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.2.4
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-5377.88
China
JN.1.65
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-5377.88
China
GM.2
N
HKU-N
CGAAGGTGTGACTTCCATG
19
52.63
29254
29236
R
-5385.48
Hong Kong
B.51
ORF1ab
Young-ORF1ab
TCATTGTTAATGCCTATATTAACC
24
29.17
14155
14178
F
-5424.4
Singapore
B.1.267
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-5467.16
Germany
B.1.444
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-5467.16
Germany
B.1.1.74
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-5467.16
Germany
BM.1.1.3
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
XS
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BA.1.9
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
MB.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BA.5.2.54
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
ED.3
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
CM.4
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BQ.1.4
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BN.1.9
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BU.1
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
BQ.1.23
ORF1ab
Charité-ORF1b
GTGARATGGTCATGTGTGGCGG
22
54.55
15431
15452
F
-5491.88
Germany
AY.52 (Delta)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
FL.20.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JN.1.30
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JR.1.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
XDE
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JN.1.1.9
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GW.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GJ.1.2.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
DV.7.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GW.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
HY.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
XBB.1.5.42
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JN.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JN.1.9
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
HK.24.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GK.2.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
B.1.587
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
B.1.333
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GK.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
HN.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
JY.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
AY.4.6 (Delta)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
BE.1.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
BA.2 (Omicron)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
AZ.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
B.1.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
B.33
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
AZ.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
AY.121.1 (Delta)
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
B.4.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
AZ.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
China
GK.1.11.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-5518.4
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
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