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
EE.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EE.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.4.6.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.4.6.4
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.5
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.2.75.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.75.5
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BF.7.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.7.8
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.40
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.40
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.6
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.2.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.8
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.2.9.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.9.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.17
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.17
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BN.1.4.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BN.1.4.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BK.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BK.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.76
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.76
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BN.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BN.4
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CK.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CK.1.4
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.11
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.11
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FL.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.1.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
FY.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FY.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
HH.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HH.2.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XCE
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XCE
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
HN.4.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HN.4.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
GU.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GU.1
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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