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
BF.7.12
N
SC2
CCTTGTGTGGTCTGCATGAGTTTAG
25
48
29554
29530
R
-25520.9
US
XBB.1.41.2
N
SC2
CCTTGTGTGGTCTGCATGAGTTTAG
25
48
29554
29530
R
-25520.9
US
B.1.1.262
N
SC2
CCTTGTGTGGTCTGCATGAGTTTAG
25
48
29554
29530
R
-25520.9
US
B.1.1.144
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.288
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.249
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.378
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.97
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.9
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.439
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.408
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.256
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
Q.7 (Alpha)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.460
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.262
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
EG.9
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBU
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.351.5 (Beta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FZ.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBB.1.9.7
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBC.1.6.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FL.4.4
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FQ.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
JB.1.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBB.1.17
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FL.3.4
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FZ.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
DV.7.2
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FL.6
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
FL.30.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBB.1.5.68
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
CD.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
AY.122.3 (Delta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.277
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
AY.28 (Delta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.272
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.371
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
AA.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.353
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.407
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
AA.4
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.160.13
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.47
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.182
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.1.218
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
XBB.1.12.1
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
A.11
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
AY.22 (Delta)
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.128
ORF1ab
NIID WH-1 F501R913
CTTTACCAGCACGTGCTAGAAGG
23
52.17
896
874
R
-25657.5
Japan
B.1.36.33
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
Page 5069 of 5293
Go to page:
Prev
1
442
883
1324
1765
2206
2647
3088
3529
3970
4411
4852
5293
Next