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
GK.2.4
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
GK.2.4
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
FL.1.5.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FL.1.5.2
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
FL.1.5.2
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FL.1.5.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
EE.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EE.2
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
EE.2
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
EE.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
DB.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
DB.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
DB.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
DB.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BW.1.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BW.1.1.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BW.1.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BW.1.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BQ.1.1.22
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BQ.1.1.22
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BQ.1.1.22
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BQ.1.1.22
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BE.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
China
BE.6
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BE.6
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BE.6
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
KB.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KB.4
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
KB.4
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
KB.4
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HF.1.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HF.1.2
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
HF.1.2
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
HF.1.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BG.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BG.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BG.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BG.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.1.42.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.42.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
JN.1.42.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-26378.9
Japan
JN.1.42.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BQ.1.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BQ.1.1.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BQ.1.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BQ.1.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.517
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.517
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
B.1.1.517
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.517
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
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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