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
A.2
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
A.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.533
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.533
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.533
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.533
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.1.525
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
AY.120.2 (Delta)
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
AY.120.2 (Delta)
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
AY.120.2 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.1.528
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.1.528
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.1.528
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.1.528
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
C.1.2
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
C.1.2
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-17103.8
China
C.1.2
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
C.1.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
AY.91 (Delta)
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
AY.91 (Delta)
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
AY.91 (Delta)
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
AY.91 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.3
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.3
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.3
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.39
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.39
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.39
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.39
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.617
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.617
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.617
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.617
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-16719.1
US
B.1.1.383
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.1.383
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.1.383
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.1.383
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.1.40
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.1.40
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.1.40
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.1.40
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
AY.95 (Delta)
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
AY.95 (Delta)
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
AY.95 (Delta)
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
AY.95 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
B.1.1.189
ORF1ab
Pasteur-ORF1ab-2
CTGGTCAAGGTTAATATAGG
20
40
14186
14167
R
-18348.8
France
B.1.1.189
E
Niu-E
TTCTTGCTTTCGTGGTATTC
20
40
26303
26322
F
-19913.4
China
B.1.1.189
E
Niu-E
CACGTTAACAATATTGCAGC
20
40
26391
26372
R
-20723.8
China
B.1.1.189
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-21115.5
US
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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