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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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Kenya

Number of isolates sequences available: 290

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_457827
EPI_ISL_457828
EPI_ISL_457829
EPI_ISL_457830
EPI_ISL_457831
EPI_ISL_457832
EPI_ISL_457833
EPI_ISL_457834
EPI_ISL_457835
EPI_ISL_457836
EPI_ISL_457837
EPI_ISL_457838
EPI_ISL_457839
EPI_ISL_457840
EPI_ISL_457841
EPI_ISL_457842
EPI_ISL_457843
EPI_ISL_457844
EPI_ISL_457845
EPI_ISL_457846
EPI_ISL_457847
EPI_ISL_457848
EPI_ISL_457849
EPI_ISL_457850
EPI_ISL_457851
EPI_ISL_457852
EPI_ISL_457853
EPI_ISL_457854
EPI_ISL_457855
EPI_ISL_457856
EPI_ISL_457857
EPI_ISL_457858
EPI_ISL_457859
EPI_ISL_457860
EPI_ISL_457861
EPI_ISL_457862The sequence is not available
EPI_ISL_457863
EPI_ISL_457864The sequence is not available
EPI_ISL_457865
EPI_ISL_457866
EPI_ISL_457867
EPI_ISL_457868
EPI_ISL_457869
EPI_ISL_457870
EPI_ISL_457871
EPI_ISL_457872
EPI_ISL_457873
EPI_ISL_457874
EPI_ISL_457875
EPI_ISL_457876
EPI_ISL_457877
EPI_ISL_457878
EPI_ISL_457879
EPI_ISL_457880
EPI_ISL_457881
EPI_ISL_457882The sequence is not available
EPI_ISL_457883
EPI_ISL_457884
EPI_ISL_457885
EPI_ISL_457886
EPI_ISL_457887
EPI_ISL_457888
EPI_ISL_457889
EPI_ISL_457890
EPI_ISL_457891
EPI_ISL_457892
EPI_ISL_457893
EPI_ISL_457894
EPI_ISL_457895
EPI_ISL_457896
EPI_ISL_457897
EPI_ISL_457898
EPI_ISL_457899
EPI_ISL_457900
EPI_ISL_457901
EPI_ISL_457902
EPI_ISL_457903
EPI_ISL_457904
EPI_ISL_457905
EPI_ISL_457906
EPI_ISL_457907
EPI_ISL_457908
EPI_ISL_457909
EPI_ISL_457910
EPI_ISL_457911
EPI_ISL_457912
EPI_ISL_457913
EPI_ISL_457914
EPI_ISL_457915
EPI_ISL_457916
EPI_ISL_457917
EPI_ISL_457918
EPI_ISL_457919
EPI_ISL_457920
EPI_ISL_457921
EPI_ISL_457922
EPI_ISL_457923
EPI_ISL_457924The sequence is not available
EPI_ISL_457925
EPI_ISL_457926The sequence is not available
EPI_ISL_457927
EPI_ISL_457928
EPI_ISL_457929
EPI_ISL_457930The sequence is not available
EPI_ISL_457931
EPI_ISL_457932
EPI_ISL_457933
EPI_ISL_457934
EPI_ISL_457935The sequence is not available
EPI_ISL_457936The sequence is not available
EPI_ISL_457999
EPI_ISL_458000
EPI_ISL_568695Kilifi
EPI_ISL_568705Kilifi
EPI_ISL_568822Kilifi
EPI_ISL_568868Kilifi
EPI_ISL_568716Kwale
EPI_ISL_568717Kwale
EPI_ISL_568800Kwale
EPI_ISL_568801Kwale
EPI_ISL_568802Kwale
EPI_ISL_568803Kwale
EPI_ISL_568804Kwale
EPI_ISL_568805Kwale
EPI_ISL_568823Kwale
EPI_ISL_568827Kwale
EPI_ISL_568828Kwale
EPI_ISL_568829Kwale
EPI_ISL_568830Kwale
EPI_ISL_568831Kwale
EPI_ISL_568832Kwale
EPI_ISL_568842Kwale
EPI_ISL_568843Kwale
EPI_ISL_568844Kwale
EPI_ISL_568845Kwale
EPI_ISL_568846Kwale
EPI_ISL_568847Kwale
EPI_ISL_568849Kwale
EPI_ISL_568850Kwale
EPI_ISL_568851Kwale
EPI_ISL_568861Kwale
EPI_ISL_568862Kwale
EPI_ISL_568863Kwale
EPI_ISL_568864Kwale
EPI_ISL_568865Kwale
EPI_ISL_568869Kwale
EPI_ISL_568870Kwale
EPI_ISL_568696Mombasa
EPI_ISL_568697Mombasa
EPI_ISL_568698Mombasa
EPI_ISL_568699Mombasa
EPI_ISL_568700Mombasa
EPI_ISL_568701Mombasa
EPI_ISL_568702Mombasa
EPI_ISL_568703Mombasa
EPI_ISL_568704Mombasa
EPI_ISL_568706Mombasa
EPI_ISL_568707Mombasa
EPI_ISL_568708Mombasa
