Table 2 Estimation of evolution rate and positive selection for HA and NA genes of pH1N1 and H3N2 viruses. Evolution rates were estimated using the Bayesian Markov Chain Monte Carlo method in the Bayesian Evolutionary Analysis Sampling Trees (BEAST) package (v1.8.4). HPD represents lower and upper limits of highest posterior density that contains 95% of the sampled values. The selective pressure at codon level was also calculated using the most conservative ‘single-likelihood ancestor counting’ algorithm (SLAC) and the ‘fixed effects likelihood’ (FEL) methods available at the DataMonkey web server of the HYPHY software. (N) refers to the number of positively selected amino acids and (AA) refers to amino acids that were found to be under positive selection. Positively selected sites were defined when dN/dS p value is less than 0.05 using the best fit model as recommended by website
Number of analysed sequences | Nucleotide substitution rate (×10−3) | Positive selection | |||||||
|---|---|---|---|---|---|---|---|---|---|
Mean | 95% HPD | SLAC | FEL | ||||||
Mean (dN/dS) | N | AA | Mean (dN/dS) | N | AA | ||||
H1 | 512 | 1.91 | 1.68–2.1 | 0.336 | 3 | 10–239-240 | 0.311 | 8 | 13–202–239-240-305-468-543-546 |
H3 | 239 | 1.47 | 1.27–1.68 | 0.299 | 1 | 239 | 0.267 | 2 | 19–69 |
N1 | 342 | 1.93 | 1.7–2 | 0.352 | – | – | 0.311 | – | – |
N2 | 132 | 3.09 | 2.5–3.1 | 0.238 | – | – | 0.208 | – | – |