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
JZ.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
HS.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
HS.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.5.73
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XBB.1.5.73
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
HT.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
HT.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FL.20
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FL.20
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
JH.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
JH.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
CK.1.1.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
CK.1.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.34.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XBB.1.34.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
EG.7
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
EG.7
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
BN.1.3.5
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
BN.1.3.5
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XCF.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XCF.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XCC
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XCC
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FK.1.5
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FK.1.5
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
HE.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
HE.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.33
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XBB.1.33
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FY.4.1.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FY.4.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.5.99
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XBB.1.5.99
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
HW.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
HW.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.4.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
XBB.1.4.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FE.1.1.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FE.1.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
HA.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
HA.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
GM.3.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
GM.3.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FT.3.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
FT.3.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
JD.1.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
JD.1.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-16669.2
Singapore
GJ.2
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
Singapore
GJ.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FL.21.1
N
Young-N
CTCAGTCCAAGATGGTATTTCT
22
40.91
28583
28604
F
-21953.9
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
Page 314 of 5293
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