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
AY.122.6 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
B.1.621.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.39.2 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.125 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.103.1 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.92 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.122.4 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
AY.101 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.57
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.49
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.9.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.13
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.69
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBF.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.44
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.37
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.54
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.52
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BL.3
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BA.2.48
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
BL.5
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
B.1.640
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-19128
Thailand
B.1.640.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-19128
Thailand
B.1.640.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-19128
Thailand
JN.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19133.4
Japan
CV.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-19157.9
Hong Kong
BT.2
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-19162.8
US
B.1.631
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-19173.1
Germany
XCR
S
NIID WH-1 Seq F24383R24865
AAGACTCACTTTCTTCCACAG
21
42.86
24366
24386
F
-19174.1
Japan
FG.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
XBB.1.16.11
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
B.1.131
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
B.1.601
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
A.11
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
XBB.1.5.8
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
AY.42.1 (Delta)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
B.1.595.2
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
B.1.1.345
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
AT.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
AY.133 (Delta)
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-19188.3
Japan
FU.1.1.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19189.2
Singapore
B.28
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.612
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.361
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.582
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.580
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.568
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
B.1.581
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-19194.1
South Korea
JN.1.28.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-19194.8
Germany
JN.1.4.8
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-19200.7
Singapore
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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