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
DJ.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13769.6
Singapore
DJ.1.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13769.6
Singapore
BF.7.27
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.5
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.4
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.3
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
BF.7.14.6
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-13753.9
France
B.1.1.261
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-13747.9
China
B.1.1.514
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-13747.9
China
BA.2.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-13747.9
China
B.1.540
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-13723.7
Germany
BA.5.2.14
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-13663.4
Japan
B.1.267
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-13655.5
Germany
B.1.1.327
E
Charité-E
ACAGGTACGTTAATAGTTAATAGCGT
26
34.62
26269
26294
F
-13655.5
Germany
B.1.36.22
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-13632.4
China
B.1.1.265
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
AY.46.6 (Delta)
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
CH.1.1.12
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
JN.1.8.2
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
BA.5.2.27
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
CH.1.1.27
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
B.1.393
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-13628.2
China
BA.2.33
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-13604.1
Singapore
B.1.177.89
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-13584.2
South Korea
AY.14 (Delta)
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-13584.2
South Korea
BA.5.1.17
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-13571.9
China
B.19
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-13571.9
China
B.1.1.61
ORF1ab
HKU-ORF1b
AACRCGCTTAACAAAGCACTC
21
42.86
18909
18889
R
-13529.3
Hong Kong
XBB.1.5.78
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-13486.5
China
BA.1.1.16
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.18
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.21
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.15.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.15.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.18
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.14
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.20
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.17
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.8
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.10
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
JN.1.39.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
JN.1.50.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.1.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
Singapore
BA.1.19
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13443.5
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
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