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A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

ABSTRACT: In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a multiple reaction monitoring we can detect the presence of two peptides specific to SARS-CoV-2 in a 2.3 min gradient run with 100% specificity and 90.5% sensitivity when compared to RT-PCR. Importantly, we further show that these peptides could be detected even in the patients who have recovered from the symptoms and have tested negative for the virus by RT-PCR highlighting the sensitivity of the technique. This method has the translational potential of in terms of the rapid diagnostics of symptomatic and asymptomatic COVID-19 and can augment current methods available for diagnosis of SARS-CoV-2.

SUBMITTER: Singh P

PROVIDER: S-EPMC7457902 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

Singh Praveen P Chakraborty Rahul R Marwal Robin R Radhakrishan V S VS Bhaskar Akash Kumar AK Vashisht Himanshu H Dhar Mahesh S MS Pradhan Shalini S Ranjan Gyan G Imran Mohamed M Raj Anurag A Sharma Uma U Singh Priyanka P Lall Hemlata H Dutta Meena M Garg Parth P Ray Arjun A Dash Debasis D Sivasubbu Sridhar S Gogia Hema H Madan Preeti P Kabra Sandhya S Singh Sujeet K SK Agrawal Anurag A Rakshit Partha P Kumar Pramod P Sengupta Shantanu S

Journal of proteins and proteomics 20200831 3

In the last few months, there has been a global catastrophic outbreak of severe acute respiratory syndrome disease caused by the novel coronavirus SARS-CoV-2 affecting millions of people worldwide. Early diagnosis and isolation are key to contain the rapid spread of the virus. Towards this goal, we report a simple, sensitive and rapid method to detect the virus using a targeted mass spectrometric approach, which can directly detect the presence of virus from naso-oropharyngeal swabs. Using a mul ...[more]

PMID: 33132628

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Project description:BackgroundThe 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.MethodsHere, 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.FindingsThe 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.InterpretationOur 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.FundingThis study was supported by DBT/Wellcome Trust India Alliance Margdarshi Fellowship grant IA/M/15/1/502023 awarded to AP and the generosity of Eric and Wendy Schmidt.

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A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

Publications

A rapid and sensitive method to detect SARS-CoV-2 virus using targeted-mass spectrometry.

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