Table 1.
Stability of secondary structure formed by genome of coronavirus.
| Genus | Virus | 5′-UTR* | TSS-to-end | Virulence grade | ||
|---|---|---|---|---|---|---|
| Free energy (kcal/mol) | Stability index | Free energy (kcal/mol) | Stability index | |||
| Alphacoronavirus | Bat CoV CDPHE15 | − 66.8 | 92 (H) | − 8,803.5 | 99 (H) | 6 |
| Bat CoV HKU10 | − 61.3 | 84 (M) | − 8,029.1 | 90 (H) | 5 | |
| Cat CoV1 | − 68.8 | 95 (H) | − 7,963.0 | 89 (M) | 5 | |
| Rat CoV | − 59.5 | 82 (M) | − 8,615.0 | 97 (H) | 5 | |
| Mink CoV1 | − 71.2 | 98 (H) | − 7,790.4 | 88 (M) | 5 | |
| Bat CoV1 | − 59.6 | 82 (M) | − 8,153.4 | 92 (H) | 5 | |
| Bat CoV Sax2011 | − 66.7 | 92 (H) | − 8,815.5 | 99 (H) | 6 | |
| Bat CoV SC2013 | − 57.3 | 79 (L) | − 8,712.4 | 98 (H) | 4 | |
| PEDV | − 62.4 | 86 (M) | − 8,671.9 | 97 (H) | 5 | |
| Bat CoV HKU2 | − 64.3 | 88 (M) | − 8,313.0 | 93 (H) | 5 | |
| Human CoV NL63 | − 58.9 | 81 (M) | − 7,223.3 | 81 (M) | 4 | |
| Human CoV 229E | − 55.6 | 76 (L) | − 7,982.5 | 90 (H) | 4 | |
| Betacoronavirus | Human CoV HKU1 | − 43.1 | 59 (L) | − 6,864.6 | 77 (L) | 2 |
| Human MERS-CoV | − 72.8 | 100 (H) | − 8,436.5 | 95 (H) | 6 | |
| Human SARS-CoV | − 63.2 | 87 (M) | − 8,054.1 | 91 (H) | 5 | |
| Human SARS-CoV-2 | − 62.4 | 86 (M) | − 7,860.4 | 88 (M) | 4 | |
| Bat CoV ZJ2013 | − 58.9 | 81 (M) | − 8,328.2 | 94 (H) | 5 | |
| Bat CoV HKU9 | − 55.2 | 76 (L) | − 8,897.8 | 100 (H) | 4 | |
| Deltacoronavirus | Wigeon CoV HKU20 | − 51.8 | 71 (L) | − 8,273.2 | 93 (H) | 4 |
| Bulbul CoV HKU11 | − 54.3 | 75 (L) | − 8,387.6 | 94 (H) | 4 | |
| Heron CoV HKU19 | − 54.9 | 75 (L) | − 7,687.2 | 86 (M) | 3 | |
| Moorhen CoV HKU21 | − 51.2 | 70 (L) | − 8,140.4 | 91 (H) | 4 | |
| Gammacoronavirus | Whale CoV SW1 | − 62.8 | 86 (M) | − 8,161.3 | 92 (H) | 5 |
| Turkey CoV | − 59.0 | 81 (M) | − 8,195.4 | 92 (H) | 5 | |
*Fee energy of 5′-UTR (untranslated region) was obtained by using 200 nucleotides immediately upstream of TSS (translation start site) for secondary structure prediction. Free energy of TSS-to-end region is normalized using the average genome size (28,085 nt) of all surveyed coronaviruses based on actual accumulated free energy of a specific genome (Table S2). 5′-UTR region of human MERS-CoV and TSS-to-end region of bat CoV HKU9 have the lowest free energy respectively, which are thus given the highest stability index (100). H (high), M (medium) and L (low) indicate stability index of ≥ 90, 80 to 89, and < 79, respectively. Virulence grade is based on stability of both 5′-UTR and TSS-to-end regions, in which H, M and L stability is given 3, 2 and 1 points respectively. For example, human SARS-CoV has M and H stability in 5′-UTR and TSS-to-end regions. Thus, its virulence is of grade 5 (i.e. 2 + 3). Various grades of virulence are interpreted as follows: 6—very high, 5—high, 4—medium, 3—low and 2—very low. MERS: Middle East respiratory syndrome. SARS: severe acute respiratory syndrome. PEDV: Porcine epidemic diarrhea virus. The viruses listed in the table were selected to represent different subgenera of coronaviruses.