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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 10 05:32:46 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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Ireland

Number of isolates sequences available: 1577

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_437684
EPI_ISL_437685
EPI_ISL_437686
EPI_ISL_437687
EPI_ISL_437688
EPI_ISL_778831
EPI_ISL_778832
EPI_ISL_778833
EPI_ISL_778834
EPI_ISL_791280
EPI_ISL_791281
EPI_ISL_791282
EPI_ISL_791290
EPI_ISL_791291
EPI_ISL_791297
EPI_ISL_791307
EPI_ISL_791308
EPI_ISL_791309
EPI_ISL_791310
EPI_ISL_791311
EPI_ISL_791312
EPI_ISL_791313
EPI_ISL_791314
EPI_ISL_791315
EPI_ISL_791316
EPI_ISL_752588Carlow
EPI_ISL_767738Carlow
EPI_ISL_525371Cavan
EPI_ISL_639849Cavan
EPI_ISL_639869Cavan
EPI_ISL_639870Cavan
EPI_ISL_639871Cavan
EPI_ISL_639872Cavan
EPI_ISL_639873Cavan
EPI_ISL_639874Cavan
EPI_ISL_639882Cavan
EPI_ISL_639884Cavan
EPI_ISL_639886Cavan
EPI_ISL_639887Cavan
EPI_ISL_639888Cavan
EPI_ISL_639889Cavan
EPI_ISL_639890Cavan
EPI_ISL_639891Cavan
EPI_ISL_639904Cavan
EPI_ISL_639905Cavan
EPI_ISL_639907Cavan
EPI_ISL_666692Cavan
EPI_ISL_671865Cavan
EPI_ISL_732463Cavan
EPI_ISL_732518Cavan
EPI_ISL_767729Cavan
EPI_ISL_767735Cavan
EPI_ISL_767736Cavan
EPI_ISL_578236Clare
EPI_ISL_578246Clare
EPI_ISL_578247Clare
EPI_ISL_578248Clare
EPI_ISL_644221Clare
EPI_ISL_644231Clare
EPI_ISL_644269Clare
EPI_ISL_644272Clare
EPI_ISL_644315Clare
EPI_ISL_644317Clare
EPI_ISL_644338Clare
EPI_ISL_671352Clare
EPI_ISL_671864Clare
EPI_ISL_681705Clare
EPI_ISL_681706Clare
EPI_ISL_681707Clare
EPI_ISL_681708Clare
EPI_ISL_681709Clare
EPI_ISL_681710Clare
EPI_ISL_681711Clare
EPI_ISL_681712Clare
EPI_ISL_681713Clare
EPI_ISL_681714Clare
EPI_ISL_681715Clare
EPI_ISL_681716Clare
EPI_ISL_681717Clare
EPI_ISL_681718Clare
EPI_ISL_732432Clare
EPI_ISL_732433Clare
EPI_ISL_732517Clare
EPI_ISL_752534Clare
EPI_ISL_752537Clare
Ireland/COR-20134/2020 EPI_ISL_414487Cork2020-03-04
Ireland/Cork2/2020 EPI_ISL_417432Cork2020-03-08
Ireland/Dublin-22361/2020 EPI_ISL_418580Cork2020-03-08
EPI_ISL_500593Cork
EPI_ISL_512093Cork
EPI_ISL_512100Cork
EPI_ISL_528470Cork
EPI_ISL_528471Cork
EPI_ISL_528480Cork
EPI_ISL_528481Cork
EPI_ISL_578249Cork
EPI_ISL_578250Cork
EPI_ISL_578251Cork
