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Status of SARS-CoV-2 detection systems (RT-PCR)
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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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Bosnia and Herzegovina

Number of isolates sequences available: 31

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_462463
EPI_ISL_462476
EPI_ISL_462450Bihac
EPI_ISL_462451Bihac
EPI_ISL_462458Bihac
EPI_ISL_462468Bihac
EPI_ISL_462462Breza
EPI_ISL_462466Cazin
EPI_ISL_462472DZ Vitez
EPI_ISL_462452Gorazde
EPI_ISL_462453Gorazde
EPI_ISL_462454Gorazde
EPI_ISL_462460Gorazde
EPI_ISL_462467Gorazde
EPI_ISL_462474Gornji Vakuf
EPI_ISL_462464Ilidza
EPI_ISL_462465Ilidza
EPI_ISL_462471Ilijas
EPI_ISL_462475KZ Kakanj
EPI_ISL_462753Livno
EPI_ISL_462461Maglaj
EPI_ISL_462459Novi Travnik
EPI_ISL_462455Sarajevo
EPI_ISL_462456Sarajevo
EPI_ISL_462457Sarajevo
EPI_ISL_462469Sarajevo
EPI_ISL_462470Sarajevo
EPI_ISL_467300Sarajevo
EPI_ISL_463893Tuzla
EPI_ISL_462473Zepce
EPI_ISL_462990Čelinac

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