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
B.1.372
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
C.8
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
B.1.1.425
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.5.55
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
HH.8.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FL.19
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FM.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FK.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.2.7.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.8.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EU.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.14
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.21
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EJ.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BM.1.1.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
AY.123.1 (Delta)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
AY.9.2.2 (Delta)
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EW.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBF.7
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.1.37
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BN.1.4.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EW.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CH.1.1.17
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.2.8
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBF.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBP
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CH.1.1.22
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.36
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.37
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.2.10
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.21
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-19343
Hong Kong
BN.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BN.1.8
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
AD.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.6
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.26.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.10.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XAY.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CY.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.3.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBT
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.1.12
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BQ.1.33
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.29
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BA.5.1.28
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CL.1.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BM.1.1.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBM
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
BF.34
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CB.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
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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