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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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Iraq

Number of isolates sequences available: 50

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_450483The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525498The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525499The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525500The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525501The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525502The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525503The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525504The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525505The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525506The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525507The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525508The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525509The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525510The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525511The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525512The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525513The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525514The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525515The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525516The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525517The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525518The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525519The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525520The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525521The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525522The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525523The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525524The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525525The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525526The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525527The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525528The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525529The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525530The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525531The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525532The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525533The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525534The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_525535The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_582029Al-Muthanna Province
EPI_ISL_582030Al-Muthanna Province
EPI_ISL_514094ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514095ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514096ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514097ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514098ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514099ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514100ErbilThe sequence is not availableThe sequence is not available
EPI_ISL_514101ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514102ErbilThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available

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