Science facts about mutations and the development of a vaccine

Writes Dr. V.E Kalodimou

Director Flow Cytometry-Research and Regenerative Medicine Department
IASO MATERNITY HOSPITAL

A mutation is an alteration/change in the genetic material, (the genome), of a cell, of a living organism or of a virus that is more or less permanent and that can be transmitted to the cell’s or the virus’s descendants. Mutations also occurred as the result of environmental factors such as UV light and cigarette smoke.

Over a lifetime our DNA can undergo changes or ‘mutations^?’ in the sequence of :, A, C, G and T. (Figure 1) This results in changes in the proteins that are made. This can be a bad or a good thing.

Figure 1: An illustration to show an example of a DNA mutation. By Genome Research Limited

Cells often can recognize any potentially mutation causing damage and repair it before it becomes a fixed mutation.

Mutations can also be inherited, particularly if they have a positive effect. For example, the disorder sickle cell anemia is caused by a mutation in the gene that instructs the building of a protein called hemoglobin. This causes the red blood cells to become an abnormal, rigid, sickle shape. However, in African populations, having this mutation also protects against malaria.

Mutation can also disrupt normal gene activity and cause diseases, like cancer. Cancer is the most common human genetic disease; it is caused by mutations occurring in a number of growth-controlling genes. Sometimes faulty cancer causing genes can exist from birth, increasing a person’s chance of getting cancer. On the other hand the beneficial mutations also known as ‘good’ mutations, lead to new versions of proteins that help organisms adapt to changes in their environment. Beneficial mutations are essential for evolution to occur. They increase an organism’s chances of surviving or reproducing, so they are likely to become more common over time.

Some mutations are hereditary because they are passed down to an offspring from a parent carrying a mutation through the germ line, meaning through an egg or sperm cell carrying the mutation.

There are also nonhereditary mutations that occur in cells outside of the germ line, which are called somatic mutations.

So, can a mutated gene be corrected? Most treatment strategies for genetic disorders do not alter the underlying genetic mutation; however, a few disorders have been treated with gene therapy. This experimental technique involves changing a person’s genes to prevent or treat a disease.

Mutations can lead to changes in the structure of an encoded protein or to a decrease or complete loss in its expression. Because a change in the DNA sequence affects all copies of the encoded protein, mutations can be particularly damaging to a cell or organism.

We have 4 types of mutation:

1. Germline mutations occur in gametes. Somatic mutations occur in other body cells.
2. Chromosomal alterations are mutations that change chromosome structure.
3. Point mutations change a single nucleotide.
4. Frame shift mutations are additions or deletions of nucleotides that cause a shift in the reading frame.

Mutations are caused by environmental factors known as mutagens, include:

• radiation,
• chemicals, and
• infectious agents.

Mutations may be spontaneous in nature.

Mutations can vary in severity from having zero consequences to majorly alter a protein and its function. Mutations can involve the substitution of one DNA base to another, a G for an A for instance. Or mutations can involve the insertion of additional DNA bases or the deletion of existing DNA bases.

Once a mutation occurs, if it changes the function of a resulting protein, a virus or organism is then changed. Because cells and viruses interact with the environment or surrounding cells, this change is either going to give the mutated cell or virus an advantage, allowing it to thrive more easily in its environment or will make it disadvantaged, making it more difficult to survive.

This is a process called natural selection. If the mutation confers an advantage, the mutated sequence then spreads within a population and if the mutation confers a disadvantage, the mutated sequence dies out.

As COVID-19 spreads around the globe, it is mutating, in other words, it is acquiring genetic changes. While the idea of “viral mutation” may sound concerning, it’s important to understand that many of these mutations are minor, and don’t have an overall impact on how fast a virus spreads or potentially how severe a viral infection might be. In fact, some mutations could make the virus less infectious.

Much of our knowledge of how viruses change to escape natural or vaccine-elicited immunity comes from observing the influenza virus and constantly updating influenza vaccines.

