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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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Croatia

Number of isolates sequences available: 22

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_454588Dubrovnik
Croatia/OY-S1/2020 EPI_ISL_429659Istria2020-03
Croatia/8U-S17/2020 EPI_ISL_429663Istria2020-03
Croatia/AU-S10/2020 EPI_ISL_429705Istria2020-03
Croatia/LG-S2/2020 EPI_ISL_429792Istria2020-03
Croatia/17-S7/2020 EPI_ISL_429802Istria2020-03
Croatia/I7-S21/2020 EPI_ISL_429803Istria2020-03
Croatia/7R-S8/2020 EPI_ISL_429805Istria2020-03
EPI_ISL_454574Istria
EPI_ISL_454605Istria
EPI_ISL_454606Istria
EPI_ISL_455566Istria
EPI_ISL_455567Istria
EPI_ISL_468591Istria
EPI_ISL_468656Istria
EPI_ISL_454602Koprivnica
EPI_ISL_454578Osijek
EPI_ISL_454595Pula
EPI_ISL_454581Split
EPI_ISL_454583Split
EPI_ISL_454592Varazdin
EPI_ISL_451934Varaždin County

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