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Status of SARS-CoV-2 detection systems (RT-PCR)
enabled by data from GISAID logo


Update: Sun Jan 10 05:32:46 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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Equatorial Guinea

Number of isolates sequences available: 95

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_648318
EPI_ISL_648372
EPI_ISL_648374
EPI_ISL_648379
EPI_ISL_648304Bioko Norte
EPI_ISL_648305Bioko Norte
EPI_ISL_648306Bioko Norte
EPI_ISL_648307Bioko Norte
EPI_ISL_648308Bioko Norte
EPI_ISL_648309Bioko Norte
EPI_ISL_648310Bioko Norte
EPI_ISL_648311Bioko Norte
EPI_ISL_648312Bioko Norte
EPI_ISL_648313Bioko Norte
EPI_ISL_648314Bioko Norte
EPI_ISL_648315Bioko Norte
EPI_ISL_648316Bioko Norte
EPI_ISL_648317Bioko Norte
EPI_ISL_648319Bioko Norte
EPI_ISL_648320Bioko Norte
EPI_ISL_648321Bioko Norte
EPI_ISL_648322Bioko Norte
EPI_ISL_648323Bioko Norte
EPI_ISL_648327Bioko Norte
EPI_ISL_648328Bioko Norte
EPI_ISL_648329Bioko Norte
EPI_ISL_648330Bioko Norte
EPI_ISL_648331Bioko Norte
EPI_ISL_648332Bioko Norte
EPI_ISL_648333Bioko Norte
EPI_ISL_648335Bioko Norte
EPI_ISL_648338Bioko Norte
EPI_ISL_648339Bioko Norte
EPI_ISL_648340Bioko Norte
EPI_ISL_648341Bioko Norte
EPI_ISL_648343Bioko Norte
EPI_ISL_648344Bioko Norte
EPI_ISL_648345Bioko Norte
EPI_ISL_648346Bioko Norte
EPI_ISL_648347Bioko Norte
EPI_ISL_648349Bioko Norte
EPI_ISL_648351Bioko Norte
EPI_ISL_648352Bioko Norte
EPI_ISL_648353Bioko Norte
EPI_ISL_648354Bioko Norte
EPI_ISL_648355Bioko Norte
EPI_ISL_648356Bioko Norte
EPI_ISL_648357Bioko Norte
EPI_ISL_648358Bioko Norte
EPI_ISL_648359Bioko Norte
EPI_ISL_648361Bioko Norte
EPI_ISL_648362Bioko Norte
EPI_ISL_648363Bioko Norte
EPI_ISL_648364Bioko Norte
EPI_ISL_648365Bioko Norte
EPI_ISL_648366Bioko Norte
EPI_ISL_648368Bioko Norte
EPI_ISL_648369Bioko Norte
EPI_ISL_648370Bioko Norte
EPI_ISL_648371Bioko Norte
EPI_ISL_648375Bioko Norte
EPI_ISL_648377Bioko Norte
EPI_ISL_648378Bioko Norte
EPI_ISL_649155Bioko Norte
EPI_ISL_649156Bioko Norte
EPI_ISL_649157Bioko Norte
EPI_ISL_649158Bioko Norte
EPI_ISL_649159Bioko Norte
EPI_ISL_649160Bioko Norte
EPI_ISL_649161Bioko Norte
EPI_ISL_649162Bioko Norte
EPI_ISL_649163Bioko Norte
EPI_ISL_649164Bioko Norte
EPI_ISL_649165Bioko Norte
EPI_ISL_649166Bioko Norte
EPI_ISL_649167Bioko Norte
EPI_ISL_649168Bioko Norte
EPI_ISL_649169Bioko Norte
EPI_ISL_649172Bioko Norte
EPI_ISL_649170Bioko Sur
EPI_ISL_649171Bioko Sur
EPI_ISL_648303Litoral
EPI_ISL_648324Litoral
EPI_ISL_648325Litoral
EPI_ISL_648326Litoral
EPI_ISL_648334Litoral
EPI_ISL_648336Litoral
EPI_ISL_648337Litoral
EPI_ISL_648342Litoral
EPI_ISL_648348Litoral
EPI_ISL_648350Litoral
EPI_ISL_648360Litoral
EPI_ISL_648367Litoral
EPI_ISL_648373Litoral
EPI_ISL_648376Litoral

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