Enabled by data from
assayM COVID-19: track sensitivity of RT-PCR primers on COVID-19 Variants
#last Updated:
Sunday, 15 September 2024 05:10:01 GMT+3 (Arabian Standard Time)
, based on 3892 variants (from 8.94 million sequences) and 34 primer sets.
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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
BA.4 (Omicron)
S
Won-S
CTACATGCACCAGCAACTGT
20
50
23114
23133
F
-22142.8
South Korea
BA.4 (Omicron)
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-21965.9
South Korea
BA.4 (Omicron)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BA.4 (Omicron)
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-19261.4
South Korea
BA.4 (Omicron)
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-22616.4
Germany
BA.4 (Omicron)
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BA.4 (Omicron)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BA.4 (Omicron)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.4 (Omicron)
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
BA.4 (Omicron)
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
BA.4 (Omicron)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.4 (Omicron)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.4 (Omicron)
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.4 (Omicron)
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.4 (Omicron)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
BA.4 (Omicron)
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-25148.4
US
BA.4 (Omicron)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
BA.4 (Omicron)
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
BA.4 (Omicron)
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BA.4 (Omicron)
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BA.4 (Omicron)
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BA.4 (Omicron)
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
BA.4 (Omicron)
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-19212.8
Germany
BA.4 (Omicron)
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
BA.4 (Omicron)
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-22388.1
South Korea
BA.4 (Omicron)
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BA.4 (Omicron)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.4 (Omicron)
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.4 (Omicron)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BA.4 (Omicron)
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-20936.4
Hong Kong
BA.4 (Omicron)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
BA.4 (Omicron)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.4 (Omicron)
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BA.4 (Omicron)
N
SC2
CCTTGTGTGGTCTGCATGAGTTTAG
25
48
29554
29530
R
-4388.79
US
BA.4 (Omicron)
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-24908.9
Japan
BA.4 (Omicron)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BA.4 (Omicron)
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.4 (Omicron)
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BA.4 (Omicron)
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
BA.4 (Omicron)
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.4 (Omicron)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BA.4 (Omicron)
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-23857.7
Japan
BA.4 (Omicron)
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-20966
Japan
BA.3.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.3.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
BA.3.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
BA.3.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
BA.3.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.3.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
BA.3.1
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20516.2
China
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
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