Selected article for: "cell culture and Illumina sequencing"
Author: LaRinda A Holland; Emily A Kaelin; Rabia Maqsood; Bereket Estifanos; Lily I Wu; Arvind Varsani; Rolf U Halden; Brenda G Hogue; Matthew Scotch; Efrem S Lim
Title: An 81 base-pair deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)
  • Document date: 2020_4_22
    • ID: mkcrl9pw_7
    Snippet: To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we 40 performed next-generation sequencing (Illumina NextSeq, 2x76) directly on specimen RNA, 41 thereby avoiding cell culture passage and potentially associated mutations. This generated an 42 NGS dataset of 20.7 to 22.7 million paired-end reads per sample. We mapped quality-filtered 43 reads to a reference SARS-CoV-2 genome (MN908947) using BBMap (version 39.6.....
    Document: To understand the evolutionary relationships and characterize the SARS-CoV-2 genomes, we 40 performed next-generation sequencing (Illumina NextSeq, 2x76) directly on specimen RNA, 41 thereby avoiding cell culture passage and potentially associated mutations. This generated an 42 NGS dataset of 20.7 to 22.7 million paired-end reads per sample. We mapped quality-filtered 43 reads to a reference SARS-CoV-2 genome (MN908947) using BBMap (version 39.64) to 44 generate three full-length genomes: AZ-ASU2922 (376x coverage), AZ-ASU2923 (50x) and AZ-45 ASU2936 (879x) (Geneious prime version 2020.0.5). We aligned a total of 222 SARS-CoV-2 46 genome sequences comprising at least 5 representative sequences from phylogenetic lineages 47 . CC-BY 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity.

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