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.4.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
EU.1.1.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
EU.1.1.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CM.2.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
CM.2.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XBB.1.43
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.43
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.122.3 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.122.3 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.132 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.132 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
B.1.160.17
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-3064.43
China
B.1.160.17
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
BA.4.1.10
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BA.4.1.10
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XBB.1.19
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XBB.1.19
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KF.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KF.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XCS
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XCS
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GA.7.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
GA.7.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
FL.15.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
FL.15.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.2.40
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BA.2.40
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CR.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
CR.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KB.3
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KB.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GK.11
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
GK.11
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CJ.1.3.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
CJ.1.3.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XAN
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XAN
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BN.1.4.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BN.1.4.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
DV.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
DV.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CS.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
CS.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.2.83
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BA.2.83
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BJ.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
BJ.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XDG
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XDG
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GA.4
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
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
Page 3651 of 5293
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