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.2.10
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BQ.1.21
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BQ.1.21
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.21
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
BN.3
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BN.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BN.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BN.1.8
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BN.1.8
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BN.1.8
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
AD.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
AD.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
AD.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
XBB.6
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XBB.6
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.6
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BQ.1.26.2
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BQ.1.26.2
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.26.2
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
BQ.1.10.3
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BQ.1.10.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.10.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
XAY.1.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XAY.1.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XAY.1.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
CY.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
CY.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CY.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
XBB.3.1
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XBB.3.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.3.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
XBT
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XBT
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBT
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BQ.1.1.12
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BQ.1.1.12
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.1.12
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
BQ.1.33
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BQ.1.33
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BQ.1.33
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21956.6
US
XBB.1.29
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
XBB.1.29
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
XBB.1.29
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BA.5.1.28
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
BA.5.1.28
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
BA.5.1.28
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
CL.1.3
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-23527.6
Germany
CL.1.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-23140.2
China
CL.1.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-22824.1
US
BM.1.1.4
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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