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Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein

View ORCID ProfileEN Nikolaev, MI Indeykina, AG Brzhozovskiy, AE Bugrova, View ORCID ProfileAS Kononikhin, NL Starodubtseva, EV Petrotchenko, G Kovalev, CH Borchers, GT Sukhikh
doi: https://doi.org/10.1101/2020.05.24.113043
EN Nikolaev
1Skolkovo Institute of Science and Technology, Moscow, Russia
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  • For correspondence: e.nikolaev@skoltech.ru
MI Indeykina
2Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
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AG Brzhozovskiy
1Skolkovo Institute of Science and Technology, Moscow, Russia
3V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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AE Bugrova
2Emanuel Institute for Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
3V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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AS Kononikhin
1Skolkovo Institute of Science and Technology, Moscow, Russia
3V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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NL Starodubtseva
3V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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EV Petrotchenko
4Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
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G Kovalev
1Skolkovo Institute of Science and Technology, Moscow, Russia
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CH Borchers
1Skolkovo Institute of Science and Technology, Moscow, Russia
4Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
5Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
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GT Sukhikh
3V. I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Moscow, Russia
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ABSTRACT

Detection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted May 25, 2020.
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Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein
EN Nikolaev, MI Indeykina, AG Brzhozovskiy, AE Bugrova, AS Kononikhin, NL Starodubtseva, EV Petrotchenko, G Kovalev, CH Borchers, GT Sukhikh
bioRxiv 2020.05.24.113043; doi: https://doi.org/10.1101/2020.05.24.113043
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Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein
EN Nikolaev, MI Indeykina, AG Brzhozovskiy, AE Bugrova, AS Kononikhin, NL Starodubtseva, EV Petrotchenko, G Kovalev, CH Borchers, GT Sukhikh
bioRxiv 2020.05.24.113043; doi: https://doi.org/10.1101/2020.05.24.113043

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