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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 31 07:00:30 2021 (UTC+2)

Author: Olivier Friard - Department of Life Sciences and Systems Biology - University of Turin - Italy

We gratefully acknowledge the Authors of the Originating and Submitting laboratories of the genetic sequence and metadata shared via GISAID, on which this research is based.
The isolates collection dates are in YYYY-MM-DD format (ISO 8601).

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Malaysia

Number of isolates sequences available: 321

Method

When the target sequence of amplification systems is available the primers and probe are aligned against the target sequence using the Smith-Waterman local sequence alignment algorithm and the alignments are classified in 3 categories:
             Full match - All primers and probe have a 100% identity with the target sequence. In case of a 2 probes system (RdRP) at least one probe must have a 100% identity.
             The identities of forward/reverse primers AND probe are greater than or equal to 80% AND the length of the amplification product is comprised between the reference length plus/minus 8 bp.
             The identity of one primer OR the probe are less than 80% OR the length of the amplification product is NOT comprised between reference length plus/minus 8 bp.

If the target sequence is not available the The sequence is not available warning is shown.
Please note that the reverse primer sequence is shown reverted-complemented in the alignments.

Results

Move the mouse cursor over elements to see the details.

Virus name / Accession IDRegionCollection date2019-nCoV_N12019-nCoV_N22019-nCoV_N3E-SarbecoRdRP
EPI_ISL_410487The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_410488The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_410489The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_430439
EPI_ISL_430440
EPI_ISL_430441
EPI_ISL_430442
EPI_ISL_430443
EPI_ISL_430444
EPI_ISL_459955
EPI_ISL_459956
EPI_ISL_459957
EPI_ISL_489994
EPI_ISL_490016
EPI_ISL_490047
EPI_ISL_490048
EPI_ISL_490092
EPI_ISL_490093
EPI_ISL_490094
EPI_ISL_490095
EPI_ISL_490096
EPI_ISL_490097
EPI_ISL_490098
EPI_ISL_490099
EPI_ISL_490100
EPI_ISL_490101
EPI_ISL_490102
EPI_ISL_490103
EPI_ISL_596449
EPI_ISL_644671
EPI_ISL_644672
EPI_ISL_718267
EPI_ISL_718268
EPI_ISL_718269
EPI_ISL_718270
EPI_ISL_718271
EPI_ISL_718272
EPI_ISL_718274
EPI_ISL_718275
EPI_ISL_718276
EPI_ISL_718277
EPI_ISL_718278
EPI_ISL_718279
EPI_ISL_718280
EPI_ISL_718281
EPI_ISL_718282
EPI_ISL_718283
EPI_ISL_718284
EPI_ISL_718285
EPI_ISL_718286
EPI_ISL_718287
EPI_ISL_718288
EPI_ISL_718289
EPI_ISL_718290
EPI_ISL_718291
EPI_ISL_718292
EPI_ISL_718293
EPI_ISL_718294
EPI_ISL_718295
EPI_ISL_718296
EPI_ISL_718297
EPI_ISL_718298
EPI_ISL_718299
EPI_ISL_718300
EPI_ISL_718301
EPI_ISL_718302
EPI_ISL_718303
EPI_ISL_718304
EPI_ISL_718305
EPI_ISL_718306
