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.33
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-1403.3
Japan
FL.29
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FL.29
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
EG.13
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
EG.13
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
GP.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
GP.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
HL.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
HL.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XCD
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XCD
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.44.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.44.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
EG.2.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
EG.2.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
1233.44
Japan
FL.37
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FL.37
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.45.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.45.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FP.4
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FP.4
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.5.102
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.5.102
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FK.1.3
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FK.1.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
GN.5
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
GN.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FL.31
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FL.31
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FL.13.3
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FL.13.3
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
EG.7
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
EG.7
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
BN.1.3.5
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
BN.1.3.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XCF.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XCF.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XCC
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XCC
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FK.1.5
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FK.1.5
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FL.21.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FL.21.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FP.2.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
FP.2.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.5.92
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.5.92
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
XBB.1.5.42
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
XBB.1.5.42
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-23366.4
Japan
FL.35.1
ORF1ab
Young-ORF1ab
CACTTAATGTAAGGCTTTGTTAAG
24
33.33
14243
14220
R
-22408
Singapore
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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