BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: #variant

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.

 

How are new COVID variants identified?

COVID variants are of high concern for scientists studying the disease. Some variants can be more infectious or cause more severe illness. Additionally, some variants can evade vaccines by having different surface proteins than the variant the vaccine was created for. This causes the antibodies produced from the vaccine to be less effective against other variants. In AP Biology class we discussed how the Delta Variant, first identified in December 2020, has a different spike protein structure than the original virus from which the vaccine was created from. This allows the variant to be more infectious, and make the vaccine less effective against it. But, what are COVID variants? And how are they discovered? Hand with surgical latex gloves holding Coronavirus and A Variant of Concern text

COVID variants are “versions” of the virus with a different genetic code than the original one discovered. However, not every mutation leads to a new variant. This is because the genetic code of the virus codes for proteins. Some mutations will not change the structure of the protein and thus not change the virus. So, COVID variants can be defined as versions of the virus with a significantly different genetic code than the original virus.

To detect new COVID variants, scientists sequence the genetic code of virus which appears in positive COVID tests. Scientists look at the similarity of the genetic sequences they find. Then, if many of the sequences they get look very similar to each other, but different to any other known virus, a variant has been discovered.

To sequence the RNA of the virus, scientists use what is called Next Generation Sequencing (NGS). To understand how NGS works, it is best to start with what is called Sanger Sequencing. Sanger Sequencing utilizes a modified PCR reaction called chain-termination PCR to generate DNA or RNA fragments of varying length. The ending nucleotide of each sequence is called a ddNTP, which contains a florescent die corresponding to the type of nucleotide. The addition of a ddNTP also terminates the copying of the particular sequence. The goal of this PCR reaction is to generate a fragment of every length from the start to the end of the sequence. The sequences can then be sorted by length using a specialized form of gel electrophoresis. The sequence is then read by using a laser to check the color of the fluorescent die at the end of each sequence. Based on the color and size, the nucleotide at that position of the genomic sequence can be found.

Sanger Sequencing Example

The difference with NGS is that many sequences can be done in parallel, allowing for very high throughput. In other words, with NGS many COVID tests can be sequenced in once.

Changing Composition of SARS-CoV-2/Understanding the Alpha Variant in England

Since its emergence in the Fall of 2020, the original SARS-CoV-2 variant of concern (VOC) rapidly became the dominant lineage across much of Europe. Although, simultaneously, several other variants of concern were identified globally. Like B.1.1.7 or the Alpha Variant (first mutation of SARS-CoV-2 found to be more transmissible), these VOCs possess mutations thought to create only partial immunity.

Researchers are understanding when and how these additional VOCs pose a threat in settings where B.1.1.7 is currently dominant. This is where scientists in the UK examined trends in the prevalence of non-B.1.1.7 lineages in London and other English regions using passive-case detection PCR data, cross-sectional community infection surveys, genomic surveillance, and wastewater monitoring. The study period spanned from January 31st of 2021 to May 15th of 2021.

Through this data, the percentage of non-B.1.1.7 variants has been increasing since late March 2021. This increase was initially driven by a variety of lineages with immune escape. From mid-April, B.1.617.2 (WHO label of Delta) spread rapidly, becoming the dominant variant in England by late May, similarly to the Alpha Variant.

Shown by many mutations in the spike protein receptor (RBD), studies suggest B.1.1.7 is 50–80% more transmissible with greater severity than previously circulating Covid Variants. B.1.1.7 rose rapidly, from near 0% to over 50% in under two months, and soon made up greater than 98% of sequenced samples in England. Its rapid spread necessitated a third lockdown in England during last January. Subsequent spread in Europe and North America has highlighted the threat this variant poses to a continued alteration of the Coronavirus.

The 69–70 deletion in B.1.1.7′s Spike gene causes PCR tests to return negative results for that gene target which is a major problem when identifying and testing for Covid. One of the most important changes in lineage of B.1.1.7 seems to be a spike protein substitution of N501Y, a change from asparagine to tyrosine in amino-acid position, that enhances transmission. These alterations can change antibody recognition while also affecting ACE2’s (receptor protein) binding specificity which can then lead to the virus becoming more infectious. We are seeing a pattern of the same type of mutation in Covid consistently.

An example of a similar mutation that has been recent is the new Omicron variant out of South Africa. Omicron is similar in which their has been a specific change in the spike protein where antibody recognition is limited and it is highly transmissible between any living organism. Our class has understood and studied the importance of our body being able to identify and create an antibody for the specific antigen being displayed by a pathogen.  These mutations within the spike protein allow another immune response to happen which a different antibody has to be created to mark the different antigen being displayed. Unfortunately, this will be a continuing problem without vaccine mandates since it gives the virus more time to mutate where outbreaks like in South Africa will continue to transpire around the world.

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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