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| 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| XBB.1.9.4 | ORF1ab | Won-ORF1ab | TGCATTAACATTGGCCGTGA | 20 | 45 | 15558 | 15539 | R | -21175.8 | South Korea |
| XBB.1.9.4 | ORF1ab | Chan-ORF1ab | CGCATACAGTCTTRCAGGCT | 20 | 50 | 16220 | 16239 | F | -11502.5 | China |
| XBB.1.9.4 | ORF1ab | Chan-ORF1ab | GTGTGATGTTGAWATGACATGGTC | 24 | 41.67 | 16353 | 16330 | R | -17292.3 | China |
| XBB.1.9.4 | ORF1ab | HKU-ORF1b | TGGGGYTTTACRGGTAACCT | 20 | 45 | 18778 | 18797 | F | -7043.36 | Hong Kong |
| XBB.1.9.4 | ORF1ab | HKU-ORF1b | AACRCGCTTAACAAAGCACTC | 21 | 42.86 | 18909 | 18889 | R | -17655.9 | Hong Kong |
| XBB.1.9.4 | S | Young-S | TATACATGTCTCTGGGACCA | 20 | 45 | 21763 | 21782 | F | -19121.1 | Singapore |
| XBB.1.9.4 | S | Young-S | ATCCAGCCTCTTATTATGTTAGAC | 24 | 37.5 | 21876 | 21853 | R | -22070.7 | Singapore |
| XBB.1.9.4 | S | Chan-S | CCTACTAAATTAAATGATCTCTGCTTTACT | 30 | 30 | 22712 | 22741 | F | -27219.1 | China |
| XBB.1.9.4 | S | Chan-S | CAAGCTATAACGCAGCCTGTA | 21 | 47.62 | 22869 | 22849 | R | -22073.5 | China |
| XBB.1.9.4 | S | Won-S | CTACATGCACCAGCAACTGT | 20 | 50 | 23114 | 23133 | F | -22142.8 | South Korea |
| XBB.1.9.4 | S | Won-S | CACCTGTGCCTGTTAAACCA | 20 | 50 | 23213 | 23194 | R | -21965.9 | South Korea |
| XBB.1.9.4 | E | Won-E | TTCGGAAGAGACAGGTACGTT | 21 | 47.62 | 26259 | 26279 | F | -15016.3 | South Korea |
| XBB.1.9.4 | E | Won-E | CACACAATCGATGCGCAGTA | 20 | 50 | 26365 | 26346 | R | -19261.4 | South Korea |
| XBB.1.9.4 | E | Charité-E | ACAGGTACGTTAATAGTTAATAGCGT | 26 | 34.62 | 26269 | 26294 | F | -19379.1 | Germany |
| XBB.1.9.4 | E | Charité-E | ATATTGCAGCAGTACGCACACA | 22 | 45.45 | 26381 | 26360 | R | -23527.6 | Germany |
| XBB.1.9.4 | E | Huang-E | ACTTCTTTTTCTTGCTTTCGTGGT | 24 | 37.5 | 26295 | 26318 | F | -25022.8 | China |
| XBB.1.9.4 | E | Huang-E | GCAGCAGTACGCACACAATC | 20 | 55 | 26376 | 26357 | R | -23540.5 | China |
| XBB.1.9.4 | E | Niu-E | TTCTTGCTTTCGTGGTATTC | 20 | 40 | 26303 | 26322 | F | -19913.4 | China |
| XBB.1.9.4 | E | Niu-E | CACGTTAACAATATTGCAGC | 20 | 40 | 26391 | 26372 | R | -20723.8 | China |
| XBB.1.9.4 | N | CN-CDC-N | GGGGAACTTCTCCTGCTAGAAT | 22 | 50 | 28881 | 28902 | F | -17926.1 | China |
| XBB.1.9.4 | N | CN-CDC-N | CAGACATTTTGCTCTCAAGCTG | 22 | 45.45 | 28979 | 28958 | R | -23140.2 | China |
| XBB.1.9.4 | N | NIH-TH_N | CGTTTGGTGGACCCTCAGAT | 20 | 55 | 28320 | 28339 | F | -22019.3 | Thailand |
| XBB.1.9.4 | N | NIH-TH_N | CCCCACTGCGTTCTCCATT | 19 | 57.89 | 28376 | 28358 | R | -3370.08 | Thailand |
| XBB.1.9.4 | N | US-CDC-N-1 | GACCCCAAAATCAGCGAAAT | 20 | 45 | 28287 | 28306 | F | -18526.8 | US |
| XBB.1.9.4 | N | US-CDC-N-1 | TCTGGTTACTGCCAGTTGAATCTG | 24 | 45.83 | 28358 | 28335 | R | -25148.4 | US |
