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
LB.1.2.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.3.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
ML.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.2.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.1.6
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
LB.1.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
MM.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JN.1.7.8
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.2.3.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
LB.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.2.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.3.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.1.1.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.2.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JN.1.7.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.1.1.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.2.15
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
KP.2.3
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
GE.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
HE.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.33
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FY.4.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.5.99
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
HW.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.4.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FE.1.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
HA.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
GM.3.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FT.3.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JD.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
GJ.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
HT.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FL.20
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JH.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
CK.1.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.34.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EG.2.5
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JK.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.5.106
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
XBB.1.5.11
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-893.215
Hong Kong
FE.1.1.2
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FY.4.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
GZ.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
FT.3.1.1
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
EG.4.4
N
HKU-N
TAATCAGACAAGGAACTGATTA
22
31.82
29145
29166
F
-18800.2
Hong Kong
JZ.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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