The changes in plasma metabolome observed in long COVID patients two years after acute infection

The authors from Mexico examined the persistence of long-term changes in plasma metabolome in long COVID patients two years after acute infection. They also assessed certain immune markers. The results have shown that mitochondrial dysfunction, redox state imbalance, impaired energy metabolism, and chronic immune dysregulation are likely to be the main hallmarks of long COVID, even two years after acute infection.

The WHO has described long COVID as a condition “that occurs in individuals with a previous history of probable or confirmed SARS-CoV-2 infection, usually three months after the onset, with symptoms lasting at least two months that cannot be explained by an alternative diagnosis”. Long COVID could be considered as a spectrum of disorders. Over 50 symptoms have been reported to be associated with long COVID. Multiple organ systems are affected, including the respiratory, cardiovascular, nervous, and gastrointestinal systems. Both untargeted and targeted metabolomics have proven to be valuable tools for studying long COVID.

The term “post-viral syndrome” has been used for over a century. The authors emphasized that certain viruses might lead to persistent physiological alterations, such as West Nile, Polio, Dengue, Zika, seasonal flu, Epstein-Barr, Ebola, MERS, and SARS. However, none of these viruses have affected so many people at the same time as SARS-CoV-2. The increasing number of patients with long COVID has become a challenge for public health systems worldwide, but, there are no guidelines for diagnosis and classification of patients with long COVID.

About the study

The authors assessed the plasma metabolome in 100 samples collected from patients with acute COVID-19, patients with long COVID and healthy controls. Stored plasma samples from 37 individuals who tested negative for SARS-CoV-2 in 2020 were used as negative controls. The patients were asked to complete a questionnaire. Long COVID was considered if patients reported at least one persistent neurological, psychiatric, gastrointestinal, cardiovascular, respiratory, or systemic symptom. A total of 30 patients with long COVID were further categorized into two classes: class A patients, who reported less than five persistent symptoms (17 patients), and class B patients, who reported more than five persistent symptoms (13 patients).

All patients were fully vaccinated between 2021 and 2022.

The Metabolomics Innovation Center Prime (TMIC PRIMER) assay was used to measure a metabolomics. This assay provides quantitative results for up to 143 endogenous metabolites, such as biogenic amines, amino acids, organic acids, lipids, and lipid-like compounds. The authors quantified 108 metabolites. Additionally, levels of IL-17 and leptin were measured. IL-17 is persistently changed in several chronic inflammatory and autoimmune diseases, and leptin is believed to cause inflammatory fatigue.


Even after 2 years, 27 metabolites remained dysregulated in long COVID patients compared to healthy controls. The concentrations of C18:2, C10:2, C10:1, as well as glutamine, choline, glucose, kynurenine, pyruvic acid, kynurenine/tryptophan ratio, and putrescine were higher in long COVID patients in comparison to the healthy controls. Long COVID patients, on the other hand, had downregulated lysoPC 14:0, lysoPC 16:0, lysoPC 16:1, lysoPC 18:0, LysoPC 17:0, LysoPC 20:4, SM(OH)22:1, PC aa 32:2, sarcosine, taurine, and glutamic acid in comparison to healthy controls. Patients with long COVID also had increased glutamine/glutamate ratio and decreased lactate/pyruvate ratio.

One of the most dysregulated metabolites was glucose. The authors speculated that the observed rise in plasma pyruvate levels is a result of glycolytic dysregulation and protein degradation, whereas increased putrescine levels could be an indicator of increased protein degradation to help fuel pyruvate metabolism. The increased levels of hippuric acid could be associated with a residual intestinal dysbiosis. The presence of elevated levels of kynurenine, and a trend toward normalization in tryptophan and the kynurenine/tryptophan ratio suggests that the inflammatory conditions attributed to the hyperactivation of this metabolic pathway are still present. A rise in glutamine levels and a decrease in glutamate (a higher glutamine/glutamate ratio) could be associated with long-term recovery. A disruption of the glutamatergic pathway can result in significant neurological consequences.

The results also revealed an increase in the concentrations of metabolites associated with collagen metabolism in long COVID patients. Among these metabolites, proline is particularly noteworthy. Taurine and spermidine were significantly decreased, although a trend toward normalization was observed when compared to healthy controls.

