Table 2.
Estimates of the ratio of recombination rate to point mutation rate (R/theta), substitutions by recombination relative to point mutation (r/m), number of substitutions per recombination event (δν), and mean length of DNA imported by homologous recombination (δ) from dataset D4. For each genome segment and analysis, the highest values are shown in bold. These analyses were conducted for the two HKU1 genotypes collectively (HKU1_all) and independently.
| Genome Segment | Coronavirus Genus/Species |
R/Theta | r/m | δν | δ |
|---|---|---|---|---|---|
| (a) Spike | alphaCoVs | 1.103 | 41.590 | 37.718 | 335.413 |
| betaCoVs | 2.193 | 28.494 | 12.994 | 208.896 | |
| (b) WGS | alphaCoVs | 0.014 | 0.840 | 58.043 | 1032.937 |
| betaCoVs | 0.025 | 0.867 | 35.369 | 780.250 | |
| (c) WGS: Interspecies analysis (between one sHCoV species and all other non-human CoVs) | 229E | 0.013 | 0.741 | 57.465 | 1146.815 |
| NL63 | 0.016 | 0.943 | 59.561 | 970.252 | |
| OC43 | 0.027 | 0.888 | 32.291 | 687.266 | |
| HKU1_all | 0.025 | 0.890 | 35.890 | 760.242 | |
| HKU1 Genotype A | 0.024 | 0.840 | 35.170 | 747.680 | |
| HKU1 Genotype B | 0.024 | 0.865 | 36.718 | 787.036 | |
| (d) WGS: Intraspecies analysis (within one sHCoV species) | 229E | 1.693 | 2.915 | 1.722 | 649.287 |
| NL63 | 0.138 | 0.885 | 6.415 | 106.019 | |
| OC43 | 0.329 | 1.636 | 4.967 | 675.283 | |
| HKU1_all | 0.029 | 1.912 | 66.927 | 743.307 | |
| HKU1 Genotype A | 0.216 | 0.537 | 2.493 | 176.197 | |
| HKU1 Genotype B | 0.056 | 2.123 | 37.595 | 811.754 |