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
B.19
ORF1ab
Won-ORF1ab
CATGTGTGGCGGTTCACTAT
20
50
15441
15460
F
-14696.5
South Korea
BA.1.1.16
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-14678.7
South Korea
B.1.1.239
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14673.5
Hong Kong
BA.2.24
S
NIID WH-1 F24381R24873
TCAAGACTCACTTTCTTCCAC
21
42.86
24364
24384
F
-14660.3
Japan
B.1.432
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-14642.7
Germany
BA.5.5.2
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-14642.7
Germany
HK.21
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14622
Hong Kong
BA.2.16
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14622
Hong Kong
B.1.160.13
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14622
Hong Kong
B.12
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14622
Hong Kong
XBB.1.28.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14622
Hong Kong
AY.112.3 (Delta)
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-14610.8
France
EG.5.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-14595.2
Japan
BA.5.2.49
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-14595.2
Japan
B.1.258.17
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-14584.6
US
BA.2.76
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-14576.8
Hong Kong
B.1.77
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-14566
Japan
A.29
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-14560.2
Thailand
B.1.357
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
L.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
BQ.1.6
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
EG.1.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
LB.1.5
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
B.1.258
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-14553.9
China
B.1.1.437
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-14547
China
B.1.1.391
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-14522.5
Hong Kong
B.1.151
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-14522.5
Hong Kong
LF.3.1.1
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-14518.2
Hong Kong
XBB.1.41.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
B.1.177.17
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
B.1.1.163
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
B.1.287
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
B.1.1.428
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
B.1.36.20
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14517.8
Singapore
AY.4.13 (Delta)
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-14490.6
US
B.1.173
S
Won-S
CACCTGTGCCTGTTAAACCA
20
50
23213
23194
R
-14485.7
South Korea
B.1.1.16
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14479.3
Singapore
B.1.596.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-14479.3
Singapore
JD.2.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1.5
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1.8
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.2.2
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1.3
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.1.7
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
KK.2
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
KK.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
JD.1.2.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-14403.2
France
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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