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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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Egypt

Number of isolates sequences available: 155

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_430819
EPI_ISL_430820
EPI_ISL_468044
EPI_ISL_468045
EPI_ISL_468046
EPI_ISL_468047
EPI_ISL_468048
EPI_ISL_468049
EPI_ISL_468050
EPI_ISL_468051
EPI_ISL_468052
EPI_ISL_468053
EPI_ISL_468054
EPI_ISL_468055
EPI_ISL_468056
EPI_ISL_468057
EPI_ISL_468058
EPI_ISL_468059
EPI_ISL_468060
EPI_ISL_468061
EPI_ISL_468062
EPI_ISL_475722
EPI_ISL_475723
EPI_ISL_475724
EPI_ISL_475745
EPI_ISL_475746
EPI_ISL_475747
EPI_ISL_475748
EPI_ISL_475749
EPI_ISL_475750
EPI_ISL_475751
EPI_ISL_475752
EPI_ISL_475753
EPI_ISL_477161
EPI_ISL_478672
EPI_ISL_479686
EPI_ISL_479687
EPI_ISL_479688
EPI_ISL_479689
EPI_ISL_479690
EPI_ISL_479691
EPI_ISL_479692
EPI_ISL_479693
EPI_ISL_479694
EPI_ISL_479695
EPI_ISL_479696
EPI_ISL_479697
EPI_ISL_479698
EPI_ISL_479699
EPI_ISL_479700
EPI_ISL_479701
EPI_ISL_479702
EPI_ISL_479703
EPI_ISL_479704
EPI_ISL_479705
EPI_ISL_479706
EPI_ISL_479707
EPI_ISL_479708
EPI_ISL_479709
EPI_ISL_479710
EPI_ISL_479711
EPI_ISL_479712
EPI_ISL_479713
EPI_ISL_479714
EPI_ISL_479715
EPI_ISL_479716
EPI_ISL_479717
EPI_ISL_479718
EPI_ISL_479719
EPI_ISL_479720
EPI_ISL_479721
EPI_ISL_479722
EPI_ISL_479723
EPI_ISL_479724
EPI_ISL_479725
EPI_ISL_479726
EPI_ISL_479727
EPI_ISL_479728
EPI_ISL_479729
EPI_ISL_479730
EPI_ISL_479731
EPI_ISL_479732
EPI_ISL_479733
EPI_ISL_479734
EPI_ISL_479735
EPI_ISL_482759
EPI_ISL_482760
EPI_ISL_482761
EPI_ISL_482762
EPI_ISL_482763
EPI_ISL_482764
EPI_ISL_482765
EPI_ISL_482766
EPI_ISL_482767
EPI_ISL_482768
EPI_ISL_482769
EPI_ISL_482770
EPI_ISL_482771
EPI_ISL_482772
EPI_ISL_482773
EPI_ISL_482774
EPI_ISL_482775
EPI_ISL_524426
EPI_ISL_524427
EPI_ISL_526975
EPI_ISL_526976
EPI_ISL_526977
EPI_ISL_526978
EPI_ISL_526979
EPI_ISL_526980
EPI_ISL_526981
EPI_ISL_526982
EPI_ISL_526983
EPI_ISL_526984
EPI_ISL_526985
EPI_ISL_526986
EPI_ISL_526987
EPI_ISL_526988
EPI_ISL_526989
EPI_ISL_526990
EPI_ISL_526991
EPI_ISL_526992
EPI_ISL_526993
EPI_ISL_526994
EPI_ISL_526995
EPI_ISL_526996
EPI_ISL_526997
EPI_ISL_526998
EPI_ISL_526999
EPI_ISL_527000
EPI_ISL_527001
EPI_ISL_527002
EPI_ISL_527003
EPI_ISL_527004
EPI_ISL_527005
EPI_ISL_527006
EPI_ISL_527007
EPI_ISL_528386
EPI_ISL_576371
EPI_ISL_576372
EPI_ISL_576373
EPI_ISL_469275Cairo
EPI_ISL_483035Cairo
EPI_ISL_483036Cairo
EPI_ISL_483038Cairo
EPI_ISL_529031Cairo
EPI_ISL_529032Cairo
EPI_ISL_529141Cairo
EPI_ISL_529142Cairo
EPI_ISL_529143Cairo
EPI_ISL_529144Cairo
EPI_ISL_529145Cairo
EPI_ISL_510526Fayoum
EPI_ISL_510532Fayoum
EPI_ISL_483037Kalyoubia

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