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Evolution of Viruses

Evolution of Viruses

Studies suggest that viruses have been on earth since the dawn of time yet, according to the criteria of life, viruses are not considered living. Viruses are responsible for the majority of diseases that plague the earth and constantly evolve by developing new ways to evade our immune defenses. So what are viruses exactly? Are they simply strands of genetic material that try to take over our bodies? Or are they something more complex? Let's dive deeper into the history and evolution of viruses to find out.

Evolution of viruses over time

The exact way that viruses evolved over time still remains a mystery to this day; however, researchers have some theories. Over the course of modern science, three hypotheses explaining viral origin have emerged:

  1. viruses are relics of a pre-cellular life form;

  2. viruses were produced by the devolution of a unicellular organism;

  3. viruses originated from fragments of genetic material that escaped from the control of the cell and became parasitic.

As the first viruses emerged, they infected their hosts which were most likely bacteria since they are the earliest life form. According to theory 3, viruses mutated into a more parasitic entity and relied more on a host species to survive. As viruses infect different hosts, the viral genomes mutate into different viral strains and this is how viruses evolve over time.

Regressive evolution theory of viruses

The regressive theory of viruses hypothesizes that viruses originated from a more complex free-living ancestor that "de-evolved" by losing genetic information over time.1 As the virus precursor/ancestor lost genetic material, the hypothesis suggests that it developed a parasitic way of surviving.

Viruses are technically not living, because they do not contain enough genetic material to form a complete cell.

Since viruses are not alive, they cannot be classified as parasites. Instead, the way that viruses replicate can be labeled as "parasitic". This is because viruses need to live inside humans to reproduce themselves.

Virus: An acellular, parasitic genetic material that is not classified within any kingdom. Parasite: An organism that lives within another organism of a different species (host) and survives by stealing nutrients from the host.

Viruses are not all identical and come in many different shapes and sizes. The viruses that exist today can be categorized into groups based on the way they store their genetic material. Classifying viruses based on their genome is known as the Baltimore classification method.

  • Double-stranded DNA viruses (dsDNA) store their genetic material as a double helix consisting of two DNA strands, while single-stranded DNA (ssDNA) viruses store their genetic material as one strand of DNA.
  • Some viruses even store their genetic materials as RNA.2 These viruses are called retroviruses. Retroviruses can either be double-stranded (dsRNA), where the genetic material is stored as two strands of RNA, or single-stranded ssRNA, where the genetic material is stored as a single strand of RNA.
  • Single-stranded RNA viruses such as SARS-COV-2 (COVID-19) can either be positive or negative sense. Negative sense RNA viruses have genetic material that is complementary to viral mRNA and cannot be translated readily into viral proteins within the host.2

Examples of negative-sense RNA viruses include Influenza and Ebola.

We will be discussing these viruses later on in this article.

Unlike influenza and Ebola, positive-sense RNA viruses are comprised of the positive mRNA strand and are able to be translated into proteins readily within the host.2

Retrovirus: A virus that stores its genetic material as RNA.

Data to support the regressive theory exists, but it is hard for researchers to know the exact way that viruses evolved without witnessing them firsthand. Analysis of multiple viral genomes provides an interesting insight into how viruses function and may have regressively evolved. Genomic analysis of a large group of DNA viruses called the NCLDV'S best highlights the regressive hypothesis.

NCLDV'S include viruses such as smallpox.1 These types of viruses are quite large and rely less on their host for replication and survival.1

For instance, smallpox is able to produce functional mRNA's within the host cell cytoplasm without the need for a complete take over the host cell's transcription machinery.1

In contrast, smaller viruses such as influenza, possess much smaller genomes and rely entirely on the host cell's transcription machinery for replication.1 Analysis of these two viruses suggests that viruses are regressive. The influenza virus could have evolved from an organism that was more dependent upon its host which could explain why the influenza virus has less genetic material.

Role of viruses in human evolution

Now that we have a general idea of where viruses come from, let's discuss their role in human evolution. Are viruses simply here to take over our bodies? Or did they help us evolve into the complex organisms that we are today?

The answer may surprise you!

Emerging research suggests that 30% of human protein adaptation since humans evolved from chimpanzees has been driven by viruses.1 This means that viruses have been partially responsible for diversifying us from our primate ancestors. This data makes sense because when a host population is faced with a pandemic, the population must genetically adapt in order to fight and withstand the infection.

If the population does not adapt, the virus will overtake each organism in the population until that population goes extinct. If you take a closer look at the human genome, you will see that a large portion of our genetic code matches the genetic code of common viruses. This is because as we are infected with a virus, our bodies store some viral genetic code within our genomes so that we are better equipped to fight that virus if it infects us again. So, viruses may be the reason why our life expectancy has generally increased over the years, but research suggests that the infiltration of viruses within human genomes may not be 100% beneficial.

