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Status of SARS-CoV-2 detection systems (RT-PCR)
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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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Number of isolates sequences available: 27


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.


Move the mouse cursor over elements to see the details.

Virus name / Accession IDRegionCollection date2019-nCoV_N12019-nCoV_N22019-nCoV_N3E-SarbecoRdRP
EPI_ISL_837553Santa Cruz
EPI_ISL_837554Santa Cruz
EPI_ISL_837555Santa Cruz
EPI_ISL_837556Santa Cruz
EPI_ISL_837557Santa Cruz
EPI_ISL_837559Santa Cruz
EPI_ISL_837563Santa Cruz
EPI_ISL_837564Santa Cruz
EPI_ISL_837565Santa Cruz
EPI_ISL_837566Santa Cruz
EPI_ISL_837567Santa Cruz
EPI_ISL_837568Santa Cruz
EPI_ISL_837569Santa Cruz
EPI_ISL_837570Santa Cruz
EPI_ISL_837571Santa Cruz
EPI_ISL_837574Santa Cruz
EPI_ISL_837575Santa Cruz
EPI_ISL_837577Santa Cruz
EPI_ISL_837578Santa Cruz
EPI_ISL_837561Santa Cruz-El Torno
EPI_ISL_837562Santa Cruz-Pailon

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