The majority of long COVID patients also had alterations in lipid metabolism with higher levels of carnitine and some short, medium, and long acylcarnitines. These cahnges have been mostly associated with altered fatty acid metabolism, dysfunctional mitochondria-dependent lipid catabolism, and immune processes or the lysis of white blood cells. Furthermore, decreased concentrations of LysoPC 16:0, LysoPC 17:0, LysoPC 18:0, and LysoPC 20:4 were found in comparison to healthy controls. Routine clinical laboratory tests exhibited elevated levels of total cholesterol, triglycerides, and VLDL, as well as normal levels of HDL and LDL, in line with the lipid dysregulation demonstrated by the targeted metabolomic analysis.

The concentrations of 30 metabolites were within the normal range. The level of phenylalanine, which is frequently associated with sepsis and COVID disease severity, decreased to normal levels. Beta-hydroxybutyric acid and citric acid were also normalized, suggesting a partial recovery of the tricarboxylic acid cycle. The levels of butyric acid and propionic acid, two short-chain fatty acids that were found to be changes during acute COVID-19, also fell within the normal range in long COVID patients. Spermidine levels were also normalized, and a decrease in levels of spermidine could reflect a trend for normalization in overall redox balance, according to the authors. The levels of sphingomyelins and long-chain monounsaturated and saturated LysoPCs were also found to be within normal range.

The multivariate analysis revealed that the most important variables that can be utilized to differentiate healthy controls from long COVID patients are phenylalanine, glutamine/glutamate ratio, taurine and glutamine.

The top five metabolic pathways were significantly dysregulated in patients with long COVID compared to healthy controls, such as phospholipids biosynthesis, gluconeogenesis, the glucose-alanine cycle, the Warburg effect, and taurine and hypotaurine metabolism.

The plasma metabolome was then assessed in three subgroups of patients: class A patients who had less than five persistent symptoms (18 patients), class B patients who had more than five symptoms (12 patients), and recovered or non-long COVID patients who didn’t have any symptoms (18 patients). The number, type of symptoms and metabolic signatures were different between patients experiencing long COVID (class A and class B patients) and recovered patients or non-long COVID patients.

Lactic acid, lactate/pyruvate ratio, ornithine/citrulline ratio, and arginine were the most relevant metabolites that distinguished long COVID patients with more than five symptoms (class B) from those with fewer than five symptoms (class A). The levels of lactic acid and the lactate/pyruvate ratio were increased in patients with more than five symptoms and systemic disorders (class B patients), as important indicators of mitochondrial dysfunction. These two markers (lactate and the lactate/pyruvate ratio) were found to be positively correlated with symptoms like fatigue, myalgia and arthralgia. The authors pointed out that elevated ornithine/citrulline ratio, observed in class B patients, actually reflects an abnormal metabolic activity in the urea cycle.

The patients in class B exhibited a decrease in arginine levels in comparison to other subgroups. Arginine was negatively correlated with levels of IL-17, and various symptoms, like anxiety, fatigue, loss of concentration, thoracic pain, dyspnea, myalgia, and arthralgia. The authors noted that the reduced availability of arginine to produce sufficient levels of nitric oxide in endothelial cells and vascular tissues results in the impairment of numerous physiological functions of skeletal muscles.

Additionally, long COVID patients with more than five symptoms had increased levels of IL-17 , but there was no statistical difference in leptin levels, despite observing higher levels in those patients.

The top five metabolic pathways were significantly dysregulated in class B patients, including pyruvate metabolism, gluconeogenesis, glycine and serine metabolism, urea cycle metabolism, and the Warburg effect, compared to recovered patients who didn’t have any symptoms. In order to distinguish class B long COVID patients from all other long COVID patients, the lactate/pyruvate ratio had the best performance.

The authors concluded that, to their knowledge, this study is the first to describe quantitative metabolic perturbations two years after the acute COVID-19 infection using targeted metabolomics. Two years after acute COVID-19 infection, mitochondrial dysfunction, redox state imbalance, impaired energy metabolism, and chronic immune dysregulation are likely to be the main hallmarks of long COVID.

Researchers have emphasized that metabolomics is not only useful for getting a picture of physiological or pathophysiological processes occuring in a living organism, it is a powerful instrument for proposing therapeutic interventions. Based on their findings, the authors suggested some interventions for the treatment of long COVID patients, including supplementation of taurine (which reduces musculoskeletal disorders), supplementation of citrulline (which enhances ammonia clearance and reduces blood lactate), supplementation of glutamine (primary source for neurotransmitters and immune function balancing), supplementation of antioxidants such as N-acetylcysteine or NAD + (redox balance), and supplementation of arginine (which targets endothelial dysfunction in Long-COVID).

This article was published in Scientific Reports.

Journal Reference

López-Hernández, Y. et al. The plasma metabolome of long COVID patients two years after infection. Sci Rep 13, 12420 (2023) (Open Access)