Hypothesis: Long COVID brain fog is caused by free glycan sugar chains in the brain

by Angela May O’Connor, Ph.D. 1

1 Independent Patient-Researcher

Cite as: O’Connor, A. M. (2023). Hypothesis: Long COVID brain fog is caused by free glycan sugar chains in the brain. Patient-Generated Hypotheses Journal for Long COVID & Associated Conditions, Vol. 1, 5-12


Coronavirus spike proteins are composed of glycoproteins, molecules that have a protein center and sugar side-chains. These coronavirus glycans interact with other protein-sugar molecules present on the outer surface of cells, known as the glycocalyx. Coronavirus spike proteins particularly interact with the glycocalyx within blood vessels, causing these protein-sugars to peel off the internal walls of blood vessels. Previous work has shown that during sepsis, protein-sugar molecules similarly slough off the internal walls of blood vessels, cross the blood-brain barrier and contribute to cognitive, memory, and mood disorders. This proposal hypothesizes that viral persistence and constant coronavirus spike protein presence in the bloodstream of Long COVID patients similarly causes an ongoing degradation of endothelial glycocalyx, resulting in free floating glycan sugar side-chains that contribute to the cognitive issues observed in this condition.


Proteoglycans are a broad group of molecules, comprised of a core protein surrounded by sugar side-chains that are composed of differentially sulphated groups of glycosaminoglycans (GAG); both the core protein and sugar chains determine binding affinity and functionality of a proteoglycan1,2. The spike proteins found on the external surface of SARS-CoV-2, the virus that causes COVID-19, are glycoproteins, also composed of a protein core and sugar side-chains3-5. During normal function, sugar side-chains are constrained to their core proteins and do not interfere with normal biological processes; however, free glycan side-chains can damage various tissues, such as during sepsis6-8.

These glycan fragments are small enough to pass the blood-brain barrier, resulting in impaired memory and cognitive functions both during and after sepsis, thought to be due to the presence of free glycan side-chains within the brain6,7. The SARS-CoV-2 proteoglycan spike protein is known to persistently circulate in patients with Long COVID10, and is known to both cross and disrupt the function of the blood-brain barrier11-13. This proposal addresses the possibility that freely circulating, persistent SARS-CoV-2 spike protein is a major contributor to the cognitive and memory deficits experienced by patients with Long COVID.


Proteoglycans play many different roles in cellular and biological processes, particularly heparan sulfate proteoglycans (HSPGs)2 like those thought to act as a co-receptor for the SARS-CoV-2 virus3-5. HSPGs mediate growth factor signaling, provide guidance during cellular migration and axonal growth within the brain, organize the extracellular matrix, enable cellular motility and adhesion, and facilitate virus-host interactions among other cell-cell crosstalk2. HSPGs may be secreted into and participate in the extracellular matrix, form intracellular secretory vesicles, or be bound to cellular membranes2, where they act as co-receptors for various growth factors, proteins and the SARS-CoV-2 virus3-5.

Proteoglycans and glycoproteins within the brain regulate neuronal health, form chemical gradients that guide cellular migration during development, provide cellular support, enable synaptic connections, regulate the availability and signaling of growth factors, and close off critical periods by helping to solidify mature neural networks2, 14-18. It has been seen that altering proteoglycans within the rodent brain results in altered behavior19-21 and neural function22,23.

Recent work has established the presence of free-floating SARS-CoV-2 spike protein within the blood of Long COVID patients8. It is hypothesized that viral persistence within patients results in a variety of immunological, neurological, and autonomic dysregulation, while also providing a constant supply of the spike glycoprotein. The presence of freely circulating glycans has also been detected, and significantly contributes to pathophysiology during sepsis6,7. Like Long COVID, sepsis is a multi-organ, multi-system inflammatory process where normal cellular activity is disrupted or completely breaks down, and the two have been compared as having similar long-term sequelae35. Proteoglycans and glycoproteins that are sloughed off blood vessel endothelia during sepsis are capable of crossing the blood-brain barrier, and are thought to contribute to the ongoing cognitive and neurological issues seen in post-sepsis syndrome6-9. Similarly, the free floating spike protein found in the blood of Long COVID patients is also capable of crossing the blood-brain barrier12,13, and high levels of HSPGs have been found in the blood of COVID-19 patients due to endothelial glycocalyx disruption3. What is not known is whether the presence of these glycans in the brain contributes to the cognitive and neurological issues seen in Long COVID, similar to the effect observed in septic and post-septic patients.

This proposal puts forward the hypothesis that the circulating SARS-CoV-2 spike protein found in Long COVID patients crosses the blood-brain barrier and interferes with normal neuronal and cellular functioning within the brain, contributing to the brain fog, speech impediments, memory issues, cognitive impairments, and other neurological disorders observed in patients with Long COVID.

How to test the hypothesis

Assessing patient tissue

  • Assess proteoglycan and glycoprotein sugar side-chain recovery from post-mortem tissue taken from the brains of severe acute COVID-19 patients. Recover glycan chains and perform liquid chromatography mass spectrometry using established techniques7 to assess the presence of the SARS-CoV-2 spike protein or free-floating HSPG sugar side-chains within various brain regions.
  • Correlate circulating glycan levels with brain glycan measurements and behavioral/cognitive performance to determine how free floating SARS-CoV-2 spike protein and elevated HSPG blood levels correlate with impaired cognitive capabilities.

Assessing animal studies

  • Use an established Long COVID animal model such as that published by Frere et al. (2022)30. Compare behavioral performance in the Puzzle-Box to assess cognitive capabilities29 across a Long COVID animal model, sepsis animal model, and possibly animal model with disturbed brain glycans (i.e. chondroitinase and heparinase injections into the hippocampus).
  • Fresh frozen brains from the above animals: recover glycan chains and perform liquid chromatography mass spectrometry7 to assess the presence of the SARS-CoV-2 spike protein and free-floating HSPG sugar side-chains within various brain regions. Stain brain samples for 3G10 and 10EF to assess the presence of broken/free floating proteoglycan side-chains versus bound/complete side-chains27, and for perineuronal nets using wisteria floribunda agglutinin (WFA) to assess the state of the glycans within the brain extracellular matrix28.
  • Collect trunk blood at sac: process for the presence of free floating proteoglycans and glycoproteins, including the SARS-CoV-2 spike protein.
  • Correlate circulating glycan levels with brain glycan measurements and behavioral performance to determine how much free floating glycans, including the SARS-CoV-2 spike protein, contribute to impaired cognitive capabilities.

Potential therapeutics

  • Nattokinase to dissolve persistent circulating SARS-CoV-2 spike protein31
  • Synthetic heparan sulfate mimetics to disrupt glycocalyx degradation caused by persistent SARS-CoV-2 spike protein32
  • Drugs used to restore endothelial functioning in diabetes treatment33,34

Unanswered questions

1. Do Long COVID patients have ongoing endothelial glycocalyx degradation similar to that observed in acute COVID patients?

2. What neurological or cognitive impacts do the free-floating SARS-CoV-2 spike protein glycans have in patients with Long COVID?

3. How can we measure or determine this?

4. What are some ways in which we can eliminate the free floating glycans from Long COVID patients’ tissues, particularly within the brain?


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