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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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Slovakia

Number of isolates sequences available: 25

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
Slovakia/SK-BMC2/2020 EPI_ISL_417878Bratislava2020-03-07
EPI_ISL_516988Bratislava
EPI_ISL_516989Bratislava
EPI_ISL_572329Bratislava
EPI_ISL_577736Bratislava
EPI_ISL_577740Bratislava
EPI_ISL_577741Bratislava
EPI_ISL_577742Bratislava
EPI_ISL_583484Bratislava
EPI_ISL_583487Bratislava
EPI_ISL_583488Bratislava
EPI_ISL_583482Jatov
EPI_ISL_583483Kamenicna
Slovakia/SK-BMC5/2020 EPI_ISL_417879Kosice2020-03-06
Slovakia/SK-BMC1/2020 EPI_ISL_417877Kostoliste2020-03-06
EPI_ISL_583489Levice
Slovakia/SK-BMC6/2020 EPI_ISL_417880Martin2020-03-08
EPI_ISL_577734Martincek
EPI_ISL_577738Pezinok
EPI_ISL_577739Pezinok
EPI_ISL_583485Surany
EPI_ISL_583486Surany
EPI_ISL_583481Tvrdosovce
EPI_ISL_577735Zehra
EPI_ISL_577737Zehra

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