Influenza viruses change in two main ways:

1. antigenic drift and
2. antigenic shift.

As a virus replicates, its genes undergo random “copying errors”, (i.e. genetic mutations). Over time, these genetic copying errors can, among other changes to the virus, lead to alterations in the virus’ surface proteins or antigens.

Figure 2: virus replication – random copying errors

Our immune system uses these antigens to recognize and fight the virus. So, the question is what happens if a virus mutates to evade our immune system?

To answer the question we going to use influenza viruses as an example where genetic mutations accumulate and cause its antigens to “drift”, meaning the surface of the mutated virus looks different than the original virus.

Figure 3: Influenza example

When influenza virus drifts enough, vaccines against old strains of the virus and immunity from previous influenza virus infections no longer work against the new, drifted strains. A person then becomes vulnerable to the newer, mutated flu viruses. Antigenic drift is one of the main reasons why the flu vaccine must be reviewed and updated each year, to keep up with the influenza virus as it changes.

Could that also happen with Covid-19; scientific observations regarding the genetic evolution of the virus it appears that the virus is mutating relatively slowly as compared to other RNA viruses. Scientists think this is due to its ability to proofread newly-made RNA copies.

This proofreading function does not exist in most other RNA viruses, including influenza. Studies to date estimate that the virus mutates at a rate approximately four times slower than the influenza virus, also known as the seasonal flu virus. It does not seem to be drifting antigenically.

Figure 4: Mutations at 4 times slower

The Antigenic Shift occurs when two different, but related, i.e. influenza virus strains infect a host cell at the same time. Sometimes these viruses can “mate,” in a process called, reassortment. During reassortment, two influenza viruses’ genome segments can combine to make a new strain of influenza virus.

A reassortment result is a new subtype of virus, with antigens that are a mixture of the original strains. When a shift happens, most people have little or no immunity against the resulting new virus (i.e. “x” marks below). Viruses emerging as a result of antigenic shift are the ones most likely to cause pandemics.

Figure 5: Antigenic shift – the result of pandemics

Coronaviruses do not have segmented genomes and cannot reassort. Instead, the coronavirus genome is made of a single, very long piece of RNA. However, when two coronaviruses infect the same cell, they can recombine, which is different than reassortment. In recombination, a new single RNA genome is stitched together from pieces of the two “parental” coronaviruses genomes.

It’s not as efficient as reassortment, but scientists believe that coronaviruses have recombined in nature. When this happens, scientists identify the resulting virus as a “novel coronavirus.” The generation of a novel coronavirus, although occurring by a different mechanism than antigenic shift in influenza viruses, can have a similar consequence, with pandemic spread.

The human immune system uses a number of tactics to fight pathogens. The pathogen’s job is to evade the immune system, create more copies of itself, and spread to other hosts. Characteristics that help a virus do its job tend to be kept from one generation to another. Characteristics that make it difficult for the virus to spread to another host tend to be lost. One way hosts protect themselves from a virus is to develop antibodies to it. Antibodies lock onto the outer surface proteins of a virus and prevent it from entering host cells. A virus that appears different from other viruses that have infected the host has an advantage: the host has no pre-existing immunity, in the form of antibodies, to that virus. Many viral adaptations involve changes to the virus’s outer surface.

In order to understand better this assumption, we are going to use the example of influenza and HIV and how evolution occurs. Both of these viruses are RNA viruses, meaning that their genetic material is encoded in RNA, not DNA.

DNA is a more stable molecule than RNA, and DNA viruses have a proofreading check as part of their reproductive process. They manage to use the host cell to verify viral DNA replication. If the virus makes a mistake in copying the DNA, the host cell can often correct the mistake. DNA viruses, therefore, do not change or mutate, much. RNA, however, is an unstable molecule, and RNA viruses don’t have a built-in proofreading step in their replication. Mistakes in copying RNA happen frequently, and the host cell does not correct these mistakes.

