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

Update:
Sun Jan 10 05:32:46 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).
Go to homeCzech Republic
Number of isolates sequences available:
283
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 ID | Region | Collection date | 2019-nCoV_N1 | 2019-nCoV_N2 | 2019-nCoV_N3 | E-Sarbeco | RdRP |
CzechRepublic/IAB20-006-16/2020 EPI_ISL_426581 | | 2020 | | | | | |
CzechRepublic/IAB_1/2020 EPI_ISL_426883 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_4/2020 EPI_ISL_426884 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_8/2020 EPI_ISL_426885 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_9/2020 EPI_ISL_426886 | | 2020-03-28 | | | | | |
CzechRepublic/IAB_10/2020 EPI_ISL_426887 | | 2020-03-31 | | | | | |
CzechRepublic/IAB_12/2020 EPI_ISL_426888 | | 2020-03-31 | | | | | |
CzechRepublic/IAB_14/2020 EPI_ISL_426889 | | 2020-04-02 | | | | | |
CzechRepublic/IAB_15/2020 EPI_ISL_426890 | | 2020-03-26 | | | | | |
CzechRepublic/IAB_16/2020 EPI_ISL_426891 | | 2020-03-26 | | | | | |
CzechRepublic/IAB_17/2020 EPI_ISL_426892 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_18/2020 EPI_ISL_426893 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_20/2020 EPI_ISL_426894 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_21/2020 EPI_ISL_426895 | | 2020-03-27 | | | | | |
CzechRepublic/IAB_22/2020 EPI_ISL_426896 | | 2020-03-28 | | | | | |
CzechRepublic/IAB_23/2020 EPI_ISL_426897 | | 2020-03-29 | | | | | |
EPI_ISL_626620 | | | | | | | |
EPI_ISL_626621 | | | | | | | |
EPI_ISL_660555 | | | | | | | |
EPI_ISL_660598 | | | | | | | |
EPI_ISL_693669 | | | | | | | |
EPI_ISL_693675 | | | | | | | |
EPI_ISL_693683 | | | | | | | |
EPI_ISL_491119 | Breclav | | | | | | |
EPI_ISL_489708 | Brno | | | | | | |
EPI_ISL_530350 | Brno | | | | | | |
EPI_ISL_779711 | Brno | | | | | | |
EPI_ISL_577623 | Central Bohemia Region | | | | | | |
EPI_ISL_577629 | Central Bohemia Region | | | | | | |
EPI_ISL_577630 | Central Bohemia Region | | | | | | |
EPI_ISL_577631 | Central Bohemia Region | | | | | | |
EPI_ISL_577632 | Central Bohemia Region | | | | | | |
EPI_ISL_577633 | Central Bohemia Region | | | | | | |
EPI_ISL_577634 | Central Bohemia Region | | | | | | |
EPI_ISL_577635 | Central Bohemia Region | | | | | | |
EPI_ISL_577636 | Central Bohemia Region | | | | | | |
EPI_ISL_577637 | Central Bohemia Region | | | | | | |
EPI_ISL_577638 | Central Bohemia Region | | | | | | |
EPI_ISL_584078 | Central Bohemia Region | | | | | | |
EPI_ISL_584081 | Central Bohemia Region | | | | | | |
EPI_ISL_584082 | Central Bohemia Region | | | | | | |
EPI_ISL_539776 | Central Bohemian Region | | | | | | |
EPI_ISL_626571 | Central Bohemian Region | | | | | | |
EPI_ISL_626575 | Central Bohemian Region | | | | | | |
EPI_ISL_626576 | Central Bohemian Region | | | | | | |
