Encephalitis After COVID-19 Vaccine Administration: Perspectives

In this video, Roger Seheult, MD of MedCram reviews an autopsy case report in a vaccinated individual where spike protein was found in the heart and brain of an individual that had died of encephalitis (inflammation of the brain). 

Vaccine side effects

Medcram in the past has reviewed the vaccines and their side effects going back to April 2021 with the Johnson and Johnson vaccine pause and September 2021 with Covid vaccines and 10 key questions answered with Rhonda Patrick. 

Side effects of medications are not a foreign concept, and Dr. Seheult has had plenty of experience in this. He himself collaborated on a study that reviewed how long people should be on anticoagulation after an unprovoked venous thromboembolism and evaluated side effects vs potential benefits of a treatment. It is important to note that any medical intervention you will be undertaking will always have some component of risk and potential side effects. 

Autopsy case report

He goes on to review a case report of multifocal necrotizing encephalitis (brain inflammation) and myocarditis (heart inflammation) after BNT162b2 (Pfizer) mRNA vaccination against COVID-19. This paper never mentions if the patient was ever tested for SARS-CoV2 infection. It involved a 76 year old male who had received 3 doses of a COVID-19 vaccine. This patient had a diagnosis of Parkinson’s disease which can be a confounder as this disease has neurological manifestations, autonomic dysfunction as well as mitochondrial dysfunction and cardiovascular manifestations. After the patient’s last vaccine dose, two weeks later,  he was reported to have collapsed while eating and collapsed again another week later. Per the paper there was no symptomatic COVID disease.

Autopsy findings

The lung autopsy results essentially showed bilateral bronchopneumonia (ie extensive pneumonia). In the heart autopsy, it showed coronary artery disease, pulmonary edema, inflammation, and fibrin clots.

Spike and nucleocapsid proteins

The heart tissue was stained for both the spike and nucleocapsid protein. The virus carries both these proteins.  The spike protein is the target of the vaccines and the nucleocapsid protein. A viral infection should have both spike and nucleocapsid proteins. The presence of nucleocapsid proteins implies that an active viral infection is present.  A control example in the paper showed in a control patient’s respiratory secretions that died of COVID, both the spike and nucleocapsid protein were present. In this current patient’s brain on autopsy, they stained for these and found that spike protein was present but the nucleocapsid protein was absent. Why is there no nucleocapsid protein? In this same patient on autopsy, the staining of the heart, spike protein was seen, but again no nucleocapsid. On the final autopsy results it was determined that death was due to bilateral bronchopneumonia, Parkinson’s disease, necrotic encephalitis, and myocarditis.  The authors of the case report concluded that since the nucleocapsid protein of SARS-CoV-2 was consistently absent, it must be assumed that the presence of the spike protein in affected tissues was not due to an infection with SARS-CoV-2 but rather to the transfection of the tissues by the gene-based COVID-19 vaccines. A caveat to this was the patient did not appear to have been tested for SARS-CoV-2 infection and that the respiratory tissue was not tested for SARS-CoV-2. The author of this report concluded that the absence of the nucleocapsid is the definitive evidence that the encephalitis lesions in the brain must have been attributed to vaccination rather than infection.  

Why is the nucleocapsid protein missing?

However, there is another paper from the Annals of Diagnostic Pathology. This paper was available online in May 2022, well before the recent autopsy case report was written. This paper was looking at deaths attributed to COVID-19 deaths. This paper found that in each COVID-19 patient that had died, there was an abundance of SARS-CoV-2 spike protein; however, the SARS-CoV2 RNA and nucleocapsid protein were rarely detected in situ in any COVID-19 heart. They concluded that the viral spike protein is endocytosed (eaten) by the macrophages and carried to the heart and brain and other organs and this is the reason why the spike protein is visible and not the nucleocapsid. Furthermore, they found that nucleocapsid protein was only evident in COVID-19 lung samples and nasopharynx, and not in other organs tested. For the spike protein, it was found in the heart and was concluded that the spike protein can transfer to organs outside of the respiratory system but this does not seem to be the case for the nucleocapsid.  

Going back to the original autopsy report there was evidence of spike protein in the heart but no evidence of any nucleocapsid protein. It is in the respiratory tissues where the virus replicates and this is where you are most likely to see a spike protein and nucleocapsid protein. The authors of the pathology study point out that in the lung the virus induces a microangiopathy that causes viral degeneration and this is likely a source of viral spike proteins to enter the circulation and dock in organs with a high perivascular based ACE2 population such as the heart.  They go on to point out that prelim studies suggest that the viral spike protein along with the matrix and envelop proteins are carried by macrophages in the circulation.  So the nucleocapsid might not be seen due to it not being picked up by the macrophages like the spike protein is.  The author of the first study concluded that the absence of the nucleocapsid protein meant the spike protein had to come from a vaccine; however, in light of the other study it appears that having spike protein alone does not necessarily mean it was from a vaccine only, but could have been from a SARS-CoV-2 infection as well. 

Are there excess deaths noted from the vaccines?

It is important to continue to look for possible vaccine side effects. When we look at the chart that reflects when the most people were vaccinated in a day, there is no increase in excess mortality noted afterward which is what we would expect if the vaccines were contributing to excess deaths. The key to understanding whether or not and how you can prevent events after any intervention is not to compare somebody who would never have an event with someone who did have an event but instead you need to compare someone who did have an event with someone who didn’t get the intervention. This is important when trying to look at things epidemiologically and with studies and with data. This is also why even when things seem logical as in this autopsy case of seeing the spike protein without the nucleocapsid, it is important to conduct studies and do research to further open up understanding before coming to definitive conclusions. There could be other factors that are preventing that nucleocapsid protein from leaving respiratory tissues and getting into non-respiratory tissue organs. The second paper highlighted where this may be the case.  Additional research is needed.

MedCram wants to send its condolences to all of those individuals that have lost someone due to COVID-19. 



A Case Report: Multifocal Necrotizing Encephalitis and Myocarditis after BNT162b2 mRNA Vaccination against COVID-19 (Vaccines) | https://www.ncbi.nlm.nih.gov/pmc/arti…

Histologic, viral, and molecular correlates of heart disease in fatal COVID-19 (Annals of Diagnostic Pathology) | https://www.sciencedirect.com/science…


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