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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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Ireland

Number of isolates sequences available: 329

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_525371Cavan
EPI_ISL_578236Clare
EPI_ISL_578246Clare
EPI_ISL_578247Clare
EPI_ISL_578248Clare
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
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_501264Galway
EPI_ISL_501265Galway
EPI_ISL_528458Galway
EPI_ISL_528459Galway
EPI_ISL_578237Galway
EPI_ISL_578238Galway
EPI_ISL_578276Galway
EPI_ISL_578277Galway
EPI_ISL_578278Galway
EPI_ISL_578279Galway
EPI_ISL_578280Galway
EPI_ISL_578281Galway
EPI_ISL_500595Kerry
EPI_ISL_578219Kerry
EPI_ISL_578220Kerry
EPI_ISL_501252Kildare
EPI_ISL_512087Kildare
EPI_ISL_512090Kildare
EPI_ISL_512091Kildare
EPI_ISL_512097Kildare
EPI_ISL_512102Kildare
EPI_ISL_512105Kildare
EPI_ISL_512106Kildare
EPI_ISL_525356Kildare
EPI_ISL_525357Kildare
EPI_ISL_525363Kildare
EPI_ISL_525375Kildare
EPI_ISL_525377Kildare
EPI_ISL_525378Kildare
EPI_ISL_525380Kildare
EPI_ISL_525381Kildare
EPI_ISL_525382Kildare
EPI_ISL_525383Kildare
EPI_ISL_525384Kildare
EPI_ISL_525385Kildare
EPI_ISL_525387Kildare
EPI_ISL_525388Kildare
EPI_ISL_525389Kildare
EPI_ISL_525390Kildare
EPI_ISL_525394Kildare
EPI_ISL_525395Kildare
EPI_ISL_525396Kildare
EPI_ISL_525400Kildare
EPI_ISL_525401Kildare
EPI_ISL_525404Kildare
EPI_ISL_525407Kildare
EPI_ISL_525414Kildare
EPI_ISL_525418Kildare
EPI_ISL_528441Kildare
EPI_ISL_528442Kildare
EPI_ISL_528454Kildare
EPI_ISL_528455Kildare
EPI_ISL_528466Kildare
EPI_ISL_528467Kildare
EPI_ISL_528468Kildare
EPI_ISL_528469Kildare
EPI_ISL_528479Kildare
EPI_ISL_578205Kildare
EPI_ISL_578209Kildare
EPI_ISL_578213Kildare
EPI_ISL_578215Kildare
EPI_ISL_578221Kildare
EPI_ISL_578222Kildare
EPI_ISL_578225Kildare
EPI_ISL_578239Kildare
EPI_ISL_578282Kildare
EPI_ISL_578283Kildare
EPI_ISL_578284Kildare
EPI_ISL_578285Kildare
EPI_ISL_578286Kildare
EPI_ISL_578287Kildare
EPI_ISL_578288Kildare
EPI_ISL_578289Kildare
EPI_ISL_578290Kildare
EPI_ISL_578291Kildare
EPI_ISL_578292Kildare
EPI_ISL_578293Kildare
EPI_ISL_578294Kildare
EPI_ISL_578295Kildare
EPI_ISL_578296Kildare
EPI_ISL_578297Kildare
EPI_ISL_578298Kildare
EPI_ISL_578299Kildare
EPI_ISL_578300Kildare
EPI_ISL_578301Kildare
EPI_ISL_500583Kilkenny
EPI_ISL_528449Kilkenny
EPI_ISL_528450Kilkenny
EPI_ISL_528451Kilkenny
EPI_ISL_528460Kilkenny
EPI_ISL_528461Kilkenny
EPI_ISL_528462Kilkenny
EPI_ISL_528463Kilkenny
EPI_ISL_528464Kilkenny
EPI_ISL_528478Kilkenny
EPI_ISL_528483Kilkenny
EPI_ISL_578302Kilkenny
EPI_ISL_578303Kilkenny
EPI_ISL_578304Kilkenny
EPI_ISL_578305Kilkenny
EPI_ISL_578306Kilkenny
EPI_ISL_578307Kilkenny