EPI_ISL_626604 | Central Bohemian Region | | | | | | |
EPI_ISL_626606 | Central Bohemian Region | | | | | | |
EPI_ISL_626608 | Central Bohemian Region | | | | | | |
EPI_ISL_626612 | Central Bohemian Region | | | | | | |
EPI_ISL_626615 | Central Bohemian Region | | | | | | |
EPI_ISL_626616 | Central Bohemian Region | | | | | | |
EPI_ISL_626619 | Central Bohemian Region | | | | | | |
EPI_ISL_660556 | Central Bohemian Region | | | | | | |
EPI_ISL_660566 | Central Bohemian Region | | | | | | |
EPI_ISL_660569 | Central Bohemian Region | | | | | | |
EPI_ISL_660574 | Central Bohemian Region | | | | | | |
EPI_ISL_660575 | Central Bohemian Region | | | | | | |
EPI_ISL_660576 | Central Bohemian Region | | | | | | |
EPI_ISL_660577 | Central Bohemian Region | | | | | | |
EPI_ISL_660578 | Central Bohemian Region | | | | | | |
EPI_ISL_660579 | Central Bohemian Region | | | | | | |
EPI_ISL_660580 | Central Bohemian Region | | | | | | |
EPI_ISL_660581 | Central Bohemian Region | | | | | | |
EPI_ISL_660582 | Central Bohemian Region | | | | | | |
EPI_ISL_693661 | Central Bohemian Region | | | | | | |
EPI_ISL_693663 | Central Bohemian Region | | | | | | |
EPI_ISL_693670 | Central Bohemian Region | | | | | | |
EPI_ISL_693674 | Central Bohemian Region | | | | | | |
EPI_ISL_693677 | Central Bohemian Region | | | | | | |
EPI_ISL_693686 | Central Bohemian Region | | | | | | |
EPI_ISL_736999 | Central Bohemian Region | | | | | | |
EPI_ISL_737003 | Central Bohemian Region | | | | | | |
EPI_ISL_737004 | Central Bohemian Region | | | | | | |
EPI_ISL_737005 | Central Bohemian Region | | | | | | |
EPI_ISL_737006 | Central Bohemian Region | | | | | | |
EPI_ISL_737008 | Central Bohemian Region | | | | | | |
EPI_ISL_737009 | Central Bohemian Region | | | | | | |
EPI_ISL_737010 | Central Bohemian Region | | | | | | |
EPI_ISL_737017 | Central Bohemian Region | | | | | | |
EPI_ISL_737019 | Central Bohemian Region | | | | | | |
EPI_ISL_737025 | Central Bohemian Region | | | | | | |
EPI_ISL_737027 | Central Bohemian Region | | | | | | |
EPI_ISL_737032 | Central Bohemian Region | | | | | | |
CzechRepublic/Seq3/2020 EPI_ISL_426356 | Central Czechia and Prague | 2020-03-21 | | | | | |
CzechRepublic/Seq4/2020 EPI_ISL_426357 | Central Czechia and Prague | 2020-03-18 | | | | | |
CzechRepublic/Seq5/2020 EPI_ISL_426358 | Central Czechia and Prague | 2020-03-19 | | | | | |
CzechRepublic/Seq6/2020 EPI_ISL_426359 | Central Czechia and Prague | 2020-03-17 | | | | | |
CzechRepublic/Seq7/2020 EPI_ISL_426360 | Central Czechia and Prague | 2020-03-18 | | | | | |
EPI_ISL_489709 | Domažlice | | | | | | |
EPI_ISL_660583 | Hradec Králové Region | | | | | | |
EPI_ISL_693664 | Hradec Králové Region | | | | | | |
EPI_ISL_476067 | Hranice na Moravě | | | | | | |
EPI_ISL_471550 | Jihlava | | | | | | |
EPI_ISL_545954 | Liberec Region | | | | | | |
