BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Omicron

Omicron’s Effect on the Vaccinated by Vaccination Status

As the world continues to be stricken by the seemingly everlasting wave of strains of Sars-Cov-2, the vaccine began to give people hope as it was extremely effective against the original disease as well as all the other strains up until now. With sudden jump in corona cases, researchers have discovered that there is a new virus that is soon to take over as the most prevalent virus in the world. It’s been named Omicron but the question that is on a lot of people’s mind is if this new strain will be hindered by the vaccine or will it continue on its rampage across the world.

Study Participant Receives NIAID-GSK Candidate Ebola Vaccine (3)

Studies show that the answer is dependent on vaccination status. Omicron has accounted for “90% of COVID cases in areas like the Midwest” states Doctor Rochelle Walensky. The article later goes on to state that the booster vaccination shot ” increased by 25-fold people’s levels of virus-fighting antibodies.” Ultimately the amount of vulnerability you have to this new strain is directly tied to how many vaccination shot you have. But why do we even need a booster shot if the first two doses should have been enough? Well to answer this question we first need to look at how the initial two doses work. The CDC states that “Vaccines work by stimulating your immune system to produce antibodies, exactly like it would if you were exposed to the disease.”  As we learned in our AP Biology class, by giving you a small amount of sars-cov-2, the dendritic cell is able to enlist the help of plasma B cells and memory B cells by sending out T helper cells. This is known as theHumorale Immunantwort humoral response and is what gives you the ability to fight off breakthrough infections as well as help hinder the symptoms of sars-cov-2. It is able to suppress symptoms as well as prevent reinfections because once your body has fought off a little bit of the virus with the antibodies created by B helper cells your body is able to make a copy of how to deal with it in your B memory cells. The memory B cells are what give you your immunity to the virus. However over time they do run out as you were only given a small amount of the virus so this is where the booster comes into affect. The booster shot is designed so that your body is able to continue to get stimulated by the virus so that you B plasma and helper cells are able to keep memorizing and keep fighting off small (in the case of the vaccine) or big (in the case of an actual infection) Covid cases. There may continue to be more booster that you must take in order to keep your immunity, and no its not because the chip is running out of battery or they want to keep injecting you, but its due to the fact that your body simply can’t remember such a small amount of the virus for very long and if you don’t get the booster you are 25x more likely to contract Omicron than those who have all three. Ultimately the vaccine is still effective against Omicron, however Omicrons ability to be more infectious than any other variant before it is why it was able to take over the world so quickly. That being said there is a very real possibility that there will be a Omicron centered booster shot that will be significantly more effective than the past three shots against this devastating variant. Feel free to let me know how you feel about Omicron, a special new booster, or about how that Vaccine works down below.

 

2021: The Year Of The Coronavirus Variants

Alpha and beta kicked off the 2021 year, and several worrisome variants later, omicron closed it out. How omicron may come to define the pandemic’s future remains uncertain. But even as omicron comes on strong, one variant, which rose to global dominance midyear in a way variants like alpha and beta never did, continues to largely define the pandemic right now: delta.

Things had actually seemed to be looking up in some parts of the world in the late spring and early summer of 2021, a year and a half into the COVID-19 pandemic. In the United States, for instance, millions of people were vaccinated, cases of the disease were falling, and people were beginning to socialize and resume normal activities. 

But then delta hit hard. First spotted in India in October 2020, this variant of SARS-CoV-2, the coronavirus known as COVID-19, quickly swept around the world, supplanting other versions of the virus in 2021. Delta overwhelmed health care systems, tore through unvaccinated populations and showed that even the vaccinated were vulnerable, causing some breakthrough cases.  

It soon became clear why delta wreaks so much havoc. People infected with delta make more of the virus and spread it for longer than people infected with other variants, researchers reported in Clinical Infectious Diseases in August. As a result, delta infections are more contagious. Consider two scenarios in a community where no one has immunity to the coronavirus: A person infected with an earlier version of the virus — the one first identified in Wuhan, China, that set off the pandemic — might spread it to two or three others. But a person infected with delta may transmit it to five or six people.

COVID-19 Coronavirus Symptoms

Mutations similar to delta’s have appeared here and there in other variants that proved themselves capable of spreading more easily or better evading the body’s immune defenses than the original virus. That includes alpha, first spotted in the United Kingdom; beta, first characterized in South Africa; and gamma, first noted in Brazil. The recently discovered omicron variant, first described in South Africa and Botswana, also shares some of the same mutations. 

Some of delta’s grab bag of mutations are identical to those found in other variants, while others change the same protein building block, or amino acid, in a different way or pop up in the same part of the virus. For instance, alpha and omicron also have the same mutation of the 203rd amino acid in the N protein, but it is a different amino acid change than seen in delta. And some mutations are entirely new to delta. 

