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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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Kenya

Number of isolates sequences available: 514

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_806622
EPI_ISL_806575Kajiado
EPI_ISL_806703Kajiado
EPI_ISL_806704Kajiado
EPI_ISL_806705Kajiado
EPI_ISL_806706Kajiado
EPI_ISL_806707Kajiado
EPI_ISL_568695Kilifi
EPI_ISL_568705Kilifi
EPI_ISL_568822Kilifi
EPI_ISL_568868Kilifi
EPI_ISL_806567Kilifi
EPI_ISL_806576Kilifi
EPI_ISL_806577Kilifi
EPI_ISL_806578Kilifi
EPI_ISL_806579Kilifi
EPI_ISL_806588Kilifi
EPI_ISL_806589Kilifi
EPI_ISL_806594Kilifi
EPI_ISL_806601Kilifi
EPI_ISL_806607Kilifi
EPI_ISL_806608Kilifi
EPI_ISL_806612Kilifi
EPI_ISL_806618Kilifi
EPI_ISL_806626Kilifi
EPI_ISL_806638Kilifi
EPI_ISL_806644Kilifi
EPI_ISL_806650Kilifi
EPI_ISL_806667Kilifi
EPI_ISL_806696Kilifi
EPI_ISL_806697Kilifi
EPI_ISL_806700Kilifi
EPI_ISL_806701Kilifi
EPI_ISL_855495Kilifi
EPI_ISL_855498Kilifi
EPI_ISL_855499Kilifi
EPI_ISL_855501Kilifi
EPI_ISL_855502Kilifi
EPI_ISL_855503Kilifi
EPI_ISL_855507Kilifi
EPI_ISL_855510Kilifi
EPI_ISL_855511Kilifi
EPI_ISL_855513Kilifi
EPI_ISL_855514Kilifi
EPI_ISL_855517Kilifi
EPI_ISL_855518Kilifi
EPI_ISL_855519Kilifi
EPI_ISL_855523Kilifi
EPI_ISL_855525Kilifi
EPI_ISL_855528Kilifi
EPI_ISL_855529Kilifi
EPI_ISL_855530Kilifi
EPI_ISL_855531Kilifi
EPI_ISL_855536Kilifi
EPI_ISL_855539Kilifi
EPI_ISL_855540Kilifi
EPI_ISL_855542Kilifi
EPI_ISL_855545Kilifi
EPI_ISL_855546Kilifi
EPI_ISL_855547Kilifi
EPI_ISL_855548Kilifi
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_806569Kwale
EPI_ISL_806586Kwale
EPI_ISL_806587Kwale
EPI_ISL_806643Kwale
EPI_ISL_806645Kwale
EPI_ISL_806648Kwale
EPI_ISL_806652Kwale
EPI_ISL_806680Kwale
EPI_ISL_806688Kwale
EPI_ISL_855496Kwale
EPI_ISL_855497Kwale
EPI_ISL_855505Kwale
EPI_ISL_855544Kwale
EPI_ISL_806548Lamu
EPI_ISL_806549Lamu
EPI_ISL_806554Lamu
EPI_ISL_806555Lamu
EPI_ISL_806556Lamu
EPI_ISL_806557Lamu
EPI_ISL_806558Lamu
EPI_ISL_806566Lamu
EPI_ISL_806570Lamu
EPI_ISL_806584Lamu
EPI_ISL_806591Lamu
EPI_ISL_806600Lamu
EPI_ISL_806609Lamu
EPI_ISL_806623Lamu
EPI_ISL_806624Lamu
EPI_ISL_806625Lamu
EPI_ISL_806630Lamu
EPI_ISL_806631Lamu
EPI_ISL_806632Lamu
EPI_ISL_806637Lamu
EPI_ISL_806698Lamu
EPI_ISL_806708Lamu
EPI_ISL_806709Lamu
EPI_ISL_806710Lamu
EPI_ISL_806711Lamu
EPI_ISL_806712Lamu
EPI_ISL_806715Lamu
EPI_ISL_806716Lamu
EPI_ISL_855504Lamu
EPI_ISL_855515Lamu
EPI_ISL_855516Lamu
EPI_ISL_855522Lamu
EPI_ISL_855535Lamu
EPI_ISL_855537Lamu
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_806550Mombasa
EPI_ISL_806551Mombasa
EPI_ISL_806552Mombasa
EPI_ISL_806553Mombasa
EPI_ISL_806559Mombasa
EPI_ISL_806560Mombasa
EPI_ISL_806562Mombasa
EPI_ISL_806563Mombasa
EPI_ISL_806564Mombasa
