Identification of SARS-CoV-2 biomarkers in saliva by transcriptomic and proteomics analysis

Clinical Proteomics

Research

George S. Katselis¹  Paulos Chumala¹  Walter L. Siqueira²  Lina M. Marin²  Lucas Julseth³  Stephen Sanche⁴  Robert Skomro⁵  Erika Penz⁵ 

[1] Canadian Centre for Health and Safety in Agriculture, Department of Medicine, College of Medicine, University of Saskatchewan, S7N 2Z4, Saskatoon, SK, Canada;College of Dentistry, University of Saskatchewan, S7N 5E5, Saskatoon, SK, Canada;College of Dentistry, University of Saskatchewan, S7N 5E5, Saskatoon, SK, Canada;Canadian Centre for Health and Safety in Agriculture, Department of Medicine, College of Medicine, University of Saskatchewan, S7N 2Z4, Saskatoon, SK, Canada;Division of Infectious Diseases, Department of Medicine, and Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, S7N 0X8, Saskatoon, SK, Canada;Division of Respirology, Critical Care and Sleep Medicine, Department of Medicine, College of Medicine, University of Saskatchewan, S7N 0X8, Saskatoon, SK, Canada;

关键词: Saliva;    SARS-CoV-2;    Peptides;    Proteins;    Proteomics;    Mass spectrometry;    Transcriptomics;    Real-time RT-PCR;    Biomarkers;   

DOI  :  10.1186/s12014-023-09417-w

 received in 2022-03-07, accepted in 2023-06-20,  发布年份 2023

来源: Springer

【 摘 要 】

The detection of SARS-CoV-2 biomarkers by real time PCR (rRT-PCR) has shown that the sensitivity of the test is negatively affected by low viral loads and the severity of the disease. This limitation can be overcome by the use of more sensitive approaches such as mass spectrometry (MS), which has not been explored for the detection of SARS-CoV-2 proteins in saliva. Thus, this study aimed at assessing the translational applicability of mass spectrometry-based proteomics approaches to identify viral proteins in saliva from people diagnosed with COVID-19 within fourteen days after the initial diagnosis, and to compare its performance with rRT-PCR. After ethics approval, saliva samples were self-collected by 42 COVID-19 positive and 16 healthy individuals. Samples from people positive for COVID-19 were collected on average on the sixth day (± 4 days) after initial diagnosis. Viable viral particles in saliva were heat-inactivated followed by the extraction of total proteins and viral RNA. Proteins were digested and then subjected to tandem MS analysis (LC-QTOF-MS/MS) using a data-dependent MS/MS acquisition qualitative shotgun proteomics approach. The acquired spectra were queried against a combined SARS-CoV-2 and human database. The qualitative detection of SARS-CoV-2 specific RNA was done by rRT-PCR. SARS-CoV-2 proteins were identified in all COVID-19 samples (100%), while viral RNA was detected in only 24 out of 42 COVID-19 samples (57.1%). Seven out of 18 SARS-CoV-2 proteins were identified in saliva from COVID-19 positive individuals, from which the most frequent were replicase polyproteins 1ab (100%) and 1a (91.3%), and nucleocapsid (45.2%). Neither viral proteins nor RNA were detected in healthy individuals. Our mass spectrometry approach appears to be more sensitive than rRT-PCR for the detection of SARS-CoV-2 biomarkers in saliva collected from COVID-19 positive individuals up to 14 days after the initial diagnostic test. Based on the novel data presented here, our MS technology can be used as an effective diagnostic test of COVID-19 for initial diagnosis or follow-up of symptomatic cases, especially in patients with reduced viral load.

【 授权许可】

CC BY   
© BioMed Central Ltd., part of Springer Nature 2023

【 图 表 】

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