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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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Ukraine

Number of isolates sequences available: 58

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_512597
EPI_ISL_512598
EPI_ISL_512599
EPI_ISL_512600
EPI_ISL_512601
EPI_ISL_512602
EPI_ISL_512603
EPI_ISL_512604
EPI_ISL_512605
EPI_ISL_512606
EPI_ISL_512607
EPI_ISL_512608
EPI_ISL_512609
EPI_ISL_512610
EPI_ISL_512611
EPI_ISL_512612
EPI_ISL_512613
EPI_ISL_512614
EPI_ISL_512615
EPI_ISL_512616
EPI_ISL_512617
EPI_ISL_512618
EPI_ISL_512619
EPI_ISL_512620
EPI_ISL_512621
EPI_ISL_512622
EPI_ISL_512623
EPI_ISL_512624
EPI_ISL_512625
EPI_ISL_512626
EPI_ISL_512627
EPI_ISL_512628
EPI_ISL_512629
EPI_ISL_512630
EPI_ISL_512631
EPI_ISL_512632
EPI_ISL_512633
EPI_ISL_512634
EPI_ISL_512635
EPI_ISL_512636
EPI_ISL_512637
EPI_ISL_512638
EPI_ISL_512639
EPI_ISL_512640
EPI_ISL_512641
EPI_ISL_512642
EPI_ISL_512643
EPI_ISL_512644
EPI_ISL_512810
EPI_ISL_576147Ivano-Frankivsk
EPI_ISL_576146Kharkiv
EPI_ISL_582509Kharkiv
EPI_ISL_582510Kharkiv
EPI_ISL_582511Kharkiv
EPI_ISL_582512Kharkiv
EPI_ISL_582513Kharkiv
EPI_ISL_576148Kyiv
EPI_ISL_576149Lutsk

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