Table 2.
Evolutionary Dynamics Within BA.1 Clade Sequences at the Positions of the S-Gene Where BA.1 Differs From the Wuhan-Hu-1 Reference Strain (WT) by an Amino Acid Change.
| Pos | WT | BA.1 | Missing, % | Total mut. % | Rev. % | Syn. mut. % | Total subs | Syn. subs | Rev. subs |
|---|---|---|---|---|---|---|---|---|---|
| 67 | A | V | 0.61 | 0.125 | 0.123 | 0.029 | 1 | 0 | 1 |
| 95 | T | I | 2.159 | 0.112 | 0.11 | 0 | 3 | 0 | 1 |
| 142 | G | D | 3.646 | 0.364 | 0.307 | 0.076 | 5 | 1 | 2 |
| 339 | G | D | 4.623 | 0.513 | 0.509 | 0 | 12 | 0 | 9 |
| 371 | S | L | 10.541 | 0.8 | 0.753 | 0.017 | 7 | 0 | 4 |
| 373 | S | P | 10.314 | 0.82 | 0.818 | 0.005 | 6 | 0 | 4 |
| 375 | S | F | 10.18 | 1.002 | 1.002 | 0.001 | 9 | 0 | 6 |
| 417 | K | N | 65.478 | 3.041 | 3.038 | 0.001 | 16 | 0 | 13 |
| 440 | N | K | 62.292 | 1.94 | 1.939 | 0 | 14 | 0 | 12 |
| 446 | G | S | 61.538 | 1.728 | 1.712 | 0.001 | 13 | 0 | 9 |
| 477 | S | N | 9.474 | 0.956 | 0.951 | 0.005 | 12 | 0 | 10 |
| 478 | T | K | 9.335 | 0.763 | 0.76 | 0.001 | 14 | 0 | 8 |
| 484 | E | A | 9.466 | 1.069 | 0.975 | 0.019 | 8 | 0 | 8 |
| 493 | Q | R | 9.161 | 0.945 | 0.938 | 0.011 | 5 | 0 | 5 |
| 496 | G | S | 10.567 | 0.93 | 0.927 | 0.001 | 4 | 0 | 4 |
| 498 | Q | R | 10.677 | 0.977 | 0.975 | 0.043 | 5 | 0 | 5 |
| 501 | N | Y | 10.496 | 0.947 | 0.942 | 0 | 6 | 0 | 4 |
| 505 | Y | H | 10.972 | 1.039 | 1.039 | 0.016 | 8 | 0 | 5 |
| 547 | T | K | 0.208 | 0.083 | 0.082 | 0 | 0 | 0 | 0 |
| 614 | D | G | 0.127 | 0.02 | 0.02 | 0.001 | 1 | 0 | 1 |
| 655 | H | Y | 0.257 | 0.101 | 0.101 | 0.001 | 2 | 0 | 2 |
| 679 | N | K | 0.336 | 0.204 | 0.204 | 0.002 | 4 | 0 | 4 |
| 681 | P | H | 0.338 | 0.21 | 0.125 | 0.001 | 5 | 0 | 1 |
| 764 | N | K | 31.574 | 0.554 | 0.554 | 0.001 | 9 | 0 | 9 |
| 796 | D | Y | 2.833 | 0.26 | 0.234 | 0.001 | 9 | 0 | 7 |
| 856 | N | K | 2 | 0.14 | 0.14 | 0.001 | 2 | 0 | 2 |
| 954 | Q | H | 2.074 | 0.07 | 0.07 | 0.001 | 2 | 0 | 2 |
| 969 | N | K | 1.888 | 0.12 | 0.118 | 0.001 | 2 | 0 | 2 |
Missing, %: fraction of complete genomes in GISAID that have partially (e.g., AAN) or completely (NNN) unresolved codons at this site. Total mut. %: the fraction of sequences where there are mutations away from the BA.1 consensus codon (resolved codons only). Rev. %: the fraction of sequences where there are mutations away from the BA.1 consensus back to the wildtype (WT). Syn. mut. %: the fraction of sequences where there are synonymous mutations that maintain the BA.1 residue. Total subs: the number of substitutions along internal branches of the BA.1 phylogeny which involve resolved nucleotides (based on the SLAC method); Syn. subs: the number of substitutions that are synonymous for the BA.1 consensus residue; Rev. subs: the number of substitutions that replace the BA.1 consensus residue with the WT residue. Bolded sites are those which are experiencing episodic positive selection along internal tree branches.