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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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Morocco

Number of isolates sequences available: 48

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_459965
EPI_ISL_459966
EPI_ISL_459967
EPI_ISL_459968
EPI_ISL_459969
EPI_ISL_459970
EPI_ISL_459971
EPI_ISL_459972
EPI_ISL_459973
EPI_ISL_459974
EPI_ISL_459975
EPI_ISL_459976
EPI_ISL_459977
EPI_ISL_459978
EPI_ISL_459979
EPI_ISL_459980
EPI_ISL_459981
EPI_ISL_459982
EPI_ISL_459983
EPI_ISL_459984
EPI_ISL_467299
EPI_ISL_469017
EPI_ISL_469049
EPI_ISL_469051
EPI_ISL_469052
EPI_ISL_469053
EPI_ISL_469054
EPI_ISL_476024
EPI_ISL_476025
EPI_ISL_476026
EPI_ISL_476559
EPI_ISL_482732
EPI_ISL_482733
EPI_ISL_482734
EPI_ISL_482735
EPI_ISL_482736
EPI_ISL_482737
EPI_ISL_482738
EPI_ISL_482739
EPI_ISL_482740
EPI_ISL_458150Casablanca
EPI_ISL_451400Ouarzazate
EPI_ISL_458287Rabat
EPI_ISL_471456Rabat
EPI_ISL_471457Rabat
EPI_ISL_471458Rabat
EPI_ISL_471459Rabat
EPI_ISL_471460Rabat

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