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
XBB.1.5.109
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
FR.1.5
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
JN.10
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
HK.12
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
HK.33
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
GK.5.1
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
XCZ
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
FL.40
ORF1ab
Yip-ORF1ab
TTGTTATAGCGGCCTTCTGT
20
45
1970
1951
R
-21075.5
China
FK.1.3
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
GA.4.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
CJ.1.2
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
EP.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
B.1.1.381
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
BM.2
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
FD.1.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
LY.1
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21062.3
US
B.1.640
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-21047.5
US
B.1.640.2
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-21047.5
US
A.29
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-21047.5
US
B.1.640.1
N
US-CDC-N-1
TCTGGTTACTGCCAGTTGAATCTG
24
45.83
28358
28335
R
-21047.5
US
B.1.112
N
US-CDC-N-3
GGGAGCCTTGAATACACCAAAA
22
45.45
28681
28702
F
-21016.2
US
FL.35.1
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-21016.1
Japan
XBB.1.25
ORF1ab
NIID WH-1 F501R913
TTCGGATGCTCGAACTGCACC
21
57.14
484
504
F
-21016.1
Japan
GW.5.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
KE.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
KE.3
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GW.5.1.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GW.5.3.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GW.5.1
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GW.5
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
KE.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GW.5.2
N
Corman-N
CACATTGGCACCCGCAATC
19
57.89
28706
28724
F
-21001.7
Germany
GC.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
B.1.1.297
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
GW.5
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
FL.20.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
GJ.1.2.4
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
DV.7.1.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
JR.1.1.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
XDE
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
EG.2.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
XBB.1.5.42
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
GW.4
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
HY.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
GK.2
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
HN.6
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
JY.1.1
N
Won-N
GTTGCGACTACGTGATGAGG
20
55
28849
28830
R
-20999.4
South Korea
BF.7.15
E
Charité-E
ATATTGCAGCAGTACGCACACA
22
45.45
26381
26360
R
-20999.1
Germany
XBB.1.5.38
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-20992.8
Japan
XBC.1.4
ORF1ab
NIID WH-1 F509R854
CTCGAACTGCACCTCATGG
19
57.89
492
510
F
-20973.1
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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