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.21
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FL.21
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
FL.21
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
FL.21
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
FW.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
FW.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FW.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
FW.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
FW.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JS.2
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JS.2
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
JS.2
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JS.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
JS.2
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GK.2.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GK.2.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GK.2.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GK.2.1.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
GK.2.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
HG.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
HG.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HG.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HG.3
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
HG.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GE.1.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GE.1.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GE.1.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GE.1.3
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
GE.1.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
XCQ
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
XCQ
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
XCQ
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
XCQ
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
XCQ
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GS.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GS.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GS.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GS.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
GS.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
EG.11
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
EG.11
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
EG.11
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
EG.11
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
EG.11
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
JC.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
JC.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
JC.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
JC.3
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
JC.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GK.4
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
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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