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A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens
BACKGROUND: The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow a...
Autores principales: | , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8253671/ https://www.ncbi.nlm.nih.gov/pubmed/34229274 http://dx.doi.org/10.1016/j.ebiom.2021.103465 |
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author | Renuse, Santosh Vanderboom, Patrick M. Maus, Anthony D. Kemp, Jennifer V. Gurtner, Kari M. Madugundu, Anil K. Chavan, Sandip Peterson, Jane A. Madden, Benjamin J. Mangalaparthi, Kiran K. Mun, Dong-Gi Singh, Smrita Kipp, Benjamin R. Dasari, Surendra Singh, Ravinder J. Grebe, Stefan K. Pandey, Akhilesh |
author_facet | Renuse, Santosh Vanderboom, Patrick M. Maus, Anthony D. Kemp, Jennifer V. Gurtner, Kari M. Madugundu, Anil K. Chavan, Sandip Peterson, Jane A. Madden, Benjamin J. Mangalaparthi, Kiran K. Mun, Dong-Gi Singh, Smrita Kipp, Benjamin R. Dasari, Surendra Singh, Ravinder J. Grebe, Stefan K. Pandey, Akhilesh |
author_sort | Renuse, Santosh |
collection | PubMed |
description | BACKGROUND: The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow assays, each with their own strengths and weaknesses, have been developed and deployed in a short time. METHODS: Here, we describe an immunoaffinity purification approach followed a by high resolution mass spectrometry-based targeted qualitative assay capable of detecting SARS-CoV-2 viral antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data. FINDINGS: The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922–0.997) (86/88) sensitivity and 100% (95% CI = 0.958–1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method. INTERPRETATION: Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures. |
format | Online Article Text |
id | pubmed-8253671 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-82536712021-07-06 A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens Renuse, Santosh Vanderboom, Patrick M. Maus, Anthony D. Kemp, Jennifer V. Gurtner, Kari M. Madugundu, Anil K. Chavan, Sandip Peterson, Jane A. Madden, Benjamin J. Mangalaparthi, Kiran K. Mun, Dong-Gi Singh, Smrita Kipp, Benjamin R. Dasari, Surendra Singh, Ravinder J. Grebe, Stefan K. Pandey, Akhilesh EBioMedicine Research Paper BACKGROUND: The COVID-19 pandemic caused by severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) has overwhelmed health systems worldwide and highlighted limitations of diagnostic testing. Several types of diagnostic tests including RT-PCR-based assays and antigen detection by lateral flow assays, each with their own strengths and weaknesses, have been developed and deployed in a short time. METHODS: Here, we describe an immunoaffinity purification approach followed a by high resolution mass spectrometry-based targeted qualitative assay capable of detecting SARS-CoV-2 viral antigen from nasopharyngeal swab samples. Based on our discovery experiments using purified virus, recombinant viral protein and nasopharyngeal swab samples from COVID-19 positive patients, nucleocapsid protein was selected as a target antigen. We then developed an automated antibody capture-based workflow coupled to targeted high-field asymmetric waveform ion mobility spectrometry (FAIMS) - parallel reaction monitoring (PRM) assay on an Orbitrap Exploris 480 mass spectrometer. An ensemble machine learning-based model for determining COVID-19 positive samples was developed using fragment ion intensities from the PRM data. FINDINGS: The optimized targeted assay, which was used to analyze 88 positive and 88 negative nasopharyngeal swab samples for validation, resulted in 98% (95% CI = 0.922–0.997) (86/88) sensitivity and 100% (95% CI = 0.958–1.000) (88/88) specificity using RT-PCR-based molecular testing as the reference method. INTERPRETATION: Our results demonstrate that direct detection of infectious agents from clinical samples by tandem mass spectrometry-based assays have potential to be deployed as diagnostic assays in clinical laboratories, which has hitherto been limited to analysis of pure microbial cultures. Elsevier 2021-07-03 /pmc/articles/PMC8253671/ /pubmed/34229274 http://dx.doi.org/10.1016/j.ebiom.2021.103465 Text en © 2021 Published by Elsevier B.V. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Research Paper Renuse, Santosh Vanderboom, Patrick M. Maus, Anthony D. Kemp, Jennifer V. Gurtner, Kari M. Madugundu, Anil K. Chavan, Sandip Peterson, Jane A. Madden, Benjamin J. Mangalaparthi, Kiran K. Mun, Dong-Gi Singh, Smrita Kipp, Benjamin R. Dasari, Surendra Singh, Ravinder J. Grebe, Stefan K. Pandey, Akhilesh A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title | A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title_full | A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title_fullStr | A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title_full_unstemmed | A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title_short | A mass spectrometry-based targeted assay for detection of SARS-CoV-2 antigen from clinical specimens |
title_sort | mass spectrometry-based targeted assay for detection of sars-cov-2 antigen from clinical specimens |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8253671/ https://www.ncbi.nlm.nih.gov/pubmed/34229274 http://dx.doi.org/10.1016/j.ebiom.2021.103465 |
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