EPI_ISL_578252Cork
EPI_ISL_578253Cork
EPI_ISL_605126Cork
EPI_ISL_605130Cork
EPI_ISL_605135Cork
EPI_ISL_605146Cork
EPI_ISL_639832Cork
EPI_ISL_671866Cork
EPI_ISL_671867Cork
EPI_ISL_671868Cork
EPI_ISL_671869Cork
EPI_ISL_671870Cork
EPI_ISL_671871Cork
EPI_ISL_671872Cork
EPI_ISL_671873Cork
EPI_ISL_671874Cork
EPI_ISL_671875Cork
EPI_ISL_671876Cork
EPI_ISL_671877Cork
EPI_ISL_671878Cork
EPI_ISL_671879Cork
EPI_ISL_671880Cork
EPI_ISL_671881Cork
EPI_ISL_671882Cork
EPI_ISL_681885Cork
EPI_ISL_681888Cork
EPI_ISL_681906Cork
EPI_ISL_681908Cork
EPI_ISL_681921Cork
EPI_ISL_681923Cork
EPI_ISL_732464Cork
EPI_ISL_732465Cork
EPI_ISL_732466Cork
EPI_ISL_732478Cork
EPI_ISL_732519Cork
EPI_ISL_752528Cork
EPI_ISL_752530Cork
EPI_ISL_752553Cork
EPI_ISL_752562Cork
EPI_ISL_752564Cork
EPI_ISL_752569Cork
EPI_ISL_752572Cork
EPI_ISL_752574Cork
EPI_ISL_752576Cork
EPI_ISL_752578Cork
EPI_ISL_752579Cork
EPI_ISL_752580Cork
EPI_ISL_767737Cork
EPI_ISL_666688Donegal
EPI_ISL_666689Donegal
EPI_ISL_666690Donegal
EPI_ISL_666695Donegal
EPI_ISL_666696Donegal
EPI_ISL_666697Donegal
EPI_ISL_666698Donegal
EPI_ISL_666699Donegal
EPI_ISL_666700Donegal
EPI_ISL_666701Donegal
EPI_ISL_666702Donegal
EPI_ISL_666703Donegal
EPI_ISL_666704Donegal
EPI_ISL_666705Donegal
EPI_ISL_666706Donegal
EPI_ISL_666707Donegal
EPI_ISL_666708Donegal
EPI_ISL_752559Donegal
EPI_ISL_752591Donegal
Ireland/Dublin-19072/2020 EPI_ISL_414584Dublin2020-03-02
Ireland/21145/2020 EPI_ISL_418548Dublin2020-03-06
Ireland/Dublin-22428/2020 EPI_ISL_418581Dublin2020-03-08
Ireland/24042/2020 EPI_ISL_418583Dublin2020-03-10
EPI_ISL_500574Dublin
EPI_ISL_500577Dublin
EPI_ISL_500579Dublin
EPI_ISL_500580Dublin
EPI_ISL_500585Dublin
EPI_ISL_500586Dublin
EPI_ISL_500587Dublin
EPI_ISL_500588Dublin
EPI_ISL_500589Dublin
EPI_ISL_500590Dublin
EPI_ISL_500592Dublin
EPI_ISL_500594Dublin
EPI_ISL_501261Dublin
EPI_ISL_501262Dublin
EPI_ISL_501263Dublin
EPI_ISL_501266Dublin
EPI_ISL_501267Dublin
EPI_ISL_501268Dublin
EPI_ISL_501269Dublin
EPI_ISL_501270Dublin
EPI_ISL_501271Dublin
EPI_ISL_501272Dublin
EPI_ISL_501273Dublin
EPI_ISL_501274Dublin
EPI_ISL_512089Dublin
EPI_ISL_512092Dublin
EPI_ISL_512094Dublin
EPI_ISL_512095Dublin
EPI_ISL_512096Dublin
EPI_ISL_512101Dublin
EPI_ISL_512103Dublin
EPI_ISL_512104Dublin
EPI_ISL_525358Dublin
EPI_ISL_525359Dublin
