Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI

SARS-CoV-2*/immunology ; SARS-CoV-2*/genetics ; Coronavirus Nucleocapsid Proteins*/immunology ; Coronavirus Nucleocapsid Proteins*/genetics ; COVID-19*/diagnosis ; COVID-19*/immunology ; COVID-19*/virology ; Antigens, Viral*/immunology ; Antigens, Viral*/genetics ; Phosphoproteins*/immunology ; Phosphoproteins*/genetics; Humans ; Enzyme-Linked Immunosorbent Assay/methods ; Enzyme-Linked Immunosorbent Assay/standards ; COVID-19 Serological Testing/methods ; COVID-19 Serological Testing/standards ; Antibodies, Viral/immunology ; Antibodies, Monoclonal/immunology ; Computational Biology/methods ; Mutation ; Animals

The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.

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U24 LM013755 United States LM NLM NIH HHS

Keywords: COVID-19 diagnostics; Enzyme-linked immunoassay; RADx; SARS-CoV-2; monoclonal and polyclonal antibodies; nucleocapsid protein; peptide epitope mapping; viral quality assurance

0 (Coronavirus Nucleocapsid Proteins)
0 (Antigens, Viral)
0 (Phosphoproteins)
0 (nucleocapsid phosphoprotein, SARS-CoV-2)
0 (Antibodies, Viral)
0 (Antibodies, Monoclonal)

SARS-CoV-2 variants

Date Created: 20240525 Date Completed: 20240525 Latest Revision: 20240530

20240530

PMC11125937

10.3390/v16050662

38793544