EPI_ISL_471528 | Litomerice-Brnay | | | | | | |
EPI_ISL_490112 | Litovel | | | | | | |
EPI_ISL_491092 | Litovel | | | | | | |
EPI_ISL_471530 | Melnik | | | | | | |
EPI_ISL_539778 | Moravian-Silesian Region | | | | | | |
EPI_ISL_539779 | Moravian-Silesian Region | | | | | | |
EPI_ISL_539782 | Moravian-Silesian Region | | | | | | |
EPI_ISL_541332 | Moravian-Silesian Region | | | | | | |
EPI_ISL_541333 | Moravian-Silesian Region | | | | | | |
EPI_ISL_541334 | Moravian-Silesian Region | | | | | | |
EPI_ISL_626593 | Moravian-Silesian Region | | | | | | |
EPI_ISL_693671 | Moravian-Silesian Region | | | | | | |
EPI_ISL_577624 | Northern Bohemia Region | | | | | | |
EPI_ISL_577625 | Northern Bohemia Region | | | | | | |
EPI_ISL_577626 | Northern Bohemia Region | | | | | | |
EPI_ISL_577627 | Northern Bohemia Region | | | | | | |
EPI_ISL_577628 | Northern Bohemia Region | | | | | | |
EPI_ISL_584073 | Northern Bohemia Region | | | | | | |
EPI_ISL_584074 | Northern Bohemia Region | | | | | | |
EPI_ISL_584075 | Northern Bohemia Region | | | | | | |
EPI_ISL_584076 | Northern Bohemia Region | | | | | | |
EPI_ISL_584077 | Northern Bohemia Region | | | | | | |
EPI_ISL_584080 | Northern Bohemia Region | | | | | | |
EPI_ISL_737020 | Olomouc | | | | | | |
EPI_ISL_539781 | Olomouc Region | | | | | | |
EPI_ISL_545580 | Olomouc Region | | | | | | |
EPI_ISL_545956 | Olomouc Region | | | | | | |
EPI_ISL_545957 | Olomouc Region | | | | | | |
EPI_ISL_541138 | Pardubice Region | | | | | | |
EPI_ISL_530348 | Plzen | | | | | | |
EPI_ISL_626622 | Plzen | | | | | | |
EPI_ISL_626605 | Plzen Region | | | | | | |
EPI_ISL_491094 | Plzeň | | | | | | |
CzechRepublic/ChVir1630/2020 EPI_ISL_416742 | Prague | 2020-02 | | | | | |
CzechRepublic/ChVir1912/2020 EPI_ISL_416743 | Prague | 2020-03 | | | | | |
CzechRepublic/2741/2020 EPI_ISL_422636 | Prague | 2020-03-08 | | | | | |
CzechRepublic/2556/2020 EPI_ISL_425228 | Prague | 2020-03-22 | | | | | |
CzechRepublic/2122/2020 EPI_ISL_425229 | Prague | 2020-03-19 | | | | | |
CzechRepublic/2282/2020 EPI_ISL_426051 | Prague | 2020-03-20 | | | | | |
EPI_ISL_437519 | Prague | | | | | | |
EPI_ISL_471547 | Prague | | | | | | |
EPI_ISL_471553 | Prague | | | | | | |
EPI_ISL_471555 | Prague | | | | | | |
EPI_ISL_491117 | Prague | | | | | | |
EPI_ISL_513314 | Prague | | | | | | |
EPI_ISL_539780 | Prague | | | | | | |
EPI_ISL_541082 | Prague | | | | | | |
EPI_ISL_541335 | Prague | | | | | | |
EPI_ISL_568577 | Prague | | | | | | |
EPI_ISL_626572 | Prague | | | | | | |
EPI_ISL_626573 | Prague | | | | | | |
EPI_ISL_626577 | Prague | | | | | | |
EPI_ISL_626578 | Prague | | | | | | |
EPI_ISL_626579 | Prague | | | | | | |
EPI_ISL_626580 | Prague | | | | | | |
EPI_ISL_626581 | Prague | | | | | | |
EPI_ISL_626582 | Prague | | | | | | |
EPI_ISL_626583 | Prague | | | | | | |
EPI_ISL_626584 | Prague | | | | | | |