Currently, the human genome consists of around 22,000 genes and roughly 8% of our DNA consists of remnants of ancient viruses and is theorized to contribute to modern-day diseases such as multiple sclerosis (MS), cancer, and amyotrophic lateral sclerosis (ALS).3 A geneticist named Barbara McClintock discovered that certain portions of our DNA are able to move around our genomes by copying and pasting themselves.3

She later names these genes "jumping genes".3 Since Barbara's discovery, later scientists determined that these jumping genes originated within the viral portion of our genome. It is possible that these jumping genes could cause frameshift mutations within our genome leading to the evolution of human diseases such as MS; however, more research is needed on this subject to know for sure.

Evolution and ecology of influenza A viruses

Genomic studies suggest that influenza viruses have existed for millions of years.4 Currently, the main reservoir for influenza are birds; however, influenza viruses frequently infect other species including humans.4 Molecular sequencing of influenza A from birds and mammals suggests that it is a highly evolving virus with a high mutation rate.4 Despite the genetic variations within the host species influenza A infects and the subtypes of influenza A viruses that exist, research reveals that the genetic diversity of current influenza A viruses originated fairly recently. Studies suggest that the current influenza A viruses originated sometime in the 19th century. Scientists hypothesize that there was a large-scale "selective sweep" of the influenza genomes sometime during the 1800s causing all avian and mammalian influenza A viral lineages to originate from the time of the sweep.4 After the sweep, the influenza A viruses continued to evolve at a fast rate.

As previously mentioned, influenza A viruses infect hosts in multiple species. Usually, many cross-species transmission infections of influenza usually result in small spillover infections, there have been many times where a spillover infection grew into a full-blown epidemic. This was seen during the early 2000s when swine flu (H1N1) spread like wildfire throughout the US and other countries.

Due to its ability to jump between host species and its fast mutation rates, influenza A viruses evolve at a rapid rate. The three mechanisms by which influenza viruses evolve are: mutation (antigenic drift), re-assortment (antigenic shift), and recombination.4

Mutations

The influenza A viruses undergo significant point mutations which causes the virus to gradually evolve. As the virus infects the host, the host's immune system learns how to fight the virus which is why viruses need to mutate in order to develop ways to evade the host's immune system attacks.

Point Mutation: A genetic alteration caused by the substitution of a single nucleotide for another nucleotide. EX. GAG turning into GUG. This is a point mutation that causes sickle cell anemia

Point mutations in the influenza A virus genome cause a conformational change in the shapes of viral proteins which allows the virus to evade the immune system and also evade influenza treatment. For example mutations in the HA protein of the influenza A virus can lead to increased infection rates while a mutation in the NA protein can lead to drug resistance within the virus.

The Hemagglutinin HA protein is responsible for binding influenza a virus to host cells. The neuraminidase (NA) protein is responsible for cleaving the host cell receptor to initiate viral entry into the host cell.

Re-assortment

Another way that influenza viruses evolve is through re-assortment. Re-assortment allows different influenza strains to exchange RNA segments with one another which results in the production of a new strain of the virus. Re-assortment is likely how the swine flu was able to affect humans. One strain of influenza from swine was able to exchange RNA segments with a human strain which produced a strain of the swine flu that was able to infect humans.

Recombination

Genetic recombination within viruses is relatively rare but is still possible. Recombination in influenza A viruses can occur in two different ways: non-homologous recombination and homologous recombination. While non-homologous recombination has occurred within the influenza A virus before, homologous recombination within the influenza A virus is incredibly rare.4

Non-homologous recombination in influenza A occurs between two different RNA segments and introduces new genes into the viral genome. Homologous recombination in influenza A is believed to result from template switching during transcription of viral RNA which is extremely rare.

The process of genetic recombination is beyond the scope of this article and your course; however, it is helpful to know that recombination can be used by the influenza A virus to evolve.

Since influenza first affected humans in 1918, re-assortment of human influenza and bird influenza has developed new subtypes. For example, in 2009, there was an outbreak of H1NI in humans. Typically, bird influenza subtypes do not infect humans however, pigs act as a viral mixer since both human and bird influenza subtypes are able to infect pigs.4 As a result, of pig infection, influenza re-assortment caused a new generation of influenza viruses to be created that can infect both humans and birds.

The origin and evolution of Ebola and Marburg viruses

Marburg and Ebola are filoviruses that cause significant hemorrhage, organ failure, and death if left untreated.4 In 2013, there was a large outbreak of Ebola in West Africa that cause widespread illness and death within that region. Molecular analysis of Ebola and Marburg viruses can give us insight into its origin and evolution. Ebola was first discovered in 1976 in the Democratic Republic of Congo and scientists do not know where it comes from.5 Research suggests that Ebola is animal borne with bats or non-human primates being suspected sources. Non-human primates act as the viral reservoir and can transmit the virus to other animals including humans.4

Unlike the airborne influenza A virus, Ebola is transmitted through direct contact with the bodily fluids such as blood, semen, and phlegm of an infected animal that is living or deceased.5 Like Ebola, the Marburg virus is transmitted via infected bodily fluids. Marburg virus was first discovered in 1967 when laboratory workers in Germany and Yugoslavia were infected via contact with African green monkeys from Uganda.4 Like Ebola, the Marburg virus most likely originated in non-human primates.