EPI_ISL_718307
EPI_ISL_718308
EPI_ISL_718309
EPI_ISL_718310
EPI_ISL_718311
EPI_ISL_718312
EPI_ISL_718313
EPI_ISL_718314
EPI_ISL_718315
EPI_ISL_728157
EPI_ISL_728158
EPI_ISL_728160
EPI_ISL_728161
EPI_ISL_728162
EPI_ISL_728163
EPI_ISL_728164
EPI_ISL_728165
EPI_ISL_728166
EPI_ISL_728167
EPI_ISL_728169
EPI_ISL_728170
EPI_ISL_728178
EPI_ISL_728209
EPI_ISL_728210
EPI_ISL_728211
EPI_ISL_728212
EPI_ISL_728241
EPI_ISL_728242
EPI_ISL_728243
EPI_ISL_728244
EPI_ISL_728245
EPI_ISL_728246
EPI_ISL_728247
EPI_ISL_728248
EPI_ISL_728249
EPI_ISL_728250
EPI_ISL_728251
EPI_ISL_728252
EPI_ISL_728253
EPI_ISL_807151
EPI_ISL_807153
EPI_ISL_861717
EPI_ISL_861718
EPI_ISL_861719
EPI_ISL_861720
EPI_ISL_861721
EPI_ISL_861722
EPI_ISL_861723
EPI_ISL_861724
EPI_ISL_861725
EPI_ISL_861726
EPI_ISL_861729
EPI_ISL_877228
EPI_ISL_877229
EPI_ISL_877230
EPI_ISL_877231
EPI_ISL_877232
EPI_ISL_877233
EPI_ISL_877234
EPI_ISL_877235
EPI_ISL_877236
EPI_ISL_877329
EPI_ISL_877330
Malaysia/189332/2020 EPI_ISL_417917Kuala Lumpur2020-03-20
Malaysia/188407/2020 EPI_ISL_417918Kuala Lumpur2020-03-18
Malaysia/186197/2020 EPI_ISL_417919Kuala Lumpur2020-03-14
Malaysia/190300/2020 EPI_ISL_417920Kuala Lumpur2020-03-22
EPI_ISL_459953Kuala Lumpur
EPI_ISL_459954Kuala Lumpur
EPI_ISL_501176Kuala Lumpur
EPI_ISL_501177Kuala Lumpur
EPI_ISL_501178Kuala Lumpur
EPI_ISL_501179Kuala Lumpur
EPI_ISL_501180Kuala Lumpur
EPI_ISL_501181Kuala Lumpur
EPI_ISL_501182Kuala Lumpur
EPI_ISL_501183Kuala Lumpur
EPI_ISL_501184Kuala Lumpur
EPI_ISL_501185Kuala Lumpur
EPI_ISL_501186Kuala Lumpur
EPI_ISL_501187Kuala Lumpur
EPI_ISL_501188Kuala Lumpur
EPI_ISL_501189Kuala Lumpur
EPI_ISL_501190Kuala Lumpur
EPI_ISL_501191Kuala Lumpur
EPI_ISL_501192Kuala Lumpur
EPI_ISL_501193Kuala Lumpur
EPI_ISL_501194Kuala Lumpur
EPI_ISL_501195Kuala Lumpur
EPI_ISL_501196Kuala Lumpur
EPI_ISL_501197Kuala Lumpur
EPI_ISL_501198Kuala Lumpur
EPI_ISL_501199Kuala Lumpur
EPI_ISL_501200Kuala Lumpur
EPI_ISL_501201Kuala Lumpur
EPI_ISL_501202Kuala Lumpur
EPI_ISL_501203Kuala Lumpur
EPI_ISL_501204Kuala Lumpur
EPI_ISL_501205Kuala Lumpur
EPI_ISL_501206Kuala Lumpur
EPI_ISL_501207Kuala Lumpur
EPI_ISL_501208Kuala Lumpur
EPI_ISL_501209Kuala Lumpur
EPI_ISL_501210Kuala Lumpur
EPI_ISL_501211Kuala Lumpur
EPI_ISL_501212Kuala Lumpur
EPI_ISL_501213Kuala Lumpur
EPI_ISL_501214Kuala Lumpur
EPI_ISL_501215Kuala Lumpur
EPI_ISL_501216Kuala Lumpur
EPI_ISL_501217Kuala Lumpur
EPI_ISL_501218Kuala Lumpur
EPI_ISL_501219Kuala Lumpur
EPI_ISL_501220Kuala Lumpur
EPI_ISL_501221Kuala Lumpur
EPI_ISL_501222Kuala Lumpur
EPI_ISL_501223Kuala Lumpur
EPI_ISL_501224Kuala Lumpur
EPI_ISL_501225Kuala Lumpur
EPI_ISL_501226Kuala Lumpur
EPI_ISL_501227Kuala Lumpur
EPI_ISL_501228Kuala Lumpur
EPI_ISL_506996Kuala Lumpur
EPI_ISL_506997Kuala Lumpur
EPI_ISL_506998Kuala Lumpur
EPI_ISL_506999Kuala Lumpur
EPI_ISL_507000Kuala Lumpur
EPI_ISL_738086Kuala Lumpur
EPI_ISL_455312Pahang
EPI_ISL_455313Pahang
EPI_ISL_807152Rembau
EPI_ISL_718132Sarawak
EPI_ISL_718133Sarawak
