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
GS.5
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15598.4
US
AY.122.5 (Delta)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15598.4
US
JN.1.58.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15598.4
US
BN.1.2.4
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-15620.7
Singapore
XBB.1.41.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-15620.7
Singapore
XBB.1.45.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
FE.1.1.4
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.232
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
AY.4.7 (Delta)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.336
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
LE.1.2
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
BL.1.4
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
AY.34.1 (Delta)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.1.413
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.466
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.1.353
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
AY.36.1 (Delta)
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.569
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.1.159
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
B.1.607
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-15625.1
US
BA.2.86.7
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.39
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.17.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.12
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FD.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.19.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.177.72
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.1.7
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.1.4.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.15.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.2.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
HN.4.1.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.2.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
XBB.1.23
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.1.27
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.1.391
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.118
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
BA.2.3.21
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
ML.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
HK.34.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.1.519
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
BF.39.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.4.7
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
B.1.115
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
BF.35
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
XBC.1.3.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
JN.11.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
XDL
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.17.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.10
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
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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