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Principal Investigator: Matthew C. Altman
Organization: BENAROYA RESEARCH INST AT VIRGINIA MASON
Fiscal Year: 2020
Award: $543,574
Funding agency: National Institute of Allergy and Infectious Diseases
Project Summary/Abstract
This application is being submitted to PA-20-135 in accordance with NOT-AI-20-034. We are requesting an
emergency supplement to R01AI32774 “Mechanisms of IL-6 mediated T cell pathogenesis in autoimmunity”
(PI: Jane H. Buckner). This supplement will directly address the NOT-AI-20-034 research area of interest
“Identification and evaluation of the innate, cellular and humoral immune response to SARS-CoV-2
infection…..”. Importantly, the proposed work is part of the NIAID Immunophenotyping assessment in a
COVID-19 Cohort (IMPACC) study tasked with performing longitudinal immunophenotyping from 1,000
subjects with COVID-19. For each subject, among other assays, transcriptomic profiling will be done on
peripheral blood, nasal swabs and endotracheal aspirates at six different time points. Specific to the
emergency supplement requested here, we will be responsible for performing both the bulk host mRNA-
sequencing (RNA-seq) and PCR quantification of viral nucleic acid from SARS-CoV-2 for each of the ~6,000
anticipated nasal swab samples. In addition, we will perform a pilot study on 60 nasal swab samples
assessing the potential utility of metagenomic sequencing on these samples to consider it in a larger scale in
this cohort. All work will be done in close coordination with NIAID, University of California, San Francisco
(endotracheal RNA-seq), Emory University (blood RNA-seq), and Icahn School of Medicine at Mount Sinai
(virology) core sites.
Terms: <2019 novel coronavirus><2019-nCoV><Address><Area><Aspirate><Aspirate substance><Assay><Autoimmune Status><Autoimmunity><B cell differentiation factor><B cell stimulating factor 2><B-Cell Differentiation Factor><B-Cell Differentiation Factor-2><B-Cell Stimulatory Factor-2><BCDF><BSF-2><BSF2><Bioassay><Biologic Assays><Biological Assay><Blood><Blood Reticuloendothelial System><COVID><COVID-19><COVID19><California><Clinical><CoV disease><Cohort Studies><Concurrent Studies><Coronaviridae><Coronavirus><Data Set><Dataset><Disease><Disorder><Emergencies><Emergency Situation><Evaluation><Functional RNA><HPGF><Hepatocyte-Stimulating Factor><Hospital Admission><Hospitalization><Hour><Hybridoma Growth Factor><IFN-beta 2><IFNB2><IL-6><IL6 Protein><Immune response><Immunologic Subtyping><Immunological response><Immunophenotyping><Infection><Interleukin-6><Investigators><Kinetics><Link><Longitudinal Studies><MGI-2><Mediating><Microbe><Myeloid Differentiation-Inducing Protein><NIAID><Nasal><Nasal Passages Nose><National Institute of Allergy and Infectious Disease><Non-Coding><Non-Coding RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><Nose><Nucleic Acids><Pathogenesis><Patients><Pattern><Pilot Projects><Plasmacytoma Growth Factor><Pneumonia><RNA Seq><RNA sequencing><RNAseq><Research><Research Personnel><Researchers><Resolution><Respiratory Infections><Respiratory System, Nose, Nasal Passages><Respiratory Tract Infections><SARS-CoV-2><SARS-CoV2><SARS-associated coronavirus 2><SARS-coronavirus-2><SARS-related coronavirus 2><Sampling><San Francisco><Severe acute respiratory syndrome coronavirus 2><Site><Swab><T-Cells><T-Lymphocyte><Time><Universities><Untranslated RNA><Viral><Viral Pneumonia><Work><Wuhan coronavirus><clinical outcome prediction><cohort><corona virus><corona virus disease><corona virus disease 2019><coronavirus disease><coronavirus disease 2019><data management><data sharing><endotracheal><host response><immunophenotype><immunoresponse><interest><interferon beta 2><long-term study><longitudinal outcome studies><longterm study><mRNA sequencing><mRNA-seq><medical college><medical schools><metagenome sequencing><metagenomic sequencing><new drug target><new druggable target><new pharmacotherapy target><new therapeutic target><new therapy target><noncoding><novel drug target><novel druggable target><novel pharmacotherapy target><novel therapeutic target><novel therapy target><pandemic><pandemic disease><peripheral blood><pilot study><predict clinical outcome><predictor of clinical outcome><school of medicine><thymus derived lymphocyte><transcriptome sequencing><transcriptomics><virology>