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.1.9
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
GK.1.9
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
GK.1.9
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
BN.1.3.13
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
BN.1.3.13
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
BN.1.3.13
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
BN.1.3.13
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
BN.1.3.13
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.385
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
B.1.385
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
B.1.385
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
B.1.385
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
B.1.385
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
XBB.1.5.45
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
XBB.1.5.45
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
XBB.1.5.45
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
XBB.1.5.45
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
XBB.1.5.45
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
B.1.1.244
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
B.1.1.244
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
B.1.1.244
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
B.1.1.244
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
B.1.1.244
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
JD.2.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
JD.2.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
JD.2.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
JD.2.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
JD.2.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EP.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
EP.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
EP.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
EP.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
EP.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FL.17.2
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
FL.17.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
FL.17.2
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
FL.17.2
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
FL.17.2
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
EG.12
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
EG.12
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-15630.5
France
EG.12
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
EG.12
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
EG.12
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
CM.7.1.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-17837.6
France
CM.7.1.1
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-18837.8
France
CM.7.1.1
N
US-CDC-N-2
GCGCGACATTCCGAAGAA
18
55.56
29230
29213
R
-21404.2
US
CM.7.1.1
N
Young-N
AGCACCATAGGGAAGTCC
18
55.56
28648
28631
R
-19874.5
Singapore
CM.7.1.1
N
Chan-N
GCGTTCTTCGGAATGTCG
18
55.56
29210
29227
F
-21207.6
China
FL.10.2
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-5342.9
France
FL.10.2
ORF1ab
Pasteur-ORF1ab-1
CTCCCTTTGTTGTGTTGT
18
44.44
12797
12780
R
-5250.36
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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