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
B.1.265
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
B.1.265
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.265
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.401
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.401
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
B.1.401
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.401
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.362
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.362
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
B.1.1.362
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.362
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.1.6
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.1.6
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BA.1.6
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BA.1.6
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
GK.2.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GK.2.3
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
GK.2.3
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
GK.2.3
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
FW.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FW.1.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
FW.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-22644.4
Japan
FW.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HN.3.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HN.3.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
HN.3.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
HN.3.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.1.1.17
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.1.1.17
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BA.1.1.17
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BA.1.1.17
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BS.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BS.1.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BS.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BS.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
CM.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
CM.1
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
CM.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
CM.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.75.7
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.75.7
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
BA.2.75.7
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
BA.2.75.7
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
CA.7
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
CA.7
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
CA.7
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
CA.7
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.453
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.453
N
SC2
CTGCAGATTTGGATGATTTCTCC
23
43.48
29463
29485
F
-23117.2
US
B.1.453
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
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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