University of Turin logo DBIOS logo


Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Nov 29 12:36:20 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).

Go to home

CotedIvoire

Number of isolates sequences available: 49

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_614391Beoumi
EPI_ISL_614347Boauké
EPI_ISL_614348Boauké
EPI_ISL_614349Boauké
EPI_ISL_614350Boauké
EPI_ISL_614351Boauké
EPI_ISL_614352Boauké
EPI_ISL_614353Boauké
EPI_ISL_614354Boauké
EPI_ISL_614355Boauké
EPI_ISL_614356Boauké
EPI_ISL_614357Boauké
EPI_ISL_614358Boauké
EPI_ISL_614359Boauké
EPI_ISL_614360Boauké
EPI_ISL_614361Boauké
EPI_ISL_614362Boauké
EPI_ISL_614363Boauké
EPI_ISL_614364Boauké
EPI_ISL_614365Boauké
EPI_ISL_614366Boauké
EPI_ISL_614367Boauké
EPI_ISL_614368Boauké
EPI_ISL_614369Boauké
EPI_ISL_614370Boauké
EPI_ISL_614371Boauké
EPI_ISL_614372Boauké
EPI_ISL_614373Boauké
EPI_ISL_614374Boauké
EPI_ISL_614375Boauké
EPI_ISL_614381Boauké
EPI_ISL_614385Boauké
EPI_ISL_614386Boauké
EPI_ISL_614387Boauké
EPI_ISL_614388Boauké
EPI_ISL_614389Boauké
EPI_ISL_614390Boauké
EPI_ISL_614392Boauké
EPI_ISL_614393Boauké
EPI_ISL_614394Boauké
EPI_ISL_614395Boauké
EPI_ISL_614377Bouafle
EPI_ISL_614382Bouafle
EPI_ISL_614383Bouafle
EPI_ISL_614384Katiola
EPI_ISL_614376Yamoussoukro
EPI_ISL_614378Yamoussoukro
EPI_ISL_614379Yamoussoukro
EPI_ISL_614380Yamoussoukro

Download all results


GISAID data provided on this website is subject to GISAID’s Terms and Conditions | Privacy policy of University of Turin.