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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: 119

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_895728
EPI_ISL_895729
EPI_ISL_895730
EPI_ISL_895731
EPI_ISL_895732
EPI_ISL_895733
EPI_ISL_895734
EPI_ISL_895735
EPI_ISL_895736
EPI_ISL_895737
EPI_ISL_895738
EPI_ISL_895739
EPI_ISL_895740
EPI_ISL_895741
EPI_ISL_895742
EPI_ISL_895743
EPI_ISL_895744
EPI_ISL_895745
EPI_ISL_895746
EPI_ISL_895747
EPI_ISL_895748
EPI_ISL_895749
EPI_ISL_895750
EPI_ISL_895751
EPI_ISL_895752
EPI_ISL_895753
EPI_ISL_895754
EPI_ISL_895755
EPI_ISL_895757
EPI_ISL_895758
EPI_ISL_895759
EPI_ISL_895760
EPI_ISL_895761
EPI_ISL_895762
EPI_ISL_895763
EPI_ISL_895764
EPI_ISL_895765
EPI_ISL_895766
EPI_ISL_895767
EPI_ISL_895768
EPI_ISL_895769
EPI_ISL_895770
EPI_ISL_895771
EPI_ISL_895772
EPI_ISL_895773
EPI_ISL_895774
EPI_ISL_895775
EPI_ISL_895776
EPI_ISL_895777
EPI_ISL_895778
EPI_ISL_895779
EPI_ISL_895780
EPI_ISL_895781
EPI_ISL_895782
EPI_ISL_895783
EPI_ISL_895784
EPI_ISL_895785
EPI_ISL_895786
EPI_ISL_895787
EPI_ISL_895788
EPI_ISL_895789
EPI_ISL_895790
EPI_ISL_895791
EPI_ISL_895792
EPI_ISL_895793
EPI_ISL_895794
EPI_ISL_895795
EPI_ISL_895796
EPI_ISL_895797
EPI_ISL_895798
EPI_ISL_895799
EPI_ISL_895800
EPI_ISL_895801
EPI_ISL_895802
EPI_ISL_895803
EPI_ISL_895804
EPI_ISL_895805
EPI_ISL_895806
EPI_ISL_895807
EPI_ISL_895808
EPI_ISL_895809
EPI_ISL_895810
EPI_ISL_895811
EPI_ISL_895812
EPI_ISL_895813
EPI_ISL_895814
EPI_ISL_895815
EPI_ISL_895816
EPI_ISL_895817
EPI_ISL_895818
EPI_ISL_895819
EPI_ISL_895820
EPI_ISL_895821
EPI_ISL_895822
EPI_ISL_895823
EPI_ISL_895824
EPI_ISL_895825
EPI_ISL_895826
EPI_ISL_895827
EPI_ISL_895828
EPI_ISL_895829
EPI_ISL_895830
EPI_ISL_895831
EPI_ISL_895832
EPI_ISL_895833
EPI_ISL_895834
EPI_ISL_895835
EPI_ISL_895836
EPI_ISL_895837
EPI_ISL_895838
EPI_ISL_895839
EPI_ISL_895840
EPI_ISL_895841
EPI_ISL_895842
EPI_ISL_895843
EPI_ISL_895844
EPI_ISL_895845
EPI_ISL_895846
EPI_ISL_895847

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