CoronaVR
Omicron-specific diagnostic primers and probes for RT-PCR assay
Probe list
| Probe ID | Probe sequence | Start-Stop | Tm (C) |
|---|---|---|---|
| 1 | TTGATAACCCTGTCCTACCATTTAATGA | 230-257 | 61.3 |
| 2 | ACCAATGGTACTAAGAGGTTTGATAACC | 211-238 | 61.3 |
| 3 | CGGCTTTAGAACCATTGGTAGATTTGCC | 653-680 | 65.56 |
| Primer ID | Primer sequence | Start-Stop | Tm (C) | Probe | Product-length |
|---|---|---|---|---|---|
| F1 R1 |
TTCCATGTTATCTCTGGGACC CTTATTATGTTAGACTTCTCAATGGAAG |
193-213 299-272 |
58.37 57.99 |
1 | 106 |
| F2 R2 |
TTCCATGTTATCTCTGGGACC ATGTTAGACTTCTCAATGGAAG |
193-213 293-272 |
58.37 55.16 |
1 | 100 |
| F3 R3 |
TTCCATGTTATCTCTGGGACC TCTTATTATGTTAGACTTCTCAATGGAAGC |
193-213 300-271 |
58.37 60.89 |
1 | 107 |
| F4 R4 |
GTTCCATGTTATCTCTGGGAC ATGTTAGACTTCTCAATGGAAG |
192-212 293-272 |
57.73 55.16 |
1 | 101 |
| F5 R5 |
GTTCCATGTTATCTCTGGGAC TCTTATTATGTTAGACTTCTCAATGGAAG |
192-212 300-272 |
57.73 58.96 |
1 | 108 |
| F6 R6 |
GTTCCATGTTATCTCTGGGAC ATTATGTTAGACTTCTCAATGGAAG |
192-212 296-272 |
57.73 56.38 |
1 | 104 |
| F7 R7 |
GGTTCCATGTTATCTCTGGGAC TATGTTAGACTTCTCAATGGAAGC |
191-212 294-271 |
60.24 57.75 |
1 | 103 |
| F8 R8 |
GGTTCCATGTTATCTCTGGGAC CTTATTATGTTAGACTTCTCAATGGAAG |
191-212 299-272 |
60.24 57.99 |
1 | 108 |
| F9 R9 |
GTTCCATGTTATCTCTGGGACC TCTTATTATGTTAGACTTCTCAATGGAAG |
192-213 300-272 |
59.89 58.96 |
1 | 108 |
| F10 R10 |
GTTCCATGTTATCTCTGGGAC TTATGTTAGACTTCTCAATGGAAGC |
192-212 295-271 |
57.73 58.33 |
1 | 103 |
| F11 R11 |
GTTCCATGTTATCTCTGGGACC ATGTTAGACTTCTCAATGGAAGC |
192-213 293-271 |
59.89 57.87 |
1 | 101 |
| F12 R12 |
GTTCCATGTTATCTCTGGGACC TTATTATGTTAGACTTCTCAATGGAAG |
192-213 298-272 |
59.89 56.92 |
1 | 106 |
| F13 R13 |
GTTCCATGTTATCTCTGGGAC TCTTATTATGTTAGACTTCTCAATGGAAGC |
192-212 300-271 |
57.73 60.89 |
1 | 108 |
| F14 R14 |
ATGTTACTTGGTTCCATGTTATCTC ACTTCTCAATGGAAGCAAAATAAAC |
182-206 286-262 |
58.66 58.22 |
2 | 104 |
| F15 R15 |
ATGTTACTTGGTTCCATGTTATCTC GACTTCTCAATGGAAGCAAAATAAAC |
182-206 287-262 |
58.66 59.29 |
2 | 105 |
| F16 R16 |
ACTTGGTTCCATGTTATCTC GACTTCTCAATGGAAGCAAAATAAAC |
187-206 287-262 |
54.32 59.29 |
2 | 100 |
| F17 R17 |
GTTACTTGGTTCCATGTTATCTC CTTCTCAATGGAAGCAAAATAAAC |
184-206 285-262 |
56.77 56.82 |
2 | 101 |
| F18 R18 |
