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
AY.61 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.61 (Delta)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AY.61 (Delta)
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BA.2.75.6
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BA.2.75.6
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-9785.9
South Korea
BA.2.75.6
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
GC.2
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-3043.11
China
GC.2
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
GC.2
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BQ.1.1.16
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BQ.1.1.16
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BQ.1.1.16
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.1.524
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.524
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.1.524
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BA.5.2.38
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18866.3
China
BA.5.2.38
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BA.5.2.38
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
BA.1.15.3
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BA.1.15.3
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
BA.1.15.3
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.1.15
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.15
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.1.15
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AY.59 (Delta)
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AY.59 (Delta)
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AY.59 (Delta)
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
XBR
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-18625.1
China
XBR
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
XBR
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
DJ.1.1.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
DJ.1.1.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
DJ.1.1.1
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
CH.1.1.21
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
CH.1.1.21
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
CH.1.1.21
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
AZ.5
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
AZ.5
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
AZ.5
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
B.1.1.193
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
B.1.1.193
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-22650
South Korea
B.1.1.193
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-18886
US
BL.4
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-22073.5
China
BL.4
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
BL.4
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
FP.3
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-7333.08
China
FP.3
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-15016.3
South Korea
FP.3
N
US-CDC-N-3
TGTAGCACGATTGCAGCATTG
21
47.62
28752
28732
R
-23779.6
US
DA.1
S
Chan-S
CAAGCTATAACGCAGCCTGTA
21
47.62
22869
22849
R
-7333.08
China
DA.1
E
Won-E
TTCGGAAGAGACAGGTACGTT
21
47.62
26259
26279
F
-18253.7
South Korea
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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