3D medical animation coronavirus structure

These mutations on the coronavirus’ spike protein are what define delta as delta. The spike protein helps the coronavirus attach to and enter human cells penetrating host cells and cause infection. Spike proteins as learned in AP Biology while talking about COVID-19, a spike protein is a protein that forms a large structure known as a spike or peplomer projecting from the surface of an enveloped virus. The delta variant’s version carries a unique collection of mutations, marked by yellow dots in this 3-D rendering. Some of these mutations may help the virus more easily infect cells or hide from antibodies.

Though more recently in 2022 most of the population is getting the omicron variant, we must not forget the dominant variant that took control of the world and harmed a lot of people within a very short frame of time. Just when we thought we were out of the woods of COVID-19 during the summer of 2021, the delta variant proved us wrong.

Paxlovid and Molnupiravir: Our First Steps Toward Covid-19 Treatment?

Currently, the new Covid-19 variant Omicron is taking the world by storm. Originating in South Africa as of late November, it was considered a variant of concern(VOC) by the WHO on November 26th and the first US case was identified on December 1st. While masks and current vaccination provide significant protection against Covid-19 strains, there is always a chance of breakthrough infections

In response, both Merck and Pfizer have developed novel antiviral pills in attempts to treat Covid-19 symptoms. It is known that cures for viral diseases do not exist, since viruses tend to mutate extremely fast. However, there exist novel drugs that promise to alleviate Covid-19 symptoms in the early stages of infection, like Pfizer’s Paxlovid and Merck’s molnupiravir. 

It is known that Covid-19 infects human cells by its outer spike proteins attaching to ACE2 receptors on the outside of the cell membrane. When in the cell, Covid-19 viral pathogens insert their viral RNA into our cytoplasmic ribosomes, which then codes for the creation of new viruses that then get excreted by the human cell. Merck’s molnupiravir consists of a five day treatment in which mutations to the viral RNA are introduced, since molnupiravir resembles viral nucleosides, causing irregular viral replication and, ultimately, an inability for the Covid-19 viral population to collectively survive in their human host. Pfizer’s Paxlovid pill, on the other hand, is administered in the early stages of Covid-19 infection to stop the progression of the disease and to prevent severe Covid-19 symptoms by inhibiting protease enzymes from functioning, which leads to the inability of virus proteins to become segmented and to spread, leading to dysfunctional Covid-19 viral pathogens and the ultimate death of Covid-19 viruses in the human host.Omicron

Fortunately, these two treatments are showing promising results in current clinical data trials. According to a Merck Sharp and Dohme (MSD) clinical study, 14.1% of placebo-treated patients were admitted to the hospital or had died of Covid-19, while only 7.3% of molnupiravir-treated patients were either hospitalized. In addition, at the end of the trial, 0 deaths were recorded in the monopiravir trial, while 8 deaths were reported among the placebo group. These results lead MSD scientists to deduce that the novel molnupiravir to reduce hospitalization or death by 50%. 

Pfizer’s Paxlovid, on the other hand, is especially promising in its clinical results. According to a recent Pfizer clinical data trial, 7% of the placebo group was hospitalized, and 7 died, while a staggering .8% of Paxlovid-treated Covid-19 patients were hospitalized, with 0 deaths by the end of the trial. These results lead Pfizer to state that “Paxlovid is 89% effective at patients in risk of serious illness,” as reported by Pfizer CEO Albert Bourla. 

In conclusion, although Covid-19 cannot have a fixed “cure,” outside of a vaccine of course, yet convenient, short-course antiviral pill treatments like Pfizer’s Paxlovid and Merck’s molnupiravir provide promising clinical trial results that show efficacy in reducing hospitalization and death rates due to Covid-19. While clinical data trials provide important markers of understanding Covid-19 treatment, it is still impossible to predict the practical applications of these pill treatments in the real world. Who will have access to these pill treatments? How will they get distributed? Will these treatments create global and regional socioeconomic disparities? In the eyes of these questions, our current vaccination protocols remain firm. While novel Covid-19 antiviral treatments are a huge step against Covid-19, the necessity for society to continue vaccination, as well as attempt to reach herd immunity levels, still holds utmost importance. 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Omicron: The Latest Invader

As it has been for the past few years, COVID-19 is the talk of the town. However, just when things seemed to be dying down, a new variant made its way into our lives. It goes by the name “Omicron”.

Unlike the past two variants, Delta and Mu, Omicron presents a whole new dilemma in the fight against COVID-19. After Delta took the world by storm with significantly greater infection rates than Mu, seemingly nothing could get worse. However, over 30 mutations to the spike proteins of the virus now trumps Omicron above all other variants. Identified in South Africa on November 24, 2021, Omicron has already made its way to many other countries around the world, including the US.

