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
FL.1.5.2
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
HE.2
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
BA.2.75.2
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17862
Japan
KL.1.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-17862
Japan
B.1.258.7
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-17866.7
Germany
B.1.1.441
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-17866.7
Germany
B.1.570
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-17866.7
Germany
AY.112.1 (Delta)
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-17866.7
Germany
DV.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17878.2
Japan
B.1.355
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-17881.2
South Korea
AY.21 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
B.1.531
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
B.1.1.396
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
AY.17 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
B.1.1.355
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
BQ.1.21
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
BN.1.3.11
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
B.1.36.35
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
B.1.610
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
CH.1.1.18
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
BF.11.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
AY.92 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
GJ.1.2.7
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
AY.118 (Delta)
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17890.7
US
XBB.1.42.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-17914.1
US
B.1.626
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-17916.5
Singapore
DN.1.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GA.9
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.75.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GC.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.16
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.524
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.38
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.15.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.15
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBR
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DJ.1.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.21
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.193
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BL.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FP.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DA.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.14
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.16.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DN.1.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DN.1.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.99
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBF.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.409
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
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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