EPI_ISL_525362Dublin
EPI_ISL_525366Dublin
EPI_ISL_525367Dublin
EPI_ISL_525368Dublin
EPI_ISL_525372Dublin
EPI_ISL_525373Dublin
EPI_ISL_525374Dublin
EPI_ISL_528440Dublin
EPI_ISL_528447Dublin
EPI_ISL_528465Dublin
EPI_ISL_528484Dublin
EPI_ISL_578203Dublin
EPI_ISL_578204Dublin
EPI_ISL_578206Dublin
EPI_ISL_578208Dublin
EPI_ISL_578210Dublin
EPI_ISL_578217Dublin
EPI_ISL_578223Dublin
EPI_ISL_578224Dublin
EPI_ISL_578231Dublin
EPI_ISL_578232Dublin
EPI_ISL_578242Dublin
EPI_ISL_578243Dublin
EPI_ISL_578254Dublin
EPI_ISL_578255Dublin
EPI_ISL_578256Dublin
EPI_ISL_578257Dublin
EPI_ISL_578258Dublin
EPI_ISL_578259Dublin
EPI_ISL_578260Dublin
EPI_ISL_578261Dublin
EPI_ISL_578262Dublin
EPI_ISL_578263Dublin
EPI_ISL_578264Dublin
EPI_ISL_578265Dublin
EPI_ISL_578266Dublin
EPI_ISL_578267Dublin
EPI_ISL_578268Dublin
EPI_ISL_578269Dublin
EPI_ISL_578270Dublin
EPI_ISL_578271Dublin
EPI_ISL_578272Dublin
EPI_ISL_578273Dublin
EPI_ISL_578274Dublin
EPI_ISL_578275Dublin
EPI_ISL_596627Dublin
EPI_ISL_596628Dublin
EPI_ISL_596629Dublin
EPI_ISL_596630Dublin
EPI_ISL_596631Dublin
EPI_ISL_596632Dublin
EPI_ISL_596633Dublin
EPI_ISL_596634Dublin
EPI_ISL_596635Dublin
EPI_ISL_596636Dublin
EPI_ISL_596637Dublin
EPI_ISL_596638Dublin
EPI_ISL_596639Dublin
EPI_ISL_596640Dublin
EPI_ISL_596641Dublin
EPI_ISL_596642Dublin
EPI_ISL_596643Dublin
EPI_ISL_596644Dublin
EPI_ISL_596645Dublin
EPI_ISL_596646Dublin
EPI_ISL_596647Dublin
EPI_ISL_596648Dublin
EPI_ISL_596649Dublin
EPI_ISL_596650Dublin
EPI_ISL_596651Dublin
EPI_ISL_596652Dublin
EPI_ISL_596653Dublin
EPI_ISL_596654Dublin
EPI_ISL_596655Dublin
EPI_ISL_596656Dublin
EPI_ISL_596657Dublin
EPI_ISL_596658Dublin
EPI_ISL_596659Dublin
EPI_ISL_596660Dublin
EPI_ISL_596661Dublin
EPI_ISL_596662Dublin
EPI_ISL_596663Dublin
EPI_ISL_596664Dublin
EPI_ISL_596665Dublin
EPI_ISL_596666Dublin
EPI_ISL_596667Dublin
EPI_ISL_596668Dublin
EPI_ISL_596669Dublin
EPI_ISL_596670Dublin
EPI_ISL_596671Dublin
EPI_ISL_596672Dublin
EPI_ISL_596673Dublin
EPI_ISL_596674Dublin
EPI_ISL_596675Dublin
EPI_ISL_596676Dublin
EPI_ISL_596892Dublin
EPI_ISL_596893Dublin
EPI_ISL_596894Dublin
EPI_ISL_596897Dublin
EPI_ISL_596899Dublin
EPI_ISL_596900Dublin
EPI_ISL_596901Dublin
EPI_ISL_596902Dublin
EPI_ISL_596903Dublin
EPI_ISL_596904Dublin
EPI_ISL_596906Dublin
EPI_ISL_596909Dublin
