#spikeprotein – BioQuakes

Tag: #spikeprotein

While in a global battle against an invisible enemy, a team of spirited scientists have found a remarkable discovery that could change the course of the pandemic and challenge everything we thought we knew about the elusive Omicron variant! The study, led by Boston University and involving international researchers, investigates the Omicron variant of the SARS-CoV-2 virus. SARS-CoV-2, short for Severe Acute Respiratory Syndrome Coronavirus 2, is an RNA virus belonging to the Coronaviridae family, known for its distinctive spike proteins that facilitate entry into host cells. This virus, causing the COVID-19 disease, primarily targets the respiratory system and spreads via aerosolized droplets, leading to symptoms ranging from mild flu-like manifestations to severe respiratory distress.

It identifies mutations that enable Omicron to evade prior immunity and introduces a new protein, NSP6, as a key factor in its reduced disease-causing potential. This study refutes earlier misconceptions about its findings and offers new insights for vaccine and therapeutic development. Hopefully, we can create a vaccine that will finally rid us of COVID for good.

Mohsan Saeed, the study’s senior author, highlights the minimal role of the spike protein in Omicron’s lower pathogenicity. We learned in AP Biology this year that a spike protein is a surface protein found on certain viruses, including the coronavirus, that facilitates their entry into host cells. These cells recognize foreign proteins, including viral spike proteins, and help orchestrate the body’s defense by binding to these proteins and signaling other immune cells to respond. This knowledge enhances our understanding of viral mechanisms and immune responses, highlighting the significance of proteins other than the spike protein in viral pathogenicity. It binds to receptors on the host cell’s surface, triggering a process that allows the viral genome to enter and infect the cell. Instead, mutations in the NSP6 protein are crucial in Omicron’s pathogenicity. This discovery opens new possibilities for future vaccines and treatments. The research, which will also be published in print, is a collaborative effort between various universities and research centers, emphasizing the need to explore non-spike regions of the viral genome.

The study began when researchers noticed the fast spread but reduced severity of Omicron. The initial focus was on the spike protein, as it was the primary differentiator between Omicron and the original virus. However, experiments showed that while the spike protein contributed to Omicron’s characteristics, it was not the sole factor. The National Institute of Health says that another reason for quick spread is several mutations of Omicron, which promote its ability to diffuse worldwide and its capability in immune evasion. It always amazes me how something so microscopic can have so many different factors at play!

Researchers adhered to strict protocols to avoid enhancing the virus’s strength, a concern known as “gain of function.” Comparing the chimeric virus (combining Omicron’s spike with the original virus) with the original strain revealed that the chimeric virus was weaker but not as weak as Omicron, indicating other factors at play.

Further research led to the discovery of the role of the NSP6 protein. This protein, previously understudied, was found to significantly reduce viral replication and infection severity. This finding shifted the focus from the spike protein to NSP6, revealing its importance in the virus’s ability to cause disease.

Understanding the role of NSP6 opens new avenues for combating COVID-19. It highlights the importance of examining genetic differences between variants to develop new treatments and vaccines. The research team plans to further investigate NSP6, potentially leading to more effective pandemic control strategies. Now that you’ve got the scoop on what’s happening with COVID-19 if you were hesitant about the vaccine, did this blog make you think differently? If it did, how so?

The Long Term Effects of COVID-19 Hidden Behind the Fog

By shaliva

On December 7, 2023

In Student Post

COVID-19 was one of the biggest pandemics in United States history. It changed everything including schooling and many other aspects of life, but do you ever seem to forget what life was like before COVID-19? You may be thinking am I just getting old? Why am I losing my memory? Well, findings in Nature Medicine have shown that you may be suffering from what they are calling “Brain Fog”. This Brain Fog can result in recurring memory and concentration lapses that can make it difficult to function every day. You may be thinking, how does this even relate to COVID? Well, It is believed that this brain fog is developed from blood clots triggered by COVID.

