Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

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

The copyright holder for this preprint (which was not peer-reviewed) is the . https: //doi.org/10.1101 //doi.org/10. /2020 Supplementary Figure 6 . Coverage of COVID samples by Index and Sample Type. Clinical samples tested by qRT-PCR (Positive, P, Negative, N) were compared to the buffer blanks (Negative Control, N and neg), Synthetic RNAs or Vero 6 cell extracts with SARS-CoV-2 infection (CP and pos) and Subway Samples (Environmental, ENV). The %identity to the SARS-CoV-2 reference (y-axis) is shown relative to the proportion of reads that mapped from NGS (x-axis). The unique, dual-index runs (left panels) are shown relative to the single-index runs (right panels). The initial set of single-index libraries were associated with a non-negligible background of viral load in clinical negative samples, this effect was eliminated with the dualindexing approach for all remaining samples. The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.04.20.048066 doi: bioRxiv preprint Supplemental Figure 8 . Proportion of RNA-seq reads mapping SARS-CoV-2. Clinical samples tested by qRT-PCR (Positive, dark red or Negative, light grey) were sequenced and compared to the buffer blanks (Negative Control), dark grey, Synthetic RNAs or Vero 6 cell extracts with SARS-CoV-2 infection (Positive Controls, light red), and Subway Samples (Environmental, blue). Read totals are shown on the y-axis. Differences between single index barcodes are plotted across each of the plates of samples that were processed. author/funder. All rights reserved. No reuse allowed without permission.