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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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Myanmar

Number of isolates sequences available: 41

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_434709
EPI_ISL_849736
EPI_ISL_849737
EPI_ISL_849738
EPI_ISL_849739
EPI_ISL_849740
EPI_ISL_849741
EPI_ISL_849742
EPI_ISL_849743
EPI_ISL_833041Nay Pyi Taw
EPI_ISL_896579Rakhine
EPI_ISL_896580Rakhine
EPI_ISL_896581Rakhine
EPI_ISL_896582Rakhine
EPI_ISL_896583Rakhine
EPI_ISL_896584Rakhine
EPI_ISL_896585Rakhine
EPI_ISL_896586Rakhine
EPI_ISL_896587Rakhine
EPI_ISL_896588Rakhine
EPI_ISL_896589Rakhine
EPI_ISL_896590Rakhine
EPI_ISL_896591Rakhine
EPI_ISL_512844Yangon
EPI_ISL_896572Yangon
EPI_ISL_896573Yangon
EPI_ISL_896574Yangon
EPI_ISL_896575Yangon
EPI_ISL_896576Yangon
EPI_ISL_896577Yangon
EPI_ISL_896578Yangon
EPI_ISL_896592Yangon
EPI_ISL_896593Yangon
EPI_ISL_896594Yangon
EPI_ISL_896595Yangon
EPI_ISL_896596Yangon
EPI_ISL_896597Yangon
EPI_ISL_896598Yangon
EPI_ISL_896599Yangon
EPI_ISL_896600Yangon
EPI_ISL_896601Yangon

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