COVID-19 biomarker discovery

National Institute Of Allergy And Infectious Diseases

Investigators

Linked publications & trials

Abstract

The focus of the proteomic approach is to identify and quantify viral structural proteins, specifically spike (S) glycoprotein as well as envelope (E) protein, membrane (M) protein, and nucleocapsid (N) protein in patient samples. The S protein mediates attachment of the virus to the host cell surface receptors and subsequent fusion of the viral and host cell membranes to facilitate viral entry into the host cell. The S1 subunit of the ectodomain mediates binding of the virion to host cell-surface receptors through its receptor-binding domain and is the immunodominant epitope. Due to its critical role in cell entry, we anticipate high expression levels of the S protein during active infection making it an attractive diagnostic marker for SARS-CoV-2 infection. Additionally, levels of this protein are expected to change during the course of infection and can be used to monitor individual disease progression. Finally, our proposed proteomic based detection of the S protein could prove helpful in studies evaluating the efficacy of novel drugs and vaccines in the light of the most current research (1). Specific goals: 1) Development of proteomic based assay for detection and quantitation of SARS-CoV-2 proteome in biological samples. Work will focus on four structural proteins: spike (S) glycoprotein (primary target), envelope (E) protein, membrane (M) protein, and nucleocapsid (N) protein. The E and N gene (coding for the envelop and nucleocapsid protein) have been used for PCR based diagnostic assays. We therefore aim to explore using their encoded products as additional targets in our proteomics assay development. 2) Characterize and compare SARS-CoV-2 protein profiles among patients, treatments (currently: a clinical study of fostamatinib as a possible therapeutic in addition to Remdesivir), different times of the course of disease and possible co-morbidities (such as RSV) using nasopharyngeal and respiratory samples from patients admitted at the NIH previously tested with N1, N2 RT-PCR CDC RT-PCR assay and using genomic data from the research proposal Genomics of SARS-CoV-2 3) Comparison of protein profiles and correlation with RNA detection assays. This will provide protein level information regarding observed differences between N1 and N2 levels among patients as observed by RT-PCR assay. 4) Selection of viral proteomic biomarker(s) for further evaluation as diagnostic and prognostic target in different clinical samples (saliva, urine, serum). 5). Comparison of cost-effectivity of the final design of the assay to the ELISA-based tests. Bibliography: 1. Buszko M, Nita-Lazar A, Park JH, Schwartzberg PL, Verthelyi D, Young HA, Rosenberg AS. Nat Immunol. 2021 Apr;22(4):404-411.