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.1.1.12
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.87
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.33
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.46
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.26
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.15
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.21
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.31
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CP.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBG
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.32
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.1.13
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EF.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XP
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DN.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BE.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.1.15
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.7.16
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.3.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CQ.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EC.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.52
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.62
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.257
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.323
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HK.18
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.164
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.275
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.419
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.560
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.286
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.369
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.39.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.12
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
HK.3.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GS.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.13.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GJ.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XY
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.9
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EG.5.2.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.45
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
GP.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
FL.4.9
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.413
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.107
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.71
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
AS.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.166
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
B.1.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
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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