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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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Burkina Faso

Number of isolates sequences available: 85

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_660470Banfora
EPI_ISL_660475Batie
EPI_ISL_660445Batié
EPI_ISL_660474Batié
EPI_ISL_660476Batié
EPI_ISL_660477Batié
EPI_ISL_660516Batié
EPI_ISL_660522Batié
EPI_ISL_660447Bobo Dioulasso
EPI_ISL_660448Bobo Dioulasso
EPI_ISL_660449Bobo Dioulasso
EPI_ISL_660450Bobo Dioulasso
EPI_ISL_660451Bobo Dioulasso
EPI_ISL_660452Bobo Dioulasso
EPI_ISL_660453Bobo Dioulasso
EPI_ISL_660454Bobo Dioulasso
EPI_ISL_660455Bobo Dioulasso
EPI_ISL_660456Bobo Dioulasso
EPI_ISL_660457Bobo Dioulasso
EPI_ISL_660458Bobo Dioulasso
EPI_ISL_660459Bobo Dioulasso
EPI_ISL_660460Bobo Dioulasso
EPI_ISL_660461Bobo Dioulasso
EPI_ISL_660462Bobo Dioulasso
EPI_ISL_660464Bobo Dioulasso
EPI_ISL_660465Bobo Dioulasso
EPI_ISL_660466Bobo Dioulasso
EPI_ISL_660467Bobo Dioulasso
EPI_ISL_660468Bobo Dioulasso
EPI_ISL_660469Bobo Dioulasso
EPI_ISL_660471Bobo Dioulasso
EPI_ISL_660472Bobo Dioulasso
EPI_ISL_660473Bobo Dioulasso
EPI_ISL_660478Bobo Dioulasso
EPI_ISL_660479Bobo Dioulasso
EPI_ISL_660480Bobo Dioulasso
EPI_ISL_660482Bobo Dioulasso
EPI_ISL_660487Bobo Dioulasso
EPI_ISL_660488Bobo Dioulasso
EPI_ISL_660489Bobo Dioulasso
EPI_ISL_660491Bobo Dioulasso
EPI_ISL_660494Bobo Dioulasso
EPI_ISL_660495Bobo Dioulasso
EPI_ISL_660497Bobo Dioulasso
EPI_ISL_660498Bobo Dioulasso
EPI_ISL_660499Bobo Dioulasso
EPI_ISL_660500Bobo Dioulasso
EPI_ISL_660504Bobo Dioulasso
EPI_ISL_660505Bobo Dioulasso
EPI_ISL_660506Bobo Dioulasso
EPI_ISL_660507Bobo Dioulasso
EPI_ISL_660508Bobo Dioulasso
EPI_ISL_660509Bobo Dioulasso
EPI_ISL_660510Bobo Dioulasso
EPI_ISL_660511Bobo Dioulasso
EPI_ISL_660512Bobo Dioulasso
EPI_ISL_660513Bobo Dioulasso
EPI_ISL_660514Bobo Dioulasso
EPI_ISL_660515Bobo Dioulasso
EPI_ISL_660517Bobo Dioulasso
EPI_ISL_660518Bobo Dioulasso
EPI_ISL_660519Bobo Dioulasso
EPI_ISL_660520Bobo Dioulasso
EPI_ISL_660521Bobo Dioulasso
EPI_ISL_660523Bobo Dioulasso
EPI_ISL_660525Bobo Dioulasso
EPI_ISL_660526Bobo Dioulasso
EPI_ISL_660527Bobo Dioulasso
EPI_ISL_660528Bobo Dioulasso
EPI_ISL_660442Dano
EPI_ISL_660446Gaoua
EPI_ISL_660463Houndé
EPI_ISL_660490Houndé
EPI_ISL_660492Houndé
EPI_ISL_660493Houndé
EPI_ISL_660503Houndé
EPI_ISL_660481N'Dorola
EPI_ISL_660483N'Dorola
EPI_ISL_660484N'Dorola
EPI_ISL_660485N'Dorola
EPI_ISL_660486N'Dorola
EPI_ISL_660502N'Dorola
EPI_ISL_660496Orodara
EPI_ISL_660501Orodara
EPI_ISL_660524Orodara

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