Table 2.
Evolutionary rate of Bangladeshi H3N2 strains over a decade (Jan 2009–Dec 2020).
| Segments (n = 531) | Evolutionary rate (95% HPD) | dN/dS1 | Total sites1 | Sites under diversifying positive selection (Amino acid position) | ||||
|---|---|---|---|---|---|---|---|---|
| SLAC2 | MEME2 | SLAC2 | MEME2 | FEL2 | FUBAR3 | |||
| HA | 4.33 × 10–3 (3.61–5.03) | 0.269 | 0.238 | 566 | (69, 160, 546) | (69, 130, 147, 151, 160, 546) | (69, 130, 160, 546) | (69, 130, 160, 188, 214, 546) |
| NA | 4.06 × 10–3 (3.41–4.75) | 0.278 | 0.247 | 470 | (345) | (253, 345) | (144, 345) | (94, 345, 381, 469) |
| MP | 3.81 × 10–3 (2.97–4.70) | 0.053 | 0.049 | 252 | – | – | – | (187) |
| NP | 2.61 × 10–3 (2.01–3.43) | 0.102 | 0.095 | 498 | – | – | – | – |
| NS | 4.54 × 10–3 (3.42–5.57) | 0.407 | 0.395 | 230 | – | (99) | – | (37, 56) |
| PA | 2.37 × 10–3 (2.04–2.70) | 0.11 | 0.102 | 716 | – | – | (256) | (216, 256) |
| PB1 | 3.03 × 10–3 (2.46–3.70) | 0.073 | 0.067 | 757 | – | (618) | (618) | (618) |
| PB2 | 2.56 × 10–3 (2.49–3.21) | 0.095 | 0.091 | 759 | – | (299, 613) | (299, 613) | (299, 480, 613) |
HPD highest probability density, dN/dS ratio of non-synonymous and synonymous sites, SLAC single-likelihood ancestor counting, MEME mixed effects model of evolution, FEL fixed effects likelihood, FUBAR fast, unconstrained Bayesian approximation.
1For MP and NS gene, respectively M1 and NS1 proteins were analyzed.
2p-value threshold of 0.1.
3Posterior probabilities of 0.9.