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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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Mayotte

Number of isolates sequences available: 84

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_855360Mamoudzou
EPI_ISL_855361Mamoudzou
EPI_ISL_855362Mamoudzou
EPI_ISL_855363Mamoudzou
EPI_ISL_855364Mamoudzou
EPI_ISL_855365Mamoudzou
EPI_ISL_855366Mamoudzou
EPI_ISL_855367Mamoudzou
EPI_ISL_855368Mamoudzou
EPI_ISL_855369Mamoudzou
EPI_ISL_855370Mamoudzou
EPI_ISL_855371Mamoudzou
EPI_ISL_855372Mamoudzou
EPI_ISL_855373Mamoudzou
EPI_ISL_855374Mamoudzou
EPI_ISL_855375Mamoudzou
EPI_ISL_855376Mamoudzou
EPI_ISL_855377Mamoudzou
EPI_ISL_855378Mamoudzou
EPI_ISL_855379Mamoudzou
EPI_ISL_855380Mamoudzou
EPI_ISL_872197Mamoudzou
EPI_ISL_872200Mamoudzou
EPI_ISL_872202Mamoudzou
EPI_ISL_872221Mamoudzou
EPI_ISL_872222Mamoudzou
EPI_ISL_872223Mamoudzou
EPI_ISL_872224Mamoudzou
EPI_ISL_872225Mamoudzou
EPI_ISL_872226Mamoudzou
EPI_ISL_872232Mamoudzou
EPI_ISL_872240Mamoudzou
EPI_ISL_872241Mamoudzou
EPI_ISL_872242Mamoudzou
EPI_ISL_872243Mamoudzou
EPI_ISL_872244Mamoudzou
EPI_ISL_872245Mamoudzou
EPI_ISL_872246Mamoudzou
EPI_ISL_872247Mamoudzou
EPI_ISL_872248Mamoudzou
EPI_ISL_872271Mamoudzou
EPI_ISL_872272Mamoudzou
EPI_ISL_872273Mamoudzou
EPI_ISL_872326Mamoudzou
EPI_ISL_872327Mamoudzou
EPI_ISL_872328Mamoudzou
EPI_ISL_872329Mamoudzou
EPI_ISL_872330Mamoudzou
EPI_ISL_872331Mamoudzou
EPI_ISL_872332Mamoudzou
EPI_ISL_872333Mamoudzou
EPI_ISL_872334Mamoudzou
EPI_ISL_872335Mamoudzou
EPI_ISL_872336Mamoudzou
EPI_ISL_872337Mamoudzou
EPI_ISL_872338Mamoudzou
EPI_ISL_884006Mamoudzou
EPI_ISL_884007Mamoudzou
EPI_ISL_890355Mamoudzou
EPI_ISL_890356Mamoudzou
EPI_ISL_890357Mamoudzou
EPI_ISL_890358Mamoudzou
EPI_ISL_894220Mamoudzou
EPI_ISL_894221Mamoudzou
EPI_ISL_894222Mamoudzou
EPI_ISL_894224Mamoudzou
EPI_ISL_894225Mamoudzou
EPI_ISL_894226Mamoudzou
EPI_ISL_894227Mamoudzou
EPI_ISL_894228Mamoudzou
EPI_ISL_894229Mamoudzou
EPI_ISL_894230Mamoudzou
EPI_ISL_894231Mamoudzou
EPI_ISL_894233Mamoudzou
EPI_ISL_894234Mamoudzou
EPI_ISL_894235Mamoudzou
EPI_ISL_894236Mamoudzou
EPI_ISL_894237Mamoudzou
EPI_ISL_894238Mamoudzou
EPI_ISL_894239Mamoudzou
EPI_ISL_894240Mamoudzou
EPI_ISL_894241Mamoudzou
EPI_ISL_894242Mamoudzou
EPI_ISL_894243Mamoudzou

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