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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 31 07:00:30 2021 (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: 122

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_875532Banovce nad Bebravou
EPI_ISL_831674Banska Bystrica
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_717975Bratislava
EPI_ISL_718250Bratislava
EPI_ISL_718251Bratislava
EPI_ISL_718252Bratislava
EPI_ISL_718253Bratislava
EPI_ISL_718254Bratislava
EPI_ISL_718255Bratislava
EPI_ISL_718256Bratislava
EPI_ISL_718259Bratislava
EPI_ISL_779403Bratislava
EPI_ISL_788982Bratislava
EPI_ISL_788983Bratislava
EPI_ISL_788984Bratislava
EPI_ISL_788986Bratislava
EPI_ISL_788987Bratislava
EPI_ISL_788988Bratislava
EPI_ISL_831666Bratislava
EPI_ISL_831669Bratislava
EPI_ISL_831670Bratislava
EPI_ISL_831671Bratislava
EPI_ISL_831673Bratislava
EPI_ISL_875520Bratislava
EPI_ISL_875521Bratislava
EPI_ISL_875528Bratislava
EPI_ISL_903979Dolný Kubín
EPI_ISL_791990Doľany
EPI_ISL_831663Hurbanovo
EPI_ISL_831664Hurbanovo
EPI_ISL_831665Hurbanovo
EPI_ISL_875539Ilava
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_788985Miloslavov
EPI_ISL_718257Nitra
EPI_ISL_718258Nitra
EPI_ISL_831667Nitra
EPI_ISL_831668Nitra
EPI_ISL_831672Nitra
EPI_ISL_875522Nitra
EPI_ISL_875523Nitra
EPI_ISL_875524Nitra
EPI_ISL_875525Nitra
EPI_ISL_875526Nitra
EPI_ISL_875527Nitra
EPI_ISL_875530Nitra
EPI_ISL_875533Nove Mesto nad Vahom
EPI_ISL_875534Nove Mesto nad Vahom
EPI_ISL_718260Nove Zamky
EPI_ISL_788979Nove Zamky
EPI_ISL_788980Nove Zamky
EPI_ISL_788981Nove Zamky
EPI_ISL_875531Nove Zamky
EPI_ISL_875535Nove Zamky
EPI_ISL_875536Nove Zamky
EPI_ISL_875537Nove Zamky
EPI_ISL_875538Oravska Lesna
EPI_ISL_875516Partizanske
EPI_ISL_779651Pavlovce nad Uhom
EPI_ISL_779652Pavlovce nad Uhom
EPI_ISL_779653Pavlovce nad Uhom
EPI_ISL_779654Pavlovce nad Uhom
EPI_ISL_779655Pavlovce nad Uhom
EPI_ISL_779656Pavlovce nad Uhom
EPI_ISL_779657Pavlovce nad Uhom
EPI_ISL_779658Pavlovce nad Uhom
EPI_ISL_779659Pavlovce nad Uhom
EPI_ISL_779660Pavlovce nad Uhom
EPI_ISL_577738Pezinok
EPI_ISL_577739Pezinok
EPI_ISL_875517Prievidza
EPI_ISL_875518Prievidza
EPI_ISL_875519Prievidza
EPI_ISL_583485Surany
EPI_ISL_583486Surany
EPI_ISL_875529Trencin
EPI_ISL_903980Trenčín
EPI_ISL_903981Trenčín
EPI_ISL_903982Trenčín
EPI_ISL_903983Trenčín
EPI_ISL_903984Trenčín
EPI_ISL_903985Trenčín
EPI_ISL_903986Trenčín
EPI_ISL_903987Trenčín
EPI_ISL_903988Trenčín
EPI_ISL_903989Trenčín
EPI_ISL_903990Trenčín
EPI_ISL_903991Trenčín
EPI_ISL_903992Trenčín
EPI_ISL_903993Trenčín
EPI_ISL_903994Trenčín
EPI_ISL_903995Trenčín
EPI_ISL_903996Trenčín
EPI_ISL_903997Trenčín
EPI_ISL_903998Trenčín
EPI_ISL_903999Trenčín
EPI_ISL_904000Trenčín
EPI_ISL_904001Trenčín
EPI_ISL_904002Trenčín
EPI_ISL_904003Trenčín
EPI_ISL_831676Trstena
EPI_ISL_583481Tvrdosovce
EPI_ISL_577735Zehra
EPI_ISL_577737Zehra
EPI_ISL_831675Zelovce

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