EPI_ISL_568709Mombasa
EPI_ISL_568710Mombasa
EPI_ISL_568711MombasaThe sequence is not available
EPI_ISL_568712Mombasa
EPI_ISL_568713Mombasa
EPI_ISL_568714Mombasa
EPI_ISL_568715Mombasa
EPI_ISL_568718Mombasa
EPI_ISL_568719Mombasa
EPI_ISL_568720Mombasa
EPI_ISL_568721Mombasa
EPI_ISL_568722Mombasa
EPI_ISL_568723Mombasa
EPI_ISL_568724Mombasa
EPI_ISL_568725Mombasa
EPI_ISL_568726Mombasa
EPI_ISL_568727Mombasa
EPI_ISL_568728Mombasa
EPI_ISL_568729Mombasa
EPI_ISL_568730Mombasa
EPI_ISL_568731Mombasa
EPI_ISL_568732Mombasa
EPI_ISL_568733Mombasa
EPI_ISL_568734Mombasa
EPI_ISL_568735Mombasa
EPI_ISL_568736Mombasa
EPI_ISL_568737Mombasa
EPI_ISL_568738Mombasa
EPI_ISL_568739Mombasa
EPI_ISL_568740Mombasa
EPI_ISL_568741Mombasa
EPI_ISL_568742Mombasa
EPI_ISL_568743Mombasa
EPI_ISL_568744Mombasa
EPI_ISL_568745Mombasa
EPI_ISL_568746Mombasa
EPI_ISL_568747Mombasa
EPI_ISL_568748Mombasa
EPI_ISL_568749Mombasa
EPI_ISL_568750Mombasa
EPI_ISL_568751Mombasa
EPI_ISL_568752Mombasa
EPI_ISL_568753Mombasa
EPI_ISL_568754Mombasa
EPI_ISL_568755Mombasa
EPI_ISL_568756Mombasa
EPI_ISL_568757Mombasa
EPI_ISL_568758Mombasa
EPI_ISL_568759Mombasa
EPI_ISL_568760Mombasa
EPI_ISL_568761Mombasa
EPI_ISL_568762Mombasa
EPI_ISL_568763Mombasa
EPI_ISL_568764Mombasa
EPI_ISL_568765Mombasa
EPI_ISL_568766Mombasa
EPI_ISL_568767Mombasa
EPI_ISL_568768Mombasa
EPI_ISL_568769Mombasa
EPI_ISL_568770Mombasa
EPI_ISL_568771Mombasa
EPI_ISL_568772Mombasa
EPI_ISL_568773Mombasa
EPI_ISL_568774Mombasa
EPI_ISL_568775Mombasa
EPI_ISL_568776Mombasa
EPI_ISL_568777Mombasa
EPI_ISL_568778Mombasa
EPI_ISL_568779Mombasa
EPI_ISL_568780Mombasa
EPI_ISL_568781Mombasa
EPI_ISL_568782Mombasa
EPI_ISL_568783Mombasa
EPI_ISL_568784Mombasa
EPI_ISL_568785Mombasa
EPI_ISL_568786Mombasa
EPI_ISL_568787Mombasa
EPI_ISL_568788Mombasa
EPI_ISL_568789Mombasa
EPI_ISL_568790Mombasa
EPI_ISL_568791Mombasa
EPI_ISL_568792Mombasa
EPI_ISL_568793Mombasa
EPI_ISL_568794Mombasa
EPI_ISL_568795Mombasa
EPI_ISL_568796Mombasa
EPI_ISL_568797Mombasa
EPI_ISL_568798Mombasa
EPI_ISL_568799Mombasa
EPI_ISL_568806Mombasa
EPI_ISL_568807Mombasa
EPI_ISL_568808Mombasa
EPI_ISL_568809Mombasa
EPI_ISL_568824Mombasa
EPI_ISL_568825MombasaThe sequence is not available
EPI_ISL_568826Mombasa
EPI_ISL_568833Mombasa
EPI_ISL_568834Mombasa
EPI_ISL_568835Mombasa
EPI_ISL_568836Mombasa
EPI_ISL_568837Mombasa
EPI_ISL_568838MombasaThe sequence is not available
EPI_ISL_568852Mombasa
EPI_ISL_568853Mombasa
EPI_ISL_568854Mombasa
EPI_ISL_568855Mombasa
EPI_ISL_568856Mombasa
EPI_ISL_568857Mombasa
EPI_ISL_568871Mombasa
EPI_ISL_568872Mombasa
EPI_ISL_568810Taita Taveta
EPI_ISL_568811Taita Taveta
EPI_ISL_568812Taita Taveta
EPI_ISL_568813Taita Taveta
EPI_ISL_568814Taita Taveta
EPI_ISL_568815Taita Taveta
EPI_ISL_568816Taita Taveta
EPI_ISL_568817Taita Taveta
EPI_ISL_568818Taita Taveta
EPI_ISL_568819Taita Taveta
EPI_ISL_568820Taita Taveta
EPI_ISL_568821Taita Taveta
EPI_ISL_568839Taita Taveta
EPI_ISL_568840Taita Taveta
EPI_ISL_568841Taita TavetaThe sequence is not available
EPI_ISL_568848Taita Taveta
EPI_ISL_568858Taita Taveta
EPI_ISL_568859Taita Taveta
EPI_ISL_568860Taita Taveta
EPI_ISL_568866Taita Taveta
EPI_ISL_568867Taita Taveta

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