Selected article for: "genome sequence and nucleotide position"
Author: Tsuyoshi Sekizuka; Kentaro Itokawa; Tsutomu Kageyama; Shinji Saito; Ikuyo Takayama; Hideki Asanuma; Nao Naganori; Rina Tanaka; Masanori Hashino; Takuri Takahashi; Hajime Kamiya; Takuya Yamagishi; Kensaku Kakimoto; Motoi Suzuki; Hideki Hasegawa; Takaji Wakita; Makoto Kuroda
Title: Haplotype networks of SARS-CoV-2 infections in the Diamond Princess cruise ship outbreak
  • Document date: 2020_3_27
    • ID: 7vuejy26_3
    Snippet: A detected Cq (cycle quantification) value of RT-qPCR for the 896 specimens is shown in Supplementary Table S1. All 148 RT-qPCR positive RNA samples were subjected to the PrimalSeq protocol to generate enriched cDNA of the SARS-CoV-2 genome. Samples were then 25 sequenced in an Illumina NextSeq 500. In total 70 WGSs have been determined. The Cq limit for successful genome sequence determination was around 32 (Fig. 1A) , which corresponds to a vir.....
    Document: A detected Cq (cycle quantification) value of RT-qPCR for the 896 specimens is shown in Supplementary Table S1. All 148 RT-qPCR positive RNA samples were subjected to the PrimalSeq protocol to generate enriched cDNA of the SARS-CoV-2 genome. Samples were then 25 sequenced in an Illumina NextSeq 500. In total 70 WGSs have been determined. The Cq limit for successful genome sequence determination was around 32 (Fig. 1A) , which corresponds to a virus copy number of less than 300. The 73 genome sequences (including 3 sequences of DP isolates deposited in GISAID) were compared with the Wuhan-Hu-1 (isolated on Dec. 26, 2020 in China) genome sequence as a reference. The frequencies of single nucleotide variations 30 (SNVs) suggested that all 73 isolates shared a single nucleotide variation: the G nucleotide at the 11,083 position on the Wuhan-Hu-1 genome sequence was mutated to T (G11083T transversion) leading to a non-synonymous amino acid substitution (Leu37Phe) in the nsp6 protein (Fig. 1B) . Some additional minor SNVs were identified throughout the genome sequence.

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