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.1.560
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
B.1.177.26
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
GM.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
KP.3.1.3
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
XDE
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
B.11
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
FL.20.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
JN.1.30
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
JN.1.1.9
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
GJ.1.2.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
DV.7.1.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
P.7
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
GK.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
HN.6
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
GK.2.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
EG.5.1.8
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
JN.1.44
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
XBB.1.5.11
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
EG.2.1
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
JN.1.2
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
XBB.1.16.15
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
GW.4
N
US-CDC-N-2
TTACAAACATTGGCCGCAAA
20
40
29164
29183
F
-6672.85
US
AY.29.2 (Delta)
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-6647.19
China
GK.1.11.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-6459.16
US
B.1.1.74
N
Won-N
CAATGCTGCAATCGTGCTAC
20
50
28732
28751
F
-6431.9
South Korea
DV.7.2
S
Chan-S
CCTACTAAATTAAATGATCTCTGCTTTACT
30
30
22712
22741
F
-6408.76
China
BA.2.58
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-6408.46
China
BA.2.58
S
Young-S
ATCCAGCCTCTTATTATGTTAGAC
24
37.5
21876
21853
R
-6402.07
Singapore
BA.2.36
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BN.1.5
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BA.2 (Omicron)
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BN.1.3.12
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
CH.1.1.13
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
CH.1.1.15
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BN.1.3.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
DV.3
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BN.1.3
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
CH.1.1.2
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
CH.1.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BA.2.18
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
BA.2.12.1
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
AY.105 (Delta)
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
B.1.177.49
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
B.1.1.74
ORF1ab
Pasteur-ORF1ab-1
ATGAGCTTAGTCCTGTTG
18
44.44
12690
12707
F
-6360.38
France
B.1.1.112
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
B.1.1.149
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
B.1.267
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
A.23
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
B.1.596.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
GA.7.2
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-6316.86
Japan
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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