Selected article for: "copy number and CT value"
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_6
    Snippet: To optimize the LAMP assay for clinical samples, we first tested the reaction on a range of sample types, dilutions, and reaction volumes. We used a set of 201 COVID-19 samples that were tested for SARS-CoV-2 by qRT-PCR, including 69 nasopharyngeal (NP) swab samples that tested positive (clinical positives, qRT-PCR Ct<40) and 132 samples that tested negative (clinical negatives, qRT-PCR Ct ≥ 40) (see Methods). Clinically positive samples showed.....
    Document: To optimize the LAMP assay for clinical samples, we first tested the reaction on a range of sample types, dilutions, and reaction volumes. We used a set of 201 COVID-19 samples that were tested for SARS-CoV-2 by qRT-PCR, including 69 nasopharyngeal (NP) swab samples that tested positive (clinical positives, qRT-PCR Ct<40) and 132 samples that tested negative (clinical negatives, qRT-PCR Ct ≥ 40) (see Methods). Clinically positive samples showed a much higher fluorescence than negative samples, with superior performance observed with higher (10µL vs 5µL) input volumes (Supp. Figure 3b) . Clinically positive samples that failed to generate LAMP fluorescence were associated with lower viral genome abundance (high cycle threshold [Ct] value qRT-PCR). We obtained similar performance on bulk oropharyngeal swab lysate (Supp. Figure 3c -e), including increasing reaction sensitivity as a function of viral copy number. This required only a 30-minute lysis time for the oral collections and 30-minute LAMP reaction time. These results indicate robust performance of the LAMP assay across a broad range of purified nucleic acids as well as crude cellular lysates (see Methods).

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