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
XCH.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XCH.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
XCH.1
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
XCH.1
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XCH.1
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18526.8
US
XCH.1
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XCH.1
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
XCT
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XCT
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XCT
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
XCT
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
XCT
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XCT
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18526.8
US
XCT
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XCT
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
BA.2.86.6
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-2539.84
China
BA.2.86.6
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
BA.2.86.6
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
BA.2.86.6
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
BA.2.86.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
BA.2.86.6
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
BA.2.86.6
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
BA.2.86.6
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-10265.3
Japan
XDD.2
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XDD.2
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XDD.2
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
XDD.2
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
XDD.2
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-13305.5
Singapore
XDD.2
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18526.8
US
XDD.2
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XDD.2
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
XBB.1.16.9
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
XBB.1.16.9
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XBB.1.16.9
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
XBB.1.16.9
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
XBB.1.16.9
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
XBB.1.16.9
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-18526.8
US
XBB.1.16.9
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
XBB.1.16.9
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
GK.6
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
GK.6
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
GK.6
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
GK.6
ORF1ab
HKU-ORF1b
TGGGGYTTTACRGGTAACCT
20
45
18778
18797
F
-7043.36
Hong Kong
GK.6
S
Young-S
TATACATGTCTCTGGGACCA
20
45
21763
21782
F
-19121.1
Singapore
GK.6
N
US-CDC-N-1
GACCCCAAAATCAGCGAAAT
20
45
28287
28306
F
-20656.7
US
GK.6
N
NIID-JP-N
AAATTTTGGGGACCAGGAAC
20
45
29125
29144
F
-20489.8
Japan
GK.6
ORF1ab
NIID WH-1 Seq F519R840
ACCTCATGGTCATGTTATGG
20
45
502
521
F
-20812.9
Japan
EG.5.2.1
ORF1ab
Yip-ORF1ab
ATGCATTTGCATCAGAGGCT
20
45
1866
1885
F
-21402.5
China
EG.5.2.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
EG.5.2.1
ORF1ab
Won-ORF1ab
TGCATTAACATTGGCCGTGA
20
45
15558
15539
R
-21175.8
South Korea
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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