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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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Poland

Number of isolates sequences available: 117

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_437625Dolnoslakie
EPI_ISL_435723Dolnoslaskie
EPI_ISL_582031Dolnośląskie
EPI_ISL_509017Lodzkie
EPI_ISL_509018Lodzkie
EPI_ISL_509019Lodzkie
EPI_ISL_509020Lodzkie
EPI_ISL_509021Lodzkie
EPI_ISL_509022Lodzkie
EPI_ISL_509023Lodzkie
EPI_ISL_509024Lodzkie
EPI_ISL_509026Lodzkie
EPI_ISL_509028Lodzkie
EPI_ISL_509029Lodzkie
EPI_ISL_509031Lodzkie
EPI_ISL_509033Lodzkie
EPI_ISL_509035Lodzkie
EPI_ISL_509037Lodzkie
EPI_ISL_509038Lodzkie
EPI_ISL_509051Lodzkie
EPI_ISL_451971Malopolska
EPI_ISL_451972Malopolska
EPI_ISL_451973Malopolska
EPI_ISL_451974Malopolska
EPI_ISL_451975Malopolska
EPI_ISL_451976Malopolska
EPI_ISL_451977Malopolska
EPI_ISL_451978Malopolska
EPI_ISL_451979Malopolska
EPI_ISL_451980Malopolska
EPI_ISL_451981Malopolska
EPI_ISL_451982Malopolska
EPI_ISL_451983Malopolska
EPI_ISL_451984Malopolska
EPI_ISL_451985Malopolska
EPI_ISL_451986Malopolska
EPI_ISL_451987Malopolska
EPI_ISL_455441Malopolska
EPI_ISL_455443Malopolska
EPI_ISL_455448Malopolska
Poland/PL_P2/2020 EPI_ISL_428925Malopolskie2020-03-28
Poland/PL_P3/2020 EPI_ISL_428926Malopolskie2020-03-28
Poland/PL_P4/2020 EPI_ISL_428927Malopolskie2020-03-28
Poland/PL_P5/2020 EPI_ISL_428928Malopolskie2020-03-30
Poland/PL_P6/2020 EPI_ISL_428929Malopolskie2020-03-29
Poland/PL_P7/2020 EPI_ISL_428930Malopolskie2020-03-29
Poland/PL_P8/2020 EPI_ISL_428931Malopolskie2020-03-28
Poland/PL_P9/2020 EPI_ISL_428932Malopolskie2020-03-28
EPI_ISL_455440Mazowieckie
EPI_ISL_455442Mazowieckie
EPI_ISL_455445Mazowieckie
EPI_ISL_455446Mazowieckie
EPI_ISL_455447Mazowieckie
EPI_ISL_455450Mazowieckie
EPI_ISL_455451Mazowieckie
EPI_ISL_455452Mazowieckie
EPI_ISL_492066Mazowieckie
EPI_ISL_492067Mazowieckie
EPI_ISL_492068Mazowieckie
EPI_ISL_492069Mazowieckie
EPI_ISL_492070Mazowieckie
EPI_ISL_492071Mazowieckie
EPI_ISL_492072Mazowieckie
EPI_ISL_492073Mazowieckie
EPI_ISL_485399Opolskie
Poland/Pom1/2020 EPI_ISL_428209Pomerania2020-04-06
EPI_ISL_450746Pomerania
Poland/1104795/2020 EPI_ISL_428232Pomorskie2020-03-18
Poland/1105644/2020 EPI_ISL_428233Pomorskie2020-03-18
Poland/1105973/2020 EPI_ISL_428234Pomorskie2020-03-19
Poland/1107355/2020 EPI_ISL_428235Pomorskie2020-03-23
Poland/1109171/2020 EPI_ISL_428236Pomorskie2020-03-27
EPI_ISL_450525Pomorskie
EPI_ISL_450526Pomorskie
EPI_ISL_450527Pomorskie
EPI_ISL_450528Pomorskie
EPI_ISL_450529Pomorskie
EPI_ISL_450530Pomorskie
EPI_ISL_512296Pomorskie
EPI_ISL_512297Pomorskie
EPI_ISL_512298Pomorskie
EPI_ISL_512299Pomorskie
EPI_ISL_512300Pomorskie
EPI_ISL_512301Pomorskie
EPI_ISL_512302Pomorskie
EPI_ISL_512303Pomorskie
EPI_ISL_451644Pomorze
EPI_ISL_451645Pomorze
EPI_ISL_451646Pomorze
EPI_ISL_451647Pomorze
EPI_ISL_451648Pomorze
EPI_ISL_451649Pomorze
EPI_ISL_451650Pomorze
EPI_ISL_451651Pomorze
EPI_ISL_451652Pomorze
EPI_ISL_451653Pomorze
EPI_ISL_451654Pomorze
EPI_ISL_451655Slask
EPI_ISL_451656Slask
EPI_ISL_451657Slask
EPI_ISL_451658Slask
EPI_ISL_451659Slask
EPI_ISL_451660Slask
EPI_ISL_451661Slask
EPI_ISL_451662Slask
EPI_ISL_451663Slask
EPI_ISL_451664Slask
EPI_ISL_455444Warminsko-Mazurskie
EPI_ISL_455453Warminsko-Mazurskie
EPI_ISL_455449Wielkopolska
EPI_ISL_450294Wielkopolskie
EPI_ISL_450295Wielkopolskie
EPI_ISL_450338Wielkopolskie
EPI_ISL_462480Wielkopolskie
EPI_ISL_582032Wielkopolskie
Poland/PL_P1/2020 EPI_ISL_416488Zielonogorskie2020-03-03
EPI_ISL_485400Łódzkie

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