EPI_ISL_626585 | Prague | | | | | | |
EPI_ISL_626586 | Prague | | | | | | |
EPI_ISL_626587 | Prague | | | | | | |
EPI_ISL_626588 | Prague | | | | | | |
EPI_ISL_626589 | Prague | | | | | | |
EPI_ISL_626590 | Prague | | | | | | |
EPI_ISL_626592 | Prague | | | | | | |
EPI_ISL_626594 | Prague | | | | | | |
EPI_ISL_626595 | Prague | | | | | | |
EPI_ISL_626596 | Prague | | | | | | |
EPI_ISL_626603 | Prague | | | | | | |
EPI_ISL_626607 | Prague | | | | | | |
EPI_ISL_626609 | Prague | | | | | | |
EPI_ISL_626610 | Prague | | | | | | |
EPI_ISL_626611 | Prague | | | | | | |
EPI_ISL_626613 | Prague | | | | | | |
EPI_ISL_626617 | Prague | | | | | | |
EPI_ISL_626618 | Prague | | | | | | |
EPI_ISL_626623 | Prague | | | | | | |
EPI_ISL_626624 | Prague | | | | | | |
EPI_ISL_626625 | Prague | | | | | | |
EPI_ISL_660553 | Prague | | | | | | |
EPI_ISL_660557 | Prague | | | | | | |
EPI_ISL_660559 | Prague | | | | | | |
EPI_ISL_660560 | Prague | | | | | | |
EPI_ISL_660561 | Prague | | | | | | |
EPI_ISL_660562 | Prague | | | | | | |
EPI_ISL_660563 | Prague | | | | | | |
EPI_ISL_660564 | Prague | | | | | | |
EPI_ISL_660567 | Prague | | | | | | |
EPI_ISL_660570 | Prague | | | | | | |
EPI_ISL_660571 | Prague | | | | | | |
EPI_ISL_660572 | Prague | | | | | | |
EPI_ISL_660573 | Prague | | | | | | |
EPI_ISL_660584 | Prague | | | | | | |
EPI_ISL_660585 | Prague | | | | | | |
EPI_ISL_660586 | Prague | | | | | | |
EPI_ISL_660587 | Prague | | | | | | |
EPI_ISL_660588 | Prague | | | | | | |
EPI_ISL_660589 | Prague | | | | | | |
EPI_ISL_660590 | Prague | | | | | | |
EPI_ISL_660591 | Prague | | | | | | |
EPI_ISL_660592 | Prague | | | | | | |
EPI_ISL_660593 | Prague | | | | | | |
EPI_ISL_660594 | Prague | | | | | | |
EPI_ISL_660595 | Prague | | | | | | |
EPI_ISL_693662 | Prague | | | | | | |
EPI_ISL_693665 | Prague | | | | | | |
EPI_ISL_693666 | Prague | | | | | | |
EPI_ISL_693667 | Prague | | | | | | |
EPI_ISL_693668 | Prague | | | | | | |
EPI_ISL_693672 | Prague | | | | | | |
EPI_ISL_693673 | Prague | | | | | | |
EPI_ISL_693676 | Prague | | | | | | |
EPI_ISL_693679 | Prague | | | | | | |
EPI_ISL_693680 | Prague | | | | | | |
EPI_ISL_693681 | Prague | | | | | | |
EPI_ISL_693684 | Prague | | | | | | |
EPI_ISL_693685 | Prague | | | | | | |
EPI_ISL_693687 | Prague | | | | | | |
EPI_ISL_736998 | Prague | | | | | | |
EPI_ISL_737000 | Prague | | | | | | |
EPI_ISL_737001 | Prague | | | | | | |
EPI_ISL_737002 | Prague | | | | | | |
EPI_ISL_737007 | Prague | | | | | | |
EPI_ISL_737011 | Prague | | | | | | |
EPI_ISL_737012 | Prague | | | | | | |
EPI_ISL_737013 | Prague | | | | | | |
EPI_ISL_737018 | Prague | | | | | | |
EPI_ISL_737021 | Prague | | | | | | |
EPI_ISL_737022 | Prague | | | | | | |
EPI_ISL_737023 | Prague | | | | | | |
EPI_ISL_737024 | Prague | | | | | | |
EPI_ISL_737026 | Prague | | | | | | |
EPI_ISL_737028 | Prague | | | | | | |
