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.1.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HV.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
BA.2.86.5
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
BA.2.86.5
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
BA.2.86.5
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
HK.8
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HK.8
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.8
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-2358.39
Japan
HK.26.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HK.26.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.26.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
XCP
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-2673.08
Thailand
XCP
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
XCP
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
FL.1.8
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FL.1.8
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FL.1.8
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
EG.6.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EG.6.1.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
EG.6.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
EG.5.1.12
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
EG.5.1.12
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
EG.5.1.12
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-2358.39
Japan
JF.1.1.2
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JF.1.1.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JF.1.1.2
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
HK.11
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HK.11
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.11
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
JN.3.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.3.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.3.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
XDE
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
XDE
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-22667.5
Germany
XDE
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-1981.59
Japan
KE.3
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
KE.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
KE.3
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
HF.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HF.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HF.1.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
HK.22
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
HK.22
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
HK.22
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-3356.01
Japan
FW.1.1.1
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
FW.1.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
FW.1.1.1
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
Japan
JN.13
N
NIH-TH_N
CCCCACTGCGTTCTCCATT
19
57.89
28376
28358
R
-3370.08
Thailand
JN.13
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-23131.5
Germany
JN.13
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-21969.5
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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