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.1.314
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.314
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
B.1.1.132
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.1.132
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.1.132
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.2.38
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.2.38
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.2.38
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.2.42
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.2.42
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.2.42
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
B.1.1.397
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
B.1.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.1.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
B.1.1.277
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.1.277
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.1.277
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
B.1.1.294
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.1.294
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.1.294
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.2.81
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.2.81
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.2.81
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
HV.1.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HV.1.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HV.1.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
FL.2.5
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FL.2.5
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FL.2.5
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
KK.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-2673.08
Thailand
KK.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
KK.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.2.3.17
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.2.3.17
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.2.3.17
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
FG.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FG.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FG.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
GN.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
GN.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
GN.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
FY.1.2.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FY.1.2.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FY.1.2.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
B.1.413
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-22126.5
Thailand
B.1.413
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
B.1.413
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-18076.7
Japan
FY.5.5
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FY.5.5
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
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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