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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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Czech Republic

Number of isolates sequences available: 483

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_626620
EPI_ISL_626621
EPI_ISL_660555
EPI_ISL_660598
EPI_ISL_693669
EPI_ISL_693675
EPI_ISL_693683
EPI_ISL_491119Breclav
EPI_ISL_489708Brno
EPI_ISL_530350Brno
EPI_ISL_779711Brno
EPI_ISL_889309Brno
EPI_ISL_889310Brno
EPI_ISL_889311Brno
EPI_ISL_889312Brno
EPI_ISL_889313Brno
EPI_ISL_889314Brno
EPI_ISL_889315Brno
EPI_ISL_889316Brno
EPI_ISL_889317Brno
EPI_ISL_889318Brno
EPI_ISL_889319Brno
EPI_ISL_889320Brno
EPI_ISL_889321Brno
EPI_ISL_889322Brno
EPI_ISL_889323Brno
EPI_ISL_889324Brno
EPI_ISL_889325Brno
EPI_ISL_889326Brno
EPI_ISL_889327Brno
EPI_ISL_889331Brno
EPI_ISL_889332Brno
EPI_ISL_889333Brno
EPI_ISL_889334Brno
EPI_ISL_889335Brno
EPI_ISL_889336Brno
EPI_ISL_889337Brno
EPI_ISL_889338Brno
EPI_ISL_889339Brno
EPI_ISL_889340Brno
EPI_ISL_889341Brno
EPI_ISL_889342Brno
EPI_ISL_889343Brno
EPI_ISL_889344Brno
EPI_ISL_889345Brno
EPI_ISL_889346Brno
EPI_ISL_889347Brno
EPI_ISL_889348Brno
EPI_ISL_889349Brno
EPI_ISL_889350Brno
EPI_ISL_889351Brno
EPI_ISL_889352Brno
EPI_ISL_889353Brno
EPI_ISL_889354Brno
EPI_ISL_889355Brno
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
EPI_ISL_626571Central Bohemian Region
EPI_ISL_626575Central Bohemian Region
EPI_ISL_626576Central Bohemian Region
EPI_ISL_626604Central Bohemian Region
EPI_ISL_626606Central Bohemian Region
EPI_ISL_626608Central Bohemian Region
EPI_ISL_626612Central Bohemian Region
EPI_ISL_626615Central Bohemian Region
EPI_ISL_626616Central Bohemian Region
EPI_ISL_626619Central Bohemian Region
EPI_ISL_660556Central Bohemian Region
EPI_ISL_660566Central Bohemian Region
EPI_ISL_660569Central Bohemian Region
EPI_ISL_660574Central Bohemian Region
EPI_ISL_660575Central Bohemian Region
EPI_ISL_660576Central Bohemian Region
EPI_ISL_660577Central Bohemian Region
EPI_ISL_660578Central Bohemian Region
EPI_ISL_660579Central Bohemian Region
EPI_ISL_660580Central Bohemian Region
EPI_ISL_660581Central Bohemian Region
EPI_ISL_660582Central Bohemian Region
EPI_ISL_693661Central Bohemian Region
EPI_ISL_693663Central Bohemian Region
EPI_ISL_693670Central Bohemian Region
EPI_ISL_693674Central Bohemian Region
EPI_ISL_693677Central Bohemian Region
EPI_ISL_693686Central Bohemian Region
EPI_ISL_736999Central Bohemian Region
EPI_ISL_737003Central Bohemian Region
EPI_ISL_737004Central Bohemian Region
EPI_ISL_737005Central Bohemian Region
EPI_ISL_737006Central Bohemian Region
EPI_ISL_737008Central Bohemian Region
EPI_ISL_737009Central Bohemian Region
EPI_ISL_737010Central Bohemian Region
EPI_ISL_737017Central Bohemian Region
EPI_ISL_737019Central Bohemian Region
EPI_ISL_737025Central Bohemian Region
EPI_ISL_737027Central Bohemian Region
EPI_ISL_737032Central Bohemian Region
EPI_ISL_792689Central Bohemian Region
EPI_ISL_792691Central Bohemian Region
EPI_ISL_792693Central Bohemian Region
EPI_ISL_792697Central Bohemian Region
EPI_ISL_850663Central Bohemian Region
EPI_ISL_850675Central Bohemian Region
EPI_ISL_850676Central Bohemian Region
EPI_ISL_882951Central 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_660583Hradec Králové Region
EPI_ISL_693664Hradec Králové Region
EPI_ISL_792707Hradec Králové Region
EPI_ISL_850677Hradec Králové Region
