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
BA.2.12.2
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
DN.1.1.3
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
DN.1.1.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
DN.1.1.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
B.1.177.51
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.177.51
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.177.51
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BF.17
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BF.17
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BF.17
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BA.2.28
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BA.2.28
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.2.28
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
XR
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XR
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XR
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.350.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.350.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.350.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.254
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.254
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.254
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
AY.39.1.1 (Delta)
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
AY.39.1.1 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
AY.39.1.1 (Delta)
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.418
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.418
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.418
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.9.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.9.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.9.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.40
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.40
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.40
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.1.122
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.1.122
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.1.122
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
XAJ
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XAJ
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XAJ
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.431
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.431
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.431
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
B.1.168
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
B.1.168
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
B.1.168
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
Q.6 (Alpha)
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
Q.6 (Alpha)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-19680.5
China
Q.6 (Alpha)
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
AZ.2
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
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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