The viral RNA was extracted from 140 μL of clinical samples using QIAamp Viral RNA Mini kit (QIAGEN, Hilden, Germany), according to the manufacturer's instructions. The libraries were prepared using AmpliSeq Plus or COVIDSeq kits (Illumina, San Diego, USA), according to the manufacturers’ protocols. AmpliSeq Plus libraries were purified with AMPure XP magnetic beads (Beckman Coulter, Brea, USA). Libraries were quantified using High Sensitivity dsDNA quantification kit with Qubit 2.0 fluorometer (Thermo Fisher Scientific, Waltham, USA), and the mean fragment size was analyzed by TapeStation 4150 with DNA HS D1000 kit (Agilent, Santa Clara, USA). Library concentration was calculated and diluted to 4 nM. Libraries were pooled, denatured, and diluted to a final concentration of up to 12 pM and sequenced on a MiSeq platform with MiSeq Reagent kit v2 (300-cycle) (Illumina, San Diego, USA) to generate reads of 2 × 150 bp. The DNA sequencing was performed at the Genomics and Bioinformatics Center (CeGenBio), from NPDM. The sequences are available in the GISAID database (https://gisaid.org/ ) (Supplementary Table S1).
Dna hs d1000 kit
Manufactured by Agilent Technologies
Sourced in United States
The DNA HS D1000 kit is a laboratory instrument designed for the analysis and quantification of DNA samples. It provides accurate and reliable measurements of DNA concentration and fragment size distribution.
Automatically generated - may contain errors
Lab products found in correlation
Novaseq, by Illumina (3 mentions)
Covidseq kit, by Illumina (3 mentions)
Ampure xp magnetic beads, by Beckman Coulter (2 mentions)
Qiaamp viral rna mini kit, by Qiagen (1 mentions)
Miseq reagent kit v2 300 cycle, by Illumina (1 mentions)
Qubit 2.0 fluorometer, by Thermo Fisher Scientific (1 mentions)
Covid seq kits, by Illumina (1 mentions)
Tapestation 4200, by Agilent Technologies (1 mentions)
Nextera xt index kit v2, by Illumina (1 mentions)
Nextera xt library preparation kit, by Illumina (1 mentions)
Qubit dsdna hs assay kit, by Thermo Fisher Scientific (1 mentions)
Miseq with v3 2x300 bp run kit, by Illumina (1 mentions)
Novaseq system, by Illumina (1 mentions)
Magna pure 96, by Roche (1 mentions)
Covidseq library preparation kit, by Illumina (1 mentions)
6 protocols using dna hs d1000 kit
1
SARS-CoV-2 Genome Sequencing Protocol
2
COVID-19 Sequencing Library Preparation
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A COVID-seq kit was used for library preparation as per the manufacturer’s instructions (Illumina). Library validation and mean fragment size were determined using TapeStation 4200 with a DNA HS D1000 kit (Agilent). Libraries were pooled, denatured, and diluted to 10 pM and sequenced on a NovaSeq instrument (Illumina).
3
COVID-19 Sequencing Library Preparation
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A COVID-seq kit was used for library preparation as per the manufacturer’s instructions (Illumina). Library validation and mean fragment size were determined using TapeStation 4200 with a DNA HS D1000 kit (Agilent). Libraries were pooled, denatured, and diluted to 10 pM and sequenced on a NovaSeq instrument (Illumina).
4
SARS-CoV-2 Genome Sequencing Using Illumina MiSeq
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Libraries were prepared using NexteraXT library preparation kit and NexteraXT index kit V2 as per manufacturer’s instructions (Illumina, San Diego, CA, USA). Libraries were purified with AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA) and library concentration was measured by Qubit dsDNA HS Assay kit (Thermo Fisher Scientific, Waltham, MA, USA). Library validation and mean fragment size was determined by TapeStation 4200 via DNA HS D1000 kit (Agilent, Santa Clara, CA, USA). The mean fragment size was ~400 bp, as expected. The library mean fragment size and concentration molarity was calculated and each library was diluted to 4 nM. Libraries were pooled, denatured and diluted to 10pM and sequenced on MiSeq with V3 2X300 bp run kit (Illumina). Sequences are available in GISAID (accession numbers: EPI_ISL_435284, EPI_ISL_435286, EPI_ISL435287, EPI_ISL435289, EPI_ISL435291, EPI_ISL_435292, EPI_ISL447250, EPI_ISL447251).
5
COVID-19 sequencing with Illumina
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A COVID-seq kit was used for library preparation as per the manufacturer’s instructions (Illumina). Library validation and mean fragment size were determined by Tapestation 4200 via a DNA HS D1000 kit (Agilent). Libraries were pooled, denatured, and diluted to 10 pM and sequenced on a NovaSeq system (Illumina).
6
Viral Genome Extraction and Sequencing
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Viral genomes were extracted from 200 µL respiratory samples with the MagNA PURE 96 (Roche, Germany), according to the manufacturer instructions. Libraries were prepared using COVID-seq library preparation kit, as per manufacturer’s instructions (Illumina). Library validation and mean fragment size was determined by TapeStation 4200 via DNA HS D1000 kit (Agilent). Libraries were pooled, denatured and diluted to 10pM and sequenced on NovaSeq (Illumina).
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