| Literature DB >> 34367265 |
Mohammad Rubayet Hasan1,2, Mohammed Suleiman1, Andrés Pérez-López1,2.
Abstract
Coronavirus disease 2019 (COVID-19) pandemic triggered an unprecedented global effort in developing rapid and inexpensive diagnostic and prognostic tools. Since the genome of SARS-CoV-2 was uncovered, detection of viral RNA by RT-qPCR has played the most significant role in preventing the spread of the virus through early detection and tracing of suspected COVID-19 cases and through screening of at-risk population. However, a large number of alternative test methods based on SARS-CoV-2 RNA or proteins or host factors associated with SARS-CoV-2 infection have been developed and evaluated. The application of metabolomics in infectious disease diagnostics is an evolving area of science that was boosted by the urgency of COVID-19 pandemic. Metabolomics approaches that rely on the analysis of volatile organic compounds exhaled by COVID-19 patients hold promise for applications in a large-scale screening of population in point-of-care (POC) setting. On the other hand, successful application of mass-spectrometry to detect specific spectral signatures associated with COVID-19 in nasopharyngeal swab specimens may significantly save the cost and turnaround time of COVID-19 testing in the diagnostic microbiology and virology laboratories. Active research is also ongoing on the discovery of potential metabolomics-based prognostic markers for the disease that can be applied to serum or plasma specimens. Several metabolic pathways related to amino acid, lipid and energy metabolism were found to be affected by severe disease with COVID-19. In particular, tryptophan metabolism via the kynurenine pathway were persistently dysregulated in several independent studies, suggesting the roles of several metabolites of this pathway such as tryptophan, kynurenine and 3-hydroxykynurenine as potential prognostic markers of the disease. However, standardization of the test methods and large-scale clinical validation are necessary before these tests can be applied in a clinical setting. With rapidly expanding data on the metabolic profiles of COVID-19 patients with varying degrees of severity, it is likely that metabolomics will play an important role in near future in predicting the outcome of the disease with a greater degree of certainty.Entities:
Keywords: COVID-19; SARS-CoV-2; diagnosis; mass-spectrometry; metabolomics; nuclear magnetic resonance; prognosis; volatile organic compounds
Year: 2021 PMID: 34367265 PMCID: PMC8343128 DOI: 10.3389/fgene.2021.721556
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
COVID-19 testing by analysis of volatile organic compounds (VOC).
| Specimen | No of patients | Reference method | Detection method | Potential breath biomarker | Results | References |
| Breath sample | 98 | RT-qPCR | GC-IMS | Ethanal, octanal, acetone, butanone, methanol, heptanal | Sensitivity: 82.4–90% Specificity: 75–80% | |
| Saliva, tracheobronchial secretions | 1012 | RT-qPCR | Sniffing dog | – | Sensitivity: 82.6% Specificity: 96.3% | |
| Breath sample | 401 | RT-qPCR | PTR-TOF MS | Methylpent-2-enal, 2,4-octadiene 1-chloroheptane, and nonanal | Sensitivity: 90% Specificity: 94% | |
| Armpit sweat samples | 177 | RT-qPCR | Sniffing dog | – | Success rate: 76–100% | |
| Breath sample | 262 | RT-qPCR | GCxGC ToF-MS | Octanal, nonanal, heptanal | Sensitivity: 100% Specificity: 66% | |
| Breath sample | 219 | RT-qPCR Antibody test | Electronic nose | – | Sensitivity: 86% NPV: 92% | |
| Pharyngeal secretion, face masks, cloths | 80 | RT-qPCR | Sniffing dog | – | Sensitivity: 86% Specificity: 92% |
COVID-19 testing by mass-spectrometry.