GTTACTTGGTTCCATGTTATCTC TAGACTTCTCAATGGAAGCAAAATAAAC |
184-206 289-262 |
56.77 60.11 |
2 | 105 |
| F19 R19 |
TATTATAGTGCGTGAGCCAGAAGATCTC AGCAAGTAAAGTTTGAAACCTAGTG |
612-639 720-696 |
63.73 59.41 |
3 | 108 |
| F20 R20 |
TTATAGTGCGTGAGCCAGAAGATCTC TGTAAAGCAAGTAAAGTTTGAAACCTAGTG |
614-639 725-696 |
63.85 62.29 |
3 | 111 |
| F21 R21 |
TATAGTGCGTGAGCCAGAAGATCTCC TATGTAAAGCAAGTAAAGTTTGAAACCTAG |
615-640 727-698 |
65.05 60.3 |
3 | 112 |
| F22 R22 |
TAGTGCGTGAGCCAGAAGATCTCC TATGTAAAGCAAGTAAAGTTTGAAACCTAG |
617-640 727-698 |
65.28 60.3 |
3 | 110 |
| F23 R23 |
TAGTGCGTGAGCCAGAAGATCTCC AAAGCAAGTAAAGTTTGAAACCTAGTG |
617-640 722-696 |
65.28 60.37 |
3 | 105 |
| F24 R24 |
TTATAGTGCGTGAGCCAGAAGATCTCC TGTAAAGCAAGTAAAGTTTGAAACCTAGTG |
614-640 725-696 |
65.32 62.29 |
3 | 111 |
Multiple sequence alignment illustrating conservation and specificity in spike region between SARS-CoV-2 variants. Omicron-specific regions and (A) Probe-1, (B) Probe-2, (C) Probe-3, for RT-PCR assays is depicted.
Omicron-specific primers for PCR assays
| Primer ID | Primer sequence | Start-Stop | Tm (C) | Product-length |
|---|---|---|---|---|
| F1 R1 |
CTTGGTTCCATGTTATCTCTGGGACC TCCATCCAACTTTTGTTGTTTTTGTGGTC |
188-213 446-418 |
64.67 64.92 |
258 |
| F2 R2 |
TGGTTCCATGTTATCTCTGGG TTTGTTGTTTTTGTGGTCCAAAAATG |
190-210 435-410 |
58.64 60.2 |
245 |
| F3 R3 |
TTGGTTCCATGTTATCTCTGGGACCAATG TCCATCCAACTTTTGTTGTTTTTGTGGTCC |
189-217 446-417 |
66.54 66.21 |
257 |
| F4 R4 |
TACTTGGTTCCATGTTATCTCTGG TGGTCCAAAAATGGATCATTAC |
186-209 422-401 |
59.37 56.34 |
236 |
| F5 R5 |
CTTGGTTCCATGTTATCTCTGG GGTCCAAAAATGGATCATTAC |
188-209 421-401 |
58.1 54.63 |
233 |
| F6 R6 |
ATGTTACTTGGTTCCATGTTATCTCTGGG CTGAGGGAGATCTTCTGGCTCAC |
182-210 645-623 |
64.24 64.15 |
463 |
| F7 R7 |
TTACTTGGTTCCATGTTATCTCTGGGAC GGAGATCTTCTGGCTCACGC |
185-212 640-621 |
64.17 62.15 |
455 |
| F8 R8 |
ATGTTACTTGGTTCCATGTTATCTCTGGG CGAAAAACCCTGAGGGAGATCTTCTGG |
182-210 654-628 |
64.24 66.53 |
472 |
| F9 R9 |
TGTTTGTTTTTCTTGTTTTATTGCCAC AACTTTTGTTGTTTTTGTGGTCC |
2-28 439-417 |
60.24 58.24 |
437 |
| F10 R10 |
AATGATCCATTTTTGGACCACAAAAAC ACCTGAAGAAGAATCACCAGGAGTC |
403-429 762-738 |
61.44 63.76 |
359 |
| F11 R11 |
GATCCATTTTTGGACCACAAAAAC TGATGTTAATACCTATTGGCAAATCTAC |
406-429 697-670 |
59.4 59.43 |
291 |
| F12 R12 |
