Table 3.
Sites prone to positive selection in astrovirus genes
| Bayes Empirical Bayes (BEB) Analysis | |||||
| BEB positively selected sites in ORF1a | |||||
| Position in Alignment | Amino acid residue | Position in H1Z25771 | Posterior mean value for dN/dS | ± SE for dN/dS | Posterior probability (dN/dS > 1) |
| 3 | Y | 3 | 0.988 | 0.576 | 0.522 |
| 109 | K | 86 | 1.474 | 0.225 | 0.951 |
| 110 | E | 87 | 1.336 | 0.407 | 0.817 |
| 812 | A | 614 | 1.316 | 0.421 | 0.796 |
| 813 | T | 615 | 1.322 | 0.416 | 0.801 |
| 821 | S | 623 | 1.357 | 0.385 | 0.835 |
| 822 | A | 624 | 1.383 | 0.351 | 0.855 |
| 1060 | V | 755 | 1.436 | 0.290 | 0.911 |
| 1078 | S | 790 | 1.087 | 0.581 | 0.623 |
| 1102 | P | 814 | 1.326 | 0.410 | 0.804 |
| 1105 | P | 817 | 1.036 | 0.585 | 0.575 |
| 1263 | T | 932 | 1.157 | 0.503 | 0.646 |
| BEB positively selected sites in ORF1b | |||||
| Position in Alignment | Amino acid residue | Position in H1Z25771 | Posterior mean value for dN/dS | ± SE for dN/dS | Posterior probability (dN/dS > 1) |
| 45 | L | 29 | 1.068 | 0.802 | 0.603 |
| 178 | N | 160 | 1.384 | 0.860 | 0.704 |
| BEB positively selected sites in ORF2 (selection) | |||||
| Position in Alignment | Amino acid residue | Position in H1Z25771 | Posterior mean value for dN/dS | ± SE for dN/dS | Posterior probability (dN/dS > 1) |
| 489 | A | 440 | 1.231 | 0.418 | 0.660 |
| 507 | D | 458 | 1.182 | 0.439 | 0.611 |
| 533 | V | 472 | 1.123 | 0.457 | 0.551 |
| 537 | L | 476 | 1.282 | 0.396 | 0.717 |
| 604 | S | 513 | 1.122 | 0.499 | 0.582 |
| 676 | G | 573 | 1.441 | 0.264 | 0.901 |
| 686 | T | 583 | 1.094 | 0.478 | 0.537 |
| 716 | K | 612 | 1.078 | 0.468 | 0.507 |
| 745 | S | 633 | 1.182 | 0.430 | 0.603 |
| 755 | S | 643 | 1.183 | 0.430 | 0.606 |
| 764 | H | 652 | 1.172 | 0.438 | 0.599 |
| 768 | S | 656 | 1.350 | 0.357 | 0.797 |
| 774 | N | 658 | 1.269 | 0.411 | 0.710 |
| 791 | T | 659 | 1.389 | 0.329 | 0.845 |
| 793 | Y | 661 | 1.182 | 0.424 | 0.603 |
| 800 | A | 668 | 1.292 | 0.391 | 0.729 |
| 802 | Q | 670 | 1.481 | 0.205 | 0.953 |
| 803 | F | 671 | 1.333 | 0.366 | 0.775 |
| 804 | D | 674 | 1.316 | 0.394 | 0.767 |
| 814 | I | 681 | 1.090 | 0.470 | 0.528 |
| 882 | I | 741 | 1.219 | 0.431 | 0.653 |
| 919 | N | 775 | 1.187 | 0.442 | 0.621 |
The Bayes-Emperical-Bayes (BEB) output of the CODEML NSsites model 8 for nucleotide substitution allows the selection of codon sites (as amino acids) with a posterior mean value for dN/dS ≥ 1 and provides a standard error as well asa value for posterior probability. The position of the selected amino acid in the alignment has been converted into the location in the H1Z25771 polyprotein. "Selection" in the ORF2 panel refers to the limitation of one representative per human serotype in ORF2 analyses.