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Status of SARS-CoV-2 detection systems (RT-PCR)
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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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Rwanda

Number of isolates sequences available: 36

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_614763
EPI_ISL_614891
EPI_ISL_614892
EPI_ISL_614980
EPI_ISL_615063
EPI_ISL_615064
EPI_ISL_615066
EPI_ISL_615067
EPI_ISL_615069
EPI_ISL_615071
EPI_ISL_615074
EPI_ISL_615075
EPI_ISL_707711
EPI_ISL_707712
EPI_ISL_707713
EPI_ISL_707771
EPI_ISL_707772
EPI_ISL_707773
EPI_ISL_707774
EPI_ISL_707776
EPI_ISL_707777
EPI_ISL_707779
EPI_ISL_707780
EPI_ISL_707783
EPI_ISL_707787
EPI_ISL_707788
EPI_ISL_707789
EPI_ISL_707790
EPI_ISL_735437
EPI_ISL_735436Kigali
EPI_ISL_735438Kigali
EPI_ISL_735444Kigali
EPI_ISL_735445Kigali
EPI_ISL_735446Kigali
EPI_ISL_735447Kigali
EPI_ISL_735448Kigali

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