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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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Oman

Number of isolates sequences available: 205

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_457995Buraimi
EPI_ISL_491153Buraymi
EPI_ISL_457993Dakhiliyah
EPI_ISL_491133Dakhiliyah
EPI_ISL_491134Dakhiliyah
EPI_ISL_491138Dakhiliyah
EPI_ISL_491147Dakhiliyah
EPI_ISL_491154Dakhiliyah
EPI_ISL_491164Dakhiliyah
EPI_ISL_491165Dakhiliyah
EPI_ISL_491171Dakhiliyah
EPI_ISL_491125Dhahirah
EPI_ISL_491136Dhahirah
EPI_ISL_491139Dhahirah
EPI_ISL_491140Dhahirah
EPI_ISL_491142Dhahirah
EPI_ISL_491162Dhahirah
EPI_ISL_491163Dhahirah
EPI_ISL_491168Dhahirah
EPI_ISL_457978Musca
EPI_ISL_457701Muscat
EPI_ISL_457702Muscat
EPI_ISL_457703Muscat
EPI_ISL_457704Muscat
EPI_ISL_457705Muscat
EPI_ISL_457706Muscat
EPI_ISL_457707Muscat
EPI_ISL_457937Muscat
EPI_ISL_457938Muscat
EPI_ISL_457939Muscat
EPI_ISL_457974Muscat
EPI_ISL_457975Muscat
EPI_ISL_457977Muscat
EPI_ISL_457979Muscat
EPI_ISL_457980Muscat
EPI_ISL_457981Muscat
EPI_ISL_457982MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_457983MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_457984MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_457985Muscat
EPI_ISL_457986Muscat
EPI_ISL_457987Muscat
EPI_ISL_457988Muscat
EPI_ISL_457989Muscat
EPI_ISL_457990Muscat
EPI_ISL_457994Muscat
EPI_ISL_457996Muscat
EPI_ISL_458116Muscat
EPI_ISL_458117Muscat
EPI_ISL_458118Muscat
EPI_ISL_458119Muscat
EPI_ISL_458120Muscat
EPI_ISL_458121Muscat
EPI_ISL_458122Muscat
EPI_ISL_458123Muscat
EPI_ISL_458124Muscat
EPI_ISL_458125MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_458126MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_458127MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_458128MuscatThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_458137MuscatThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_491116Muscat
EPI_ISL_491121Muscat
EPI_ISL_491123Muscat
EPI_ISL_491124Muscat
EPI_ISL_491126Muscat
EPI_ISL_491128Muscat
EPI_ISL_491135Muscat
EPI_ISL_491137Muscat
EPI_ISL_491141Muscat
EPI_ISL_491146Muscat
EPI_ISL_491158Muscat
EPI_ISL_491159Muscat
EPI_ISL_491968Muscat
EPI_ISL_491969Muscat
EPI_ISL_491970Muscat
EPI_ISL_491971MuscatThe sequence is not availableThe sequence is not available
EPI_ISL_491972MuscatThe sequence is not availableThe sequence is not available
EPI_ISL_491973Muscat
EPI_ISL_491974Muscat
EPI_ISL_491975Muscat
EPI_ISL_491976Muscat
EPI_ISL_491977MuscatThe sequence is not available
EPI_ISL_491978Muscat
EPI_ISL_491979Muscat
EPI_ISL_491980Muscat
EPI_ISL_491981Muscat
EPI_ISL_491982Muscat
EPI_ISL_491983Muscat
EPI_ISL_491984Muscat
EPI_ISL_491985Muscat
EPI_ISL_491986Muscat
EPI_ISL_491987MuscatThe sequence is not available