EPI_ISL_850681Hradec Králové Region
EPI_ISL_850682Hradec Králové Region
EPI_ISL_882943Hradec Králové Region
EPI_ISL_476067Hranice na Moravě
EPI_ISL_471550Jihlava
EPI_ISL_815258Klatovy
EPI_ISL_545954Liberec Region
EPI_ISL_792685Liberec Region
EPI_ISL_850666Liberec 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_626593Moravian-Silesian Region
EPI_ISL_693671Moravian-Silesian Region
EPI_ISL_850668Moravian-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_737020Olomouc
EPI_ISL_889371Olomouc
EPI_ISL_889372Olomouc
EPI_ISL_889373Olomouc
EPI_ISL_889374Olomouc
EPI_ISL_889375Olomouc
EPI_ISL_889376Olomouc
EPI_ISL_889377Olomouc
EPI_ISL_889378Olomouc
EPI_ISL_889379Olomouc
EPI_ISL_889380Olomouc
EPI_ISL_889381Olomouc
EPI_ISL_889382Olomouc
EPI_ISL_889383Olomouc
EPI_ISL_889384Olomouc
EPI_ISL_889385Olomouc
EPI_ISL_889386Olomouc
EPI_ISL_889387Olomouc
EPI_ISL_889388Olomouc
EPI_ISL_889389Olomouc
EPI_ISL_889390Olomouc
EPI_ISL_889391Olomouc
EPI_ISL_889392Olomouc
EPI_ISL_889393Olomouc
EPI_ISL_889394Olomouc
EPI_ISL_889395Olomouc
EPI_ISL_889396Olomouc
EPI_ISL_889397Olomouc
EPI_ISL_889398Olomouc
EPI_ISL_889399Olomouc
EPI_ISL_889400Olomouc
EPI_ISL_889401Olomouc
EPI_ISL_889402Olomouc
EPI_ISL_889403Olomouc
EPI_ISL_889404Olomouc
EPI_ISL_889405Olomouc
EPI_ISL_889406Olomouc
EPI_ISL_889407Olomouc
EPI_ISL_889408Olomouc
EPI_ISL_889409Olomouc
EPI_ISL_889410Olomouc
EPI_ISL_889411Olomouc
EPI_ISL_889412Olomouc
EPI_ISL_889413Olomouc
EPI_ISL_889414Olomouc
EPI_ISL_889415Olomouc
EPI_ISL_889416Olomouc
EPI_ISL_889417Olomouc
EPI_ISL_889418Olomouc
EPI_ISL_889419Olomouc
EPI_ISL_889420Olomouc
EPI_ISL_889421Olomouc
EPI_ISL_889422Olomouc
EPI_ISL_889423Olomouc
EPI_ISL_889424Olomouc
EPI_ISL_889425Olomouc
EPI_ISL_889426Olomouc
EPI_ISL_889427Olomouc
EPI_ISL_889428Olomouc
EPI_ISL_889429Olomouc
EPI_ISL_889430Olomouc
EPI_ISL_889431Olomouc
EPI_ISL_889432Olomouc
EPI_ISL_889433Olomouc
EPI_ISL_889434Olomouc
EPI_ISL_889435Olomouc
EPI_ISL_889436Olomouc
EPI_ISL_889437Olomouc
EPI_ISL_889438Olomouc
EPI_ISL_889439Olomouc
EPI_ISL_891218Olomouc
EPI_ISL_539781Olomouc Region
EPI_ISL_545580Olomouc Region
EPI_ISL_545956Olomouc Region
EPI_ISL_545957Olomouc Region
EPI_ISL_541138Pardubice Region
EPI_ISL_889328Pilsen
EPI_ISL_889329Pilsen
EPI_ISL_889330Pilsen
EPI_ISL_815259Pivo
EPI_ISL_530348Plzen
EPI_ISL_626622Plzen
EPI_ISL_626605Plzen Region
EPI_ISL_491094Plzeň
EPI_ISL_792684Plzeň Region
EPI_ISL_882948Plzeň Region
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_626572Prague
EPI_ISL_626573Prague
EPI_ISL_626577Prague
EPI_ISL_626578Prague
EPI_ISL_626579Prague
EPI_ISL_626580Prague
EPI_ISL_626581Prague
EPI_ISL_626582Prague
EPI_ISL_626583Prague
EPI_ISL_626584Prague
EPI_ISL_626585Prague
EPI_ISL_626586Prague
EPI_ISL_626587Prague
EPI_ISL_626588Prague
EPI_ISL_626589Prague
EPI_ISL_626590Prague
EPI_ISL_626592Prague
EPI_ISL_626594Prague
EPI_ISL_626595Prague
EPI_ISL_626596Prague
EPI_ISL_626603Prague
EPI_ISL_626607Prague
EPI_ISL_626609Prague
EPI_ISL_626610Prague
EPI_ISL_626611Prague
EPI_ISL_626613Prague
EPI_ISL_626617Prague
EPI_ISL_626618Prague
EPI_ISL_626623Prague
EPI_ISL_626624Prague
EPI_ISL_626625Prague
EPI_ISL_660553Prague
EPI_ISL_660557Prague
EPI_ISL_660559Prague
EPI_ISL_660560Prague
EPI_ISL_660561Prague
EPI_ISL_660562Prague
EPI_ISL_660563Prague
EPI_ISL_660564Prague
EPI_ISL_660567Prague
EPI_ISL_660570Prague
EPI_ISL_660571Prague
EPI_ISL_660572Prague
EPI_ISL_660573Prague
EPI_ISL_660584Prague
