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
HQ.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
FD.1.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.2.3.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
GK.1.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
EG.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.1.5.8
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-2539.84
China
EG.2.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
FK.1.1.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
FT.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBF.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
GJ.1.2.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.5.1.25
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XAG
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.5.1.6
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.5.2.8
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.2.9.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.5.1.17
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BN.1.4.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BK.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
DJ.1.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.16
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-17079.9
China
BA.5.1.21
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.5.1.12
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BF.11.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
EE.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BN.3.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BE.4.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BY.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.26
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.1.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.76
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BN.4
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
CK.1.4
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.11
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.4.6.4
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.3
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BA.2.75.5
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BF.7.8
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.40
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
DM.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.60
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.1.49
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
CK.2.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
BQ.1.13
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
JN.1.9.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XDK.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.1.16.16
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
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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