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
KE.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KE.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HV.1.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HV.1.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.86.5
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.86.5
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.8
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.26.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.26.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XCP
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XCP
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
FL.1.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FL.1.8
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
EG.6.1.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EG.6.1.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
EG.5.1.12
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
EG.5.1.12
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JF.1.1.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JF.1.1.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.11
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.11
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.3.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.3.3
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XDE
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XDE
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
KE.3
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KE.3
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HF.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HF.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.22
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.22
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
FW.1.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
FW.1.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.13
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.13
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
KH.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
KH.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
LM.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
LM.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.1.17
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.17
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.15
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.15
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.1.1.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.1.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.1.63.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JN.1.63.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JN.1.27
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GJ.1.2.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-17507.2
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 4641 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next