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
DV.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CH.1.1.10
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.10
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CH.1.1.26
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.26
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
DV.7
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DV.7
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CH.1.1.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CM.10
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CM.10
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.2.11
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.2.11
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.2.25
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.25
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.42
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.42
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.69
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.69
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.70
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.70
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BE.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BE.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.3.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.3.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CR.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CR.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.2.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.2.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BF.7.13
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.7.13
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
AY.99.1 (Delta)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-21977.3
China
AY.99.1 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
KT.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
KT.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
JC.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JC.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.334
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-22844.7
China
B.1.334
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.359
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-22844.7
China
B.1.359
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CK.2.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CK.2.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
EE.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EE.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
DB.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DB.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BW.1.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BW.1.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.22
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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