Table 5.
Comparison of the Mutation Rates in SARS-CoV, Influenza Virus, and HIV*
| Virus | ORF | Size (nt) | No. of substitutions | Substitute rate (%) | No. of non-synonymous substitution | Non-synonymous substitute rate (%) | dN/dS | Ka | Ks | Ka/Ks |
|---|---|---|---|---|---|---|---|---|---|---|
| SARS-CoV |
R | 21,222 | 92 | 0.43 | 65 | 0.31 | 2.38 | 0.075 | 0.111 | 0.67 |
| S | 3,768 | 22 | 0.58 | 13 | 0.35 | 2.00 | 0.108 | 0.188 | 0.57 | |
| PUP1 | 825 | 9 | 1.09 | 6 | 0.73 | 1.77 | 0.171 | 0.340 | 0.50 | |
| PUP2 | 465 | 5 | 1.08 | 4 | 0.86 | 4.88 | 0.217 | 0.152 | 1.43 | |
| E | 231 | 1 | 0.43 | 1 | 0.43 | 0.093 | 0.000 | |||
| M | 666 | 4 | 0.60 | 4 | 0.60 | 0.126 | 0.000 | |||
| PUP3 | 192 | 2 | 1.04 | 2 | 1.04 | 0.492 | 0.000 | |||
| PUP4 | 369 | 0 | 0.00 | 0 | 0.00 | 0.000 | 0.000 | |||
| N | 1,269 | 4 | 0.32 | 3 | 0.24 | 3.00 | 0.049 | 0.054 | 0.91 | |
| PUP5 | 297 | 0 | 0.00 | 0 | 0.00 | 0.000 | 0.000 | |||
| Total | 29,725 | 137(142) | 0.46 | 98 | 0.33 | 2.52 | 0.085 | 0.119 | 0.72 | |
| Influenza Virus A |
HA | 1,701 | 698 | 41.03 | 323 | 18.99 | 0.62 | 64.5 | 382.8 | 0.17 |
| M2 | 294 | 98 | 33.33 | 60 | 20.41 | 0.83 | 178.0 | 815.9 | 0.22 | |
| M1 | 759 | 243 | 32.02 | 79 | 10.41 | 0.24 | 79.9 | 1,112 | 0.07 | |
| NA | 1,413 | 418 | 29.58 | 181 | 12.81 | 0.67 | 12.3 | 69.4 | 0.18 | |
| NP | 1,497 | 573 | 38.28 | 186 | 12.42 | 0.31 | 107.0 | 1,231 | 0.09 | |
| NS | 366 | 128 | 34.97 | 56 | 15.30 | 0.34 | 90.6 | 1,087 | 0.08 | |
| PA | 2,151 | 689 | 32.03 | 181 | 8.41 | 0.20 | 31.4 | 596.4 | 0.05 | |
| PB1 | 2,274 | 851 | 37.42 | 204 | 8.97 | 0.13 | 27.5 | 805.7 | 0.03 | |
| PB2 | 2,280 | 805 | 35.31 | 203 | 8.90 | 0.18 | 36.2 | 719.3 | 0.05 | |
| Total | 13,638 | 4,784(4,803) | 35.08 | 1,473 | 10.80 | 0.27 | 48.1 | 659.1 | 0.07 | |
| HIV-1 | Gag | 1,476 | 979 | 66.33 | 676 | 45.80 | 0.88 | 5,917 | 25,290 | 0.23 |
| Pol | 3,000 | 1,894 | 63.13 | 1,232 | 41.07 | 0.61 | 3,974 | 24,510 | 0.16 | |
| Vif | 579 | 392 | 67.70 | 300 | 51.81 | 1.42 | 7,613 | 21,014 | 0.36 | |
| Vpr | 291 | 202 | 69.42 | 140 | 48.11 | 0.76 | 5,924 | 28,054 | 0.21 | |
| Tat | 306 | 216 | 70.59 | 172 | 56.21 | 2.64 | 11,101 | 16,108 | 0.69 | |
| Rev | 303 | 237 | 78.22 | 189 | 62.38 | 1.70 | 10,107 | 19,080 | 0.53 | |
| Vpu | 249 | 215 | 86.35 | 182 | 73.09 | 2.23 | 14,947 | 25,620 | 0.58 | |
| Env | 2,574 | 1,992 | 77.39 | 1,531 | 59.48 | 1.70 | 10,765 | 23,342 | 0.46 | |
| Nef | 624 | 473 | 75.80 | 370 | 59.29 | 1.12 | 8,632 | 29,346 | 0.29 | |
| Total | 9,680 | 6,536(7,141) | 67.52 | 4,792 | 49.50 | 1.15 | 7,445 | 24,094 | 0.31 | |
*
SARS-CoV data are from 17 isolates and referred to the notes of Table 2. Influenza Virus data are from 50 strains of HA segment, 100 strains of M segment, 24 strains of NA segment, 88 strains of NP segment, 89 strains of NS segment, 53 strains of PA segment, 58 strains of PB1 segment, and 58 strains of PB2 segment, downloaded from http://www.flu.lanl.gov. HIV data are from 405 strains, downloaded from http://hiv-web.lanl.gov/. Only those minor alleles that are present in at least two sequences were considered as real substitutions.