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.1.6
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.35
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.8
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XAY.2.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CH.1.1.8
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.2.36
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BV.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BF.26
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.1.33
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CP.5
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.45
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BN.1.7
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BF.5.5
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.1.41
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.75.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.1.20
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CR.1.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
DV.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BT.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BE.1.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.9.5
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.6.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.34
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CH.1.1.12
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.9.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BN.1.4.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.2.58
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XAY.2.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.71
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBC.1.2.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CP.6
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
DN.1.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CL.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBB.3.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BN.1.2.4
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CH.1.1.25
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
DB.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CH.1.1.16
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
CZ.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.1.18
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BQ.1.1.29
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.4.1.2
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.2.47
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
FK.1.2.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
XBC.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BQ.1.26.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
DS.3
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
BA.5.1.11
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
Japan
FS.1
ORF1ab
NIID WH-1 Seq F519R840
GACATAGCGAGTGTATGCC
19
52.63
823
805
R
-20165.2
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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