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.
Menu
Home
WHO Primers
New Primers
Simple Primers
LAMP Primers
Browse
NCBI
GISAID
Search
NCBI
GISAID
Genome Scan
Mutants
Substitution
Deletion
Tutorial
Contact
Browse
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.1.346
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.93
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.93
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.512
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.512
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.349
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.1.349
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.265
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
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
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
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
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
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
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
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
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
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
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
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
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
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.637.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
B.1.637.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.79
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.79
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BG.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BG.3
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.3.10
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.3.10
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
KN.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KN.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XBB.1.10
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.1.10
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BQ.1.1.61
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BQ.1.1.61
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.5.2.37
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.5.2.37
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.5.2.10
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
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
Page 4554 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next