| Browse |
| Prediction results retrieved after performance evaluation of WHO approved 34 primers to estimate their binding affinities for 3892 SARS-CoV-2 variants. |
| Lineage (WHO label)   | Target Gene | Primer Name | Primer Sequence | Primer Length | Primer GC Content (%) | Start Position | End Position | Primer Direction | ΔG (cal) | Primer first used |
|---|---|---|---|---|---|---|---|---|---|---|
| B.1.1.360 | S | WuhanCoV-spk1 | TTGGCAAAATTCAAGACTCACTTT | 24 | 33.33 | 24354 | 24377 | F | -13169.3 | Japan |
| JN.1.8.4 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -13103.9 | Singapore |
| B.1.1.524 | ORF1ab | NIID WH-1 Seq F519R840 | ACCTCATGGTCATGTTATGG | 20 | 45 | 502 | 521 | F | -13100.3 | Japan |
| GA.7.2 | ORF1ab | Chan-ORF1ab | CGCATACAGTCTTRCAGGCT | 20 | 50 | 16220 | 16239 | F | -13080 | China |
| JN.1.4.7 | ORF1ab | NIID WH-1 F501R913 | TTCGGATGCTCGAACTGCACC | 21 | 57.14 | 484 | 504 | F | -13045.7 | Japan |
| B.46 | E | Won-E | CACACAATCGATGCGCAGTA | 20 | 50 | 26365 | 26346 | R | -13011.1 | South Korea |
| XBB.2.6.1 | ORF1ab | NIID WH-1 F509R854 | CTCGAACTGCACCTCATGG | 19 | 57.89 | 492 | 510 | F | -13008.1 | Japan |
| AY.90 (Delta) | ORF1ab | HKU-ORF1b | AACRCGCTTAACAAAGCACTC | 21 | 42.86 | 18909 | 18889 | R | -12995.1 | Hong Kong |
| EG.2.1 | N | HKU-N | TAATCAGACAAGGAACTGATTA | 22 | 31.82 | 29145 | 29166 | F | -12991.9 | Hong Kong |
| HW.1.1 | N | Chan-N | TTGGATCTTTGTCATCCAATTTG | 23 | 34.78 | 29306 | 29284 | R | -12971.4 | China |
| XBB.1.16.11 | S | Won-S | CTACATGCACCAGCAACTGT | 20 | 50 | 23114 | 23133 | F | -12970.4 | South Korea |
| XBB.1.16.11 | S | Chan-S | CAAGCTATAACGCAGCCTGTA | 21 | 47.62 | 22869 | 22849 | R | -12926.6 | China |
| JN.1.8.2 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12905.4 | Singapore |
| JN.1.36.1 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12905.4 | Singapore |
| XDT | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12905.4 | Singapore |
| XBB.1.5.77 | E | Niu-E | CACGTTAACAATATTGCAGC | 20 | 40 | 26391 | 26372 | R | -12869.4 | China |
| P.2 (Zeta) | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -12859 | China |
| B.1.1.253 | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -12859 | China |
| B.50 | N | NIID-JP-N | TGGCAGCTGTGTAGGTCAAC | 20 | 55 | 29282 | 29263 | R | -12842.3 | Japan |
| B.1.1.12 | ORF1ab | NIID WH-1 Seq F519R840 | ACCTCATGGTCATGTTATGG | 20 | 45 | 502 | 521 | F | -12780.2 | Japan |
| B.1.540 | S | Chan-S | CCTACTAAATTAAATGATCTCTGCTTTACT | 30 | 30 | 22712 | 22741 | F | -12757.3 | China |
| B.1.258.17 | ORF1ab | CN-CDC-ORF1ab | CCCTGTGGGTTTTACACTTAA | 21 | 42.86 | 13342 | 13362 | F | -12723.1 | China |
| FR.1.4 | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -12683.7 | China |
| B.1.1.440 | ORF1ab | Pasteur-ORF1ab-2 | CTGGTCAAGGTTAATATAGG | 20 | 40 | 14186 | 14167 | R | -12661.2 | France |
