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
B.1.1.216
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.471
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
C.16
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.420
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
L.3
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.36
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.518
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.551
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
C.17
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.207
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.604
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.111
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.619
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
C.36.3.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
C.36.3
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
A.23.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.316
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
AZ.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.436
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.558
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.518
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.368
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.404
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.306
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.328
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
A.2
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.533
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
B.1.1.525
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
KW.1.1.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
JN.1.28.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
JN.1.7.6
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
LG.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
KW.1.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
KW.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
AJ.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18597
US
AP.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18597.1
US
BQ.1.1.70
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18597.1
US
XBB.1.5
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-18609.9
South Korea
JD.1.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
GK.1.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.425
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
HG.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
FY.1.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
XBB.2.3.9
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.221.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.221.4
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.221.3
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
C.31
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.221
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
B.1.221.2
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
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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