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


Update: Sun Oct 25 07:18:47 2020 (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: 122

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
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_455312Pahang
EPI_ISL_455313Pahang
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

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