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

Abstract

We have applied nuclear magnetic resonance spectroscopy based plasma phenotyping to reveal diagnostic molecular signatures of SARS-CoV-2 infection <i>via</i> combined diffusional and relaxation editing (DIRE). We compared plasma from healthy age-matched controls (<i>n</i> = 26) with SARS-CoV-2 negative non-hospitalized respiratory patients and hospitalized respiratory patients (<i>n</i> = 23 and 11 respectively) with SARS-CoV-2 rRT-PCR positive respiratory patients (<i>n</i> = 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 <i>N</i>-acetyl signals from α-1-acid glycoprotein and other glycoproteins (designated GlycA and GlycB) that were elevated in SARS-CoV-2 positive patients [<i>p</i> = 2.52 × 10^-10 (GlycA) and 1.25 × 10^-9 (GlycB) <i>vs</i> 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 (SPC_total) were reduced in SARS-CoV-2 positive patients relative to both controls (<i>p</i> = 1.40 × 10^-7) and SARS-CoV-2 negative patients (<i>p</i> = 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 SPC_total/GlycA ratios were also significantly different for control <i>versus</i> SARS-CoV-2 positive patients (<i>p</i> = 1.23 × 10^-10) and for SARS-CoV-2 negatives <i>versus</i> positives (<i>p</i> = 1.60 × 10^-9). Thus, plasma SPC_total and SPC_total/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 with long-term symptoms.