Before we get into the brain fog, I want to explain how the body first reacts to COVID-19 entering your cells. AP Bio we learned, that your body activates its innate and adaptive immune systems. First, the innate system releases mast cells which release histamine along with macrophages that secrete cytokines. Cytokines are small proteins that are crucial in controlling the growth and activity of other immune system cells and blood cells. When released, they signal the immune system to do its job. We then see natural killer cells take out any damaged or infected cells while cytokines attract smaller phagocytes called neutrophils and digest pathogens. Along with the Innate response we see the Adaptive response. The adaptive response relies on B lymphocytes and T lymphocytes. The B lymphocytes create the humoral response while the T activates the cell-mediated response. Both are just as important but different. When T-helper cells recognize the antigen it triggers both responses. In the cell-mediated response, the T-memory cells prevent reinfection while the T-killer cells go and kill any infected cells. In the Humoral response the B-plasma cells, secrete antibodies that bind to and neutralize the pathogen which is then engulfed by a macrophage, while B-memory cells also prevent reinfection. Even with all this protection people may still be left with long last symptoms including brain fog.

To find out if this brain fog really came from COVID, a psychiatrist from Oxford named Maxime Taquet took samples of over 1,800 people in the U.K. who had been hospitalized due to COVID-19 and made 6 six-month checks on their symptoms. When examining the blood, they found that people who still had “brain fog” tended to have elevated levels of at least one of two proteins. The first protein is called a D-dimer protein which is produced when a blood clot breaks down. Patients with high amounts of D-dimer tend to have memory problems yet the cognitive side seems to still be intact. Doctors believe these effects were caused by blood clots in the lungs, which lead to low oxygen levels in the brain. The second and seemingly more dangerous protein to find mass amounts of is fibrinogen. This protein is produced in the liver and causes clotting to stop bleeding. When patients have elevated amounts of fibrinogen during COVID-19, they seem to have memory loss along with scoring poorly on the cognitive test. These patients show signs of dementia. Taquet believes that fibrinogen may have caused blood clots in the brain or somewhere else that directly affects the brain.

After hearing about the findings Resia Pretorius was very excited. From her own research, she has found connections between COVID and brain fog. She believes that the spike protein of COVID binds to the fibrinogen and causes it to change shape. But she believes this discovery can help determine ways to cure long COVID symptoms. So have you been affected by COVID’s brain fog or are you just getting old?

COVID-19 Vaccine Going Retro?

By samuelosaurus

On December 5, 2023

In Student Post

Have you ever wondered why the world started to use mRNA vaccines all of a sudden ever since the COVID-19 pandemic? Where did the traditional methods of vaccination go? This sudden shift in vaccine technology didn’t just happen by chance but was a result of years of scientific research and experiments. As the world faced an unprecedented pandemic, the traditional method of vaccination, while reliable, was slower and less effective to adapt to mutating virus than the mRNA vaccines, which is faster and more flexible when combating COVID-19 viruses. However, the traditional methods have returned! The new Novavax COVID-19 vaccine is an old-fashioned, protein-based approach to vaccination, a contrast to the mRNA technology used in Pfizer and Moderna vaccines. The Novavax vaccine especially targets the SARS-CoV-2 variant XBB.1.5, which is a descendent of Omicron.

Novavax’s Differences: A Protein-Based Approach
Unlike the mRNA vaccines, which use modified viral genetic materials to cause an immune response, Novavax relies on a more traditional approach which injects proteins that resemble SARS-CoV-2 directly into the body. This method has over 30 years of application in vaccines such as the Hepatitis B Vaccine. The Novavax Company also uses insect cells, such as moth cells, to produce SARS-CoV-2’s unique spike proteins. The reason why Novavax researchers use moth cells is because of its efficiency in producing spike proteins. They first select the desired genes that create the spike proteins, and then they put these kinds of genes into a baculovirus, which is basically an insect virus. The baculovirus will then infect moth cells and replicate rapidly inside them creating lots of spike proteins. Finally, the researchers will extract and use the spike proteins for vaccines. Additionally, Novavax’s formula also includes Matrix-M, a compound from Chilean Soapbark Trees, which will further enhance our immune system’s response to the spike protein.

Targeted Variants and Efficiency: Novavax vaccines are developed specifically for the XBB.1.5 variant, and they are not optimized for the newer Eris and Pirola variants. However, vaccinologist Gregory Poland notes that all vaccinations, including Pfizer and Moderna, have all been “chasing the tail” of the emerging variants all over the pandemic, so Novavax is not alone in this situation. Additionally, all of the vaccine boosters seem to be able to provide some protection against new variants, but protein vaccinations are way slower to adapt to the new variants than mRNA vaccines. In terms of efficiency, according to infectious disease researcher Kirsten Lyke, Novavax stands on par with other mRNA vaccines. It is 55% effective in preventing COVID-19 symptoms and 31% effective at preventing infections, and this is very similar to the mRNA vaccines.

