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.2.5
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FL.2.5
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
KK.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
KK.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BA.2.3.17
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BA.2.3.17
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
FG.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FG.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
GN.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
GN.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
FY.1.2.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FY.1.2.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.413
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.413
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
FY.5.5
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FY.5.5
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
JD.1.2.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
JD.1.2.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.1.268
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.1.268
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.409
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.409
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
FG.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FG.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
KV.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
KV.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
GK.1.6
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
GK.1.6
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BA.5.2.31
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BA.5.2.31
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.587
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.587
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.232
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.232
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BA.5.2.60
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BA.5.2.60
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
CD.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
CD.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
CM.4.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
CM.4.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BA.5.1.7
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BA.5.1.7
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
DE.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
DE.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
BQ.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BQ.2
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
B.1.333
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
B.1.333
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
Japan
CM.6.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
CM.6.1
ORF1ab
NIID WH-1 F509R854
CAGAAGTTGTTATCGACATAGC
22
40.91
837
816
R
-21257.9
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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