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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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Gambia

Number of isolates sequences available: 360

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_471158Kombo
EPI_ISL_471159Kombo
EPI_ISL_471160Kombo
EPI_ISL_471161Kombo
EPI_ISL_471162Kombo
EPI_ISL_471163Kombo
EPI_ISL_471164Kombo
EPI_ISL_471165Kombo
EPI_ISL_471166Kombo
EPI_ISL_471167Kombo
EPI_ISL_471168Kombo
EPI_ISL_471169Kombo
EPI_ISL_471170Kombo
EPI_ISL_471171Kombo
EPI_ISL_560992Kombo
EPI_ISL_560993Kombo
EPI_ISL_560994Kombo
EPI_ISL_560995Kombo
EPI_ISL_560996Kombo
EPI_ISL_560997Kombo
EPI_ISL_560998Kombo
EPI_ISL_560999Kombo
EPI_ISL_561000Kombo
EPI_ISL_561001Kombo
EPI_ISL_561002Kombo
EPI_ISL_561003Kombo
EPI_ISL_561004Kombo
EPI_ISL_561005Kombo
EPI_ISL_561006Kombo
EPI_ISL_561007Kombo
EPI_ISL_561008Kombo
EPI_ISL_561009Kombo
EPI_ISL_561010Kombo
EPI_ISL_561011Kombo
EPI_ISL_561012Kombo
EPI_ISL_561013Kombo
EPI_ISL_561014Kombo
EPI_ISL_561015Kombo
EPI_ISL_561016Kombo
EPI_ISL_561017Kombo
EPI_ISL_561018Kombo
EPI_ISL_561019Kombo
EPI_ISL_561020Kombo
EPI_ISL_561021Kombo
EPI_ISL_561022Kombo
EPI_ISL_561023Kombo
EPI_ISL_561024Kombo
EPI_ISL_561025Kombo
EPI_ISL_561026Kombo
EPI_ISL_561027Kombo
EPI_ISL_561028Kombo
EPI_ISL_561029Kombo
EPI_ISL_561030Kombo
EPI_ISL_561031Kombo
EPI_ISL_561032Kombo
EPI_ISL_561033Kombo
EPI_ISL_561034Kombo
EPI_ISL_561035Kombo
EPI_ISL_561036Kombo
EPI_ISL_561037Kombo
EPI_ISL_561038Kombo
EPI_ISL_561039Kombo
EPI_ISL_561040Kombo
EPI_ISL_561041Kombo
EPI_ISL_561042Kombo
EPI_ISL_561043Kombo
EPI_ISL_561044Kombo
EPI_ISL_561045Kombo
EPI_ISL_561046Kombo
EPI_ISL_561047Kombo
EPI_ISL_561048Kombo
EPI_ISL_561049Kombo
EPI_ISL_561050Kombo
EPI_ISL_561051Kombo
EPI_ISL_561052Kombo
EPI_ISL_561053Kombo
EPI_ISL_561054Kombo
EPI_ISL_561055Kombo
EPI_ISL_561056Kombo
EPI_ISL_561057Kombo
EPI_ISL_561058Kombo
EPI_ISL_561059Kombo
EPI_ISL_561060Kombo
EPI_ISL_561061Kombo
EPI_ISL_561062Kombo
EPI_ISL_561063Kombo
EPI_ISL_561064Kombo
EPI_ISL_561065Kombo
EPI_ISL_561066Kombo
EPI_ISL_561067Kombo
EPI_ISL_561068Kombo
EPI_ISL_561069Kombo
EPI_ISL_561070Kombo
EPI_ISL_561071Kombo
EPI_ISL_561072Kombo
EPI_ISL_561073Kombo
EPI_ISL_561074Kombo
EPI_ISL_561075Kombo
EPI_ISL_561076Kombo
EPI_ISL_561077Kombo
EPI_ISL_561078Kombo
EPI_ISL_561079Kombo
EPI_ISL_561080Kombo
EPI_ISL_561081Kombo
EPI_ISL_561082Kombo
EPI_ISL_561083Kombo
EPI_ISL_561084Kombo
EPI_ISL_561085Kombo
EPI_ISL_561086Kombo
EPI_ISL_561087Kombo
EPI_ISL_561088Kombo
EPI_ISL_561089Kombo
EPI_ISL_561090Kombo
EPI_ISL_561091Kombo
