Table 4.
Candidate regions of positive selection within hosts.
| Gene producta | Codonsb | Length (codons) | π N (×104)c | π S (×104)c | π N/πS (P-value)c,d | Codons with nonsynonymous differencesb,e |
|---|---|---|---|---|---|---|
| nsp2 | 331–369 | 39 | 2.98 (±1.14) | 1.21 (±0.69) | 2.46 | 332, 336, 338, 340+, 345, 355, 359, 360, 362, 365 |
| (0.176) | ||||||
| nsp3 | 103–155 | 53 | 1.69 (±0.75) | 0.07 (±0.08) | 22.92 | 112+, 113, 126+, 132, 142, 143, 153 |
| (0.033)* | ||||||
| nsp3 | 220–255 | 36 | 1.09 (±0.37) | 0 (–) | – | 224, 230, 231+, 233, 236, 247, 249 |
| (0.003)** | ||||||
| nsp3 | 419–457 | 39 | 1.68 (±0.60) | 0 (–) | – | 422, 424+, 441, 442, 445, 448, 449, 457 |
| (0.005)** | ||||||
| nsp3 | 511–540 | 30 | 2.60 (±1.19) | 0.61 (±0.60) | 4.27 | 511, 517, 520, 523, 528 |
| (0.072) | ||||||
| nsp3 | 962–1,007 | 46 | 2.55 (±1.65) | 0.39 (±0.38) | 6.56 | 966, 980, 981, 985+, 991 |
| (0.206) | ||||||
| nsp3 | 1,156–1,274 | 119 | 3.31 (±1.24) | 0 (–) | – | 1175 , 1177, 1186, 1198, 1200, 1202, 1203, 1205, 1216, 1226, 1245, 1246, 1247 |
| (0.008)** | ||||||
| nsp3 | 1,433–1,493 | 61 | 1.87 (±0.71) | 0 (–) | – | 1437, 1449, 1451, 1462, 1464, 1475, 1481, 1482 |
| (0.008)** | ||||||
| nsp3 | 1,589–1,644 | 56 | 1.17 (±0.41) | 0.23 (±0.23) | 5.03 | 1595, 1597, 1599, 1615, 1617, 1618, 1620, 1641 |
| (0.049)* | ||||||
| nsp3 | 1,733–1,765 | 33 | 1.98 (±1.14) | 0.43 (±0.44) | 4.58 | 1738, 1748, 1760, 1761 |
| (0.223) | ||||||
| nsp3 | 1,774–1,824 | 51 | 2.05 (±1.06) | 0.47 (±0.46) | 4.40 | 1789, 1795+, 1796, 1803, 1804, 1807 |
| (0.186) | ||||||
| nsp4 | 140–173 | 34 | 3.76 (±1.48) | 0.61 (±0.61) | 6.16 | 140, 144, 148, 151, 152, 161, 162, 170 |
| (0.059) | ||||||
| nsp6 | 65–127 | 63 | 5.88 (±2.66) | 0.88 (±0.86) | 6.71 | 74, 76, 83, 84, 86, 90, 91, 94, 98, 104, 106+, 112, 119 |
| (0.077) | ||||||
| nsp6 | 169–206 | 38 | 7.83 (±6.23) | 0.86 (±0.84) | 9.08 | 189, 190, 195, 197 |
| (0.266) | ||||||
| nsp8 | 21–190 | 170 | 3.51 (±2.03) | 0.10 (±0.10) | 36.12 | 50 , 57, 59, 60, 85, 91, 92, 106, 107, 110, 112, 119, 129, 138, 141, 145, 159, 163, 174 |
| (0.097) | ||||||
| nsp13 | 565–594 | 30 | 17.55 (±11.66) | 0.83 (±0.87) | 21.09 | 565, 566, 586, 588 |
| (0.158) | ||||||
| nsp14 | 248–289 | 42 | 7.09 (±4.54) | 0.52 (±0.47) | 13.71 | 255+, 267, 269, 272, 274, 276, 278, 286, 289 |
| (0.151) | ||||||
| nsp15 | 83–120 | 38 | 0.82 (±0.41) | 0.08 (±0.08) | 10.46 | 92 , 97, 107, 112+ |
| (0.044)* | ||||||
| nsp15 | 236–337 | 102 | 5.10 (±3.35) | 0 (–) | – | 250, 256, 267, 270+, 282, 287, 321, 324, 327, 336, 337 |
| (0.130) | ||||||
| nsp16 | 85–115 | 31 | 1.76 (±0.84) | 0 (–) | – | 86, 91, 98, 104, 114 |
| (0.037)* | ||||||
| ORF3af | 97–136 | 40 | 5.99 (±3.11) | 1.32 (±1.30) | 4.55 | 100, 103, 117, 118, 121, 123, 125, 126, 128, 130 |
| (0.080) | ||||||
| E | 44–76 | 33 | 4.51 (±2.00) | 1.17 (±0.81) | 3.86 | 50, 52, 58, 60, 68, 71, 72 |
| (0.130) | ||||||
| M | 135–201 | 67 | 1.96 (±0.60) | 0 (–) | – | 154, 158, 160, 161, 163, 164, 167, 187, 189, 193, 196, 198 |
| (0.001)** | ||||||
| ORF7b | 1–38 | 38 | 0.28 (±0.28) | 0 (–) | – | 9 |
| (0.307) |
Genes are ordered 5′ to 3′ by start site in the genome.
Codons are numbered with respect to mature gene products, that is each nonstructural protein (nsp) is re-numbered starting at 1.
Undefined values are indicated with a horizontal line (–).
P-values refer to Z tests of the hypothesis that πN = πS, evaluated for the indicated region using 10,000 bootstrap replicates (codon unit) *P<0.05; **P<0.01.
The codon with the highest πN (best candidate) for each region is shown with underline and bold; codons with evidence for between-host pervasive and episodic positive selection and an increasing frequency trend (Pond 2020) are shown with a ‘+’.
Note that the hypothesized overlapping gene ORF3d occupies codons 44–102 of ORF3a.