| Specimen | No of patients | Reference method | Specimen preprocessing | Target | *MS approach | Results | References |
| NPS, OPS | 985 | RT-qPCR | Ethanol precipitation, lysis, trypsin digestion; automated magnetic bead-based preparation | Nucleoprotein | TFC-MS/MS | Sensitivity: 84% Specificity: 97% | |
| NPS | 362 | RT-qPCR | No preprocessing required, 1:1 mixing with matrix solution | Untargeted | MALDI-TOF MS; machine learning – SVM | Accuracy: 93.9%) FP: 7%, FN: 5% | |
| Gargle solution | 3 | RT-qPCR | Acetone precipitation, tryptic digestion | Nucleoprotein | LC-MS | SARS-CoV-2 nucleoprotein identified in 2 of the three samples | |
| NPS | 8 | RT-qPCR | Heating, isopropanol precipitation, tryptic digestion | Nucleoprotein | LC-MS/MS | N protein detection in SARS-CoV-2 positive samples | |
| NPS | 311 | RT-qPCR | No preprocessing required, 1 μl specimen mixed with 1 μl matrix solution | Untargeted | MALDI-TOF MS; Multivariate analysis | Accuracy:67.66%, Sensitivity:61.76%, Specificity:71.72% | |
| NPS, OPS | 103 | RT-qPCR | Lysis, TCA precipitation | Spike, replicase | LC-MS/MS | Sensitivity: 90.5% Specificity: 100% | |
| Serum | 298 | RT-qPCR | Dilution, 1:1 mixing with matrix solution | Untargeted | MALDI-TOF MS; machine learning – logistic regression | Accuracy: 99% Sensitivity: 98% Specificity: 100% | |
| NPS | 199 | RT-qPCR | No preprocessing required, 1:1 mixing with matrix solution | Untargeted | MALDI-TOF MS; machine learning – | Accuracy: 98.3%, PPA:100% NPA: 96% | |
| NPS | 16 | RT-qPCR | Heat inactivation, denaturation, tryptic digestion | Nucleoprotein, spike | LC-MS/MS | 94% concordance | |
| NPS | 237 | RT-qPCR | Virus inactivation with guanidine thiocyanate, dilution, 1:1 mixing with matrix solution | Untargeted | MALDI-TOF MS; machine learning | Accuracy, sensitivity and specificity: >90% | |
| Plasma | 815 | RT-qPCR | Dilution, homogenization, centrifugation, formic acid ionization | Untargeted | HESI-MS; machine learning | Sensitivity > 83% Specificity > 96% |
Metabolomics based potential prognostic markers for COVID-19.
| Specimen | No. of patients | Metabolomics approach (N) | Patient groups | Severity marker/criteria | Metabolic pathway/s affected | Potential metabolomic markers | Association | Strength/weakness | References |
| Serum | 65 | GC-MS (46) | Mild vs. severe COVID-19 patients | Respiratory failure, respiratory rate > 30 bpm, O2 saturation < 92%, PaO2/FiO2 < 300 mmHg52. | Valine and threonine catabolism | α-hydroxyl acids | Correlation with O2 saturation/lung damage FC: 1.8–2.3; adjusted | Limited data | |
| Plasma | 104 | GC-MS UHPLC/MS (77) | COVID-19 PCR positive vs. negative patients with flu-like symptoms | Mild – symptoms, no CT scan or hospitalization Moderate – dyspnea, pneumonia by CT scan, hospitalization, O2 supplementation Critical – ICU admission, respiratory distress, intubation and mechanical ventilation | Kynurenine pathway | Anthranilic acid | Correlation with poor prognosis and high IL-10/18 ( | Correlation with known immunosuppressive role Small sample size | |
| Plasma | 30 | LC-MS/MS, NMR (162) | COVID-19 positive and negative ICU patients and healthy controls | ICU admission, mortality | – | Kynurenine Creatinine/arginine ratio | Prediction of COVID-19 associated death (accuracy = 100%) | KP pathway involvement confirmed in multiple studies Small sample size | |
| Serum | 49 | UHPLC-MS | COVID-19 positive and negative patients | Severity inferred from IL-6 levels, CRP and BUN | Tryptophan metabolism/kynurenine pathway | Acylcarnitines, kynurenine, and methionine sulfoxide | Positive correlation with IL-6 [–log( | KP pathway involvement confirmed in multiple studies Small sample size | |
| Free fatty acid and tryptophan levels | Negative correlation with CRP [–log( | ||||||||
