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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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Viet Nam

Number of isolates sequences available: 25

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_654866Ho Chi Minh city
EPI_ISL_654867Ho Chi Minh city
EPI_ISL_654868Ho Chi Minh city
EPI_ISL_654869Ho Chi Minh city
EPI_ISL_654870Ho Chi Minh city
EPI_ISL_654872Ho Chi Minh city
EPI_ISL_654873Ho Chi Minh city
EPI_ISL_654874Ho Chi Minh city
EPI_ISL_654875Ho Chi Minh city
EPI_ISL_654876Ho Chi Minh city
EPI_ISL_654877Ho Chi Minh city
EPI_ISL_654878Ho Chi Minh city
EPI_ISL_654879Ho Chi Minh city
EPI_ISL_654880Ho Chi Minh city
EPI_ISL_654881Ho Chi Minh city
EPI_ISL_654882Ho Chi Minh city
EPI_ISL_654883Ho Chi Minh city
EPI_ISL_654884Ho Chi Minh city
EPI_ISL_654885Ho Chi Minh city
EPI_ISL_654886Ho Chi Minh city
EPI_ISL_654887Ho Chi Minh city
EPI_ISL_654888Ho Chi Minh city
EPI_ISL_654889Ho Chi Minh city
EPI_ISL_654890Ho Chi Minh city
EPI_ISL_654891Ho Chi Minh city

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