Selected article for: "genome coverage and high coverage"
Author: Daniel J Butler; Christopher Mozsary; Cem Meydan; David C Danko; Jonathan Foox; Joel Rosiene; Alon Shaiber; Ebrahim Afshinnekoo; Matthew MacKay; Fritz J Sedlazeck; Nikolay A Ivanov; Maria A Sierra; Diana Pohle; Michael Zeitz; Vijendra Ramlall; Undina Gisladottir; Craig D Westover; Krista Ryon; Benjamin Young; Chandrima Bhattacharya; Phyllis Ruggiero; Bradley W Langhorst; Nathan A Tanner; Justyn Gawrys; Dmitry Meleshko; Dong Xu; Jenny Xiang; Angelika Iftner; Daniela Bezdan; John Sipley; Lin Cong; Arryn Craney; Priya Velu; Ari Melnick; Iman A Hajirasouliha; Thomas Iftner; Mirella Salvatore; Massimo Loda; Lars F Westblade; Shawn Levy; Melissa Cushing; Nicholas P Tatonetti; Marcin Imielinski; Hanna Rennert; Christopher Mason
Title: Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)
  • Document date: 2020_4_20
    • ID: kyoa5gsf_11
    Snippet: Clinical positive samples showed higher viral content (0.1%-62.2% of total RNA) than clinical negative samples (p-value < 2.2E -16 , Wilcoxon rank-sum test). Comparing quantitative estimates of viral load from all three assays (LAMP, total-RNA Seq), we observed consistent profiles between the total RNA-seq viral abundance and the quantification by qRT-PCR and LAMP (Rseq_vs_Ct = -0.84, Rseq_vs_lamp = 0.82, Rlamp_vs_Ct = -0.80) (Figure 2b , Supp. F.....
    Document: Clinical positive samples showed higher viral content (0.1%-62.2% of total RNA) than clinical negative samples (p-value < 2.2E -16 , Wilcoxon rank-sum test). Comparing quantitative estimates of viral load from all three assays (LAMP, total-RNA Seq), we observed consistent profiles between the total RNA-seq viral abundance and the quantification by qRT-PCR and LAMP (Rseq_vs_Ct = -0.84, Rseq_vs_lamp = 0.82, Rlamp_vs_Ct = -0.80) (Figure 2b , Supp. Figure 5) . Indeed, 97% of clinical negative samples (199/205) demonstrated fewer than 0.01% of total RNA-seq reads mapping to the SARS-CoV-2 reference. Three of the remaining six demonstrated high SARS-CoV-2 read proportion (>0.01%), high SARS-CoV-2 genome coverage (>99%), and high LAMP fluorescence, suggesting that these were qRT-PCR false negatives (Supp. Figure 6) . The remaining three showed lower coverage (97%-99%) of the SARS-CoV-2 genome and low signal with LAMP. These data provide evidence that false negatives from qRT-PCR are likely rare (3-6/205, or 1.4-2.8%), but may require orthogonal assays to reliably detect.

    Search related documents:
    Co phrase search for related documents
    • clinical negative sample and negative sample: 1, 2, 3, 4, 5
    • clinical positive sample and negative sample: 1, 2, 3
    • false negative and high SARS: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • false negative and high SARS genome coverage: 1
    • false negative and LAMP fluorescence: 1
    • false negative and low coverage: 1
    • false negative and low signal: 1
    • false negative and negative sample: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25
    • great proportion and high SARS: 1
    • high LAMP fluorescence and LAMP fluorescence: 1, 2, 3
    • high SARS and LAMP fluorescence: 1, 2, 3
    • high SARS and low coverage: 1, 2, 3, 4, 5, 6
    • high SARS and low signal: 1
    • high SARS and negative sample: 1, 2, 3, 4, 5
    • high SARS genome coverage and low coverage: 1
    • LAMP low signal and low signal: 1
    • low signal and negative sample: 1, 2