Table 1.
Selective pressure analysis on SARS-CoV-2 protein coding gene sub-sets.
| sub- set | Positively selected sites (ω for sites >1)∗ | Negatively selected sites (ω for sites <1)∗ |
|---|---|---|
| nsp1 | ∖ | 65 (E); 83 (H) |
| nsp2 | 198 (V; I), 248 (S; G), 347 (K; C), 348 (S; V), 559 (I; V) | 287 (F); 488 (A); 565 (E) |
| nsp3 | 1454 (N; Y; D); 1507 (A; E), 1527 (A; V; E) | 106(F); 152 (Q), 353 (T), 380 (Q), 432 (T), 561 (L), 995 (Q), 1047 (D), |
| 1138 (K), 1303 (T), 1455 (S), 1456 (T), 1502 (A), 1544 (S), 1719 (P) | ||
| nsp4 | 33 (M; I) | 15 (L), 71 (F), 212 (V), 235 (V) |
| 3C-like proteinase | ∖ | 239 (Y) |
| nsp6 | 37 (L; F) | 222 (T), 289 (V) |
| nsp7 | ∖ | ∖ |
| nsp8 | ∖ | ∖ |
| nsp9 | ∖ | ∖ |
| nsp10 | ∖ | 128 (C) |
| nsp11 | ∖ | ∖ |
| nsp12 | 25 (G; Y); 323 (P; L); 644 (T; M) | 24 (T), 28 (T), 85 (T), 105 (R), 142 (L), 455 (Y), 591 (T), 643 (T), 896 (T) |
| helicase | 504 (P; L); 598 (A; S; V) | 337 (R); 521 (V); 547 (T), 553 (A) |
| 3′-to-5′ exonuclease | ∖ | 7 (L); 490 (E) |
| endoRNAse | ∖ | 73 (N), 127 (V), 216 (L) |
| 2′-O-ribose | ∖ | 4 (A); 36 (L), 138 (N), 163 (L) |
| methyltransferase | ||
| S | ||
| surface glycoprotein | 943 (S; P) | 348 (A); 669 (G); 681 (P); 795 (K); 853 (Q); 890 (A); 921 (K); 982 (S), 1044 (G), 1100 (T), 1166 (L) |
| ORF3a | 99 (A; S; V) | ∖ |
| E | ∖ | 63 (K) |
| M | ∖ | 69 (A) |
| ORF6 | ∖ | 61 (D) |
| ORF7a | ∖ | 69 (D); 70 (G); 92 (E) |
| ORF8 | 62 (V; L) | ∖ |
| N | 13 (P; L; S); 103 (D; Y) | 173 (A); 274 (F) |
| ORF10 | ∖ | 15 (S); 19 (C) |
∗
Only the sites with a p-value < 0.1 (FEL, SLAC) and with a posterior probability >0.90 (FUBAR) were considered as candidates for selection and statistically supported.