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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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Ecuador

Number of isolates sequences available: 90

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_539785Azuay
EPI_ISL_539786Azuay
EPI_ISL_539787Azuay
EPI_ISL_539788Azuay
EPI_ISL_527809Bolivar
EPI_ISL_527810Bolivar
EPI_ISL_527811Bolivar
EPI_ISL_491932Carchi
EPI_ISL_486842Chimborazo
EPI_ISL_486843Chimborazo
EPI_ISL_486844Chimborazo
EPI_ISL_491944Daule
EPI_ISL_527812Esmeraldas
EPI_ISL_527813Esmeraldas
EPI_ISL_527814Esmeraldas
EPI_ISL_527815Esmeraldas
EPI_ISL_527816Esmeraldas
EPI_ISL_527817Esmeraldas
EPI_ISL_491941Galapagos
EPI_ISL_490201Guayaquil
EPI_ISL_574292Guayaquil
EPI_ISL_574293Guayaquil
EPI_ISL_574294Guayaquil
EPI_ISL_491933Guayas
EPI_ISL_491934Guayas
EPI_ISL_491935Guayas
EPI_ISL_491951Guayas
EPI_ISL_491952Guayas
EPI_ISL_527818Guayas
EPI_ISL_527819Guayas
EPI_ISL_594118Guayas
EPI_ISL_486846Imbabura
EPI_ISL_486847Imbabura
EPI_ISL_486848Imbabura
EPI_ISL_486849Imbabura
EPI_ISL_486850Imbabura
EPI_ISL_486851Imbabura
EPI_ISL_525436Imbabura
EPI_ISL_525437Imbabura
EPI_ISL_539789Loja
EPI_ISL_539790Loja
EPI_ISL_539791Loja
EPI_ISL_539792Loja
EPI_ISL_539793Loja
EPI_ISL_471267Los Rios
EPI_ISL_471268Los Rios
EPI_ISL_481244Los Rios
EPI_ISL_481245Los Rios
EPI_ISL_481246Los Rios
EPI_ISL_481247Los Rios
EPI_ISL_481248Los Rios
EPI_ISL_491946Los Rios
EPI_ISL_491950Los Rios
EPI_ISL_491953Los Rios
EPI_ISL_516651Los Rios
EPI_ISL_525433Los Rios
EPI_ISL_525434Los Rios
EPI_ISL_574431Los Rios
EPI_ISL_491936Manabi
EPI_ISL_491937Manabi
EPI_ISL_491938Manabi
EPI_ISL_491945Manabi
EPI_ISL_491947Manabi
EPI_ISL_491948Manabi
EPI_ISL_491949Manabi
EPI_ISL_539783Napo
EPI_ISL_539784Napo
EPI_ISL_491939Orellana
EPI_ISL_491940Orellana
EPI_ISL_516652Orellana
EPI_ISL_525435Orellana
Ecuador/HGSQ-USFQ-018/2020 EPI_ISL_422563Pichincha2020-03-30
Ecuador/HGSQ-USFQ-007/2020 EPI_ISL_422564Pichincha2020-03-30
Ecuador/HGSQ-USFQ-010/2020 EPI_ISL_422565Pichincha2020-03-30
EPI_ISL_477014Pichincha
EPI_ISL_486845Pichincha
EPI_ISL_516650Pichincha
EPI_ISL_525430Pichincha
EPI_ISL_525438Pichincha
Ecuador/HEE-01/2020 EPI_ISL_417482Quito2020-03-09
EPI_ISL_471269Quito
EPI_ISL_471270Quito
EPI_ISL_471271Quito
EPI_ISL_477015Quito
EPI_ISL_477016Quito
EPI_ISL_491954Santa Elena
EPI_ISL_516648Zamora-Chinchipe
EPI_ISL_516649Zamora-Chinchipe
EPI_ISL_525431Zamora-Chinchipe
EPI_ISL_525432Zamora-Chinchipe

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