SARS-CoV-2 Lineage Identification by Genomic Sequencing

We prepared a genome library by using an amplicon-based next-generation sequencing assay, the research-use-only COVIDSeq Test (RUO Version; Illumina, https://www.illmina.com), and sequenced samples by using the NovaSeq6000, NextSeq1000, NextSeq550, or MiniSeq platforms (Illumina). We processed the data by using DRAGEN COVID Lineage App version 3.5.3 (Illumina), and generated consensus sequences by using the SARS-CoV-2 reference genome (GenBank accession no. NC_045512). Using Pangolin version 3.1.20 (12 (link)), we assigned lineages to sequenced genomes that had >90% breadth of coverage of the reference genome and for genome data from Japan obtained from the GISAID database (https://www.gisaid.org) on July 13, 2021. We defined VOCs according to the World Health Organization designations as of June 22, 2021 (13 ). We used IQ-TREE multicore version 2.1.2 COVID-edition (http://www.iqtree.org) for phylogenetic analysis. We submitted SARS-CoV-2 sequences obtained in this study to GISAID (Appendix 1).

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Matsumura Y., Nagao M., Yamamoto M., Tsuchido Y., Noguchi T., Shinohara K., Yukawa S., Inoue H, & Ikeda T. (2022). Transmissibility of SARS-CoV-2 B.1.1.214 and Alpha Variants during 4 COVID-19 Waves, Kyoto, Japan, January 2020–June 2021. Emerging Infectious Diseases, 28(8), 1569-1577.

Publication 2022

COVIDSeq Test (RUO Version; NovaSeq6000 NextSeq1000 NextSeq550 MiniSeq DRAGEN COVID Lineage App

Assay Consensus sequences Genome Genome library Pangolin Sars cov 2 Tree

Corresponding Organization :

Other organizations : Kyoto University

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Variable analysis

independent variables

Genome library preparation using an amplicon-based next-generation sequencing assay, the research-use-only COVIDSeq Test (RUO Version; Illumina)
Sequencing samples using the NovaSeq6000, NextSeq1000, NextSeq550, or MiniSeq platforms (Illumina)

dependent variables

Generation of consensus sequences using the SARS-CoV-2 reference genome (GenBank accession no. NC_045512)
Assignment of lineages to sequenced genomes using Pangolin version 3.1.20

control variables

Sequenced genomes with >90% breadth of coverage of the reference genome
Genome data from Japan obtained from the GISAID database on July 13, 2021

positive controls

SARS-CoV-2 reference genome (GenBank accession no. NC_045512)

negative controls

Not explicitly mentioned

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