EPI_ISL_578308Kilkenny
EPI_ISL_512099Laois
EPI_ISL_525352Laois
EPI_ISL_525353Laois
EPI_ISL_525355Laois
EPI_ISL_525376Laois
EPI_ISL_525379Laois
EPI_ISL_525386Laois
EPI_ISL_525397Laois
EPI_ISL_578226Laois
EPI_ISL_578229Laois
EPI_ISL_500584Leitrim
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
EPI_ISL_500578Limerick
EPI_ISL_528443Limerick
EPI_ISL_528444Limerick
EPI_ISL_528445Limerick
EPI_ISL_528446Limerick
EPI_ISL_528475Limerick
EPI_ISL_578216Limerick
EPI_ISL_578310Limerick
EPI_ISL_578311Limerick
EPI_ISL_578312Limerick
EPI_ISL_578313Limerick
EPI_ISL_578314Limerick
EPI_ISL_578315Limerick
Ireland/22901/2020 EPI_ISL_418582Louth2020-03-10
EPI_ISL_501253Louth
EPI_ISL_501257Louth
EPI_ISL_501258Louth
EPI_ISL_501259Louth
EPI_ISL_501260Louth
EPI_ISL_512098Louth
EPI_ISL_525364Louth
EPI_ISL_578211Louth
EPI_ISL_578233Louth
EPI_ISL_578309Louth
EPI_ISL_578245Mayo
EPI_ISL_501255Meath
EPI_ISL_512088Meath
EPI_ISL_525361Meath
EPI_ISL_525365Meath
EPI_ISL_528456Meath
EPI_ISL_528457Meath
EPI_ISL_528473Meath
EPI_ISL_528474Meath
EPI_ISL_528482Meath
EPI_ISL_578212Meath
EPI_ISL_578218Meath
EPI_ISL_578244Meath
EPI_ISL_578316Meath
EPI_ISL_501254Monaghan
EPI_ISL_501256Monaghan
EPI_ISL_525354Offaly
EPI_ISL_525360Offaly
EPI_ISL_525391Offaly
EPI_ISL_525392Offaly
EPI_ISL_525393Offaly
EPI_ISL_525398Offaly
EPI_ISL_525399Offaly
EPI_ISL_525402Offaly
EPI_ISL_525403Offaly
EPI_ISL_525405Offaly
EPI_ISL_525406Offaly
EPI_ISL_525408Offaly
EPI_ISL_525409Offaly
EPI_ISL_525410Offaly
EPI_ISL_525411Offaly
EPI_ISL_525412Offaly
EPI_ISL_525413Offaly
EPI_ISL_525415Offaly
EPI_ISL_525416Offaly
EPI_ISL_525417Offaly
EPI_ISL_528448Offaly
EPI_ISL_528476Offaly
EPI_ISL_528477Offaly
EPI_ISL_578202Offaly
EPI_ISL_578317Offaly
EPI_ISL_578318Offaly
EPI_ISL_528453Roscommon
EPI_ISL_578214Roscommon
EPI_ISL_578319Roscommon
EPI_ISL_500573Sligo
EPI_ISL_578320Sligo
Ireland/21023/2020 EPI_ISL_418516Tipperary2020-03-06
EPI_ISL_578228Tipperary
EPI_ISL_500576Waterford
EPI_ISL_500581Waterford
EPI_ISL_500582Waterford
EPI_ISL_528452Waterford
EPI_ISL_528472Waterford
EPI_ISL_578227Waterford
EPI_ISL_578235Waterford
EPI_ISL_578240Waterford
EPI_ISL_578241Waterford
EPI_ISL_578321Waterford
EPI_ISL_578322Waterford
EPI_ISL_578323Waterford
EPI_ISL_578324Waterford
EPI_ISL_578325Waterford
EPI_ISL_578326Waterford
EPI_ISL_578327Waterford
EPI_ISL_578234Westmeath
EPI_ISL_525369Wexford
EPI_ISL_525370Wexford
EPI_ISL_578230Wexford
EPI_ISL_578333Wexford
EPI_ISL_578334Wexford
Ireland/24052/2020 EPI_ISL_418584Wicklow2020-03-10
EPI_ISL_500575Wicklow
EPI_ISL_500591Wicklow
EPI_ISL_578207Wicklow
EPI_ISL_578328Wicklow
EPI_ISL_578329Wicklow
EPI_ISL_578330Wicklow
EPI_ISL_578331Wicklow
EPI_ISL_578332Wicklow

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