EPI_ISL_596911Dublin
EPI_ISL_596913Dublin
EPI_ISL_596914Dublin
EPI_ISL_596915Dublin
EPI_ISL_596916Dublin
EPI_ISL_596917Dublin
EPI_ISL_596919Dublin
EPI_ISL_596920Dublin
EPI_ISL_596921Dublin
EPI_ISL_596923Dublin
EPI_ISL_596924Dublin
EPI_ISL_596925Dublin
EPI_ISL_596926Dublin
EPI_ISL_603266Dublin
EPI_ISL_605058Dublin
EPI_ISL_605060Dublin
EPI_ISL_605061Dublin
EPI_ISL_605062Dublin
EPI_ISL_605063Dublin
EPI_ISL_605064Dublin
EPI_ISL_605065Dublin
EPI_ISL_605066Dublin
EPI_ISL_605067Dublin
EPI_ISL_605069Dublin
EPI_ISL_605070Dublin
EPI_ISL_605071Dublin
EPI_ISL_605072Dublin
EPI_ISL_605075Dublin
EPI_ISL_605077Dublin
EPI_ISL_605078Dublin
EPI_ISL_605080Dublin
EPI_ISL_605081Dublin
EPI_ISL_605083Dublin
EPI_ISL_605084Dublin
EPI_ISL_605085Dublin
EPI_ISL_605086Dublin
EPI_ISL_605089Dublin
EPI_ISL_605090Dublin
EPI_ISL_605091Dublin
EPI_ISL_605092Dublin
EPI_ISL_605093Dublin
EPI_ISL_605095Dublin
EPI_ISL_605096Dublin
EPI_ISL_605097Dublin
EPI_ISL_605099Dublin
EPI_ISL_605100Dublin
EPI_ISL_605101Dublin
EPI_ISL_605102Dublin
EPI_ISL_605103Dublin
EPI_ISL_605104Dublin
EPI_ISL_605105Dublin
EPI_ISL_605106Dublin
EPI_ISL_605107Dublin
EPI_ISL_605108Dublin
EPI_ISL_605109Dublin
EPI_ISL_605110Dublin
EPI_ISL_605112Dublin
EPI_ISL_605113Dublin
EPI_ISL_605114Dublin
EPI_ISL_605115Dublin
EPI_ISL_605117Dublin
EPI_ISL_605118Dublin
EPI_ISL_605120Dublin
EPI_ISL_605122Dublin
EPI_ISL_605124Dublin
EPI_ISL_605125Dublin
EPI_ISL_605127Dublin
EPI_ISL_605128Dublin
EPI_ISL_605129Dublin
EPI_ISL_605131Dublin
EPI_ISL_605132Dublin
EPI_ISL_605133Dublin
EPI_ISL_605134Dublin
EPI_ISL_605136Dublin
EPI_ISL_605137Dublin
EPI_ISL_605138Dublin
EPI_ISL_605139Dublin
EPI_ISL_605140Dublin
EPI_ISL_605141Dublin
EPI_ISL_605142Dublin
EPI_ISL_605143Dublin
EPI_ISL_605144Dublin
EPI_ISL_605145Dublin
EPI_ISL_605798Dublin
EPI_ISL_639853Dublin
EPI_ISL_639865Dublin
EPI_ISL_644209Dublin
EPI_ISL_644210Dublin
EPI_ISL_644212Dublin
EPI_ISL_644214Dublin
EPI_ISL_644215Dublin
EPI_ISL_644217Dublin
EPI_ISL_644218Dublin
EPI_ISL_644219Dublin
EPI_ISL_644220Dublin
EPI_ISL_644223Dublin
EPI_ISL_644226Dublin
EPI_ISL_644227Dublin
EPI_ISL_644228Dublin
EPI_ISL_644230Dublin
EPI_ISL_644232Dublin
EPI_ISL_644233Dublin
EPI_ISL_644235Dublin
EPI_ISL_644237Dublin
EPI_ISL_644238Dublin
EPI_ISL_644239Dublin
EPI_ISL_644240Dublin
