by Xiaomeng Han

If your best friend Betty told you that she has a sore throat, a runny nose, and has lost her sense of smell or taste, you might immediately recognize the symptoms of COVID-19. But what if she had become very forgetful lately, instead? Recent emerging evidence suggests that SARS-CoV-2, the virus that causes COVID-19, can infect cells in the brain. In fact, some people who contracted the virus developed neurological symptoms like loss of memory, altered mental state, and even strokes. To study how the virus affects the brain, two groups of scientists turned to a novel technology called brain organoids. By using organoids, laboratory structures that partially mimic the brain’s complexity, the scientists described how the virus infects and destroys human brain cells and also found several potential therapies to halt this unanticipated symptom.

Brain organoids are tools to study the human brain 

Brain organoids are miniature brain-like structures that scientists grow in laboratories used to model diseases like Zika virus and microcephaly: a disease where a baby’s brain is much smaller than expected because it didn’t develop properly. Such diseases are difficult to study with animal models like mice, since these animals often lack the structures and connectivity of the human brain. 

To make a versatile model for studying the human brain, Dr. Juergen Knoblich’s lab developed brain organoids in 2013 using a technology called induced pluripotent stem cells, or iPSCs for short. Scientists can cause iPSCs to mimic a variety of different cell types, such as immune cells or brain cells, which are tricky or impossible to grow outside of the body. 

To make brain organoids, scientists grow iPSCs around a 3D structure while treating them with certain chemical compounds. The resulting small, 3D bundle of cells that contains similar cell types and displays similar connectivity with a real human brain can be used to study diseases which animal models cannot fully recapitulate, such as COVID-19 (Figure 1).

Figure 1: Brain organoids can model COVID-19 because they, unlike mice, can be infected by the SARS-CoV-2 virus.

In fact, this is the case with COVID-19 too: SARS-CoV-2 cannot infect normal lab mice, so mice are an imperfect model to study the disease’s progression. As such, two recently published reports used brain organoids to study SARS-CoV-2. To find out if SARS-CoV-2 can attack the brain and how the attack takes place, the groups of Prof. Alysson Muotri and Prof. Akiko Iwasaki infected brain organoids with the virus and assessed what happened to the cells in these mini-structures. So, what does SARS-CoV-2 do to the brain organoids?

SARS-CoV-2 kills neurons and reduces connectivity

In a preprint published in May, scientists in Prof. Alysson Muotri’s lab at UCSD used brain organoids to study whether SARS-CoV-2 infects cells in the brain and, if so, which cell types. Preprints are papers made public prior to the lengthy peer review process, which allows other scientists to see data sooner, before they have been reviewed and published in a research journal. The scientists classified the cells in the brain organoids into two major types: neurons, the main cell type making up our nervous system; and astrocytes, important supporting cells for neurons. They discovered that SARS-CoV-2 can infect and kill not just one, but both of these types of cells (Figure 2). 

Since SARS-CoV-2 could infect and kill brain cells, the scientists then asked whether the virus affected the pattern of structures and interactions connecting brain cells to one another. Specifically, they looked at how SARS-CoV-2 impacted synapses, the connections between neurons that are essential for signal transmission within the brain. Their data shows that infected neurons have a dramatically decreased number of synapses, hinting that SARS-CoV-2 not only kills neurons but also impairs neuronal connectivity (Figure 2). The question then is, how does SARS-CoV-2 result in neuronal death and loss of connectivity?

SARS-CoV-2 kills neurons by messing with their oxygen supply

In January, Prof. Akiko Iwasaki’s lab at Yale published their own study on how SARS-CoV-2 causes the death of neurons. These scientists took a closer look at the infected neurons in their brain organoid system and surprisingly found that most of the dying neurons were not those that were actually infected by the virus. Rather, the uninfected neurons surrounding the infected ones were dying (Figure 2)! To explain this surprising phenomenon, the scientists examined the life-sustaining metabolism of these cells. 

Their data showed that the infected neurons have a hyperactive metabolism, which means the cells are spending more energy compared to nearby non-infected neurons. Additionally, they showed that infected neurons have signs of the cellular metabolic state called hyperoxia, which indicates that their oxygen supply is much higher than needed; the neighboring neurons, on the other hand, have signs of the opposite cellular metabolic state, called hypoxia, which means that they don’t have enough oxygen for normal function and survival (Figure 2). But why would infected cells be more metabolically active? 

The scientists’ hypothesis is that when SARS-CoV-2 infects cells, the virus turns them into efficient virus-making factories; with more oxygen, these cells might be able to churn out even more viruses (Figure 2). According to this model, SARS-CoV-2 hijacks the otherwise well-balanced supply of oxygen to the brain to produce more of itself. The neighboring uninfected cells likely die because there is not enough oxygen to sustain themselves. The work of these two groups offered a better understanding of the unanticipated neurological symptoms of COVID-19; SARS-CoV-2 kills neurons by depleting their oxygen supply. But can anything be done to stop this invasion?

Figure 2: Prof. Alysson Muotri’s lab showed that SARS-CoV-2 kills neurons and reduces their connectivity. Prof. Akiko Iwasaki’s lab showed that the virus kills the neurons by messing with their oxygen supply.

Searching for drugs to protect the brain against SARS-CoV-2

Brain organoids can also be used for developing novel therapies and testing them for potential side effects more quickly. Since the Muotri and Iwasaki groups had these organoid systems up and running, they could also use them to look for drug candidates that could prevent brain cell infection by SARS-CoV-2. 

The study by Muotri’s group identified an antiviral drug called Sofobuvir, which is a FDA-approved anti-hepatitis C drug that targets enzymes essential for viral reproduction. They showed that Sofobuvir not only rescued neurons but also restored their impaired connectivity. The Iwasaki study, on the other hand, successfully employed specific antibodies, proteins counteracting certain viral molecules, to fight the infection. The antibodies they tested blocked the ACE-2 receptor molecules on neurons’ surface that help the virus enter cells. With these receptors blocked, the virus can no longer infect neurons in brain organoids.

These two groups successfully used brain organoids to study the unanticipated invasion of the human brain by SARS-CoV-2. Their results further support organoids as an invaluable model for disease and drug discovery. Moreover, these findings give theories for why some COVID-19 patients experience neurological symptoms. Although doctors may still need months or years to fully characterize the exact consequences of COVID-19 on the brains of patients, at least now we are aware of this unexpected and unwanted attack and are able to begin actively developing “weapons” to fight back!


Xiaomeng Han is a graduate student in the Harvard Ph.D. Program in Neuroscience. She uses electron microscopy to study neuronal connectivity.

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2 thoughts on “An Unexpected Invasion: How SARS-CoV-2 affects the human brain

  1. I would think that THC would protect a certain amount just like it does for MS Paients.
    A side note here is a Scientist told me that the spots seen on an MRI of MS patients are actually proteins made by Mycobacteria, and that the proteins can unfortunately pass thru the Blood Brain Barrier.
    Mycobacteria may be worse than Covid for its the cause of Leprosy, Tuberculosis, Crohn’s Disease and MS.

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