Nasopharyngeal swab samples collected at two drive-through testing centers (Toulouse Purpan and Toulouse Rangueil sites) from 8 January 2021 to 7 February 2021 were tested using the ThermoFisher TaqPath RT-PCR assay (Scientific TaqPath COVID-19 Combo Kit, Thermo Fisher, Waltham, USA) after nucleic acid extraction using the MGI automated extraction system (MGI Easy Nucleic Acid Extraction Kit). All positive nasopharyngeal samples with cycle threshold (Ct) values below 28 (Ct ≤ 28 for N-gene) were tested using the Illumina CovidSeq test (COVIDSeq, Illumina, USA) on the Illumina Nova Seq 6000 Sequencing System (Genotoul platform, GeTPlaGe, Toulouse). SARS-CoV-2 sequences were analyzed using the Illumina DRAGEN COVIDSeq test pipeline.
Dragen covidseq test pipeline
Manufactured by Illumina
The DRAGEN COVIDSeq test pipeline is a bioinformatics solution designed for the analysis of SARS-CoV-2 sequencing data. The pipeline provides a streamlined workflow for the detection and identification of the SARS-CoV-2 virus from sequencing data.
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Lab products found in correlation
3 protocols using dragen covidseq test pipeline
1
SARS-CoV-2 Sequencing from Nasopharyngeal Swabs
2
SARS-CoV-2 Whole-Genome Sequencing
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Pooled purified libraries were clustered onto a flow cell to perform whole-genome next-generation sequencing (NGS) applying sequencing by synthesis (SBS) chemistry using Illumina-NovaSeq 6000 Sequencing System (NovaSeq Xp S4 flow cell workflow). Sequencing of all the samples and generation of consensus sequences in FASTA format using Illumina DRAGEN™ COVIDSeq Test Pipeline was accomplished at BandrGen, Laboratory Madina, KSA. All the sequences were submitted to NCBI Sequence Read Archive (SRA) under Bio-project accession number PRJNA947168 (SAMN33843589, SAMN33843590, SAMN33843591, SAMN33843592, SAMN33843593, SAMN33843594, and SAMN33843595).
3
SARS-CoV-2 Whole Genome Sequencing Protocol
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The full-length SARS-CoV-2 genome of the virus isolated from the patient was sequenced using next-generation sequencing. Viral RNA was extracted from the nasopharyngeal swab in viral transport medium. Sequencing was performed with the Illumina COVIDSeq Test (Illumina, San Diego, California), using 98-target multiplex amplifications along the full SARS-CoV-2 genome. The libraries were sequenced with NextSeq 500/550 High Output Kit v2.5 (75 Cycles) on a NextSeq 500 device (Illumina). The sequences were demultiplexed and assembled as full-length genomes using the DRAGEN COVIDSeq Test Pipeline on a local DRAGEN server (Illumina). The sample was identified as AY4.2 according to the Pangolin nomenclature, before being submitted to the GISAID database.34 (link)
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