EPI_ISL_561092Kombo
EPI_ISL_561093Kombo
EPI_ISL_561094Kombo
EPI_ISL_561095Kombo
EPI_ISL_561096Kombo
EPI_ISL_561097Kombo
EPI_ISL_561098Kombo
EPI_ISL_561099Kombo
EPI_ISL_561100Kombo
EPI_ISL_561101Kombo
EPI_ISL_561102Kombo
EPI_ISL_561103Kombo
EPI_ISL_561104Kombo
EPI_ISL_561105Kombo
EPI_ISL_561106Kombo
EPI_ISL_561107Kombo
EPI_ISL_561108Kombo
EPI_ISL_561109Kombo
EPI_ISL_561110Kombo
EPI_ISL_561111Kombo
EPI_ISL_561112Kombo
EPI_ISL_561113Kombo
EPI_ISL_561114Kombo
EPI_ISL_561115Kombo
EPI_ISL_561116Kombo
EPI_ISL_561117Kombo
EPI_ISL_561118Kombo
EPI_ISL_561119Kombo
EPI_ISL_561120Kombo
EPI_ISL_561121Kombo
EPI_ISL_561122Kombo
EPI_ISL_561123Kombo
EPI_ISL_561124Kombo
EPI_ISL_561125Kombo
EPI_ISL_561126Kombo
EPI_ISL_561127Kombo
EPI_ISL_561128Kombo
EPI_ISL_561129Kombo
EPI_ISL_561130Kombo
EPI_ISL_561131Kombo
EPI_ISL_561132Kombo
EPI_ISL_561133Kombo
EPI_ISL_561134Kombo
EPI_ISL_561135Kombo
EPI_ISL_561136Kombo
EPI_ISL_561137Kombo
EPI_ISL_561138Kombo
EPI_ISL_561139Kombo
EPI_ISL_561140Kombo
EPI_ISL_561141Kombo
EPI_ISL_561142Kombo
EPI_ISL_561143Kombo
EPI_ISL_561144Kombo
EPI_ISL_561145Kombo
EPI_ISL_561146Kombo
EPI_ISL_561147Kombo
EPI_ISL_561148Kombo
EPI_ISL_561149Kombo
EPI_ISL_561150Kombo
EPI_ISL_561151Kombo
EPI_ISL_561152Kombo
EPI_ISL_561153Kombo
EPI_ISL_561154Kombo
EPI_ISL_561155Kombo
EPI_ISL_561156Kombo
EPI_ISL_561157Kombo
EPI_ISL_561158Kombo
EPI_ISL_561159Kombo
EPI_ISL_561160Kombo
EPI_ISL_561161Kombo
EPI_ISL_561162Kombo
EPI_ISL_561163Kombo
EPI_ISL_561164Kombo
EPI_ISL_561165Kombo
EPI_ISL_561166Kombo
EPI_ISL_561167Kombo
EPI_ISL_561168Kombo
EPI_ISL_561169Kombo
EPI_ISL_561170Kombo
EPI_ISL_561171Kombo
EPI_ISL_561172Kombo
EPI_ISL_561173Kombo
EPI_ISL_561174Kombo
EPI_ISL_561175Kombo
EPI_ISL_561176Kombo
EPI_ISL_561177Kombo
EPI_ISL_561178Kombo
EPI_ISL_561179Kombo
EPI_ISL_561180Kombo
EPI_ISL_561181Kombo
EPI_ISL_561182Kombo
EPI_ISL_561183Kombo
EPI_ISL_561184Kombo
EPI_ISL_561185Kombo
EPI_ISL_561186Kombo
EPI_ISL_561187Kombo
EPI_ISL_561188Kombo
EPI_ISL_561189Kombo
EPI_ISL_561190Kombo
EPI_ISL_561191Kombo
EPI_ISL_561192Kombo
EPI_ISL_561193Kombo
EPI_ISL_561194Kombo
EPI_ISL_561195Kombo
EPI_ISL_561196Kombo
EPI_ISL_561197Kombo
EPI_ISL_561198Kombo
EPI_ISL_561199Kombo
EPI_ISL_561200Kombo
EPI_ISL_561201Kombo
EPI_ISL_561202Kombo
EPI_ISL_561203Kombo
EPI_ISL_561204Kombo
EPI_ISL_561205Kombo
EPI_ISL_561206Kombo
EPI_ISL_561207Kombo
EPI_ISL_561208Kombo
EPI_ISL_561209Kombo
EPI_ISL_561210Kombo
EPI_ISL_561211Kombo
EPI_ISL_561212Kombo
EPI_ISL_561213Kombo
EPI_ISL_561214Kombo
EPI_ISL_561215Kombo
EPI_ISL_561216Kombo
EPI_ISL_561217Kombo
EPI_ISL_561218Kombo
EPI_ISL_561219Kombo
