe specific to Asian genotype was 1242. For AM/AF genotype, 320 sequences were used. The remaining 72 sequences among the 1634 DENV-1 sequences belonged to South Pacific genotype (data not shown).
*
Degenerate bases in the parenthesis are present in the primers
a
Position in the whole genome 1917-1937 and in the E gene 983-1003
b
Position in the whole genome 1973-1995 and in the E gene 1039-1061
c
Position in the whole genome 1924-1951 and in the E gene 1010-1037
d
Position in the whole genome 1942-1971 and in the E gene 1008-1037