(mRNA coding protein)

Side Effects and Availability:
When it comes to side effects, the Novavax booster demonstrates a lower risk of myocarditis(inflammation of heart muscle) or pericarditis(inflammation of the outer lining of the heart) compared to mRNA vaccines, but of course, it is not entirely risk-free. It also tends to have fewer side effects like muscle fatigue and nausea post-vaccination. A huge advantage of the Novavax vaccine is its availability, it can be stored in a typical refrigerator, making it considerably more accessible than mRNA vaccines, which require subfreezing storage. The Novavax booster is now available in pharmacies across the country, with the CDC recommending having two doses that are eight weeks apart for unvaccinated people.

Which one should I get?
Both the protein vaccines and the mRNA vaccines can help you fight against the SARS-CoV-2 virus, and neither is better than the other. The mRNA vaccine has a faster efficiency in preventing COVID and has a higher adaptability to new variants, while the Novavax vaccine uses a more familiar technology, has a more accessible storage requirement, and has a lower risk of side effects post-vaccination. But no matter which kind of vaccine you think is better, Lyke suggests that the most important thing is to “pick one and get it.”

(SARS-CoV-2)

Connecting to AP Biology:
In AP Biology, we’ve learned about how our bodies fight bacterial and viral infections and specifically talked about how the spike proteins on SARS-CoV-2 work to attack our bodies. When our body first recognizes the SARS-CoV-2 virus, white blood cells like Macrophages and Dendritic cells will engulf the virus, breaking it down into small pieces and displaying it to Helper T cells on their MHC proteins. The Helper T cells will then release Cytokines which will trigger both the Cell-mediated response and the Humoral response of your immune system. These responses will ultimately kill most of the bacteria/viruses in your body. Additionally, your immune system will then remember the SARS-CoV-2 virus, and if you ever get affected again, your immune system will immediately respond to it. Understanding how vaccines help your body defend against real viruses links directly to our studies on the human body’s defense mechanisms against foreign pathogens.

Leave a Comment!
COVID-19 is a years-long pandemic that still hasn’t ended today, I think it is really important for everyone to know how they can protect themselves through modern technologies and minimize the impact of the virus. I am also intrigued by how fast different vaccine technologies have evolved to help mankind to combat the virus. How do you feel about the re-introduction of protein-based vaccines like Novavax? Do you think this will change the public’s preferences on COVID-19 vaccines? Feel free to leave a comment below and we can discuss more about this topic! For more information on this post, go to ScientificAmerican.com for the latest research and updates.

Why Nearly Every Human on the Planet Has Contracted Covid-19

By almoschetto

On December 8, 2022

In Student Post

While some have only heard the term ‘Coronavirus’ starting in 2020, the drama around this type of infectious disease is not new. This type of virus brings on illnesses that you have most likely contracted long before the start of the pandemic in March of 2020. For example, the common cold. But of course, Coronavirus is not responsible for just that– they also bring on SARS (severe acute respiratory syndrome) and MERS (middle eastern respiratory syndrome). With SARS-CoV-2 being the virus that causes COVID-19, this extremely contagious disease is, in fact, a strain of SARS.

But if the Coronavirus has been around long before now and there are so many types of it, what makes SARS-CoV-2 special? The answer to this is its relationship with a particular enzyme, ACE-2, whose shape, function and location opens doors right up for COVID-19 to enter and infect our healthy cells.

While other types of SARS also attached to this enzyme, the ingenious design of the SARS-Cov-2 protruding spike protein is what makes this virus particularly contagious; Throughout the evolution of this virus from other versions of SARS, the shape of their spike protein has become more refined and specific through compaction of its structure to better mimic the shape of the receptor dock of a naturally-occurring enzyme called ACE-2. This mutation allows the virus to strengthen the grip that they can have on human’s cells, making their infection rate much more high and effective.

The function and location of ACE-2 also practically facilitates the infection of SARS-CoV-2 within us. These enzymes play a critical role in the renin-angiotensin system (infection-fighting system), and while this virus utilizes them as an entrance to the body as a means to infect, it is reducing the function of the very cells that are supposed to be fighting it. Additionally, this suppresses the rest of the functions of our immune system.

