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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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Colombia

Number of isolates sequences available: 175

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_445085
EPI_ISL_456144Amazonas
EPI_ISL_526932Amazonas
EPI_ISL_526933Amazonas
EPI_ISL_526934Amazonas
EPI_ISL_526949Amazonas
EPI_ISL_526950Amazonas
EPI_ISL_526951Amazonas
Colombia/Antioquia79256/2020 EPI_ISL_417924Antioquia2020-03-11
EPI_ISL_447761Antioquia
EPI_ISL_447762Antioquia
EPI_ISL_447763Antioquia
EPI_ISL_447764Antioquia
EPI_ISL_447765Antioquia
EPI_ISL_447766Antioquia
EPI_ISL_447767Antioquia
EPI_ISL_447768Antioquia
EPI_ISL_456117Antioquia
EPI_ISL_456118Antioquia
EPI_ISL_456119Antioquia
EPI_ISL_456146Antioquia
EPI_ISL_526962Antioquia
EPI_ISL_536399Antioquia
EPI_ISL_456145Atlantico
EPI_ISL_498155Atlantico
EPI_ISL_498156Atlantico
Colombia/Bogota78390/2020 EPI_ISL_418262Bogota2020-03-06
EPI_ISL_456116Bogota
EPI_ISL_456120Bogota
EPI_ISL_526954Bogota
EPI_ISL_526957Bogota
EPI_ISL_526960Bogota
EPI_ISL_526961Bogota
EPI_ISL_526967Bogota
EPI_ISL_526968Bogota
EPI_ISL_526969Bogota
EPI_ISL_526970Bogota
EPI_ISL_526971Bogota
EPI_ISL_526973Bogota
EPI_ISL_526974Bogota
EPI_ISL_456121Bolivar
EPI_ISL_456122Bolivar
EPI_ISL_456148Bolivar
EPI_ISL_497738Bolivar
EPI_ISL_498161Bolivar
EPI_ISL_447738Boyaca
EPI_ISL_447739Boyaca
EPI_ISL_447740Boyaca
EPI_ISL_447741Boyaca
EPI_ISL_447742Boyaca
EPI_ISL_447743Boyaca
EPI_ISL_447747Boyaca
EPI_ISL_447797Boyaca
EPI_ISL_447805Boyaca
EPI_ISL_498157Boyaca
EPI_ISL_498158Boyaca
EPI_ISL_447734Caldas
EPI_ISL_447751Caldas
EPI_ISL_456123Caldas
EPI_ISL_456124Cauca
EPI_ISL_498159Cauca
EPI_ISL_447799Cesar
EPI_ISL_498153Cesar
EPI_ISL_498160Cesar
EPI_ISL_447750Choco
EPI_ISL_447816Cordoba
EPI_ISL_447817Cordoba
EPI_ISL_498163Cordoba
EPI_ISL_447744Cundinamarca
EPI_ISL_447745Cundinamarca
EPI_ISL_447746Cundinamarca
EPI_ISL_447754Cundinamarca
EPI_ISL_447769Cundinamarca
EPI_ISL_447800Cundinamarca
EPI_ISL_447812Cundinamarca
EPI_ISL_447813Cundinamarca
EPI_ISL_447815Cundinamarca
EPI_ISL_498154Cundinamarca
EPI_ISL_498167Cundinamarca
EPI_ISL_498168Cundinamarca
EPI_ISL_498169Cundinamarca
EPI_ISL_498170Cundinamarca
EPI_ISL_526958Cundinamarca
EPI_ISL_447752Huila
EPI_ISL_447753Huila
EPI_ISL_447758Huila
EPI_ISL_447759Huila
EPI_ISL_447806Huila
EPI_ISL_447807Huila
EPI_ISL_447811Huila
EPI_ISL_447777Magdalena
EPI_ISL_447778Magdalena
EPI_ISL_456125Magdalena
EPI_ISL_456153Magdalena
EPI_ISL_498152Magdalena
EPI_ISL_498166Magdalena
EPI_ISL_447802Meta
EPI_ISL_447803Meta
EPI_ISL_447804Meta
EPI_ISL_498164Meta
EPI_ISL_526953Meta
EPI_ISL_447748Narino
EPI_ISL_447749Narino
EPI_ISL_447798Narino
EPI_ISL_456154Narino
EPI_ISL_498162Narino
EPI_ISL_526955Narino
EPI_ISL_526956Narino
EPI_ISL_456126Norte de Santander
EPI_ISL_456130Norte de Santander
EPI_ISL_447801Norte de santander
EPI_ISL_456127Quindio
EPI_ISL_456128Quindio
EPI_ISL_497744Quindio
EPI_ISL_447760Risaralda
EPI_ISL_447809Risaralda
EPI_ISL_447810Risaralda
EPI_ISL_456129Risaralda
EPI_ISL_456155Risaralda
EPI_ISL_497736Risaralda
EPI_ISL_497745Risaralda
EPI_ISL_498165Risaralda
EPI_ISL_456131Santander
EPI_ISL_456149Santander
EPI_ISL_456156Santander
EPI_ISL_447757Tolima
EPI_ISL_447808Tolima
EPI_ISL_456132Tolima
EPI_ISL_526963Tolima
EPI_ISL_526964Tolima
EPI_ISL_526965Tolima
EPI_ISL_445219Valle del Cauca
EPI_ISL_447735Valle del Cauca
EPI_ISL_447736Valle del Cauca
EPI_ISL_447737Valle del Cauca
EPI_ISL_447755Valle del Cauca
EPI_ISL_447756Valle del Cauca
EPI_ISL_447771Valle del Cauca
EPI_ISL_447772Valle del CaucaThe sequence is not available
EPI_ISL_447774Valle del Cauca
EPI_ISL_447775Valle del Cauca
EPI_ISL_447776Valle del Cauca
EPI_ISL_447779Valle del Cauca
EPI_ISL_447780Valle del Cauca
EPI_ISL_447781Valle del Cauca
EPI_ISL_447782Valle del Cauca
EPI_ISL_447783Valle del Cauca
EPI_ISL_447784Valle del Cauca
EPI_ISL_447785Valle del Cauca
EPI_ISL_447786Valle del Cauca
EPI_ISL_447787Valle del Cauca
EPI_ISL_447789Valle del Cauca
EPI_ISL_447790Valle del Cauca
EPI_ISL_447791Valle del Cauca
EPI_ISL_447792Valle del Cauca
EPI_ISL_447793Valle del Cauca
EPI_ISL_447794Valle del Cauca
EPI_ISL_447795Valle del Cauca
EPI_ISL_447796Valle del Cauca
EPI_ISL_447814Valle del Cauca
EPI_ISL_456133Valle del Cauca
EPI_ISL_456134Valle del Cauca
EPI_ISL_456135Valle del Cauca
EPI_ISL_456136Valle del Cauca
EPI_ISL_456137Valle del Cauca
EPI_ISL_456138Valle del Cauca
EPI_ISL_456139Valle del Cauca
EPI_ISL_456140Valle del Cauca
EPI_ISL_456141Valle del Cauca
EPI_ISL_456142Valle del Cauca
EPI_ISL_456143Valle del Cauca
EPI_ISL_456147Valle del Cauca
EPI_ISL_456150Valle del Cauca
EPI_ISL_456151Valle del Cauca
EPI_ISL_456152Valle del Cauca

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