EPI_ISL_561220Kombo
EPI_ISL_561221Kombo
EPI_ISL_561222Kombo
EPI_ISL_561223Kombo
EPI_ISL_561224Kombo
EPI_ISL_561225Kombo
EPI_ISL_561226Kombo
EPI_ISL_561227Kombo
EPI_ISL_561228Kombo
EPI_ISL_561229Kombo
EPI_ISL_561230Kombo
EPI_ISL_561231Kombo
EPI_ISL_561232Kombo
EPI_ISL_561233Kombo
EPI_ISL_561234Kombo
EPI_ISL_561235Kombo
EPI_ISL_561236Kombo
EPI_ISL_561237Kombo
EPI_ISL_561238Kombo
EPI_ISL_561239Kombo
EPI_ISL_561240Kombo
EPI_ISL_561241Kombo
EPI_ISL_561242Kombo
EPI_ISL_561243Kombo
EPI_ISL_561244Kombo
EPI_ISL_561245Kombo
EPI_ISL_561246Kombo
EPI_ISL_561247Kombo
EPI_ISL_561248Kombo
EPI_ISL_561249Kombo
EPI_ISL_561250Kombo
EPI_ISL_561251Kombo
EPI_ISL_561252Kombo
EPI_ISL_561253Kombo
EPI_ISL_561254Kombo
EPI_ISL_561255Kombo
EPI_ISL_561256Kombo
EPI_ISL_561257Kombo
EPI_ISL_561258Kombo
EPI_ISL_561259Kombo
EPI_ISL_561260Kombo
EPI_ISL_561261Kombo
EPI_ISL_561262Kombo
EPI_ISL_561263Kombo
EPI_ISL_561264Kombo
EPI_ISL_561265Kombo
EPI_ISL_561266Kombo
EPI_ISL_561267Kombo
EPI_ISL_561268Kombo
EPI_ISL_561269Kombo
EPI_ISL_561270Kombo
EPI_ISL_561271Kombo
EPI_ISL_561272Kombo
EPI_ISL_561273Kombo
EPI_ISL_561274Kombo
EPI_ISL_561275Kombo
EPI_ISL_561276Kombo
EPI_ISL_561277Kombo
EPI_ISL_561278Kombo
EPI_ISL_561279Kombo
EPI_ISL_561280Kombo
EPI_ISL_561281Kombo
EPI_ISL_561282Kombo
EPI_ISL_561283Kombo
EPI_ISL_561284Kombo
EPI_ISL_561285Kombo
EPI_ISL_561286Kombo
EPI_ISL_561287Kombo
EPI_ISL_561288Kombo
EPI_ISL_561289Kombo
EPI_ISL_561290Kombo
EPI_ISL_561291Kombo
EPI_ISL_561292Kombo
EPI_ISL_561293Kombo
EPI_ISL_561294Kombo
EPI_ISL_561295Kombo
EPI_ISL_561296Kombo
EPI_ISL_561297Kombo
EPI_ISL_561298Kombo
EPI_ISL_561299Kombo
EPI_ISL_561300Kombo
EPI_ISL_561301Kombo
EPI_ISL_561302Kombo
EPI_ISL_561303Kombo
EPI_ISL_561304Kombo
EPI_ISL_561305Kombo
EPI_ISL_561306Kombo
EPI_ISL_561307Kombo
EPI_ISL_561308Kombo
EPI_ISL_561309Kombo
EPI_ISL_561310Kombo
EPI_ISL_561311Kombo
EPI_ISL_561312Kombo
EPI_ISL_561313Kombo
EPI_ISL_561314Kombo
EPI_ISL_561315Kombo
EPI_ISL_561316Kombo
EPI_ISL_561317Kombo
EPI_ISL_561318Kombo
EPI_ISL_561319Kombo
EPI_ISL_561320Kombo
EPI_ISL_561321Kombo
EPI_ISL_561322Kombo
EPI_ISL_561323Kombo
EPI_ISL_561324Kombo
EPI_ISL_561325Kombo
EPI_ISL_561326Kombo
EPI_ISL_561327Kombo
EPI_ISL_561328Kombo
EPI_ISL_561329Kombo
EPI_ISL_561330Kombo
EPI_ISL_561331Kombo
EPI_ISL_561332Kombo
EPI_ISL_561333Kombo
EPI_ISL_561334Kombo
Gambia/GC19-015/2020 EPI_ISL_428855West Coast Region2020-03-17
Gambia/GC19-026/2020 EPI_ISL_428856West Coast Region2020-03-21
Gambia/GC19-029/2020 EPI_ISL_428857West Coast Region2020-04-20

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