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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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Kazakhstan

Number of isolates sequences available: 56

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_514093AlmatyThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514126AlmatyThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_514127AlmatyThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_435045Nur-Sultan
EPI_ISL_435046Nur-Sultan
EPI_ISL_435047Nur-Sultan
EPI_ISL_435048Nur-Sultan
EPI_ISL_454497Nur-Sultan
EPI_ISL_454498Nur-Sultan
EPI_ISL_454499Nur-Sultan
EPI_ISL_454500Nur-Sultan
EPI_ISL_454501Nur-Sultan
EPI_ISL_454502Nur-Sultan
EPI_ISL_454503Nur-Sultan
EPI_ISL_454504Nur-Sultan
EPI_ISL_454505Nur-Sultan
EPI_ISL_454506Nur-Sultan
EPI_ISL_454507Nur-Sultan
EPI_ISL_454508Nur-Sultan
EPI_ISL_454509Nur-Sultan
EPI_ISL_454510Nur-Sultan
EPI_ISL_454511Nur-Sultan
EPI_ISL_454512Nur-Sultan
EPI_ISL_454513Nur-Sultan
EPI_ISL_454514Nur-Sultan
EPI_ISL_454515Nur-Sultan
EPI_ISL_454516Nur-Sultan
EPI_ISL_454517Nur-Sultan
EPI_ISL_454518Nur-Sultan
EPI_ISL_454519Nur-Sultan
EPI_ISL_454520Nur-Sultan
EPI_ISL_454571Nur-Sultan
EPI_ISL_454572Nur-Sultan
EPI_ISL_454575Nur-Sultan
EPI_ISL_454576Nur-Sultan
EPI_ISL_454577Nur-Sultan
EPI_ISL_454579Nur-Sultan
EPI_ISL_454580Nur-Sultan
EPI_ISL_454582Nur-Sultan
EPI_ISL_454584Nur-Sultan
EPI_ISL_454585Nur-Sultan
EPI_ISL_454586Nur-Sultan
EPI_ISL_454587Nur-Sultan
EPI_ISL_454589Nur-Sultan
EPI_ISL_454590Nur-Sultan
EPI_ISL_454591Nur-Sultan
EPI_ISL_454593Nur-Sultan
EPI_ISL_454594Nur-Sultan
EPI_ISL_454596Nur-Sultan
EPI_ISL_454597Nur-Sultan
EPI_ISL_454598Nur-Sultan
EPI_ISL_454599Nur-Sultan
EPI_ISL_454600Nur-Sultan
EPI_ISL_454601Nur-Sultan
EPI_ISL_454603Nur-Sultan
EPI_ISL_454604Nur-Sultan

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