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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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Greece

Number of isolates sequences available: 133

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
Greece/10/2020 EPI_ISL_418263Athens2020-03-18
Greece/12/2020 EPI_ISL_418264Athens2020-03-18
Greece/16/2020 EPI_ISL_418265Athens2020-03-18
Greece/13/2020 EPI_ISL_427043Athens2020-03-18
EPI_ISL_430469Athens
EPI_ISL_434455Athens
EPI_ISL_434456Athens
EPI_ISL_434457Athens
EPI_ISL_434458Athens
EPI_ISL_434459Athens
EPI_ISL_434460Athens
EPI_ISL_434461Athens
EPI_ISL_434462Athens
EPI_ISL_434463Athens
EPI_ISL_434464Athens
EPI_ISL_434465Athens
EPI_ISL_434466Athens
EPI_ISL_434467Athens
EPI_ISL_434468Athens
EPI_ISL_434469Athens
EPI_ISL_434470Athens
EPI_ISL_434471Athens
EPI_ISL_434472Athens
EPI_ISL_434473Athens
EPI_ISL_434474Athens
EPI_ISL_434475Athens
EPI_ISL_434476Athens
EPI_ISL_434477Athens
EPI_ISL_434478Athens
EPI_ISL_434479Athens
EPI_ISL_434480Athens
EPI_ISL_434481Athens
EPI_ISL_434482Athens
EPI_ISL_434483Athens
EPI_ISL_434484Athens
EPI_ISL_434485Athens
EPI_ISL_434486Athens
EPI_ISL_437874Athens
EPI_ISL_437875Athens
EPI_ISL_437876Athens
EPI_ISL_437877Athens
EPI_ISL_437878Athens
EPI_ISL_437879Athens
EPI_ISL_437880Athens
EPI_ISL_437881Athens
EPI_ISL_437882Athens
EPI_ISL_437883Athens
EPI_ISL_437884Athens
EPI_ISL_437885Athens
EPI_ISL_437886Athens
EPI_ISL_437887Athens
EPI_ISL_437888Athens
EPI_ISL_437889Athens
EPI_ISL_437890Athens
EPI_ISL_437891Athens
EPI_ISL_437892Athens
EPI_ISL_437893Athens
EPI_ISL_437894Athens
EPI_ISL_437895Athens
EPI_ISL_437896Athens
EPI_ISL_437897Athens
EPI_ISL_437898Athens
EPI_ISL_437899Athens
EPI_ISL_437900Athens
EPI_ISL_437901Athens
EPI_ISL_437902Athens
EPI_ISL_437903Athens
EPI_ISL_437904Athens
EPI_ISL_437905Athens
EPI_ISL_437906Athens
EPI_ISL_437907Athens
EPI_ISL_437908Athens
EPI_ISL_437909Athens
EPI_ISL_437910Athens
EPI_ISL_437911Athens
EPI_ISL_447635Athens
EPI_ISL_447636Athens
EPI_ISL_447637Athens
EPI_ISL_447638Athens
EPI_ISL_447639Athens
EPI_ISL_447640Athens
EPI_ISL_447641Athens
EPI_ISL_447642Athens
EPI_ISL_447643Athens
EPI_ISL_447644Athens
EPI_ISL_447645Athens
EPI_ISL_447646Athens
EPI_ISL_447647Athens
EPI_ISL_447648Athens
EPI_ISL_447649Athens
EPI_ISL_447650Athens
EPI_ISL_447651Athens
EPI_ISL_447652Athens
EPI_ISL_447653Athens
EPI_ISL_447832Athens
EPI_ISL_447833Athens
EPI_ISL_447834Athens
EPI_ISL_447835Athens
EPI_ISL_447836Athens
EPI_ISL_451310Athens
EPI_ISL_451311Athens
EPI_ISL_487370Athens
EPI_ISL_487377Athens
EPI_ISL_487379Athens
EPI_ISL_487381Athens
EPI_ISL_501231Athens
EPI_ISL_501232Athens
EPI_ISL_501233Athens
EPI_ISL_501234Athens
EPI_ISL_501235Athens
EPI_ISL_501236Athens
EPI_ISL_501237Athens
EPI_ISL_501238Athens
EPI_ISL_501241Athens
EPI_ISL_501242Athens
EPI_ISL_501246Athens
EPI_ISL_501248Athens
EPI_ISL_501249Athens
EPI_ISL_501250Athens
EPI_ISL_501251Athens
EPI_ISL_529147Athens
EPI_ISL_529148Athens
EPI_ISL_501230Livadia
EPI_ISL_476835Thessaloniki
EPI_ISL_476836Thessaloniki
EPI_ISL_476837Thessaloniki
EPI_ISL_476838Thessaloniki
EPI_ISL_476839Thessaloniki
EPI_ISL_476841Thessaloniki
EPI_ISL_476843Thessaloniki
EPI_ISL_476845Thessaloniki
EPI_ISL_476847Thessaloniki
EPI_ISL_476851Thessaloniki

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