Table III.
Selection pressure analysis based on the whole-genome sequences using the methods Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting, available in the Datamonkey server
| Clade | Gene | Site | Variable amino acid residues | P MEME | P SLAC |
|---|---|---|---|---|---|
| G | nsp3 | 994 | A/D | 0.01 | 0.042 |
| nsp6 | 37 | L/F | 0.01 | 0.036 | |
| nsp12 | 323 | L/P | 0.01 | 0.008 | |
| GR | nsp3 | 994 | D/A | 0.01 | 0.05 |
| nsp3 | 1103 | P/L/S | 0.02 | 0.085 | |
| nsp4 | 380 | A/V | 0.05 | 0.088 | |
| nsp7 | 54 | S/L/P | 0.07 | 0.066 | |
| nsp16 | 298 | N/L/I | 0 | 0.037 | |
| ORF3a | 46 | L/F | 0.01 | 0.06 | |
| GH | nsp6 | 37 | L/F | 0.02 | 0.04 |
| nsp12 | 323 | L/P | 0.03 | 0.059 | |
| nsp14 | 372 | T/I | 0.03 | 0.062 | |
| nsp16 | 298 | N/L/H/I | 0 | 0.062 | |
| S | - | - | - | - | - |
| O | nsp3 | 1197 | S/R/K | 0 | 0.021 |
| nsp3 | 1198 | K/T | 0.07 | 0.022 | |
| nsp3 | 1768 | V/G | 0 | 0.004 | |
| nsp6 | 37 | F/L | 0.02 | 0.009 |
Sites were identified as showing evidence of positive selection as per the statistical significance level (P<0.1) by both the methods. MEME, Mixed Effects Model of Evolution; SLAC, Single-Likelihood Ancestor Counting