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
JN.1.6
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JG.3.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JG.3.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.4
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.4
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.22
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.22
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.15
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.15
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.9
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.44
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.44
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.32
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.32
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
EG.5.1.19
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
EG.5.1.19
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XDK.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDK.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KS.1.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KS.1.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
MK.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MK.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.4.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.4.1.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
KP.4.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.4.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LB.1.7.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LB.1.7.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XDV.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDV.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.48.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
JN.1.48.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LR.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LR.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LF.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LF.5
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
LB.1.4.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LB.1.4.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.64
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.64
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JN.1.48.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JN.1.48.3
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
LR.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
LR.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
LF.5
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
LF.5
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
LB.1.4.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
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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