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
B.1.258.23
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
BA.2.75.3
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.164
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.104
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
A.2.2
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.559
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
AY.28 (Delta)
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.47
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.405
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
XBB.1.29
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
DE.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
BA.2.9.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.322
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.241
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
C.13
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
C.4
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.59
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
B.1.1.99
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
A.2.4
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
AY.39.1.3 (Delta)
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
AY.91.1 (Delta)
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
AY.5.6 (Delta)
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
XBB.1.28
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4751.81
US
GM.2
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-4702.17
US
BA.5.2.14
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.5.2.20
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.4.1.8
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.5.2.3
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BQ.1.1.66
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.5.2.6
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.5.1.5
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BQ.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BA.4.6.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
BF.7.16
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-4671.25
France
JN.1.4.6
S
WuhanCoV-spk1
TGTGGTTCATAAAAATTCCTTTGTG
25
32
24900
24876
R
-4630.36
Japan
AY.4.6 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
GK.1.11.1
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
AY.121.1 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BQ.1.1.70
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
B.1.537
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
B.1.177.49
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BF.28
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BF.7.4.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BQ.1.1.43
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
BM.1.1.3
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
B.1.420
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
AY.79 (Delta)
N
CN-CDC-N
CAGACATTTTGCTCTCAAGCTG
22
45.45
28979
28958
R
-4625.82
China
B.19
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-4616.71
Japan
BA.2.33
S
NIID WH-1 Seq F24383R24865
CAAAGACACCTTCACGAGG
19
52.63
24848
24830
R
-4566.9
Japan
B.1.1.112
S
NIID WH-1 Seq F24383R24865
CAAAGACACCTTCACGAGG
19
52.63
24848
24830
R
-4566.9
Japan
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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