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.2.3.13
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
XBB.2.3.13
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
XBB.2.3.13
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.160
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.160
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.160
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.160
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JV.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JV.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JV.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JV.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
XCY
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
XCY
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
XCY
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
XCY
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
HK.16
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
HK.16
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
HK.16
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
HK.16
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JN.1.1.4
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JN.1.1.4
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JN.1.1.4
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JN.1.1.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
EK.4
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
EK.4
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
EK.4
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
EK.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
HV.1.10
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
HV.1.10
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
HV.1.10
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
HV.1.10
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
HV.1.6.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
HV.1.6.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
HV.1.6.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
HV.1.6.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
EF.1.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
EF.1.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
EF.1.2
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
EF.1.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
BU.3
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
BU.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
BU.3
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
BU.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
BA.5.1.38
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-15125.9
France
BA.5.1.38
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
BA.5.1.38
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
BA.5.1.38
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
BA.5.2.34
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
BA.5.2.34
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
BA.5.2.34
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
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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