The threat of Omicron derives from its ability to resist the effects of the antibodies of the vaccine due to the changes in the protein structures. As we learned in our AP Biology class recently, the vaccine works by stimulating the production of plasma B cells, which secrete antibodies to identify and neutralize the antigen of the COVID-19 virus by recognizing the spike proteins, as well as B memory cells that exist to prevent further infection of the virus. The many changes to the spike protein make the antibodies unable to properly detect and neutralize it, allowing for the virus to continue to spread throughout our bodies. Virologist Penny Moore warns of the reduced effects the vaccine will have against Omicron, as well as the exponentially faster infection rates that pose threat to the world.

6VSB spike protein SARS-CoV-2 monomer in homotrimer

A recent study from a South African virologist, Alex Sigal, isolates blood samples from 12 Omicron infected patients who have been vaccinated with the Pfizer vaccine. The study shows that the antibodies from the vaccine are nearly forty times less effective against Omicron than the other two variants. This uncovers that the vaccine may not be efficient enough to combat the new virus. Sigal’s experiment also found that people previously infected with the virus held stronger immunity to Omicron than those with the vaccination. This is due to the fact that natural B memory cells made are able to evolve for multiple months to help fight against COVID-19 while B memory cells from the vaccine only evolve for a few weeks. Though, the experiment was not done with enough patients to make a certain conclusion.

Although, there is a glimpse of hope to retain some immunity against Omicron using the booster shot. Pfizer-BioNtech research has indicated that the third dose of the vaccine can produce antibody levels against Omicron that closely resemble the antibody levels of only two shots against the prior variants. Scientists have begun to branch off from the traditional concept of stimulating production of plasma B-cells to create antibodies in hope to find a new way to trigger the immune system to adapt to new COVID-19 variants. Biologist Jesse Bloom suggests a deeper dive into the function of T-cells, particularly cytotoxic T-killer cells, and their ability to destroy cells already infected with the virus.

Omicron poses severe potential threats to the state of the world with its fast infection rate and immunity to the vaccine. The studies of the few infected patients with Omicron do not seem to promising, but not enough has been collected about Omicron to determine its true potential. The only thing we can do now is hope for the best!

 

 

How Killer T Cells Could Increase Immunity Against New COVID Variants.

In recent news, there are concerns about the newly discovered COVID variant named Omicron. Preliminary evidence suggests an increased risk of reinfection with this variant, as compared to other variants of concern. Scientists are hopeful that T cells could provide some immunity to COVID-19, even if antibodies become less effective at fighting the disease.

Along with antibodies, the human body’s immune system produces a plethora of T cells which target viruses. Helper T cell’s stimulate killer T cells, macrophages, and B cells to make immune responses. T cells do not prevent infection because they kick into action only after a virus has infiltrated the body. But, they are important for clearing an infection that has already started. If killer T cell’s are able to kill virus-infected cells before they are able to spread to from the upper respiratory tract, it will affect how you feel and will be the difference between a mild infection and a severe one.

Studies by Sette and his colleagues have shown that people who have been infected with SARS-CoV-2 typically generate T cells that target at least 15–20 different fragments of coronavirus proteins. But, the protein particles that are targeted vary from person to person. This means that a variety of T cells will be generated, making it difficult for the virus to mutate in attempt to escape cell recognition. Research suggests that most T-cell responses to COVID variations or previous infection do not target regions that were mutated in recently discovered variants. If T Cells remain active within your immune system against specific variants, they might protect against severe diseases.

Ultimately, in my opinion, this is extremely important since researchers have been analyzing clinical-trial data for several coronavirus vaccines in attempt to find clues as to whether their effectiveness fades in the face of new emerging COVID variants such as Omicron. As of now, coronavirus vaccine developers are already looking at ways to develop next-generation vaccines that stimulate T cells more effectively. Antibodies only detect proteins outside cells, and many coronavirus vaccines target spike proteins, located on the surface of the virus. Since spike proteins are liable to change, it may be prone to mutating and raising the risk that emerging variants will be able to evade antibody detection. T cells, on the other hand, can target viral proteins located inside infected cells, and some of those proteins are very stable. This raises the possibility of designing vaccines against proteins that mutate less frequently than spike proteins, and incorporating targets from multiple proteins into one vaccine.

Biotechnology firm Gritstone Oncology of Emeryville, California, is designing an experimental vaccine that incorporates the genetic code for fragments of several coronavirus proteins known to elicit T-cell responses, as well as for the full spike protein, to ensure that antibody responses are robust. Clinical trials are due to start in the first quarter of next year. If approved, this vaccine could revolutionize how we approach the creation and experimentation of COVID vaccines in the future.

Omicron Variant: How Will it Affect the Vaccinated?