EPI_ISL_491988Muscat
EPI_ISL_491989Muscat
EPI_ISL_491990Muscat
EPI_ISL_491991Muscat
EPI_ISL_491992Muscat
EPI_ISL_491993Muscat
EPI_ISL_491994Muscat
EPI_ISL_491995Muscat
EPI_ISL_491996Muscat
EPI_ISL_491997Muscat
EPI_ISL_491998Muscat
EPI_ISL_491999Muscat
EPI_ISL_492000Muscat
EPI_ISL_492001Muscat
EPI_ISL_492002Muscat
EPI_ISL_492003Muscat
EPI_ISL_492004MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_492005Muscat
EPI_ISL_492006Muscat
EPI_ISL_492007Muscat
EPI_ISL_492008Muscat
EPI_ISL_492009Muscat
EPI_ISL_492010Muscat
EPI_ISL_492011Muscat
EPI_ISL_492012Muscat
EPI_ISL_492013MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_492014Muscat
EPI_ISL_492015MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_492016Muscat
EPI_ISL_492017Muscat
EPI_ISL_492018MuscatThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_492019Muscat
EPI_ISL_492020Muscat
EPI_ISL_492021Muscat
EPI_ISL_492022Muscat
EPI_ISL_492023Muscat
EPI_ISL_492024Muscat
EPI_ISL_492025Muscat
EPI_ISL_492026Muscat
EPI_ISL_492065Muscat
EPI_ISL_518821Muscat
EPI_ISL_518822Muscat
EPI_ISL_518823Muscat
EPI_ISL_518824Muscat
EPI_ISL_518825Muscat
EPI_ISL_518826Muscat
EPI_ISL_518827Muscat
EPI_ISL_518828Muscat
EPI_ISL_518829Muscat
EPI_ISL_518830Muscat
EPI_ISL_518831Muscat
EPI_ISL_518832Muscat
EPI_ISL_518833Muscat
EPI_ISL_518834Muscat
EPI_ISL_518835Muscat
EPI_ISL_518836Muscat
EPI_ISL_518837Muscat
EPI_ISL_518838Muscat
EPI_ISL_518839Muscat
EPI_ISL_518840Muscat
EPI_ISL_518841Muscat
EPI_ISL_518842Muscat
EPI_ISL_518843Muscat
EPI_ISL_518844Muscat
EPI_ISL_518845Muscat
EPI_ISL_518846Muscat
EPI_ISL_518847Muscat
EPI_ISL_518848Muscat
EPI_ISL_518849Muscat
EPI_ISL_518850Muscat
EPI_ISL_518851Muscat
EPI_ISL_518852Muscat
EPI_ISL_518853Muscat
EPI_ISL_518854Muscat
EPI_ISL_525425Muscat
EPI_ISL_525426Muscat
EPI_ISL_525427Muscat
EPI_ISL_525428Muscat
EPI_ISL_525429Muscat
EPI_ISL_525466Muscat
EPI_ISL_766569Muscat
EPI_ISL_766570Muscat
EPI_ISL_457997Muscta
EPI_ISL_457976North Batinah
EPI_ISL_457991North Batinah
EPI_ISL_491161North Sharqiyah
EPI_ISL_457992South Batinah
EPI_ISL_457998South Batinah
EPI_ISL_491122South Batinah
EPI_ISL_491127South Batinah
EPI_ISL_491129South Batinah
EPI_ISL_491130South Batinah
EPI_ISL_491131South Batinah
EPI_ISL_491132South Batinah
EPI_ISL_491143South Batinah
EPI_ISL_491144South Batinah
EPI_ISL_491145South Batinah
EPI_ISL_491148South Batinah
EPI_ISL_491149South Batinah
EPI_ISL_491150South Batinah
EPI_ISL_491151South Batinah
EPI_ISL_491152South Batinah
EPI_ISL_491155South Batinah
EPI_ISL_491156South Batinah
EPI_ISL_491157South Batinah
EPI_ISL_491160South Batinah
EPI_ISL_491166South Batinah
EPI_ISL_491167South Batinah
EPI_ISL_491169South Batinah
EPI_ISL_491170South Batinah
EPI_ISL_525423South Batinah
EPI_ISL_525424South Batinah

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