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
JN.5
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
JG.3.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
JG.3.4
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.27.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.27.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HV.1.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HV.1.8
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
GK.1.11
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GK.1.11
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
GK.8.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GK.8.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
GK.8
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GK.8
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XE
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XE
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XCV
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XCV
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.31.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.31.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.50
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.50
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.78
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.78
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.2.43
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.2.43
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HR.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HR.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HK.7
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HK.7
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HS.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HS.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HH.5
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HH.5
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
HU.1.1
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HU.1.1
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-18162
Japan
HV.1.5
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
HV.1.5
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BA.5.11
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BA.5.11
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BQ.1.1.27
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BQ.1.1.27
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
BF.7.22
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
BF.7.22
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
GP.2
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
GP.2
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XBB.3.4
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBB.3.4
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
XBV
N
Chan-N
TTGGATCTTTGTCATCCAATTTG
23
34.78
29306
29284
R
-21867.4
China
XBV
S
NIID WH-1 F24381R24873
ATTTGAAACAAAGACACCTTCAC
23
34.78
24856
24834
R
-22193.2
Japan
B.1.1.397
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
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