EPI_ISL_737029 | Prague | | | | | | |
EPI_ISL_737030 | Prague | | | | | | |
EPI_ISL_737031 | Prague | | | | | | |
EPI_ISL_737033 | Prague | | | | | | |
EPI_ISL_513511 | Prague-Miskovice | | | | | | |
EPI_ISL_626570 | South Bohemian Region | | | | | | |
EPI_ISL_626574 | South Bohemian Region | | | | | | |
EPI_ISL_626591 | South Bohemian Region | | | | | | |
EPI_ISL_626597 | South Bohemian Region | | | | | | |
EPI_ISL_626598 | South Bohemian Region | | | | | | |
EPI_ISL_626599 | South Bohemian Region | | | | | | |
EPI_ISL_626600 | South Bohemian Region | | | | | | |
EPI_ISL_626601 | South Bohemian Region | | | | | | |
EPI_ISL_626602 | South Bohemian Region | | | | | | |
EPI_ISL_660565 | South Bohemian Region | | | | | | |
EPI_ISL_660568 | South Bohemian Region | | | | | | |
EPI_ISL_539493 | South Moravian Region | | | | | | |
EPI_ISL_541336 | South Moravian Region | | | | | | |
EPI_ISL_541337 | South Moravian Region | | | | | | |
EPI_ISL_560408 | South Moravian Region | | | | | | |
EPI_ISL_560409 | South Moravian Region | | | | | | |
EPI_ISL_560410 | South Moravian Region | | | | | | |
EPI_ISL_560411 | South Moravian Region | | | | | | |
EPI_ISL_560412 | South Moravian Region | | | | | | |
EPI_ISL_660554 | South Moravian Region | | | | | | |
EPI_ISL_660558 | South Moravian Region | | | | | | |
EPI_ISL_660596 | South Moravian Region | | | | | | |
EPI_ISL_660597 | South Moravian Region | | | | | | |
EPI_ISL_693660 | South Moravian Region | | | | | | |
EPI_ISL_737016 | South Moravian Region | | | | | | |
EPI_ISL_584079 | Southern Bohemia Region | | | | | | |
CzechRepublic/951/2020 EPI_ISL_414477 | Usti nad Labem | 2020-03-01 | | | | | |
EPI_ISL_491118 | Usti nad Labem | | | | | | |
EPI_ISL_530349 | Usti nad Labem | | | | | | |
EPI_ISL_539494 | Usti nad Labem | | | | | | |
EPI_ISL_539777 | Usti nad Labem Region | | | | | | |
EPI_ISL_471540 | Vysocina | | | | | | |
EPI_ISL_471544 | Vysocina | | | | | | |
EPI_ISL_434572 | Vysocina Region | | | | | | |
EPI_ISL_491093 | Zlin | | | | | | |
EPI_ISL_513512 | Zlin | | | | | | |
EPI_ISL_530347 | Zlin | | | | | | |
EPI_ISL_491095 | Ústí nad Labem | | | | | | |
EPI_ISL_546436 | Ústí nad Labem Region | | | | | | |
EPI_ISL_546935 | Ústí nad Labem Region | | | | | | |
EPI_ISL_546936 | Ústí nad Labem Region | | | | | | |
EPI_ISL_547966 | Ústí nad Labem Region | | | | | | |
EPI_ISL_547967 | Ústí nad Labem Region | | | | | | |
EPI_ISL_547968 | Ústí nad Labem Region | | | | | | |
EPI_ISL_626614 | Ústí nad Labem Region | | | | | | |
EPI_ISL_660599 | Ústí nad Labem Region | | | | | | |
EPI_ISL_693678 | Ústí nad Labem Region | | | | | | |
EPI_ISL_693682 | Ústí nad Labem Region | | | | | | |
EPI_ISL_737014 | Ústí nad Labem Region | | | | | | |
EPI_ISL_737015 | Ústí nad Labem Region | | | | | | |
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