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.2.65
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BG.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.61
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.1.23
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BF.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.2.74
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.12
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BM.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.2.28
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.2.62
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.2.24
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.8
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.2.13.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BF.28
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BE.1.1.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
XAZ
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BE.4
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.5.1.24
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.5.1.16
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.2.26
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-9655.77
Japan
BA.5.2.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BN.1.3.7
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BF.25
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BF.7.4.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BN.1.3.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-19681.5
Japan
BL.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
BA.5.2.47
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
ED.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BN.1.2.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
CQ.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-4248.57
Japan
CH.1.1.24
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.5.2.43
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-3736.75
Japan
BA.5.2.19
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BF.38.3
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-6001.99
Japan
BF.7.19.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BQ.1.1.43
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.5.2.12
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BF.7.23
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.214
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.284
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.351.3 (Beta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.318
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
R.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
AY.29 (Delta)
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
ML.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.5
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
B.1.1.283
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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