Table 2. Estimation of selection pressure and sequence variability for H5N1 influenza virus.
| Gene | Length (nt) | Positively selected sitea | Sites under positive selection | dN/dS (95% CI)b | Variability (%)c | ||
| SLAC | FEL | IFEL | |||||
| PB2 | 2277 | None | None | None | 0 | 0.102 (0.094–0.110) | 1.559 |
| PB1 | 2271 | 215, 384, 610 | 215, 384, 610 | 64, 215, 573, 577, 610 | 6 | 0.103 (0.094–0.111) | 1.593 |
| PA | 2148 | 337, 544 | 101, 201, 237, 337, 544, 669, 712 | 237, 337, 544 | 7 | 0.162 (0.151–0.173) | 1.810 |
| HA | 1656 | 138, 140, 156 | 115, 138, 140, 141, 156 | 45, 115, 138, 140, 141, 156 | 6 | 0.287 (0.266–0.308) | 1.914 |
| NP | 1494 | None | 452, 482 | 452 | 2 | 0.089 (0.080–0.100) | 1.470 |
| NA | 1407 | 2, 340 | 2, 46, 70, 73, 74, 84, 100, 427 | 8, 46, 74, 76, 100, 340 | 11 | 0.246 (0.226–0.268) | 1.934 |
| M1 | 756 | None | None | None | 0 | 0.129 (0.110–0.150) | 1.385 |
| M2 | 291 | 18, 82 | 18, 82 | 14, 18, 82 | 3 | 0.636 (0.531–0.753) | 1.823 |
| NS1 | 690 | 197 | 127, 197, 205 | 127, 171, 185, 197, 209, 212, 227 | 8 | 0.434 (0.395–0.477) | 2.428 |
| NS2 | 363 | None | 14, 34 | 14, 52, 111 | 4 | 0.398 (0.340–0.462) | 2.098 |
a
FEL, iFEL, SLAC significance levels are indicated by P values and site under positive selection (P<0.05) are detected by at least one method.
b
The dN/dS ratios are estimated using the FEL method available in the Hyphy package.
c
The variability of each segment is calculated at the amino acid level.