EPI_ISL_806565Mombasa
EPI_ISL_806572Mombasa
EPI_ISL_806580Mombasa
EPI_ISL_806583Mombasa
EPI_ISL_806585Mombasa
EPI_ISL_806596Mombasa
EPI_ISL_806598Mombasa
EPI_ISL_806599Mombasa
EPI_ISL_806610Mombasa
EPI_ISL_806611Mombasa
EPI_ISL_806617Mombasa
EPI_ISL_806627Mombasa
EPI_ISL_806628Mombasa
EPI_ISL_806629Mombasa
EPI_ISL_806633Mombasa
EPI_ISL_806634Mombasa
EPI_ISL_806635Mombasa
EPI_ISL_806639Mombasa
EPI_ISL_806640Mombasa
EPI_ISL_806641Mombasa
EPI_ISL_806642Mombasa
EPI_ISL_806646Mombasa
EPI_ISL_806647Mombasa
EPI_ISL_806649Mombasa
EPI_ISL_806651Mombasa
EPI_ISL_806654Mombasa
EPI_ISL_806655Mombasa
EPI_ISL_806656Mombasa
EPI_ISL_806657Mombasa
EPI_ISL_806658Mombasa
EPI_ISL_806660Mombasa
EPI_ISL_806661Mombasa
EPI_ISL_806664Mombasa
EPI_ISL_806668Mombasa
EPI_ISL_806669Mombasa
EPI_ISL_806670Mombasa
EPI_ISL_806671Mombasa
EPI_ISL_806672Mombasa
EPI_ISL_806673Mombasa
EPI_ISL_806674Mombasa
EPI_ISL_806675Mombasa
EPI_ISL_806676Mombasa
EPI_ISL_806677Mombasa
EPI_ISL_806679Mombasa
EPI_ISL_806681Mombasa
EPI_ISL_806682Mombasa
EPI_ISL_806684Mombasa
EPI_ISL_806686Mombasa
EPI_ISL_806687Mombasa
EPI_ISL_806689Mombasa
EPI_ISL_806690Mombasa
EPI_ISL_806691Mombasa
EPI_ISL_806693Mombasa
EPI_ISL_806694Mombasa
EPI_ISL_806695Mombasa
EPI_ISL_806699Mombasa
EPI_ISL_806702Mombasa
EPI_ISL_806713Mombasa
EPI_ISL_806714Mombasa
EPI_ISL_855506Mombasa
EPI_ISL_855512Mombasa
EPI_ISL_855520Mombasa
EPI_ISL_855521Mombasa
EPI_ISL_855524Mombasa
EPI_ISL_855526Mombasa
EPI_ISL_855527Mombasa
EPI_ISL_855534Mombasa
EPI_ISL_855541Mombasa
EPI_ISL_855543Mombasa
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
EPI_ISL_855500Taita Taveta
EPI_ISL_855508Taita Taveta
EPI_ISL_855509Taita Taveta
EPI_ISL_855533Taita Taveta
EPI_ISL_855538Taita Taveta
EPI_ISL_806561Taita taveta
EPI_ISL_806568Taita taveta
EPI_ISL_806571Taita taveta
EPI_ISL_806573Taita taveta
EPI_ISL_806574Taita taveta
EPI_ISL_806581Taita taveta
EPI_ISL_806582Taita taveta
EPI_ISL_806590Taita taveta
EPI_ISL_806593Taita taveta
EPI_ISL_806595Taita taveta
EPI_ISL_806602Taita taveta
EPI_ISL_806603Taita taveta
EPI_ISL_806604Taita taveta
EPI_ISL_806605Taita taveta
EPI_ISL_806606Taita taveta
EPI_ISL_806613Taita taveta
EPI_ISL_806614Taita taveta
EPI_ISL_806615Taita taveta
EPI_ISL_806616Taita taveta
EPI_ISL_806619Taita taveta
EPI_ISL_806620Taita taveta
EPI_ISL_806621Taita taveta
EPI_ISL_806653Taita taveta
EPI_ISL_806659Taita taveta
EPI_ISL_806662Taita taveta
EPI_ISL_806663Taita taveta
EPI_ISL_806665Taita taveta
EPI_ISL_806666Taita taveta
EPI_ISL_806678Taita taveta
EPI_ISL_806683Taita taveta
EPI_ISL_806685Taita taveta
EPI_ISL_806692Taita taveta
EPI_ISL_806717Taita taveta
EPI_ISL_855494Tana River
EPI_ISL_806592Tana river
EPI_ISL_806597Tana river
EPI_ISL_806636Tana river

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