TATTATAGTGCGTGAGCCAGAAGATCTC TAGGACAGAATAATCAGCAACACAGTTGC |
612-639 1095-1067 |
63.73 64.83 |
483 |
| F13 R13 |
ATAGTGCGTGAGCCAGAAGATCTC ATAGGACAGAATAATCAGCAACACAG |
616-639 1096-1071 |
63.85 60.72 |
480 |
| F14 R14 |
TTATAGTGCGTGAGCCAGAAGATCTC GTAGGAGACACTCCATAACACTTAAAAG |
614-639 1145-1118 |
63.85 61.31 |
531 |
| F15 R15 |
ATTATAGTGCGTGAGCCAGAAGATCTC ATAAACAGATGCAAATCTGGTGGC |
613-639 1044-1021 |
64.05 61.4 |
431 |
| F16 R16 |
TGCGTGAGCCAGAAGATCTC GGACAGAATAATCAGCAACACAGTTGC |
620-639 1093-1067 |
61.53 64.39 |
473 |
| F17 R17 |
TATTCTAAGCACACGCCTATTATAGTGC ACACTTAAAAGTGAAAAATGGTGCGAG |
595-622 1128-1102 |
62.28 62.66 |
533 |
| F18 R18 |
AAATATATTCTAAGCACACGCCTATTATAG ACTTAAAAGTGAAAAATGGTGCGAG |
590-619 1126-1102 |
59.42 60.36 |
536 |
| F19 R19 |
CTAAGCACACGCCTATTATAGTGC CACTTAAAAGTGAAAAATGGTGCGAG |
599-622 1127-1102 |
60.92 61.55 |
528 |
| F20 R20 |
CTAAGCACACGCCTATTATAGTGCG AACACTTAAAAGTGAAAAATGGTGCGAG |
599-623 1129-1102 |
63.07 63.01 |
530 |
| F21 R21 |
CCTATTATAGTGCGTGAGCCAG ACTTAAAAGTGAAAAATGGTGCGAG |
610-631 1126-1102 |
60.24 60.36 |
516 |
| F22 R22 |
ACGCCTATTATAGTGCGTGAG TAAAAGTGAAAAATGGTGCGAG |
607-627 1123-1102 |
59.22 57.25 |
516 |
| F23 R23 |
ATTCTAAGCACACGCCTATTATAGTGCG TAACACTTAAAAGTGAAAAATGGTGCGAG |
596-623 1130-1102 |
64.41 62.74 |
534 |
| F24 R24 |
TATATTCTAAGCACACGCCTATTATAGTGC TTAAAAGTGAAAAATGGTGCGAG |
593-622 1124-1102 |
62.26 57.9 |
531 |
| F25 R25 |
TATTCTAAGCACACGCCTATTATAG CACTTAAAAGTGAAAAATGGTGCGAG |
595-619 1127-1102 |
57.8 61.55 |
532 |
| F26 R26 |
CTAAGCACACGCCTATTATAGTGCGTG ATAACACTTAAAAGTGAAAAATGGTGCGAG |
599-625 1131-1102 |
65.46 62.95 |
532 |
| F27 R27 |
AAGCACACGCCTATTATAGTG CTTAAAAGTGAAAAATGGTGCGAG |
601-621 1125-1102 |
57.41 59.07 |
524 |
| F28 R28 |
AGCACACGCCTATTATAGTGC TTAAAAGTGAAAAATGGTGCGAG |
602-622 1124-1102 |
59.48 57.9 |
522 |
| F29 R29 |
ACACGCCTATTATAGTGCGTGAG TAACACTTAAAAGTGAAAAATGGTGCGAG |
605-627 1130-1102 |
61.99 62.74 |
525 |
| F30 R30 |
TCGGCTTTAGAACCATTGGTAGATTTGC TAACACTTAAAAGTGAAAAATGGTGCGAG |
652-679 1130-1102 |
65.04 62.74 |
478 |
| F31 R31 |
TAGAACCATTGGTAGATTTGC AAAAGTGAAAAATGGTGCGAG |
659-679 1122-1102 |
54.96 57.36 |
463 |
| F32 R32 |
GGTTTCAAACTTTACTTGCTTTACATAG TTAAAAGTGAAAAATGGTGCGAG |
701-728 1124-1102 |
59.55 57.9 |
423 |