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.1.1.53
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
BQ.1.30
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
CH.1.1.18
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
XBR
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
CH.1.1.30
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
BA.5.2.59
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
BQ.1.25.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
BQ.1.25
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
FU.2.1
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18622.3
Singapore
B.1.264.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-18617.7
China
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
B.1.221.1
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
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
XBB.2.3.9
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
EG.1.5
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
B.1.343
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-18611
Singapore
XBB.1.5
E
Won-E
CACACAATCGATGCGCAGTA
20
50
26365
26346
R
-18609.9
South Korea
BQ.1.1.70
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18597.1
US
AP.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18597.1
US
AJ.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-18597
US
KW.1
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
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
KW.1.1.1
S
WuhanCoV-spk1
TTGGCAAAATTCAAGACTCACTTT
24
33.33
24354
24377
F
-18584.5
Japan
BA.5.2.20
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BQ.1.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
DV.3
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.4.1.8
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BN.1.3
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.5.1.22
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.2.75
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.5 (Omicron)
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BA.5.5
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
CH.1.1.2
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BE.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BR.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
CH.1.1.28
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BF.5
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
CH.1.1
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
BF.7.6
ORF1ab
Pasteur-ORF1ab-2
GGTAACTGGTATGATTTCG
19
42.11
14080
14098
F
-18581.4
France
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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