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

Number of isolates sequences available: 37

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_483542
EPI_ISL_483543
EPI_ISL_483544
EPI_ISL_483545
EPI_ISL_483546
EPI_ISL_483547
EPI_ISL_483548
EPI_ISL_483549
EPI_ISL_483550
EPI_ISL_483551
EPI_ISL_483552
EPI_ISL_483553
EPI_ISL_483554
EPI_ISL_483555
EPI_ISL_483556
EPI_ISL_483557
EPI_ISL_483558
EPI_ISL_483559
EPI_ISL_483560
EPI_ISL_483561
EPI_ISL_483562
EPI_ISL_483563
EPI_ISL_483564
EPI_ISL_483565
EPI_ISL_483638
EPI_ISL_483639
EPI_ISL_483640
EPI_ISL_486887
EPI_ISL_486888
EPI_ISL_486889
EPI_ISL_487270
EPI_ISL_487272
EPI_ISL_487273
EPI_ISL_487274
EPI_ISL_485401Manama
EPI_ISL_510528Manama
EPI_ISL_510531Manama

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