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
HV.1.6.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
EF.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EF.1.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
EF.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BU.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BU.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BU.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.5.1.38
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.5.1.38
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.5.1.38
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.5.2.34
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BA.5.2.34
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.5.2.34
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BF.7.12
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.12
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BF.7.12
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
CJ.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
CJ.1.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
CJ.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BQ.1.1.21
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BQ.1.1.21
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BQ.1.1.21
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.4.6.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.4.6.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-19212.8
Germany
BA.4.6.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
CM.7.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
CM.7.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
CM.7.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.5.3.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.5.3.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.5.3.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-17733.1
Japan
BQ.1.22
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BQ.1.22
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BQ.1.22
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BF.7.19
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
BF.7.19
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BF.7.19
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
FA.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FA.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FA.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
EE.4
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EE.4
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
EE.4
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-18319.2
Japan
BQ.1.1.72
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BQ.1.1.72
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BQ.1.1.72
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
XBJ.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
XBJ.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
XBJ.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BF.14
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-4270.22
Thailand
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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