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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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Indonesia

Number of isolates sequences available: 114

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_538503Bali
EPI_ISL_438546BantenThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_438547BantenThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_438548BantenThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_438549BantenThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_518819Banten
EPI_ISL_574611Banten
EPI_ISL_525492Central Java
EPI_ISL_576383Central Java
EPI_ISL_538502Central Kalimantan
EPI_ISL_437187East Java
EPI_ISL_437188East Java
EPI_ISL_458079East Java
EPI_ISL_458081East Java
EPI_ISL_458082East Java
EPI_ISL_458083East Java
EPI_ISL_529138East Java
EPI_ISL_529961East Java
EPI_ISL_529962East Java
EPI_ISL_529963East Java
EPI_ISL_529964East Java
EPI_ISL_529965East Java
EPI_ISL_529966East Java
EPI_ISL_529967East Java
EPI_ISL_538498East Java
EPI_ISL_538499East Java
EPI_ISL_538511East Java
EPI_ISL_560991East Java
EPI_ISL_568686East Java
EPI_ISL_467374East Kalimantan
EPI_ISL_414375JakartaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_414376JakartaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_414377JakartaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_428207JakartaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_428208JakartaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_435281Jakarta
EPI_ISL_435282Jakarta
EPI_ISL_435283Jakarta
EPI_ISL_437189Jakarta
EPI_ISL_437190Jakarta
EPI_ISL_437191Jakarta
EPI_ISL_437192Jakarta
EPI_ISL_467376Jakarta
EPI_ISL_518820Jakarta
EPI_ISL_538504Jakarta
EPI_ISL_538505Jakarta
EPI_ISL_538508Jakarta
EPI_ISL_538509Jakarta
EPI_ISL_568687Jakarta
EPI_ISL_568688Jakarta
EPI_ISL_568689Jakarta
EPI_ISL_568690Jakarta
EPI_ISL_568691Jakarta
EPI_ISL_568692Jakarta
EPI_ISL_574433Jakarta
EPI_ISL_574607Jakarta
EPI_ISL_574608Jakarta
EPI_ISL_574609Jakarta
EPI_ISL_574610Jakarta
EPI_ISL_574613Jakarta
EPI_ISL_574614Jakarta
EPI_ISL_574615Jakarta
EPI_ISL_574616Jakarta
EPI_ISL_574617Jakarta
EPI_ISL_574618Jakarta
EPI_ISL_576386Jakarta
EPI_ISL_576387Jakarta
EPI_ISL_467375North Sulawesi
EPI_ISL_568694North Sulawesi
EPI_ISL_574604North Sulawesi
EPI_ISL_574619North Sulawesi
EPI_ISL_574620North Sulawesi
EPI_ISL_574621North Sulawesi
EPI_ISL_574622North Sulawesi
EPI_ISL_574623North Sulawesi
EPI_ISL_538500North Sumatra
EPI_ISL_538501North Sumatra
EPI_ISL_538506Papua
EPI_ISL_538507Papua
EPI_ISL_538512Papua
EPI_ISL_568693Papua
EPI_ISL_574603Papua
EPI_ISL_538510South Kalimantan
EPI_ISL_576385South Kalimantan
EPI_ISL_516800Special Region of Yogyakarta
EPI_ISL_516806Special Region of Yogyakarta
EPI_ISL_516829Special Region of Yogyakarta
EPI_ISL_574605Special Region of Yogyakarta
EPI_ISL_575331Special Region of Yogyakarta
EPI_ISL_576113Special Region of Yogyakarta
EPI_ISL_576114Special Region of Yogyakarta
EPI_ISL_576115Special Region of Yogyakarta
EPI_ISL_576116Special Region of Yogyakarta
EPI_ISL_576128Special Region of Yogyakarta
EPI_ISL_576130Special Region of Yogyakarta
EPI_ISL_576145Special Region of Yogyakarta
EPI_ISL_413219West JavaThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not availableThe sequence is not available
EPI_ISL_511878West Java
EPI_ISL_511879West Java
EPI_ISL_528745West Java
EPI_ISL_528746West Java
EPI_ISL_528747West Java
EPI_ISL_528748West Java
EPI_ISL_528749West Java
EPI_ISL_528750West Java
EPI_ISL_528751West Java
EPI_ISL_528752West Java
EPI_ISL_528753West Java
EPI_ISL_528759West Java
EPI_ISL_529718West Java
EPI_ISL_529719West Java
EPI_ISL_538513West Java
EPI_ISL_574606West Java
EPI_ISL_574612West Java

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