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.1.401
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
B.1.1.362
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
B.1.1.362
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
B.1.1.362
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
B.1.1.362
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
B.1.1.362
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.1.6
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.1.6
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.1.6
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
BA.1.6
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BA.1.6
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
GK.2.3
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
GK.2.3
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
GK.2.3
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
GK.2.3
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
GK.2.3
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
FW.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
FW.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
FW.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
FW.1.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
FW.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
HN.3.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
HN.3.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
HN.3.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
HN.3.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
HN.3.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.1.1.17
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.1.1.17
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.1.1.17
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
BA.1.1.17
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BA.1.1.17
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BS.1.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BS.1.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BS.1.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
BS.1.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BS.1.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
CM.1
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CM.1
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CM.1
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
CM.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
CM.1
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
BA.2.75.7
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
BA.2.75.7
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
BA.2.75.7
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
BA.2.75.7
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
BA.2.75.7
N
NIID-JP-N
TGGCAGCTGTGTAGGTCAAC
20
55
29282
29263
R
-20522.3
Japan
CA.7
E
Huang-E
GCAGCAGTACGCACACAATC
20
55
26376
26357
R
-23540.5
China
CA.7
N
NIH-TH_N
CGTTTGGTGGACCCTCAGAT
20
55
28320
28339
F
-22019.3
Thailand
CA.7
N
Corman-N
GAGGAACGAGAAGAGGCTTG
20
55
28833
28814
R
-22527.5
Germany
CA.7
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-23088.1
South Korea
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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