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
BQ.1.3
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.75.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.7.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.40
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DM.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.60
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.1.49
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CK.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.13
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.1.9.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XDK.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XBB.1.16.16
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
KT.1.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
LE.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.1.7.7
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.1.49.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.3.2.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
LB.1.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
JN.3.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XM
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.1.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.70
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.63
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.4.1.4
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.8.2
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EC.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BM.1.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XL
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BD.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.23.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XN
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BM.5
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.1.31
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.30
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CG.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.5.2.16
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BQ.1.20
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CH.1.1.30
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.8
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.7.11
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
CE.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
EA.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BA.2.22
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DH.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
XG
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BF.6
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
DV.6.1
N
CN-CDC-N
GGGGAACTTCTCCTGCTAGAAT
22
50
28881
28902
F
-17926.1
China
BN.1.2.1
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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