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Status of SARS-CoV-2 detection systems (RT-PCR)
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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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Bermuda

Number of isolates sequences available: 30

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_780382
EPI_ISL_780383
EPI_ISL_780384
EPI_ISL_780385
EPI_ISL_780386
EPI_ISL_780387
EPI_ISL_780388
EPI_ISL_780389
EPI_ISL_780390
EPI_ISL_780391
EPI_ISL_780392
EPI_ISL_780393
EPI_ISL_780394
EPI_ISL_780395
EPI_ISL_780396
EPI_ISL_780397
EPI_ISL_780398
EPI_ISL_780399
EPI_ISL_780400
EPI_ISL_780401
EPI_ISL_780402
EPI_ISL_780403
EPI_ISL_780404
EPI_ISL_780405
EPI_ISL_780406
EPI_ISL_780407
EPI_ISL_780408
EPI_ISL_780409
EPI_ISL_780410
EPI_ISL_783850

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