The rapid rate of HIV evolution has important consequences. HIV can quickly develop resistance to anti-HIV drugs. Additionally, targeting a vaccine to a rapidly changing virus is challenging. To date, researchers have developed several candidate HIV vaccines, but none has performed well enough in clinical trials to warrant licensure.

According to researchers such as Kupferschmidt the pandemic virus is slowly mutating. Therefore, the million-dollar question is if the Covid-19 virus is getting more dangerous; it’s only a tiny change.

In part that’s because it changes more slowly than most other viruses, giving virologists fewer mutations to study. But some virologists also raise an intriguing possibility Covid-19 was already well adapted to humans when it burst onto the world stage at the end of 2019, having quietly honed its ability to infect people beforehand.

Take a look at the scientific data published we know that one of the earliest candidates was the wholesale deletion of 382 base pairs in a gene called ORF8, whose function is unknown. First reported by Linfa Wang and others at the Duke-NUS Medical School in Singapore in a March preprint, the deletion has since been reported from Taiwan as well.

A deletion in the same gene occurred early in the 2003 severe acute respiratory syndrome (SARS) outbreak, caused by a closely related coronavirus when lab experiments later showed that variant replicates less efficiently than its parent, suggesting the mutation may have slowed the SARS epidemic. Cell culture experiments suggest the mutation does not have the same benign effect in Covid-19, Wang says, “but there are indications that it may cause milder disease in patients.”

The genetic science about viruses indicates that viruses are continuously changing as a result of genetic selection. They undergo subtle genetic changes through mutation and major genetic changes through recombination. Mutation occurs when an error is incorporated into the viral genome. Recombination occurs when co-infecting viruses exchange genetic information, creating a novel virus.

The mutation rates of DNA viruses approximate those of eukaryotic cells, yielding in theory one mutant virus in several hundred to many thousand genome copies. RNA viruses have much higher mutation rates, perhaps one mutation per virus genome copy. Mutations can be deleterious, neutral, or occasionally favorable. Only mutations that do not interfere with essential virus functions can persist in a virus population.

It’s hard to measure exactly how much of an impact the new variants are having on the pandemic, since there are many factors that contribute to how quickly a virus spreads, including human behaviors. Experts are taking this seriously and are working to better understand what these and other mutations could mean for the pandemic. They are also watching other emerging variants.

So far, experts say there’s no clear evidence that the new virus variants are deadlier, cause more severe disease or will make COVID-19 vaccines ineffective.

The Advisory Committee on Immunization Practices (ACIP) has been trying to solve many complex questions regarding the COVID-19 vaccine, even before it started in clinical trials.

In the past with other diseases and immunizations, it would take years to provide a vaccine recommendation.

The committee had studies three key elements that can lead to potential vaccination:

1. It verifies that the vaccine is safe and effective.

2. How a vaccine would be distributed and how much of the product is available.

3. How it determines who gets the vaccine, especially the first doses of a limited supply.

The facts till now are:

• On December 1, 2020, ACIP recommended that once the FDA passed Emergency Use Authorization (EUA), it should first be offered to healthcare workers and residents of long-term care facilities.
• On December 11, 2020, the FDA issued the first emergency use of the Pfizer-BioNTech COVID-19 vaccine to be distributed in the U.S. to those who are 16 years and older.
• Then on December 13, 2020, after the FDA approved first emergency use authorization, ACIP officially recommended the vaccine to U.S. residents, specifically for healthcare workers and those in long-term care facilities.
• And on December 18, 2020, Moderna received Emergency Use Authorization (EUA), from the FDA for its COVID-19 vaccine.

It usually takes years and years to roll out a vaccine, says Dr. Gordon. From review to distribution, everything that has happened over the past nine months has been at warp speed. We’ve never pushed out a vaccine this quickly before, so there will be many questions we need to answer as this happens in real-time.

More research is needed about the vaccine for those under 16 and when it comes to pregnant and breastfeeding women, the FDA is still deliberating.

If these studies give positive results, such directed generation of recombinant viruses may become an important tool in the development of vaccines and gene therapy in the future.

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