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
C.33
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
C.33
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.635
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.635
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.635
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
C.21
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
C.21
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
C.21
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
C.14
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
C.14
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
C.14
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AY.19 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.19 (Delta)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AY.19 (Delta)
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
N.4
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
N.4
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
N.4
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AM.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AM.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AM.2
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AY.15 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.15 (Delta)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AY.15 (Delta)
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.1.113
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.113
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.1.113
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
GA.10
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
GA.10
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GA.10
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BF.5.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BF.5.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BF.5.2
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.423
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.423
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AP.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AP.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AP.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AK.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AK.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AK.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AY.98.1.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.98.1.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AY.98.1.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BA.1.13.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BA.1.13.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BA.1.13.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
HK.34.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
HK.34.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
HK.34.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AY.124.1.1 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
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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