Diffusion and Relaxation Edited Proton NMR Spectroscopy of Plasma Reveals a High-Fidelity Supramolecular Biomarker Signature of SARS-CoV‑2 Infection

• Published in: Analytical chemistry (Washington) 2021-03, Vol.93 (8), p.3976-3986
• Main Authors: Lodge, Samantha, Nitschke, Philipp, Kimhofer, Torben, Wist, Julien, Bong, Sze-How, Loo, Ruey Leng, Masuda, Reika, Begum, Sofina, Richards, Toby, Lindon, John C, Bermel, Wolfgang, Reinsperger, Tony, Schaefer, Hartmut, Spraul, Manfred, Holmes, Elaine, Nicholson, Jeremy K
• Format: Article
• Language: English
• Subjects: Aged; Analytical chemistry; Biomarkers; Biomarkers - blood; Chemistry; Choline; COVID-19; COVID-19 - blood; COVID-19 - diagnosis; Density; Diagnostic systems; Discriminant analysis; Female; Glycoproteins; Humans; Infections; Magnetic resonance spectroscopy; Male; Metabolites; Middle Aged; Multivariate Analysis; NMR; NMR spectroscopy; Nuclear magnetic resonance; Nuclear Magnetic Resonance, Biomolecular - methods; Operators (mathematics); Orosomucoid - analysis; Orosomucoid - chemistry; Phenotyping; Phospholipids; Phospholipids - blood; Phospholipids - chemistry; Plasma; Principal components analysis; Proton Magnetic Resonance Spectroscopy - methods; Proton Magnetic Resonance Spectroscopy - statistics & numerical data; ROC Curve; SARS-CoV-2; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Signs and symptoms; Spectroscopy; Spectrum analysis; Statistics; Viral diseases
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/acs.analchem.0c04952

We have applied nuclear magnetic resonance spectroscopy based plasma phenotyping to reveal diagnostic molecular signatures of SARS-CoV-2 infection via combined diffusional and relaxation editing (DIRE). We compared plasma from healthy age-matched controls (n = 26) with SARS-CoV-2 negative non-hospitalized respiratory patients and hospitalized respiratory patients (n = 23 and 11 respectively) with SARS-CoV-2 rRT-PCR positive respiratory patients (n = 17, with longitudinal sampling time-points). DIRE data were modelled using principal component analysis and orthogonal projections to latent structures discriminant analysis (O-PLS-DA), with statistical cross-validation indices indicating excellent model generalization for the classification of SARS-CoV-2 positivity for all comparator groups (area under the receiver operator characteristic curve = 1). DIRE spectra show biomarker signal combinations conferred by differential concentrations of metabolites with selected molecular mobility properties. These comprise the following: (a) composite N-acetyl signals from α-1-acid glycoprotein and other glycoproteins (designated GlycA and GlycB) that were elevated in SARS-CoV-2 positive patients [p = 2.52 × 10–10 (GlycA) and 1.25 × 10–9 (GlycB) vs controls], (b) two diagnostic supramolecular phospholipid composite signals that were identified (SPC-A and SPC-B) from the –+N–(CH3)3 choline headgroups of lysophosphatidylcholines carried on plasma glycoproteins and from phospholipids in high-density lipoprotein subfractions (SPC-A) together with a phospholipid component of low-density lipoprotein (SPC–B). The integrals of the summed SPC signals (SPCtotal) were reduced in SARS-CoV-2 positive patients relative to both controls (p = 1.40 × 10–7) and SARS-CoV-2 negative patients (p = 4.52 × 10–8) but were not significantly different between controls and SARS-CoV-2 negative patients. The identity of the SPC signal components was determined using one and two dimensional diffusional, relaxation, and statistical spectroscopic experiments. The SPCtotal/GlycA ratios were also significantly different for control versus SARS-CoV-2 positive patients (p = 1.23 × 10–10) and for SARS-CoV-2 negatives versus positives (p = 1.60 × 10–9). Thus, plasma SPCtotal and SPCtotal/GlycA are proposed as sensitive molecular markers for SARS-CoV-2 positivity that could effectively augment current COVID-19 diagnostics and may have value in functional assessment of the disease recovery process in patients w