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.1.13
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.13
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FL.11
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.11
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FL.4.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.4.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
DM.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DM.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.60
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.60
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.49
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.49
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CK.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CK.2.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.13
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.13
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
JN.1.9.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.1.9.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19646.7
China
BN.3.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BN.3.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BE.4.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BE.4.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BY.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BY.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.26
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.26
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FK.1.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FK.1.1.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FT.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FT.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBF.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBF.5
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
GJ.1.2.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GJ.1.2.5
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.25
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.25
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XAG
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XAG
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
DJ.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DJ.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.16
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.16
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.21
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.21
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.12
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.12
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BF.11.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.11.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
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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