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
HK.3.12
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
HK.3.12
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
HK.3.12
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
HK.3.12
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
GN.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
GN.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
GN.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
GN.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JG.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JG.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JG.2
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JG.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JD.1.2.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JD.1.2.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JD.1.2.2
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JD.1.2.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JD.1.1.3
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JD.1.1.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JD.1.1.3
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JD.1.1.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JR.1.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JR.1.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JR.1.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JR.1.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
GJ.1.2.6
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
GJ.1.2.6
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
GJ.1.2.6
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
GJ.1.2.6
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JN.1.30
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JN.1.30
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JN.1.30
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-3779.86
China
JN.1.30
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
XDA.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
XDA.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
XDA.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
XDA.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JN.1.58.3
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JN.1.58.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JN.1.58.3
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JN.1.58.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
XBB.1.5.33
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
XBB.1.5.33
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
XBB.1.5.33
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
XBB.1.5.33
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
JN.13.1
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
JN.13.1
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
JN.13.1
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
JN.13.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
GK.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
XDK.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
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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