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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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Senegal

Number of isolates sequences available: 136

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
Senegal/003/2020 EPI_ISL_418206Dakar2020-02-28
Senegal/016/2020 EPI_ISL_418207Dakar2020-03-02
Senegal/020/2020 EPI_ISL_418208Dakar2020-03-04
Senegal/026/2020 EPI_ISL_418209Dakar2020-03-03
Senegal/136/2020 EPI_ISL_418216Dakar2020-03-13
Senegal/306/2020 EPI_ISL_420069Dakar2020-03-17
Senegal/315/2020 EPI_ISL_420070Dakar2020-03-17
Senegal/382/2020 EPI_ISL_420073Dakar2020-03-19
Senegal/610/2020 EPI_ISL_420075Dakar2020-03-20
Senegal/611/2020 EPI_ISL_420076Dakar2020-03-20
Senegal/618/2020 EPI_ISL_420077Dakar2020-03-20
EPI_ISL_476148Dakar
EPI_ISL_476149Dakar
EPI_ISL_476150Dakar
EPI_ISL_476151Dakar
EPI_ISL_476491Dakar
EPI_ISL_476492Dakar
EPI_ISL_476493Dakar
EPI_ISL_476494Dakar
EPI_ISL_476495Dakar
EPI_ISL_476497Dakar
EPI_ISL_476514Dakar
EPI_ISL_476516Dakar
EPI_ISL_476558Dakar
EPI_ISL_476560Dakar
EPI_ISL_476562Dakar
EPI_ISL_476564Dakar
EPI_ISL_476566Dakar
EPI_ISL_476569Dakar
EPI_ISL_476570Dakar
EPI_ISL_476572Dakar
EPI_ISL_476574Dakar
EPI_ISL_477141Dakar
EPI_ISL_477142Dakar
EPI_ISL_477143Dakar
EPI_ISL_477144Dakar
EPI_ISL_477145Dakar
EPI_ISL_477146Dakar
EPI_ISL_477147Dakar
EPI_ISL_477148Dakar
EPI_ISL_477149Dakar
EPI_ISL_477150Dakar
EPI_ISL_477151Dakar
EPI_ISL_477152Dakar
EPI_ISL_477153Dakar
EPI_ISL_477154Dakar
EPI_ISL_477155Dakar
EPI_ISL_477156Dakar
EPI_ISL_477157Dakar
EPI_ISL_477158Dakar
EPI_ISL_477159Dakar
EPI_ISL_480554Dakar
EPI_ISL_480782Dakar
EPI_ISL_480786Dakar
EPI_ISL_480787Dakar
EPI_ISL_480788Dakar
EPI_ISL_481220Dakar
EPI_ISL_481234Dakar
EPI_ISL_481235Dakar
EPI_ISL_481236Dakar
EPI_ISL_481237Dakar
EPI_ISL_481238Dakar
EPI_ISL_481239Dakar
EPI_ISL_481240Dakar
EPI_ISL_481243Dakar
EPI_ISL_482874Dakar
EPI_ISL_482875Dakar
EPI_ISL_482876Dakar
EPI_ISL_482877Dakar
EPI_ISL_482878Dakar
EPI_ISL_485635Dakar
EPI_ISL_485708Dakar
EPI_ISL_485710Dakar
EPI_ISL_485711Dakar
EPI_ISL_485712Dakar
EPI_ISL_485713Dakar
EPI_ISL_485715Dakar
EPI_ISL_485716Dakar
EPI_ISL_485717Dakar
EPI_ISL_486857Dakar
EPI_ISL_486858DakarThe sequence is not available
EPI_ISL_486859Dakar
EPI_ISL_486860Dakar
EPI_ISL_486861Dakar
EPI_ISL_486862Dakar
EPI_ISL_486863Dakar
EPI_ISL_486864Dakar
EPI_ISL_486865Dakar
EPI_ISL_486866Dakar
EPI_ISL_486867Dakar
EPI_ISL_486868Dakar
EPI_ISL_486869Dakar
EPI_ISL_486870Dakar
EPI_ISL_486871Dakar
EPI_ISL_486872Dakar
EPI_ISL_486873Dakar
EPI_ISL_498229Dakar
EPI_ISL_498230Dakar
EPI_ISL_498231Dakar
EPI_ISL_498232Dakar
EPI_ISL_498233Dakar
EPI_ISL_498235Dakar
EPI_ISL_498236Dakar
EPI_ISL_498237Dakar
EPI_ISL_498238Dakar
EPI_ISL_498239Dakar
EPI_ISL_498240Dakar
EPI_ISL_498241Dakar
EPI_ISL_498242Dakar
EPI_ISL_498243Dakar
EPI_ISL_498244Dakar
EPI_ISL_498245Dakar
EPI_ISL_498246Dakar
EPI_ISL_498247Dakar
EPI_ISL_498248Dakar
EPI_ISL_498249Dakar
EPI_ISL_498250Dakar
EPI_ISL_498251DakarThe sequence is not available
EPI_ISL_498252Dakar
EPI_ISL_476515Dakarhuman
Senegal/073/2020 EPI_ISL_418210Diourbel2020-03-10
Senegal/082/2020 EPI_ISL_418211Diourbel2020-03-11
Senegal/087/2020 EPI_ISL_418212Diourbel2020-03-11
Senegal/094/2020 EPI_ISL_418213Diourbel2020-03-12
Senegal/102/2020 EPI_ISL_418214Diourbel2020-03-12
Senegal/119/2020 EPI_ISL_418215Diourbel2020-03-12
EPI_ISL_480789Kolda
EPI_ISL_498234Pikine
Senegal/600/2020 EPI_ISL_420074Saint-Louis2020-03-20
EPI_ISL_480556Saint-Louis
EPI_ISL_480783Saint-Louis
Senegal/139/2020 EPI_ISL_418217Thies2020-03-13
Senegal/328/2020 EPI_ISL_420071Thies2020-03-17
Senegal/370/2020 EPI_ISL_420072Thies2020-03-18
Senegal/620/2020 EPI_ISL_420078Thies2020-03-20
Senegal/640/2020 EPI_ISL_420079Thies2020-03-20

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