| XBB.1.9.4 | N | US-CDC-N-2 | TTACAAACATTGGCCGCAAA | 20 | 40 | 29164 | 29183 | F | -21115.5 | US |
| XBB.1.9.4 | N | US-CDC-N-2 | GCGCGACATTCCGAAGAA | 18 | 55.56 | 29230 | 29213 | R | -21404.2 | US |
| XBB.1.9.4 | N | US-CDC-N-3 | GGGAGCCTTGAATACACCAAAA | 22 | 45.45 | 28681 | 28702 | F | -22824.1 | US |
| XBB.1.9.4 | N | US-CDC-N-3 | TGTAGCACGATTGCAGCATTG | 21 | 47.62 | 28752 | 28732 | R | -23779.6 | US |
| XBB.1.9.4 | N | Young-N | CTCAGTCCAAGATGGTATTTCT | 22 | 40.91 | 28583 | 28604 | F | -17480.9 | Singapore |
| XBB.1.9.4 | N | Young-N | AGCACCATAGGGAAGTCC | 18 | 55.56 | 28648 | 28631 | R | -16947.8 | Singapore |
| XBB.1.9.4 | N | Corman-N | CACATTGGCACCCGCAATC | 19 | 57.89 | 28706 | 28724 | F | -23131.5 | Germany |
| XBB.1.9.4 | N | Corman-N | GAGGAACGAGAAGAGGCTTG | 20 | 55 | 28833 | 28814 | R | -22527.5 | Germany |
| XBB.1.9.4 | N | Won-N | CAATGCTGCAATCGTGCTAC | 20 | 50 | 28732 | 28751 | F | -22388.1 | South Korea |
| XBB.1.9.4 | N | Won-N | GTTGCGACTACGTGATGAGG | 20 | 55 | 28849 | 28830 | R | -23088.1 | South Korea |
| XBB.1.9.4 | N | NIID-JP-N | AAATTTTGGGGACCAGGAAC | 20 | 45 | 29125 | 29144 | F | -20489.8 | Japan |
| XBB.1.9.4 | N | NIID-JP-N | TGGCAGCTGTGTAGGTCAAC | 20 | 55 | 29282 | 29263 | R | -20522.3 | Japan |
| XBB.1.9.4 | N | HKU-N | TAATCAGACAAGGAACTGATTA | 22 | 31.82 | 29145 | 29166 | F | -18800.2 | Hong Kong |
| XBB.1.9.4 | N | HKU-N | CGAAGGTGTGACTTCCATG | 19 | 52.63 | 29254 | 29236 | R | -20936.4 | Hong Kong |
| XBB.1.9.4 | N | Chan-N | GCGTTCTTCGGAATGTCG | 18 | 55.56 | 29210 | 29227 | F | -21207.6 | China |
| XBB.1.9.4 | N | Chan-N | TTGGATCTTTGTCATCCAATTTG | 23 | 34.78 | 29306 | 29284 | R | -21867.4 | China |
| XBB.1.9.4 | N | SC2 | CTGCAGATTTGGATGATTTCTCC | 23 | 43.48 | 29463 | 29485 | F | -23117.2 | US |
| XBB.1.9.4 | N | SC2 | CCTTGTGTGGTCTGCATGAGTTTAG | 25 | 48 | 29554 | 29530 | R | -26482.3 | US |
| XBB.1.9.4 | ORF1ab | NIID WH-1 F501R913 | TTCGGATGCTCGAACTGCACC | 21 | 57.14 | 484 | 504 | F | -24908.9 | Japan |
| XBB.1.9.4 | ORF1ab | NIID WH-1 F501R913 | CTTTACCAGCACGTGCTAGAAGG | 23 | 52.17 | 896 | 874 | R | -25657.5 | Japan |
| XBB.1.9.4 | ORF1ab | NIID WH-1 F509R854 | CTCGAACTGCACCTCATGG | 19 | 57.89 | 492 | 510 | F | -21969.5 | Japan |
| XBB.1.9.4 | ORF1ab | NIID WH-1 F509R854 | CAGAAGTTGTTATCGACATAGC | 22 | 40.91 | 837 | 816 | R | -21257.9 | Japan |
| XBB.1.9.4 | ORF1ab | NIID WH-1 Seq F519R840 | ACCTCATGGTCATGTTATGG | 20 | 45 | 502 | 521 | F | -20812.9 | Japan |
| XBB.1.9.4 | ORF1ab | NIID WH-1 Seq F519R840 | GACATAGCGAGTGTATGCC | 19 | 52.63 | 823 | 805 | R | -20165.2 | Japan |
| XBB.1.9.4 | S | WuhanCoV-spk1 | TTGGCAAAATTCAAGACTCACTTT | 24 | 33.33 | 24354 | 24377 | F | -23366.4 | Japan |
| 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 |