During August 2021, 180 SARS-CoV-2 positive samples with N1 Cq values less than 30 were randomly selected from a total of 710 saliva isolates collected from Clemson students and employees. These heat-treated positive saliva samples were then sent for sequencing to an external reference lab (Premier Medical Sciences, Greenville SC, USA). RNA was extracted from saliva samples via magnetic beads (Omega) and recovered SARS-CoV-2 RNA quantity was assessed via Codiagnostics Logix smart assay. Samples were processed and sequenced on either an Illumina NovaSeq 6000 or NextSeq500/550 flow cell. Sequences were demultiplexed, assembled, and analyzed in DRAGEN COVID Lineage (Illumina, v.3.5.3). The delta variant was present in 95.6% of sequenced university samples. Between 8/22/2021 and 9/18/2021, it is estimated that the delta variant was present in 98.9% (95% CI: 93.5-99.9%) of SARS-CoV-2 positive samples in SC49 .
Dragen covid lineage
Manufactured by Illumina
Sourced in United States
The DRAGEN COVID Lineage is a bioinformatics software tool developed by Illumina. It is designed to accurately identify and classify SARS-CoV-2 viral lineages and variants from sequencing data. The core function of the DRAGEN COVID Lineage is to provide rapid and accurate analysis of SARS-CoV-2 genomic sequences.
Automatically generated - may contain errors
5 protocols using dragen covid lineage
1
Delta Variant Prevalence in University Samples
2
SARS-CoV-2 Genome Phylogenetic Analysis
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The raw FASTQ data generated in Illumina MiSeq was processed and assembled using DRAGEN COVID Lineage v3.5.3 (Illumina Inc.) in Illumina BaseSpace. Phylogenetic tree was constructed using multiple genome sequence alignment MAFFT (v.7.407) [26 (link)] by mapping against the Wuhan-Hu-1 reference genome with accession: NC_045512.2. Genomic isolates of SARS-CoV-2 were assigned lineages using the PANGOLIN algorithms [27 (link)] and listed in S2 Table with their GISAID sequence IDs and dates of sampling. Subsequently, highly homoplasic sites of SARS-CoV-2 genome alignment output were masked to correct for the error prone regions of 5’-UTR and 3’-UTR without losing key sites [28 ]. A maximum likelihood tree was constructed using IQTREE (v.1.5.5) with 1,000 bootstrap replicates and GTR nucleotide substitution model [29 (link)–31 (link)]. The phylogenetic tree output was visualised using Figtree (v.1.4.4), annotation, and heatmap generated using a custom R script [32 ].
3
SARS-CoV-2 Sequencing from Saliva Samples
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Ethical review for this study was obtained by the Institutional Review Board of Clemson University. This study uses archived deidentified samples and data. The samples and data sets were striped of patient identifiers prior to any SARS-CoV2 sequencing and experiments for this study. Heat treated saliva samples were sequenced at a commercial lab (Premier Medical Laboratory Services, Greenville SC, USA). RNA was extracted from saliva samples via magnetic beads (Omega Bio-Tek, Norcross GA, USA) and recovered SARS-CoV-2 RNA quantity was assessed via Logix smart assay (Codiagnostics, Salt Lake City UT, USA). Samples with sufficient RNA quality were processed and sequenced on either an Illumina NovaSeq 6000 or NextSeq500/550 flow cell. Sequences were demultiplexed, assembled, and analyzed with DRAGEN COVID Lineage (Illumina, v.3.5.3).
4
SARS-CoV-2 Lineage Identification Protocol
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Sequencing data was analyzed using DRAGEN COVID Lineage (version 3.5.9; Illumina Inc., USA) and method as described previously [11 (link),12 (link)]. In brief, sequencing reads of human origin were removed using NCBI Human Read Scrubber algorithm. ARTIC primer sequences were removed from the reads, followed by aligning to the reference genome Wuhan-Hu-1 (GenBank accession number MN908947.3) using DRAGEN (Illumina Inc., USA). Samples with less than 90 amplicons detected are filtered. Variant calling and consensus genome assembly with respect to the reference genome were performed using DRAGEN (Illumina Inc., USA) using default parameters. Nucleotide and amino acid positions were numbered according to the reference genome. All genome sequences analyzed in this study were submitted to GISAID under accession numbers EPI_ISI_13822514 to 13822565 and EPI_ISI_14336314 to 14336324. Pangolin lineages of the consensus genomes were assigned using Pangolin COVID-19 Lineage Assigner (version 4.0.2) [13 (link)]. Phylogenetic clades of the consensus genomes were mapped using Nextclade (version 1.11.0) [14 (link)].
5
SARS-CoV-2 Sequencing from Saliva Samples
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Ethical review for this study was obtained by the Institutional Review Board of Clemson University. This study uses archived deidentified samples and data. The samples and data sets were stripped of patient identifiers prior to any SARS-CoV-2 sequencing and experiments for this study. Heat-treated saliva samples were sequenced at a commercial lab (Premier Medical Laboratory Services, Greenville, SC). RNA was extracted from saliva samples via magnetic beads (Omega Bio-Tek, Norcross, GA) and recovered SARS-CoV-2 RNA quantity was assessed via Logix Smart Assay (Codiagnostics, Salt Lake City, UT). Samples with sufficient RNA quality were processed and sequenced on either an Illumina NovaSeq 6000 or NextSeq500/550 flow cell. Sequences were demultiplexed, assembled, and analyzed with DRAGEN COVID Lineage (Illumina, v.3.5.3).
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