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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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Egypt

Number of isolates sequences available: 366

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_794593
EPI_ISL_794594
EPI_ISL_794595
EPI_ISL_794596
EPI_ISL_794597
EPI_ISL_794598
EPI_ISL_794599
EPI_ISL_794600
EPI_ISL_794601
EPI_ISL_794602
EPI_ISL_794603
EPI_ISL_794604
EPI_ISL_794605
EPI_ISL_794606
EPI_ISL_794607
EPI_ISL_794608
EPI_ISL_794634
EPI_ISL_812783
EPI_ISL_812784
EPI_ISL_812785
EPI_ISL_812786
EPI_ISL_812787
EPI_ISL_812788
EPI_ISL_812789
EPI_ISL_812790
EPI_ISL_812791
EPI_ISL_812792
EPI_ISL_812793
EPI_ISL_812794
EPI_ISL_812795
EPI_ISL_812796
EPI_ISL_812797
EPI_ISL_812798
EPI_ISL_812799
EPI_ISL_812800
EPI_ISL_812801
EPI_ISL_812802
EPI_ISL_812803
EPI_ISL_812804
EPI_ISL_812805
EPI_ISL_812806
EPI_ISL_812807
EPI_ISL_812808
EPI_ISL_812809
EPI_ISL_812810
EPI_ISL_812811
EPI_ISL_812812
EPI_ISL_812813
EPI_ISL_812814
EPI_ISL_812815
EPI_ISL_812816
EPI_ISL_812817
EPI_ISL_812818
EPI_ISL_812819
EPI_ISL_812820
EPI_ISL_812821
EPI_ISL_812822
EPI_ISL_812823
EPI_ISL_812824
EPI_ISL_812825
EPI_ISL_812826
EPI_ISL_812827
EPI_ISL_812828
EPI_ISL_812829
EPI_ISL_812830
EPI_ISL_812831
EPI_ISL_812832
EPI_ISL_812833
EPI_ISL_812834
EPI_ISL_812835
EPI_ISL_812836
EPI_ISL_812837
EPI_ISL_812838
EPI_ISL_812839
EPI_ISL_812840
EPI_ISL_812841
EPI_ISL_812842
EPI_ISL_812843
EPI_ISL_812844
EPI_ISL_812845
EPI_ISL_812846
EPI_ISL_812847
EPI_ISL_812848
EPI_ISL_812849
EPI_ISL_812850
EPI_ISL_812851
EPI_ISL_812852
EPI_ISL_812853
EPI_ISL_812854
EPI_ISL_812855
EPI_ISL_812856
EPI_ISL_812857
EPI_ISL_812858
EPI_ISL_812859
EPI_ISL_812860
EPI_ISL_812861
EPI_ISL_812862
EPI_ISL_812863
EPI_ISL_812864
EPI_ISL_812865
EPI_ISL_812866
EPI_ISL_812867
EPI_ISL_812868
EPI_ISL_812869
EPI_ISL_812870
EPI_ISL_812871
EPI_ISL_812872
EPI_ISL_857315
EPI_ISL_857316
EPI_ISL_857317
EPI_ISL_857318
EPI_ISL_857319
EPI_ISL_857320
EPI_ISL_857321
EPI_ISL_857322
EPI_ISL_857323
EPI_ISL_857324
EPI_ISL_857325
EPI_ISL_857326
EPI_ISL_857327
EPI_ISL_857328
EPI_ISL_857329
EPI_ISL_857330
EPI_ISL_857331
EPI_ISL_857332
EPI_ISL_857333
EPI_ISL_857334
EPI_ISL_857335
EPI_ISL_857336
EPI_ISL_857337
EPI_ISL_857338
EPI_ISL_857339
EPI_ISL_857340
EPI_ISL_857341
EPI_ISL_857342
EPI_ISL_857343
EPI_ISL_857344
EPI_ISL_857345
EPI_ISL_857346
EPI_ISL_857347
EPI_ISL_862783
EPI_ISL_862784
EPI_ISL_862785
EPI_ISL_862786
EPI_ISL_862787
EPI_ISL_862788
EPI_ISL_862789
EPI_ISL_862790
EPI_ISL_862791
EPI_ISL_862792
EPI_ISL_862793
EPI_ISL_862794
EPI_ISL_862795
EPI_ISL_862796
EPI_ISL_862797
EPI_ISL_862798
EPI_ISL_862799
EPI_ISL_862800
EPI_ISL_862801
EPI_ISL_862802
EPI_ISL_862803
EPI_ISL_862804
EPI_ISL_862805
EPI_ISL_862806
EPI_ISL_862807
EPI_ISL_862808
EPI_ISL_862809
EPI_ISL_862810
EPI_ISL_862811
EPI_ISL_862812
EPI_ISL_862813
EPI_ISL_890195
EPI_ISL_890196
EPI_ISL_890197
EPI_ISL_890198
EPI_ISL_890199
EPI_ISL_890200
EPI_ISL_890201
EPI_ISL_890202
EPI_ISL_890203
EPI_ISL_890204
EPI_ISL_890205
EPI_ISL_890206
EPI_ISL_890207
EPI_ISL_890208
EPI_ISL_890209
EPI_ISL_890210
EPI_ISL_890211
EPI_ISL_890212
EPI_ISL_890213
EPI_ISL_890214
EPI_ISL_890215
EPI_ISL_890216
EPI_ISL_890217
EPI_ISL_890218
EPI_ISL_890219
EPI_ISL_890220
EPI_ISL_890221
EPI_ISL_890222
EPI_ISL_890223
EPI_ISL_890224
EPI_ISL_890225
EPI_ISL_890226
EPI_ISL_890227
EPI_ISL_890228
EPI_ISL_890229
EPI_ISL_890230
EPI_ISL_890231
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_605780Cairo
EPI_ISL_605781Cairo
EPI_ISL_605782Cairo
EPI_ISL_510526Fayoum
EPI_ISL_510532Fayoum
EPI_ISL_483037Kalyoubia

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