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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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Serbia

Number of isolates sequences available: 47

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_450415The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450443The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_454419The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_482744
EPI_ISL_514425
EPI_ISL_514426
EPI_ISL_514427
EPI_ISL_514428
EPI_ISL_514429
EPI_ISL_514430
EPI_ISL_514431
EPI_ISL_454795Cacak
EPI_ISL_455480Cacak
EPI_ISL_582525Cuprija
EPI_ISL_541651Kosovska Mitrovica
EPI_ISL_541655Kosovska Mitrovica
EPI_ISL_541657Kosovska Mitrovica
EPI_ISL_541658Kosovska Mitrovica
EPI_ISL_582530Kosovska Mitrovica
EPI_ISL_582524Kragujevac
EPI_ISL_437435Kraljevo
EPI_ISL_445086Kraljevo
EPI_ISL_445087Kraljevo
EPI_ISL_462435Kraljevo
EPI_ISL_462437Kraljevo
EPI_ISL_462438Kraljevo
EPI_ISL_541656Kraljevo
EPI_ISL_541660Kraljevo
EPI_ISL_541662Kraljevo
EPI_ISL_582531Kraljevo
EPI_ISL_582532Kraljevo
EPI_ISL_582533Kraljevo
EPI_ISL_582534Kraljevo
EPI_ISL_582526Krusevac
EPI_ISL_582527Krusevac
EPI_ISL_582528Krusevac
EPI_ISL_582529Krusevac
EPI_ISL_437436Novi Pazar
EPI_ISL_541649Novi Pazar
EPI_ISL_541650Novi Pazar
EPI_ISL_541652Novi Pazar
EPI_ISL_541653Novi Pazar
EPI_ISL_541654Novi Pazar
EPI_ISL_541659Novi Pazar
EPI_ISL_541661Novi Pazar
EPI_ISL_462434Novi Sad
EPI_ISL_462436Uzice

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