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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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Tunisia

Number of isolates sequences available: 84

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_450490The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450491The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450492The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450493The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_450494The sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_463001
EPI_ISL_463002
EPI_ISL_463003
EPI_ISL_463004
EPI_ISL_463005
EPI_ISL_463006
EPI_ISL_803817Ariana
EPI_ISL_458286Ben Arous
EPI_ISL_632310Ben Arous
EPI_ISL_634977Ben Arous
EPI_ISL_654018Ben Arous
EPI_ISL_654020Ben Arous
EPI_ISL_683329Ben Arous
EPI_ISL_733500Ben Arous
EPI_ISL_803120Ben Arous
EPI_ISL_458285Bizerte
EPI_ISL_855557Bizerte
EPI_ISL_855562Bizerte
EPI_ISL_855565Bizerte
EPI_ISL_855566Bizerte
EPI_ISL_811145Djerba
EPI_ISL_707791Gafsa
EPI_ISL_796782Ksar Hellal
EPI_ISL_699657Monastir
EPI_ISL_710532Monastir
EPI_ISL_710534Monastir
EPI_ISL_710537Monastir
EPI_ISL_710540Monastir
EPI_ISL_710541Monastir
EPI_ISL_710575Monastir
EPI_ISL_711057Monastir
EPI_ISL_712060Monastir
EPI_ISL_635061Nabeul
EPI_ISL_654017Nabeul
EPI_ISL_699655Nabeul
EPI_ISL_707697Nabeul
EPI_ISL_707699Nabeul
EPI_ISL_707700Nabeul
EPI_ISL_733499Nabeul
EPI_ISL_794737Nabeul
EPI_ISL_803119Nabeul
EPI_ISL_803430Nabeul
EPI_ISL_803851Nabeul
EPI_ISL_712062Sfax
EPI_ISL_712063Sfax
EPI_ISL_712064Sfax
EPI_ISL_712065Sfax
EPI_ISL_712066Sfax
EPI_ISL_712067Sfax
EPI_ISL_712068Sfax
EPI_ISL_712069Sfax
EPI_ISL_712568Sfax
EPI_ISL_855564Sidi Bouzid
EPI_ISL_707698Soliman
EPI_ISL_450482TunisThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_635059Tunis
EPI_ISL_635060Tunis
EPI_ISL_635062Tunis
EPI_ISL_654016Tunis
EPI_ISL_654019Tunis
EPI_ISL_699656Tunis
EPI_ISL_707792Tunis
EPI_ISL_707793Tunis
EPI_ISL_763065Tunis
EPI_ISL_763067Tunis
EPI_ISL_794735Tunis
EPI_ISL_794736Tunis
EPI_ISL_794738Tunis
EPI_ISL_855558Tunis
EPI_ISL_855559Tunis
EPI_ISL_855560Tunis
EPI_ISL_855561Tunis
EPI_ISL_855563Tunis
EPI_ISL_855567Tunis
EPI_ISL_855568Tunis
EPI_ISL_855569Tunis
EPI_ISL_855570Tunis
EPI_ISL_855571Tunis
EPI_ISL_855572Tunis

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