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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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Uruguay

Number of isolates sequences available: 75

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_480345Maldonado
Uruguay/UY-1/2020 EPI_ISL_426476Montevideo2020-03-16
Uruguay/UY-2/2020 EPI_ISL_426477Montevideo2020-03-16
Uruguay/UY-3/2020 EPI_ISL_426478Montevideo2020-04-17
Uruguay/UY-4/2020 EPI_ISL_426479Montevideo2020-03-17
Uruguay/UY-5/2020 EPI_ISL_426480Montevideo2020-03-17
Uruguay/UY-6/2020 EPI_ISL_426481Montevideo2020-03-17
Uruguay/UY-6-2/2020 EPI_ISL_426482Montevideo2020-03-17
Uruguay/UY-8/2020 EPI_ISL_426583Montevideo2020-03-17
Uruguay/UY-9/2020 EPI_ISL_426584Montevideo2020-03-19
Uruguay/UY-10/2020 EPI_ISL_429257Montevideo2020-03-19
EPI_ISL_444493Montevideo
EPI_ISL_457940Montevideo
EPI_ISL_457941Montevideo
EPI_ISL_457942Montevideo
EPI_ISL_457943Montevideo
EPI_ISL_457944Montevideo
EPI_ISL_457945Montevideo
EPI_ISL_457946Montevideo
EPI_ISL_457947Montevideo
EPI_ISL_457948Montevideo
EPI_ISL_457949Montevideo
EPI_ISL_457950Montevideo
EPI_ISL_457951Montevideo
EPI_ISL_457952Montevideo
EPI_ISL_457953Montevideo
EPI_ISL_457954Montevideo
EPI_ISL_457955Montevideo
EPI_ISL_457956Montevideo
EPI_ISL_457957Montevideo
EPI_ISL_457958Montevideo
EPI_ISL_457959Montevideo
EPI_ISL_457960Montevideo
EPI_ISL_457961Montevideo
EPI_ISL_457962Montevideo
EPI_ISL_457963Montevideo
EPI_ISL_457964Montevideo
EPI_ISL_457965Montevideo
EPI_ISL_457966Montevideo
EPI_ISL_457967Montevideo
EPI_ISL_457968Montevideo
EPI_ISL_457969Montevideo
EPI_ISL_457970Montevideo
EPI_ISL_457971Montevideo
EPI_ISL_457972Montevideo
EPI_ISL_457973Montevideo
EPI_ISL_480331Montevideo
EPI_ISL_480332Montevideo
EPI_ISL_480333Montevideo
EPI_ISL_480334Montevideo
EPI_ISL_480335Montevideo
EPI_ISL_480336Montevideo
EPI_ISL_480337Montevideo
EPI_ISL_480342Montevideo
EPI_ISL_480343Montevideo
EPI_ISL_480344Montevideo
EPI_ISL_480347Montevideo
EPI_ISL_480348Montevideo
EPI_ISL_480428Montevideo
EPI_ISL_480429Montevideo
EPI_ISL_480430Montevideo
EPI_ISL_480431Montevideo
EPI_ISL_480432Montevideo
EPI_ISL_480433Montevideo
EPI_ISL_480434Montevideo
EPI_ISL_480435Montevideo
EPI_ISL_480436Montevideo
EPI_ISL_480437Montevideo
EPI_ISL_480438Montevideo
EPI_ISL_540430Montevideo
EPI_ISL_480338Rivera
EPI_ISL_480339Rivera
EPI_ISL_480340Rivera
EPI_ISL_480341Rivera
EPI_ISL_480346Rivera

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