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_12
Snippet: Analysis of total RNA-seq sequences enabled mapping of co-infections and colonization with commensal species across both clinical positives and negatives in our sample set. We identified additional RNA viruses and organisms that distinguished high, medium, and lower viral load patients (Supp Table 1) , with overall similarity observed across patients in the bacterial RNA fractions (Supp. Figure 7a) . However, there were distinct variations in kno.....
Document: Analysis of total RNA-seq sequences enabled mapping of co-infections and colonization with commensal species across both clinical positives and negatives in our sample set. We identified additional RNA viruses and organisms that distinguished high, medium, and lower viral load patients (Supp Table 1) , with overall similarity observed across patients in the bacterial RNA fractions (Supp. Figure 7a) . However, there were distinct variations in known respiratory viruses, including human coronaviruses 229E, NL63, and HKU1, as well as influenza A, rhinovirus (A and C), and respiratory syncytial virus (Supp Figure 7a ). As expected, most patients (129/133) that presented with the SARS-CoV-2 virus lacked reads associated with other respiratory viruses. A subset of patients (4/133, 3.0%) also harbored Influenza A. These cases were enriched in the lower titer (bottom third) of COVID-19 positive (3/4) patients. One patient carried SARS-CoV-2, human metapneumovirus, and coronavirus NL63 at the same time (Supp Figure 7a,b) . These results indicate that a positive test for common respiratory viruses does not rule out the presence of SARS-CoV-2. There was also an associated depletion of several species of Streptococcus, Veillonella, and Prevotella in the high viral patient category (Supp Figure 7c ) that was co-incident with SARS-CoV-2 infection, indicating a possible disruption of the host microbiome at the airway site of the NP swab collection.
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