EPI_ISL_718134Sarawak
EPI_ISL_718135Sarawak
EPI_ISL_718136Sarawak
EPI_ISL_718137Sarawak
EPI_ISL_718138Sarawak
EPI_ISL_718139Sarawak
EPI_ISL_718140Sarawak
EPI_ISL_718141Sarawak
EPI_ISL_718142Sarawak
EPI_ISL_718143Sarawak
EPI_ISL_718144Sarawak
EPI_ISL_718145Sarawak
EPI_ISL_718146Sarawak
EPI_ISL_718147Sarawak
EPI_ISL_718148Sarawak
EPI_ISL_718149Sarawak
EPI_ISL_718150Sarawak
EPI_ISL_718151Sarawak
EPI_ISL_718152Sarawak
EPI_ISL_718153Sarawak
EPI_ISL_718154Sarawak
EPI_ISL_718155Sarawak
EPI_ISL_718156Sarawak
EPI_ISL_718157Sarawak
EPI_ISL_718158Sarawak
EPI_ISL_718159Sarawak
EPI_ISL_718160Sarawak
EPI_ISL_718161Sarawak
EPI_ISL_718162Sarawak
EPI_ISL_718163Sarawak
EPI_ISL_718164Sarawak
EPI_ISL_718165Sarawak
EPI_ISL_718166Sarawak
EPI_ISL_718167Sarawak
EPI_ISL_718168Sarawak
EPI_ISL_718169Sarawak
EPI_ISL_718170Sarawak
EPI_ISL_718171Sarawak
EPI_ISL_718172Sarawak
EPI_ISL_718173Sarawak
EPI_ISL_718174Sarawak
EPI_ISL_718175Sarawak
EPI_ISL_718176Sarawak
EPI_ISL_718177Sarawak
EPI_ISL_718178Sarawak
EPI_ISL_718179Sarawak
EPI_ISL_718180Sarawak
EPI_ISL_718181Sarawak
EPI_ISL_718182Sarawak
EPI_ISL_718183Sarawak
EPI_ISL_718184Sarawak
EPI_ISL_718185Sarawak
EPI_ISL_718186Sarawak
EPI_ISL_718187Sarawak
EPI_ISL_718188Sarawak
EPI_ISL_718189Sarawak
EPI_ISL_718190Sarawak
EPI_ISL_718191Sarawak
EPI_ISL_718192Sarawak
EPI_ISL_718193Sarawak
EPI_ISL_718194Sarawak
EPI_ISL_718195Sarawak
EPI_ISL_718196Sarawak
EPI_ISL_718197Sarawak
EPI_ISL_718198Sarawak
EPI_ISL_718199Sarawak
EPI_ISL_718200Sarawak
EPI_ISL_718201Sarawak
EPI_ISL_718202Sarawak
EPI_ISL_718203Sarawak
EPI_ISL_718204Sarawak
EPI_ISL_718205Sarawak
EPI_ISL_718206Sarawak
EPI_ISL_718207Sarawak
EPI_ISL_718208Sarawak
EPI_ISL_718209Sarawak
EPI_ISL_718210Sarawak
EPI_ISL_718211Sarawak
EPI_ISL_718212Sarawak
EPI_ISL_718213Sarawak
EPI_ISL_718214Sarawak
EPI_ISL_718215Sarawak
EPI_ISL_718216Sarawak
EPI_ISL_718217Sarawak
EPI_ISL_718218Sarawak
EPI_ISL_718219Sarawak
EPI_ISL_718220Sarawak
EPI_ISL_718221Sarawak
EPI_ISL_718222Sarawak
Malaysia/MKAK-CL-2020-5045/2020 EPI_ISL_416829Selangor2020-02-20
Malaysia/MKAK-CL-2020-5047/2020 EPI_ISL_416866Selangor2020-02-20
Malaysia/MKAK-CL-2020-5049/2020 EPI_ISL_416884Selangor2020-02-20
Malaysia/MKAK-CL-2020-5096/2020 EPI_ISL_416885Selangor2020-02-20
Malaysia/MKAK-CL-2020-6430/2020 EPI_ISL_416886Selangor2020-02-20
Malaysia/MKAK-CL-2020-7554/2020 EPI_ISL_416907Selangor2020-02-20
EPI_ISL_455790Selangor
EPI_ISL_455791Selangor
EPI_ISL_455792Selangor
EPI_ISL_455793Selangor
EPI_ISL_489992Selangor
EPI_ISL_489993Selangor
EPI_ISL_490014Selangor
EPI_ISL_490015Selangor
EPI_ISL_490089Selangor
EPI_ISL_490090Selangor
EPI_ISL_490091Selangor
EPI_ISL_528738Selangor
EPI_ISL_528739Selangor
EPI_ISL_528740Selangor
EPI_ISL_528741Selangor
EPI_ISL_528742Selangor
EPI_ISL_528743Selangor
EPI_ISL_528744Selangor
EPI_ISL_568873Selangor
EPI_ISL_568874Selangor
EPI_ISL_568875Selangor
EPI_ISL_582124Selangor
EPI_ISL_807150Selangor

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