| B.19 | E | Charité-E | ACAGGTACGTTAATAGTTAATAGCGT | 26 | 34.62 | 26269 | 26294 | F | -12650.3 | Germany |
| P.7 | E | Charité-E | ATATTGCAGCAGTACGCACACA | 22 | 45.45 | 26381 | 26360 | R | -12640.7 | Germany |
| DV.7.1.4 | E | Huang-E | GCAGCAGTACGCACACAATC | 20 | 55 | 26376 | 26357 | R | -12594.2 | China |
| BA.5.2.1 | ORF1ab | CN-CDC-ORF1ab | CCCTGTGGGTTTTACACTTAA | 21 | 42.86 | 13342 | 13362 | F | -12591.1 | China |
| HH.8.1 | S | Won-S | CTACATGCACCAGCAACTGT | 20 | 50 | 23114 | 23133 | F | -12525.5 | South Korea |
| JN.1.63 | E | Huang-E | GCAGCAGTACGCACACAATC | 20 | 55 | 26376 | 26357 | R | -12504.8 | China |
| XDQ | E | Charité-E | ACAGGTACGTTAATAGTTAATAGCGT | 26 | 34.62 | 26269 | 26294 | F | -12500.3 | Germany |
| XBB.3.4 | ORF1ab | NIID WH-1 Seq F519R840 | ACCTCATGGTCATGTTATGG | 20 | 45 | 502 | 521 | F | -12500 | Japan |
| GE.1.6 | ORF1ab | Pasteur-ORF1ab-1 | ATGAGCTTAGTCCTGTTG | 18 | 44.44 | 12690 | 12707 | F | -12482.5 | France |
| GE.1.2.1 | S | Chan-S | CAAGCTATAACGCAGCCTGTA | 21 | 47.62 | 22869 | 22849 | R | -12456.3 | China |
| B.1.1.464 | ORF1ab | NIID WH-1 F509R854 | CAGAAGTTGTTATCGACATAGC | 22 | 40.91 | 837 | 816 | R | -12454 | Japan |
| BA.1.15.3 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12444.8 | Singapore |
| JN.17 | ORF1ab | Pasteur-ORF1ab-1 | CTCCCTTTGTTGTGTTGT | 18 | 44.44 | 12797 | 12780 | R | -12423.2 | France |
| JG.3.4 | ORF1ab | Pasteur-ORF1ab-1 | CTCCCTTTGTTGTGTTGT | 18 | 44.44 | 12797 | 12780 | R | -12423.2 | France |
| JN.9 | ORF1ab | Pasteur-ORF1ab-1 | CTCCCTTTGTTGTGTTGT | 18 | 44.44 | 12797 | 12780 | R | -12423.2 | France |
| EG.5.2.2 | ORF1ab | Pasteur-ORF1ab-1 | CTCCCTTTGTTGTGTTGT | 18 | 44.44 | 12797 | 12780 | R | -12423.2 | France |
| BF.7.15 | N | NIH-TH_N | CCCCACTGCGTTCTCCATT | 19 | 57.89 | 28376 | 28358 | R | -12402 | Thailand |
| BF.7.13 | N | NIH-TH_N | CCCCACTGCGTTCTCCATT | 19 | 57.89 | 28376 | 28358 | R | -12402 | Thailand |
| FL.39.1 | E | Charité-E | ATATTGCAGCAGTACGCACACA | 22 | 45.45 | 26381 | 26360 | R | -12382.3 | Germany |
| AY.39.3 (Delta) | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -12360.1 | China |
| BA.5.1.22 | S | WuhanCoV-spk1 | TTGGCAAAATTCAAGACTCACTTT | 24 | 33.33 | 24354 | 24377 | F | -12345.8 | Japan |
| B.1.258.17 | N | NIH-TH_N | CCCCACTGCGTTCTCCATT | 19 | 57.89 | 28376 | 28358 | R | -12329.1 | Thailand |
| B.1.258.17 | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -12321.1 | China |
| BQ.1.1.76 | N | US-CDC-N-2 | TTACAAACATTGGCCGCAAA | 20 | 40 | 29164 | 29183 | F | -12311.6 | US |
| LE.2 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12306.8 | Singapore |
| LB.1.6 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -12306.8 | Singapore |
| Lineage (WHO label) | Target Gene | Primer Name | Primer Sequence | Primer Length | Primer GC Content (%) | Start Position | End Position | Primer Direction | ΔG (cal) | Primer first used |