EPI_ISL_644241Dublin
EPI_ISL_644242Dublin
EPI_ISL_644243Dublin
EPI_ISL_644244Dublin
EPI_ISL_644245Dublin
EPI_ISL_644246Dublin
EPI_ISL_644247Dublin
EPI_ISL_644248Dublin
EPI_ISL_644249Dublin
EPI_ISL_644250Dublin
EPI_ISL_644251Dublin
EPI_ISL_644252Dublin
EPI_ISL_644253Dublin
EPI_ISL_644254Dublin
EPI_ISL_644257Dublin
EPI_ISL_644258Dublin
EPI_ISL_644260Dublin
EPI_ISL_644261Dublin
EPI_ISL_644262Dublin
EPI_ISL_644263Dublin
EPI_ISL_644265Dublin
EPI_ISL_644266Dublin
EPI_ISL_644267Dublin
EPI_ISL_644268Dublin
EPI_ISL_644271Dublin
EPI_ISL_644273Dublin
EPI_ISL_644274Dublin
EPI_ISL_644276Dublin
EPI_ISL_644278Dublin
EPI_ISL_644279Dublin
EPI_ISL_644281Dublin
EPI_ISL_644284Dublin
EPI_ISL_644285Dublin
EPI_ISL_644286Dublin
EPI_ISL_644287Dublin
EPI_ISL_644288Dublin
EPI_ISL_644289Dublin
EPI_ISL_644290Dublin
EPI_ISL_644292Dublin
EPI_ISL_644293Dublin
EPI_ISL_644294Dublin
EPI_ISL_644296Dublin
EPI_ISL_644297Dublin
EPI_ISL_644304Dublin
EPI_ISL_644305Dublin
EPI_ISL_644307Dublin
EPI_ISL_644308Dublin
EPI_ISL_644310Dublin
EPI_ISL_644314Dublin
EPI_ISL_644316Dublin
EPI_ISL_644318Dublin
EPI_ISL_644319Dublin
EPI_ISL_644321Dublin
EPI_ISL_644322Dublin
EPI_ISL_644323Dublin
EPI_ISL_644324Dublin
EPI_ISL_644325Dublin
EPI_ISL_644326Dublin
EPI_ISL_644328Dublin
EPI_ISL_644329Dublin
EPI_ISL_644331Dublin
EPI_ISL_644332Dublin
EPI_ISL_644333Dublin
EPI_ISL_644335Dublin
EPI_ISL_644336Dublin
EPI_ISL_644339Dublin
EPI_ISL_644340Dublin
EPI_ISL_644341Dublin
EPI_ISL_644342Dublin
EPI_ISL_644344Dublin
EPI_ISL_671337Dublin
EPI_ISL_671338Dublin
EPI_ISL_671339Dublin
EPI_ISL_671340Dublin
EPI_ISL_671341Dublin
EPI_ISL_671343Dublin
EPI_ISL_671344Dublin
EPI_ISL_671345Dublin
EPI_ISL_671346Dublin
EPI_ISL_671355Dublin
EPI_ISL_671356Dublin
EPI_ISL_671358Dublin
EPI_ISL_671359Dublin
EPI_ISL_671360Dublin
EPI_ISL_671362Dublin
EPI_ISL_671363Dublin
EPI_ISL_671364Dublin
EPI_ISL_671370Dublin
EPI_ISL_671373Dublin
EPI_ISL_671374Dublin
EPI_ISL_671376Dublin
EPI_ISL_671382Dublin
EPI_ISL_671383Dublin
EPI_ISL_671384Dublin
EPI_ISL_671386Dublin
EPI_ISL_671387Dublin
EPI_ISL_671388Dublin
EPI_ISL_671390Dublin
EPI_ISL_671395Dublin
EPI_ISL_671397Dublin
EPI_ISL_671398Dublin
EPI_ISL_671399Dublin
EPI_ISL_671402Dublin
EPI_ISL_671883Dublin
EPI_ISL_671884Dublin
EPI_ISL_671885Dublin
EPI_ISL_671886Dublin
EPI_ISL_671887Dublin
