TABLE 1.
TABLE of current literature examining the structure of the SARS-CoV-2 genomea
| Region investigated | Author | Method/tool |
|---|---|---|
| Whole genome | Sanders et al. (90) | SHAPE-MaPseq |
| Whole genome | Huston et al. (101) | SHAPE-MaPseq |
| Whole genome | Rangan et al. (59) | MSA |
| Whole genome | Andrews et al. (103) | ScanFold |
| Whole genome | Manfredonia et al. (105) | SHAPE-MaPseq DMS-MaPseq |
| Whole genome | Alhatlani (273) | Mfold RNAfold |
| Whole genome | Sun et al. (89) | icSHAPE |
| Whole genome | Lan et al. (88) | DMS-MaPseq |
| Whole genome | Cao et al. (266) | vRIC-seq RNAstructure |
| Whole genome | Tavares et al. (274) | SuperFold |
| Whole genome | Ziv et al. (37) | COMRADES |
| Whole genome | Yang et al. (122) | SHAPE-MaP |
| SL1–8 in the extended 5′ UTR and the reverse complement of the 5′ UTR SL1–4, FSE, and 3′ UTR | Rangan et al. (106) | FARFAR2 |
| 5′ UTR | Miao et al. (65) | In-line probing RNAse V1 probing |
| 5′ Terminus and frame-shift element | Iserman et al. (119) | SHAPE-MaP |
| Nsp2 and 3′ UTR | Ali Hosseini Rad and McLellan (141) | RNAfold |
| Genome-scale ordered RNA structure (GORS) | Simmonds (275) | RNAfold |
| 5′ Terminus, frame-shift element, and 3′ UTR | Wacker et al. (63) | NMR DMS footprinting |
| 5′ UTR | Vankadari et al. (276) | RNAfold |
| 3′ UTR | Zhao et al. (123) | DMS-MaPseq |
| Frame-shift element | Zhang et al. (178) | SHAPE-MaPseq DMS-MaPseq |
aFSE, frame-shifting element; UTR, untranslated region.