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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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Morocco

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_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_728220The sequence is not available
EPI_ISL_728221
EPI_ISL_728222
EPI_ISL_728223
EPI_ISL_728224
EPI_ISL_728235
EPI_ISL_728236
EPI_ISL_728237
EPI_ISL_728239
EPI_ISL_728240
EPI_ISL_728367
EPI_ISL_768835
EPI_ISL_768838
EPI_ISL_768839
EPI_ISL_775264
EPI_ISL_775265
EPI_ISL_778870
EPI_ISL_775254Ain Aouda
EPI_ISL_458150Casablanca
EPI_ISL_769863Casablanca
EPI_ISL_728353Harhoura
EPI_ISL_728355Harhoura
EPI_ISL_775252Harhoura
EPI_ISL_728340Mohammedia
EPI_ISL_451400Ouarzazate
EPI_ISL_458287Rabat
EPI_ISL_471456Rabat
EPI_ISL_471457Rabat
EPI_ISL_471458Rabat
EPI_ISL_471459Rabat
EPI_ISL_471460Rabat
EPI_ISL_723469Rabat
EPI_ISL_728219Rabat
EPI_ISL_728272Rabat
EPI_ISL_728273Rabat
EPI_ISL_728274Rabat
EPI_ISL_728275Rabat
EPI_ISL_728276Rabat
EPI_ISL_728277Rabat
EPI_ISL_728289Rabat
EPI_ISL_728290Rabat
EPI_ISL_728291Rabat
EPI_ISL_728295Rabat
EPI_ISL_728297Rabat
EPI_ISL_728301Rabat
EPI_ISL_728322Rabat
EPI_ISL_728332Rabat
EPI_ISL_728334Rabat
EPI_ISL_728336Rabat
EPI_ISL_728344Rabat
EPI_ISL_728349Rabat
EPI_ISL_728359Rabat
EPI_ISL_728363Rabat
EPI_ISL_768836Rabat
EPI_ISL_768840Rabat
EPI_ISL_775226Rabat
EPI_ISL_775249Rabat
EPI_ISL_775262Rabat
EPI_ISL_775263Rabat
EPI_ISL_775222Sale
EPI_ISL_775224Sale
EPI_ISL_775250Sale
EPI_ISL_768831Salé
EPI_ISL_728339Temara
EPI_ISL_728342Temara
EPI_ISL_728347Temara
EPI_ISL_728352Temara
EPI_ISL_728360Temara
EPI_ISL_728366Temara
EPI_ISL_768832Temara
EPI_ISL_768834Temara
EPI_ISL_768837Temara
EPI_ISL_775219Temara
EPI_ISL_775220Temara
EPI_ISL_775221Temara
EPI_ISL_775223Temara
EPI_ISL_775225Temara
EPI_ISL_775247Temara
EPI_ISL_775255Temara
EPI_ISL_775256Temara
EPI_ISL_775258Temara
EPI_ISL_775260Temara

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