EPI_ISL_671888Dublin
EPI_ISL_671889Dublin
EPI_ISL_671890Dublin
EPI_ISL_671891Dublin
EPI_ISL_671892Dublin
EPI_ISL_671893Dublin
EPI_ISL_671894Dublin
EPI_ISL_671895Dublin
EPI_ISL_671896Dublin
EPI_ISL_671897Dublin
EPI_ISL_671898Dublin
EPI_ISL_671899Dublin
EPI_ISL_671900Dublin
EPI_ISL_671901Dublin
EPI_ISL_681887Dublin
EPI_ISL_681899Dublin
EPI_ISL_681900Dublin
EPI_ISL_681903Dublin
EPI_ISL_681905Dublin
EPI_ISL_681914Dublin
EPI_ISL_681919Dublin
EPI_ISL_681922Dublin
EPI_ISL_681925Dublin
EPI_ISL_708508Dublin
EPI_ISL_708510Dublin
EPI_ISL_708511Dublin
EPI_ISL_708512Dublin
EPI_ISL_708515Dublin
EPI_ISL_708516Dublin
EPI_ISL_708518Dublin
EPI_ISL_708521Dublin
EPI_ISL_708523Dublin
EPI_ISL_708524Dublin
EPI_ISL_708525Dublin
EPI_ISL_708527Dublin
EPI_ISL_732374Dublin
EPI_ISL_732375Dublin
EPI_ISL_732376Dublin
EPI_ISL_732377Dublin
EPI_ISL_732379Dublin
EPI_ISL_732380Dublin
EPI_ISL_732381Dublin
EPI_ISL_732382Dublin
EPI_ISL_732383Dublin
EPI_ISL_732384Dublin
EPI_ISL_732385Dublin
EPI_ISL_732386Dublin
EPI_ISL_732388Dublin
EPI_ISL_732389Dublin
EPI_ISL_732390Dublin
EPI_ISL_732391Dublin
EPI_ISL_732392Dublin
EPI_ISL_732394Dublin
EPI_ISL_732397Dublin
EPI_ISL_732398Dublin
EPI_ISL_732399Dublin
EPI_ISL_732400Dublin
EPI_ISL_732402Dublin
EPI_ISL_732403Dublin
EPI_ISL_732404Dublin
EPI_ISL_732405Dublin
EPI_ISL_732407Dublin
EPI_ISL_732409Dublin
EPI_ISL_732423Dublin
EPI_ISL_732435Dublin
EPI_ISL_732438Dublin
EPI_ISL_732439Dublin
EPI_ISL_732440Dublin
EPI_ISL_732441Dublin
EPI_ISL_732442Dublin
EPI_ISL_732443Dublin
EPI_ISL_732444Dublin
EPI_ISL_732446Dublin
EPI_ISL_732447Dublin
EPI_ISL_732448Dublin
EPI_ISL_732449Dublin
EPI_ISL_732450Dublin
EPI_ISL_732451Dublin
EPI_ISL_732452Dublin
EPI_ISL_732453Dublin
EPI_ISL_732455Dublin
EPI_ISL_732457Dublin
EPI_ISL_732458Dublin
EPI_ISL_732479Dublin
EPI_ISL_732480Dublin
EPI_ISL_732483Dublin
EPI_ISL_732484Dublin
EPI_ISL_732490Dublin
EPI_ISL_732491Dublin
EPI_ISL_732497Dublin
EPI_ISL_732498Dublin
EPI_ISL_732499Dublin
EPI_ISL_732500Dublin
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Ireland/Limerick-19933/2020 EPI_ISL_414585Limerick2020-03-03
Ireland/Limerick-19934/2020 EPI_ISL_414586Limerick2020-03-03
Ireland/Limerick-19935/2020 EPI_ISL_414587Limerick2020-03-03
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