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
BA.2.58
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
GE.1.2.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
B.1.1.112
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
AY.125.1 (Delta)
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
BA.5.2.54
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
CJ.1.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
BA.1.9
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-3680.15
Singapore
CM.8.1.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
P.7
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.177.26
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
AY.4.10 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
BQ.1.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
AY.121.1 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.160.26
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
Q.6 (Alpha)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
BA.2.58
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.1.371
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.160.27
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.177.68
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
AY.79 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
AY.134
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.1.74
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
FL.13.3.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
AY.29.2 (Delta)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.258.17
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.46
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.165
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.1.444
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
P.1.9 (Gamma)
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-3660.47
China
B.19
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-3643.27
China
B.50
ORF1ab
Chan-ORF1ab
GTGTGATGTTGAWATGACATGGTC
24
41.67
16353
16330
R
-3643.27
China
B.1.165
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.178
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.403
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
A.27
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
AY.125.1 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.160.33
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
FM.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.51
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
FL.2.5
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
BQ.1.1.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
BG.2
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.1.180
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.243
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.1.291
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
JN.1.48.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
B.1.293
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
AY.39 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
AY.26 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
AY.3 (Delta)
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-3635.26
China
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 5178 of 5293
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