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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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Jordan

Number of isolates sequences available: 28

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_429992Amman
EPI_ISL_429993Amman
EPI_ISL_429994Amman
EPI_ISL_429995Amman
EPI_ISL_429996Amman
EPI_ISL_429997Amman
EPI_ISL_429998Amman
EPI_ISL_429999Amman
EPI_ISL_430000Amman
EPI_ISL_430001Amman
EPI_ISL_430002Amman
EPI_ISL_430003Amman
EPI_ISL_430004Amman
EPI_ISL_430005Amman
EPI_ISL_430006Amman
EPI_ISL_430007Amman
EPI_ISL_430008Amman
EPI_ISL_430011Amman
EPI_ISL_430013Amman
EPI_ISL_430014Amman
EPI_ISL_430015Amman
EPI_ISL_434516Amman
EPI_ISL_450186Amman
EPI_ISL_450187Amman
EPI_ISL_450188Amman
EPI_ISL_450189Amman
EPI_ISL_430009Irbid
EPI_ISL_430012Irbid

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