When looking back over the past 2 years, many think about the need for and effectiveness of the COVID-19 vaccines, but regardless of what many may think it has been proven that the COVID-19 vaccine is effective against the original variant of COVID-19 that was most prominent during the production of vaccines. However, what many people are wondering is if these vaccines & boosters are still effective against the Omicron variant?

Before going over the effectiveness of the current vaccines and booster shots on the Omicron variant, we first have to look at the Omicron variant itself. First off, we know that Omicron was “first identified [in] South Africa,” which is a place where full vaccination rates are at 25%: a low percent that is not high enough for herd immunity. Despite this, the Omicron is still viewed as a threat to more vaccinated communities. This is because in order for variants of COVID-19 to be labeled a variant, it needs at least one mutation to its spike protein, and Omicron has dozens of mutations to its spike protein, and the more mutations it has, the more potential it has to infect the vaccinated.

It is important to note that the COVID-19 vaccines help to produce antibodies that latch onto and render spike proteins inactive. Since this Omicron variant has dozens of mutations to its spike protein. As seen through activities and lessons learned in our Bio class, different variants of COVID-19 just have pieces of the protein structure changed, which leads to a changed shape of their spike proteins. This leads to existing vaccines being less effective as the original vaccine was meant for a specific spike protein shape, not the shapes of the new variants. The changes to the Omicron spike protein makes it very different to the original COVID-19 spike protein, so the vaccine will be less effective.

Even if a break through the vaccinations defenses doesn’t happen with the Omicron variant, “some version of this coronavirus is bound to flummox our vaccines.” Despite all of this information, we still know very little about the Omicron variant and its effects. It’s just too early to know what will happen. Because of this lack of information, it is important for people to make sure they are vaccinated and get their boosters as it does still make a difference. Overall, people, vaccinated or not, should err on the side of caution with this new potential threat of Omicron out there and should try to stay safe.

 

 

“US braces for Omicron!”…Whats all the hubbub really about?

I was studying for AP Bio one day, when I first heard about the fears around the omicron variant. All over instagram, facebook, I even received emails about it: there seems to be major concern among many, including prominent medical researchers, according to WHO.

World Health Organization Logo

“What is the omicron variant?” You may ask.  This variant was first reported from South Africa  Wednesday, November 24th. In the recent weeks, cases of infection have been increasing rapidly in South Africa, likely as a result of this mutated variant. According to WHO, this variant has a large number of concerning mutations (discussed in detail below), some of which increase the risk of infection. Luckily, current SARS-CoV-2 PCR tests still can be used as a marker in detecting this new omicron variant. Because of this fact, officials have been able to detect this variant faster than previous surges in infection cases.

OmicronDespite being able to detect this variant faster than previously, researchers are still concerned over the mutations this variant poses and the implications that could have in this pandemic. Being the fastest spreading variant yet, some of these concerns include the specific mutations on the spike proteins. As we learned before, Spike Proteins protrude from the SARS-CoV-2 cell, allowing for it to bind to receptors on the host cell. Penny Moore, a virologist at the University of the Witwatersrand in Johannesburg, South Africa, says there are more than 30 mutations to the spike protein in omicron, which could possibly make it more contagious and/or allow this variant to evade our vaccines. 

Many of the mutations detected on the omicron variant have been found in the delta and Alpha variants, and are linked to heightened infections, as well as the ability to evade infection-blocking antibodies and other immune responses. Mutations to regions of the spike protein in the omicron variant has changed the way the antibodies recognize the pathogens, hindering their ability to bind to the spike proteins. If the spike proteins have mutated and changed shape, then the antibodies will not be as effective in binding. Additionally, hints from computer modeling have revealed the omicron variant could dodge the immunity given by the T cells. However, Scientists have yet to understand the true significance of these mutations and what it means for the response to the pandemic. Penny Moore and her team hope to have their first results in two weeks. 

What does this mean for vaccine efficacy?

Solo-mrna-vaccine-4 Well, two quarantined travelers in Hong Kong have tested positive for the omicron variant despite being vaccinated using the Pfizer vaccine. Additionally, Moore says that breakthrough infections have been reported in South Africa among people who have received the vaccine. Again, researchers in South Africa will soon find whether this omicron variant causes illness that is more severe or milder than that produced by the other variants. We should hear their results soon. According to Researchers, the greater threat that this omicron variant poses beyond South Africa is unclear. In the meantime, a way to fight for a healthy future would be to continually take the measures necessary to reduce the risk of COVID-19, including proven public health measures such as wearing masks, hand hygiene, social distancing, and getting vaccinated.

Let me know your thoughts below on this new variant! Stay Safe!

 

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

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 proteinVariants of COVID-19 have mutations present in the spike protein due to copying errors in our DNA.

File:Omicron.jpg - Wikimedia Commons

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.

Free COVID-19 Illustrations - Innovative Genomics Institute (IGI)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.

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