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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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Czech Republic

Number of isolates sequences available: 115

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
CzechRepublic/IAB20-006-16/2020 EPI_ISL_4265812020
CzechRepublic/IAB_1/2020 EPI_ISL_4268832020-03-27
CzechRepublic/IAB_4/2020 EPI_ISL_4268842020-03-27
CzechRepublic/IAB_8/2020 EPI_ISL_4268852020-03-27
CzechRepublic/IAB_9/2020 EPI_ISL_4268862020-03-28
CzechRepublic/IAB_10/2020 EPI_ISL_4268872020-03-31
CzechRepublic/IAB_12/2020 EPI_ISL_4268882020-03-31
CzechRepublic/IAB_14/2020 EPI_ISL_4268892020-04-02
CzechRepublic/IAB_15/2020 EPI_ISL_4268902020-03-26
CzechRepublic/IAB_16/2020 EPI_ISL_4268912020-03-26
CzechRepublic/IAB_17/2020 EPI_ISL_4268922020-03-27
CzechRepublic/IAB_18/2020 EPI_ISL_4268932020-03-27
CzechRepublic/IAB_20/2020 EPI_ISL_4268942020-03-27
CzechRepublic/IAB_21/2020 EPI_ISL_4268952020-03-27
CzechRepublic/IAB_22/2020 EPI_ISL_4268962020-03-28
CzechRepublic/IAB_23/2020 EPI_ISL_4268972020-03-29
EPI_ISL_491119Breclav
EPI_ISL_489708Brno
EPI_ISL_530350Brno
EPI_ISL_577623Central Bohemia Region
EPI_ISL_577629Central Bohemia Region
EPI_ISL_577630Central Bohemia Region
EPI_ISL_577631Central Bohemia Region
EPI_ISL_577632Central Bohemia Region
EPI_ISL_577633Central Bohemia Region
EPI_ISL_577634Central Bohemia Region
EPI_ISL_577635Central Bohemia Region
EPI_ISL_577636Central Bohemia Region
EPI_ISL_577637Central Bohemia Region
EPI_ISL_577638Central Bohemia Region
EPI_ISL_584078Central Bohemia Region
EPI_ISL_584081Central Bohemia Region
EPI_ISL_584082Central Bohemia Region
EPI_ISL_539776Central Bohemian Region
CzechRepublic/Seq3/2020 EPI_ISL_426356Central Czechia and Prague2020-03-21
CzechRepublic/Seq4/2020 EPI_ISL_426357Central Czechia and Prague2020-03-18
CzechRepublic/Seq5/2020 EPI_ISL_426358Central Czechia and Prague2020-03-19
CzechRepublic/Seq6/2020 EPI_ISL_426359Central Czechia and Prague2020-03-17
CzechRepublic/Seq7/2020 EPI_ISL_426360Central Czechia and Prague2020-03-18
EPI_ISL_489709Domažlice
EPI_ISL_476067Hranice na Moravě
EPI_ISL_471550Jihlava
EPI_ISL_545954Liberec Region
EPI_ISL_471528Litomerice-Brnay
EPI_ISL_490112Litovel
EPI_ISL_491092Litovel
EPI_ISL_471530Melnik
EPI_ISL_539778Moravian-Silesian Region
EPI_ISL_539779Moravian-Silesian Region
EPI_ISL_539782Moravian-Silesian Region
EPI_ISL_541332Moravian-Silesian Region
EPI_ISL_541333Moravian-Silesian Region
EPI_ISL_541334Moravian-Silesian Region
EPI_ISL_577624Northern Bohemia Region
EPI_ISL_577625Northern Bohemia Region
EPI_ISL_577626Northern Bohemia Region
EPI_ISL_577627Northern Bohemia Region
EPI_ISL_577628Northern Bohemia Region
EPI_ISL_584073Northern Bohemia Region
EPI_ISL_584074Northern Bohemia Region
EPI_ISL_584075Northern Bohemia Region
EPI_ISL_584076Northern Bohemia Region
EPI_ISL_584077Northern Bohemia Region
EPI_ISL_584080Northern Bohemia Region
EPI_ISL_539781Olomouc Region
EPI_ISL_545580Olomouc Region
EPI_ISL_545956Olomouc Region
EPI_ISL_545957Olomouc Region
EPI_ISL_541138Pardubice Region
EPI_ISL_530348Plzen
EPI_ISL_491094Plzeň
CzechRepublic/ChVir1630/2020 EPI_ISL_416742Prague2020-02
CzechRepublic/ChVir1912/2020 EPI_ISL_416743Prague2020-03
CzechRepublic/2741/2020 EPI_ISL_422636Prague2020-03-08
CzechRepublic/2556/2020 EPI_ISL_425228Prague2020-03-22
CzechRepublic/2122/2020 EPI_ISL_425229Prague2020-03-19
CzechRepublic/2282/2020 EPI_ISL_426051Prague2020-03-20
EPI_ISL_437519Prague
EPI_ISL_471547Prague
EPI_ISL_471553Prague
EPI_ISL_471555Prague
EPI_ISL_491117Prague
EPI_ISL_513314Prague
EPI_ISL_539780Prague
EPI_ISL_541082Prague
EPI_ISL_541335Prague
EPI_ISL_568577Prague
EPI_ISL_513511Prague-Miskovice
EPI_ISL_539493South Moravian Region
EPI_ISL_541336South Moravian Region
EPI_ISL_541337South Moravian Region
EPI_ISL_560408South Moravian Region
EPI_ISL_560409South Moravian Region
EPI_ISL_560410South Moravian Region
EPI_ISL_560411South Moravian Region
EPI_ISL_560412South Moravian Region
EPI_ISL_584079Southern Bohemia Region
CzechRepublic/951/2020 EPI_ISL_414477Usti nad Labem2020-03-01
EPI_ISL_491118Usti nad Labem
EPI_ISL_530349Usti nad Labem
EPI_ISL_539494Usti nad Labem
EPI_ISL_539777Usti nad Labem Region
EPI_ISL_471540Vysocina
EPI_ISL_471544Vysocina
EPI_ISL_434572Vysocina Region
EPI_ISL_491093Zlin
EPI_ISL_513512Zlin
EPI_ISL_530347Zlin
EPI_ISL_491095Ústí nad Labem
EPI_ISL_546436Ústí nad Labem Region
EPI_ISL_546935Ústí nad Labem Region
EPI_ISL_546936Ústí nad Labem Region
EPI_ISL_547966Ústí nad Labem Region
EPI_ISL_547967Ústí nad Labem Region
EPI_ISL_547968Ústí nad Labem Region

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