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
AY.25 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.25 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.25.1 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.25.1 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.25.3 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.25.3 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.75 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.75 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
AY.100 (Delta)
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
AY.100 (Delta)
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KP.2.8
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KP.2.8
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JN.1.11
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.11
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JN.1.24.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.24.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-3384
China
JN.1.18.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.18.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
LU.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
LU.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JN.1.40
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.40
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
MB.1.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
MB.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KP.3.2.4
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KP.3.2.4
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JN.1.50
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
JN.1.50
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KP.2.14
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KP.2.14
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
unclassifiable
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
unclassifiable
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
KS.1.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
KS.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
FL.1.2
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
FL.1.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
FY.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
FY.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
HH.2.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HH.2.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XCE
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
XCE
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
HN.4.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
HN.4.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GU.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-24325.8
China
GU.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
LQ.1.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
LQ.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
LY.1
E
Huang-E
ACTTCTTTTTCTTGCTTTCGTGGT
24
37.5
26295
26318
F
-25022.8
China
LY.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
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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