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
GK.7
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.1.1.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.3.3.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XDY
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
JN.1.18.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.4.1.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KS.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
MM.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
JN.1.48.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.4.2.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.3.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
MC.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LP.1.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
JN.1.50.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
MH.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.3.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.3.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.3.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.2.6
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
MA.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
KP.3.1.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
LB.1.8
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.1.5.81
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CH.1.1.20
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBL.3.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.2.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.1.28.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
GA.6.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
B.1.160.20
ORF1ab
CN-CDC-ORF1ab
CCCTGTGGGTTTTACACTTAA
21
42.86
13342
13362
F
-20179.2
China
B.1.438.4
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.438.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.252
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.438.3
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.182
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.1.218
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.438
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.587
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
B.1.588
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-20190.6
US
AY.21 (Delta)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-20194.6
China
BE.12
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.11
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.6
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.9
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.13
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BA.5.3.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.8
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
BE.7
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-20194.8
US
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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