Table 6.
Rates of change in different genomic regions of enterovirus (EV) 71-B4 derived from this study
| Evolutionary rate (changes/site/year) | ||||||
|---|---|---|---|---|---|---|
| Region | By linear regression | By Bayesian Markov chain Monte Carlo | ||||
| Synonymous sites | R2 | All sites | R2 |
Third codon position (95% HPD) |
All sites (95% HPD) |
|
| VP1 | 2.2 × 10-2 | 0.36 | 4.6 × 10-3 | 0.36 | 1.48 × 10-2 (1.43 × 10-2~1.54 × 10-2) |
5.7 × 10-3 (4.6 × 10-3~6.7 × 10-3) |
| 2A | 3.5 × 10-2 | 0.70 | 6.8 × 10-3 | 0.58 | 1.66 × 10-2 (1.54 × 10-2~1.74 × 10-2) |
6.7 × 10-3 5.2 × 10-3~8.5 × 10-3 |
| 3C | 3.2 × 10-2 | 0.59 | 7.1 × 10-3 | 0.54 | 1.51 × 10-2 (1.41 × 10-2~1.61 × 10-2) |
6.3 × 10-3 4.9 × 10-3~7.7 × 10-3 |
| 5'UTR | - | - | 5.3 × 10-3 | 0.60 | - | 5.5 × 10-3 4.1 × 10-3~7.0 × 10-3 |
Bayesian Markov chain Monte Carlo was conducted by BEAST v1.4.8 using the GTR+Γ+SRD06 [75] model of nucleotide substitution and strict molecular clock (see Methods for details).
R2, regression coefficient.
HPD, highest posterior density; UTR, untranslated region.