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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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Costa Rica

Number of isolates sequences available: 91

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_434533
EPI_ISL_434535
EPI_ISL_434536
EPI_ISL_434538
EPI_ISL_434539
EPI_ISL_434540
EPI_ISL_512674
EPI_ISL_527739
EPI_ISL_480312Alajuela
EPI_ISL_480314Alajuela
EPI_ISL_480316Alajuela
EPI_ISL_480318Alajuela
EPI_ISL_491438Alajuela
EPI_ISL_491440Alajuela
EPI_ISL_491446Alajuela
EPI_ISL_491448Alajuela
EPI_ISL_491449Alajuela
EPI_ISL_491452Alajuela
EPI_ISL_491453Alajuela
EPI_ISL_491455Alajuela
EPI_ISL_512659Alajuela
EPI_ISL_512660Alajuela
EPI_ISL_512661Alajuela
EPI_ISL_512663Alajuela
EPI_ISL_512664Alajuela
EPI_ISL_512669Alajuela
EPI_ISL_512670Alajuela
EPI_ISL_527740Alajuela
EPI_ISL_527741Alajuela
EPI_ISL_527746Alajuela
EPI_ISL_527759Alajuela
EPI_ISL_512846Cartago
EPI_ISL_491450Guanacaste
EPI_ISL_512666Guanacaste
EPI_ISL_512667Guanacaste
EPI_ISL_527747Guanacaste
EPI_ISL_480313Heredia
EPI_ISL_480319Heredia
EPI_ISL_480326Heredia
EPI_ISL_512672Heredia
EPI_ISL_512675Heredia
EPI_ISL_527750Heredia
EPI_ISL_527753Heredia
EPI_ISL_527754Heredia
EPI_ISL_512673Limon
EPI_ISL_527748Limon
EPI_ISL_512658Puntarenas
EPI_ISL_512668Puntarenas
EPI_ISL_527751Puntarenas
EPI_ISL_458236San Jose
EPI_ISL_480315San Jose
EPI_ISL_480317San Jose
EPI_ISL_480320San Jose
EPI_ISL_480321San Jose
EPI_ISL_480322San Jose
EPI_ISL_480323San Jose
EPI_ISL_480324San Jose
EPI_ISL_480325San Jose
EPI_ISL_480327San Jose
EPI_ISL_480328San Jose
EPI_ISL_491437San Jose
EPI_ISL_491439San Jose
EPI_ISL_491441San Jose
EPI_ISL_491442San Jose
EPI_ISL_491443San Jose
EPI_ISL_491444San Jose
EPI_ISL_491445San Jose
EPI_ISL_491447San Jose
EPI_ISL_491451San Jose
EPI_ISL_491454San Jose
EPI_ISL_491456San Jose
EPI_ISL_491457San Jose
EPI_ISL_512653San Jose
EPI_ISL_512654San Jose
EPI_ISL_512655San Jose
EPI_ISL_512656San Jose
EPI_ISL_512657San Jose
EPI_ISL_512662San Jose
EPI_ISL_512665San Jose
EPI_ISL_512671San Jose
EPI_ISL_527742San Jose
EPI_ISL_527743San Jose
EPI_ISL_527744San Jose
EPI_ISL_527745San Jose
EPI_ISL_527749San Jose
EPI_ISL_527752San Jose
EPI_ISL_527755San Jose
EPI_ISL_527756San Jose
EPI_ISL_527757San Jose
EPI_ISL_527758San Jose
EPI_ISL_527760San Jose

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