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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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Costa Rica

Number of isolates sequences available: 181

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_434539
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_682235Alajuela
EPI_ISL_682244Alajuela
EPI_ISL_682247Alajuela
EPI_ISL_682248Alajuela
EPI_ISL_682258Alajuela
EPI_ISL_682259Alajuela
EPI_ISL_682265Alajuela
EPI_ISL_769990Alajuela
EPI_ISL_769991Alajuela
EPI_ISL_769992Alajuela
EPI_ISL_770024Alajuela
EPI_ISL_434540Cartago
EPI_ISL_512846Cartago
EPI_ISL_682241Cartago
EPI_ISL_682246Cartago
EPI_ISL_682249Cartago
EPI_ISL_682257Cartago
EPI_ISL_682270Cartago
EPI_ISL_682271Cartago
EPI_ISL_682272Cartago
EPI_ISL_769993Cartago
EPI_ISL_769994Cartago
EPI_ISL_769995Cartago
EPI_ISL_769996Cartago
EPI_ISL_769997Cartago
EPI_ISL_769998Cartago
EPI_ISL_769999Cartago
EPI_ISL_770025Cartago
EPI_ISL_770026Cartago
EPI_ISL_491450Guanacaste
EPI_ISL_512666Guanacaste
EPI_ISL_512667Guanacaste
EPI_ISL_527747Guanacaste
EPI_ISL_682238Guanacaste
EPI_ISL_770000Guanacaste
EPI_ISL_770001Guanacaste
EPI_ISL_770002Guanacaste
EPI_ISL_770003Guanacaste
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_682242Heredia
EPI_ISL_682255Heredia
EPI_ISL_682276Heredia
EPI_ISL_769987Heredia
EPI_ISL_770004Heredia
EPI_ISL_770005Heredia
EPI_ISL_770027Heredia
EPI_ISL_512673Limon
EPI_ISL_527748Limon
EPI_ISL_682267Limon
EPI_ISL_682273Limon
EPI_ISL_770028Limon
EPI_ISL_512658Puntarenas
EPI_ISL_512668Puntarenas
EPI_ISL_527751Puntarenas
EPI_ISL_682237Puntarenas
EPI_ISL_682239Puntarenas
EPI_ISL_682243Puntarenas
EPI_ISL_682256Puntarenas
EPI_ISL_682261Puntarenas
EPI_ISL_770006Puntarenas
EPI_ISL_770007Puntarenas
EPI_ISL_770008Puntarenas
EPI_ISL_770029Puntarenas
EPI_ISL_770030Puntarenas
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
EPI_ISL_682236San Jose
EPI_ISL_682240San Jose
EPI_ISL_682245San Jose
EPI_ISL_682250San Jose
EPI_ISL_682251San Jose
EPI_ISL_682252San Jose
EPI_ISL_682253San Jose
EPI_ISL_682254San Jose
EPI_ISL_682260San Jose
EPI_ISL_682262San Jose
EPI_ISL_682263San Jose
EPI_ISL_682264San Jose
EPI_ISL_682266San Jose
EPI_ISL_682268San Jose
EPI_ISL_682269San Jose
EPI_ISL_682274San Jose
EPI_ISL_682275San Jose
EPI_ISL_682277San Jose
EPI_ISL_769986San Jose
EPI_ISL_769988San Jose
EPI_ISL_769989San Jose
EPI_ISL_770009San Jose
EPI_ISL_770010San Jose
EPI_ISL_770011San Jose
EPI_ISL_770012San Jose
EPI_ISL_770013San Jose
EPI_ISL_770014San Jose
EPI_ISL_770015San Jose
EPI_ISL_770016San Jose
EPI_ISL_770017San Jose
EPI_ISL_770018San Jose
EPI_ISL_770019San Jose
EPI_ISL_770020San Jose
EPI_ISL_770021San Jose
EPI_ISL_770022San Jose
EPI_ISL_770023San Jose
EPI_ISL_770031San Jose
EPI_ISL_770032San Jose
EPI_ISL_434538Tibas

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