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
XBB.1.19.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GE.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.6.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FU.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DV.7.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.86.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HK.3.12
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GN.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JG.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JD.1.2.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JD.1.1.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JR.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GJ.1.2.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XDA.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.1.58.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.5.33
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.13.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GK.1.6.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GY.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XCW
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GA.2.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GK.3.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.2.3.21
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.36
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.5.108
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JS.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.5.104
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HH.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.1.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GW.5.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JE.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.5.2.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DV.7.1.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.16.23
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GN.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JH.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GJ.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GJ.1.2.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HN.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HK.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.10.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.41.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JG.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XCK
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GN.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.16.27
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GY.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HH.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HK.25
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.5.1.11
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
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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