In the human body, one way in which our immune system works is by the release of T lymphocytes, or T-cells, along with macrophages and monocytes to fight off infections. However, with SARS-CoV-2 having already hijacked ACE-2 at the time when T-cell release is activated, the immune system becomes dysfunctional; the three aforementioned immunity cells are released via a positive feedback loop in a much greater magnitude than usual/ than with other illnesses. Lastly, ACE-2 positive cells are present in over 70 types of our bodily cells, and are especially abundant in oral, nasal, and nasopharynx tissues, which are hot spot entrances for this virus (and many others).

With the involvement of just one enzyme within our bodies, SARS-CoV-2 throws all aspects of our immune system into a disarray. With the many adaptations and evolutions of SARS viruses, infectious diseases such as these are just getting smarter and smarter each time they sweep through the human population.

SARS-CoV-2 Spike Protein

How does the Omicron variant of COVID-19 compare to the deadly Delta variant?

By cytokinesav

On December 6, 2021

In Student Post

With news of the new variant of the COVID-19 virus reaching 16 states here in the US, many are asking: What is this Omicron variant?

The Omicron variant of COVID-19 was first reported to the World Health Organization by the Head of South African Medical Association, Dr. Angelique Coetzee. As of December 6, 2021, there are about 59,000 Americans hospitalized due to said variant. The Delta variant, more than twice as contagious than previous variants according to the CDC, still continues to be the leading cause of COVID-related hospitalization and deaths today in the US and many other countries. However, medical experts are saying that Omicron has a few different key mutations that make it very likely to outperform Delta. How does this Omicron variant compare to the deadly Delta variant which we’ve been battling this year? Here are the main things you need to know.

Symptoms of the Omicron variant:

Fever or chills
Cough
Shortness of breath or difficulty breathing
Fatigue
Muscle or body aches
Headache
New loss of taste or smell
Sore throat
Congestion or runny nose
Nausea or vomiting
Diarrhea

Infection and Spread:

So far, people who have been diagnosed with the Omicron variant of SARS-Cov-2 in the US have or had mild symptoms, yet it is said to be much more contagious. Why? The difference in the structure of the spike protein. Variants of COVID-19 have mutations present in the spike protein due to copying errors in our DNA.

Omicron Structure pictured

The Delta variant has 18 mutations in its spike proteins…Omicron has a whopping 43! That is many, many more than Delta. Jeremy Kamil, associate professor of microbiology and immunology at Louisiana State University Health Shreveport, said, “The number of changes blew people’s minds…It’s an exaggeration to say we’re back at square one, but this is not a good development.”

Around 30 countries have detected said variant so far; 19 states in the US have. The high number of mutations it contains does not necessarily mean it’s more dangerous. As previously stated, Omicron patients have thus far exhibited milder symptoms. Dr. Coatzee said that she first discovered Omicron’s appearance as her patients exhibited “unusual symptoms” in comparison to the Delta variant. However, don’t be too scared; experts say our immune systems have grown more equipped to fight the COVID-19 virus.

We still have yet to learn more about Omicron and its nature, infection, etc., as it is very new.

The original COVID-19 virus’s structure is pictured above

With Omicron having more than double the mutations as Delta, the likeliness of transmission/level of contagiousness is quite high–also meaning that the efficacy of our vaccine could be compromised. The Omicron spike protein has similar components that of the Delta, beta, and gamma variants, meaning that the rate of transmissibility is similar. With Omicron having the largest number of mutations, however, transmissibility can be increased more than 2x!

What should you do?

Well, continue to follow the standard COVID-19 measures. Wear a mask, social distance, wash your hands, travel less, and just be careful. These methods have proven time and time again to help. Travel restrictions on the rise can be tough with the holidays coming, but remember that they are only in place for the sake of our safety. It is important to follow these rules as the pandemic is not over.

BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: #spikeprotein

Unlocking Omicron’s Secrets: Breakthrough in COVID-19 Research Reveals NSP6 Protein’s Key Role

The Long Term Effects of COVID-19 Hidden Behind the Fog

COVID-19 Vaccine Going Retro?

Why Nearly Every Human on the Planet Has Contracted Covid-19

How does the Omicron variant of COVID-19 compare to the deadly Delta variant?

Symptoms of the Omicron variant:

Infection and Spread:

Omicron Structure pictured

The original COVID-19 virus’s structure is pictured above

What should you do?

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