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
HN.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HN.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HK.13
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.13
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GK.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GK.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
FL.24.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FL.24.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GK.1.8.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GK.1.8.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GE.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GE.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
XDQ.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
XDQ.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.18
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.18
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GJ.1.2.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GJ.1.2.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HK.3.2.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.3.2.2
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HK.2.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.2.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.16
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.16
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
LN.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
LN.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.25.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.25.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.16.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.16.2
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.57.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.57.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.44.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.44.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JD.1.1.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JD.1.1.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JR.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JR.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GJ.1.2.6
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GJ.1.2.6
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.30
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.30
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
XDA.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
XDA.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JN.1.58.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.1.58.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HK.8.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.8.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
XBB.1.19.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
XBB.1.19.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
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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