Table 2.
Markov chain Monte Carlo (MCMC) results and other parameters for different CV-A6 datasets.
| Geographic set and datasets | Number of strains |
Regression (R) |
dN/dS |
MCMC (BEAST)
a
|
|||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All | From this study |
Substitution rate
(10-−3)(95%HPD) |
TMRCA(95%HPD) |
||||||||||||
| Mild cases | Severe/fatal cases | P1 | 3D | ORF | P1 | 3D | ORF | P1 | 3D | ORF | P1 | 3D | ORF | ||
| Worldwide | |||||||||||||||
| Selected | 142 | NA | NA | 0.69 | 0.05 | 0.22 | 0.017 | 0.020 | 0.019 | 4.73 (4.14, 5.30) | NA | NA | 87.63(69.06, 146.15) | NA | NA |
| Lineage –A | 400 | NA | NA | 0.91 | 0.82 | 0.92 | 0.022 | 0.031 | 0.022 | 5.48(4.86, 6.10) | 4.83(4.41, 5.24) | 4.16(3.97, 4.37) | 13.01(12.18, 13.93) | 12.91(12.06, 13.88) | 13.30(12.84, 13.77) |
| Mainland China | |||||||||||||||
| All | 336 | 137 | 19 | 0.81 | 0.44 | 0.51 | 0.023 | 0.022 | 0.020 | 5.20(4.74, 5.68) | NA | NA | 22.08(16.56, 28.53) | NA | NA |
| Lineage –A | 222 | 116 | 12 | 0.88 | 0.82 | 0.90 | 0.025 | 0.024 | 0.020 | 4.40(4.01, 4.81) | 3.83(3.41, 4.26) | 3.89(3.66, 4.11) | 13.38(12.36, 14.48) | 13.36(11.96, 14.91) | 14.21(13.51, 15.05) |
| Lineage –J | 62 | 8 | 2 | 0.74 | 0.73 | 0.87 | 0.027 | 0.062 | 0.042 | 5.21(4.52, 5.94) | 5.17(4.18, 6.21) | 4.68(4.25, 5.11) | 6.28(5.48 7.31) | 5.86(5.24, 6.66) | 5.95(5.62, 6.30) |
| Lineage –L | 32 | 13 | 5 | 0.93 | 0.85 | 0.93 | 0.033 | 0.030 | 0.031 | 4.85(4.07, 5.59) | 5.09(3.92, 6.20) | 4.72(4.26 5.24) | 5.76(5.27, 6.30) | 5.68(5.04, 6.38) | 5.49(5.20 5.78) |
a
NA, MCMC values were not calculated for the 3Dpol and ORF datasets, which were not monophyletic.