| Acylcarnitines | Positive correlation with BUN [–log( | ||||||||
| Serum | 187 | GC-MS (75) | Mild vs. severe disease | Dyspnea, respiratory rate ≥ 30/min; O2 saturation ≤ 93%, PaO2/FiO2 < 300 mmHg52, lung infiltrates > 50% | – | 2-hydroxy-3- methylbutyric acid, 3-hydroxybutyric acid, cholesterol, succinic acid, | Progression from mild to severe COVID-19 (AUC 0.969) | Free fatty acid changes observed in multiple studies Small sample size | |
| Plasma | 49 | LC-MS/MS (221) | Moderate, severe and critical | O2 saturation, analytical parameters and radiological findings | Ceramides, tryptophan metabolism, and NAD-consuming reactions | Kynurenine/tryptophan, 3-hydroxykynurenine/kynurenine, and 3-hydroxykynurenine/tryptophan | Increase with COVID-19 severity ( | KP pathway involvement confirmed in multiple studies Small sample size | |
| Serum | 61 | Targeted: UHPLC-MS/MS (258) Untargeted: UHPLC quadruple TOF high-resolution MS/MS system (155) | Mild, severe COVID-19 patients and healthy control | Respiratory distress, respiratory rate ≥ 30/min; O2 saturation ≤ 93%, PaO2/FiO2 < 300 mmHg5 | Nicotinate and nicotinamide metabolism, tryptophan metabolism, and citrate cycle | – | Correlation with IL-6, IP-10, and M-CSF | KP pathway involvement confirmed in multiple studies Supporting data from longitudinal study Small sample size | |
| Plasma | 341 (700 samples – longitudinal over 3 months) | Untargeted: LC-MS/machine learning (235 polar metabolite and 472 lipid metabolite) | COVID-19 positive patients with different levels of severity and COVID-19 negative patients | Symptoms, hospital and ICU admission, mechanical ventilation, death | – | 25 predictor metabolites | Predict disease severity | Results confirmed by animal testing Longitudinal study Predictor metabolites remained uncharacterized | |
| Plasma | 161 | Untargeted: UPLC-MS/MS GCxGC-MS (2075 lipids and 500 small molecules) | Critical and non-critical COVID-19 patients and healthy controls | Mild to severe – O2 supplementation, no mechanical or non-invasive ventilation Critical – respiratory failure, ICU admission, mechanical ventilation | Gluconeogenesis and the metabolism of porphyrins | Arachidonic acid and oleic acid | Correlated to severity of the disease (AUC > 0.98) | Free fatty acid changes observed in multiple studies Small sample size | |
| Plasma | 85 | NMR, LC-MS/MS; Multi-omics (348) | Mild to severe vs. critical | Mild – clinical signs of pneumonia but without O2 support Severe – with O2 support using non-invasive ventilation, tracheal tube, tracheotomy assist ventilation, or ECMO | Lipoprotein metabolism | HDL1, HDL4, LDL1, LDL4, LDL5, VLDL5, ApoA1, triglycerides, cholesterol | Disease severity | Preliminary data on potential biomarkers | |
| Blood, urine | 30 | LC-MS Multi-omics: proteome, amino acids and lipidome (1254 proteins 664 lipids) | Severe vs. non-severe | Common – symptoms, pneumonia Severe – respiratory distress, respiratory rate > 30 bpm, O2 saturation < 92% at rest, PaO2/FiO2 < 300 mmHg52. Critical – respiratory failure, mechanical ventilation, shock, ICU admission | – | 21 lipids and 4 proteins | AUC: 0.993 to classify severe patients | Limited data | |
| – | 96 | Bioinformatics analysis of published metabolomics data of COVID-19 | Non-severe and severe COVID-19 patients, healthy controls and non-COVID-disease controls | Mild – symptoms without pneumonia Typical – fever or respiratory tract symptoms with pneumonia Severe – respiratory distress, respiratory rate > 30 bpm, O2 saturation < 92% at rest, PaO2/FiO2 < 300 mmHg52 Critical – respiratory failure, mechanical ventilation, shock, ICU admission, other organ failure | Nucleic acid and amino acid metabolism | Taurochenodeoxycholic acid 3-sulfate, glucuronate and | Top classifier of severe disease (ROC 0.805) |