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.1.18.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LU.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.40
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MG.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.59
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LG.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.10
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LK.2.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LB.1.7.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.25 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.25.1 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.25.3 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.75 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.100 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.44 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.7
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LD.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-17519.3
Japan
KP.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KW.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KR.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.15.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.50.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LB.1.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LF.3.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDK.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.4.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.26
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.37
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JQ.2.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
JN.1.23.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
DY.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
KP.2.4
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LJ.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LE.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
MD.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
EG.5.1.16
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
LE.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDQ
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.502
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.285
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.582
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.580
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.306
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.280
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.329
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.396
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.595.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
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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