EPI_ISL_660585Prague
EPI_ISL_660586Prague
EPI_ISL_660587Prague
EPI_ISL_660588Prague
EPI_ISL_660589Prague
EPI_ISL_660590Prague
EPI_ISL_660591Prague
EPI_ISL_660592Prague
EPI_ISL_660593Prague
EPI_ISL_660594Prague
EPI_ISL_660595Prague
EPI_ISL_693662Prague
EPI_ISL_693665Prague
EPI_ISL_693666Prague
EPI_ISL_693667Prague
EPI_ISL_693668Prague
EPI_ISL_693672Prague
EPI_ISL_693673Prague
EPI_ISL_693676Prague
EPI_ISL_693679Prague
EPI_ISL_693680Prague
EPI_ISL_693681Prague
EPI_ISL_693684Prague
EPI_ISL_693685Prague
EPI_ISL_693687Prague
EPI_ISL_736998Prague
EPI_ISL_737000Prague
EPI_ISL_737001Prague
EPI_ISL_737002Prague
EPI_ISL_737007Prague
EPI_ISL_737011Prague
EPI_ISL_737012Prague
EPI_ISL_737013Prague
EPI_ISL_737018Prague
EPI_ISL_737021Prague
EPI_ISL_737022Prague
EPI_ISL_737023Prague
EPI_ISL_737024Prague
EPI_ISL_737026Prague
EPI_ISL_737028Prague
EPI_ISL_737029Prague
EPI_ISL_737030Prague
EPI_ISL_737031Prague
EPI_ISL_737033Prague
EPI_ISL_792687Prague
EPI_ISL_792690Prague
EPI_ISL_792692Prague
EPI_ISL_792696Prague
EPI_ISL_792698Prague
EPI_ISL_792699Prague
EPI_ISL_792700Prague
EPI_ISL_792701Prague
EPI_ISL_792702Prague
EPI_ISL_792703Prague
EPI_ISL_792704Prague
EPI_ISL_792705Prague
EPI_ISL_792706Prague
EPI_ISL_850664Prague
EPI_ISL_850665Prague
EPI_ISL_850671Prague
EPI_ISL_850672Prague
EPI_ISL_850674Prague
EPI_ISL_850678Prague
EPI_ISL_850679Prague
EPI_ISL_850680Prague
EPI_ISL_850683Prague
EPI_ISL_850684Prague
EPI_ISL_850685Prague
EPI_ISL_850686Prague
EPI_ISL_850687Prague
EPI_ISL_850688Prague
EPI_ISL_882944Prague
EPI_ISL_882945Prague
EPI_ISL_882946Prague
EPI_ISL_882947Prague
EPI_ISL_882949Prague
EPI_ISL_882950Prague
EPI_ISL_882952Prague
EPI_ISL_882953Prague
EPI_ISL_882954Prague
EPI_ISL_882955Prague
EPI_ISL_889307Prague
EPI_ISL_889308Prague
EPI_ISL_889356Prague
EPI_ISL_889357Prague
EPI_ISL_889358Prague
EPI_ISL_889359Prague
EPI_ISL_889360Prague
EPI_ISL_889361Prague
EPI_ISL_889362Prague
EPI_ISL_889363Prague
EPI_ISL_889364Prague
EPI_ISL_889365Prague
EPI_ISL_889366Prague
EPI_ISL_889367Prague
EPI_ISL_889368Prague
EPI_ISL_889369Prague
EPI_ISL_889370Prague
EPI_ISL_891217Prague
EPI_ISL_513511Prague-Miskovice
EPI_ISL_626570South Bohemian Region
EPI_ISL_626574South Bohemian Region
EPI_ISL_626591South Bohemian Region
EPI_ISL_626597South Bohemian Region
EPI_ISL_626598South Bohemian Region
EPI_ISL_626599South Bohemian Region
EPI_ISL_626600South Bohemian Region
EPI_ISL_626601South Bohemian Region
EPI_ISL_626602South Bohemian Region
EPI_ISL_660565South Bohemian Region
EPI_ISL_660568South Bohemian Region
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_660554South Moravian Region
EPI_ISL_660558South Moravian Region
EPI_ISL_660596South Moravian Region
EPI_ISL_660597South Moravian Region
EPI_ISL_693660South Moravian Region
EPI_ISL_737016South 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_850673Zlín Region
EPI_ISL_792686unknown
EPI_ISL_491095Ústí nad Labem
EPI_ISL_792688Ústí nad Labem
EPI_ISL_850667Ústí 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
EPI_ISL_626614Ústí nad Labem Region
EPI_ISL_660599Ústí nad Labem Region
EPI_ISL_693678Ústí nad Labem Region
EPI_ISL_693682Ústí nad Labem Region
EPI_ISL_737014Ústí nad Labem Region
EPI_ISL_737015Ústí nad Labem Region
EPI_ISL_792694Ústí nad Labem Region
EPI_ISL_792695Ústí nad Labem Region
EPI_ISL_850669Ústí nad Labem Region
EPI_ISL_850670Ústí nad Labem Region

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