Just like the influenza A virus, Ebola and Marburg viruses evolve by mutations, re-assortment, and recombination; however, these viruses evolve at a much slower rate compared to influenza A viruses.

Evolution of Viruses - Key takeaways

  • The regressive theory of viruses hypothesizes that viruses originated from some sort of more complex free-living ancestor that "de-evolved" by losing genetic information over time.
  • A retrovirus is a virus that stores its genetic material as RNA.
  • Marburg and Ebola are filoviruses that cause significant hemorrhage, organ failure, and death if left untreated.
  • The three mechanisms by which influenza viruses evolve are: mutation (antigenic drift), re-assortment (antigenic shift), and recombination.

References

  1. Wessner, D. R. (2010) The Origins of Viruses. Nature Education 3(9):37
  2. Prabarna Ganguly, Ph.D. (2022) Retrovirus. National Human Genome Research Institute
  3. Arnold, C. (2020) The non-human living inside of you. Cold Spring Harbor Laboratory
  4. Shao, W., Li, X., Goraya, M. U., Wang, S., & Chen, J. (2017). Evolution of Influenza A Virus by Mutation and Re-Assortment. National Library of Medicine
  5. Brauburger, K., Hume, A. J., Mühlberger, E., & Olejnik, J. (2012). Forty-five years of Marburg virus research. Viruses, 4(10), 1878–1927.
  6. What is Ebola Virus Disease? (2021, April 27). Retrieved from https://www.cdc.gov/vhf/ebola/about.

Frequently Asked Questions about Evolution of Viruses

Viruses evolve using three different methods: mutations, re-assortment, and recombination. 

Viruses promote genetic diversity in the host organisms they infect. When a host is infected with a virus, their bodies modify their genome to better prepare the organism to fight the virus during a second infection. 

It is estimated that the first viruses evolved 3.5 billion years before humans evolved. 

Vaccines that reduce the replication and transmission of viruses do not speed up viral evolution as these types of vaccines reduce the chance of viral mutations. 

RNA viruses such as influenza and SARS-COV-2 mutate the fastest. 

Final Evolution of Viruses Quiz

Question

What theory of viral origin suggests that viruses originated from a complex free-living ancestor that devolved over time by losing genetic material?

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Answer

Regressive Theory 

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Question

This term refers to an acellular, parasitic piece of genetic material that is not classified within any kingdom. 

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Answer

Virus 

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Question

Viruses are all identical and have the same genetic code. 

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Answer

False 

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Question

Viruses that store their genetic information as RNA are called dsDNA viruses. 

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Answer

False 

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Question

What is a retrovirus?

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Answer

A virus that stores its genetic material as RNA. 

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What is a negative sense RNA virus?

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Answer

A virus that has genetic code that is complimentary to the viral mRNA.

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Why are viruses important for human evolution?

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Answer

They help us diversify our genomes 

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What percentage of our genome contains viral DNA?

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Answer

8%

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Question

What term refers to the viral DNA naturally found in humans that randomly copies and pastes itself into different parts of the human genome? 

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Answer

Jumping genes 

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What is the main reservoir for influenza? 

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Answer

Birds 

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Which organism acts as a viral mixer between human and avian strains of influenza?

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Answer

Pigs 

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What are three ways that the influenza A virus is able to evolve?

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Answer

Mutations 

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What mutation results from the substitution of a single nucleotide for another nucleotide?

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Answer

Point Mutation 

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What term refers to different strains of a virus exchanging genetic information to produce a new strain of that virus?

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Answer

Reassortment 

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What are two ways that viruses can evolve via recombination? 

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Answer

Non-homologous 

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What term is used to classify the Marburg and Ebola viruses?

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Answer

Filoviruses

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How are Ebola and Marburg viruses transmitted?

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Infectious bodily fluids 

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Viruses are small, obligate ______ parasites that can infect different host cells. 

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unicellular 

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True or false: Viruses contain a capsid, nucleic acid (either DNA or RNA) and sometimes an envelope. 

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True

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Viruses that have RNA as their genetic material can be:

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single-stranded or double-stranded viruses

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Parvoviruses have _____ as their genetic material.

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double-stranded DNA (dsDNA)

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The viral _____ gives protection to the genome, and is made up of repeated protein subunits called capsomeres. 


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capsid 

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A(n) ______ is a lipid membrane structure derived from the cell membrane of the host.


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envelope

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Another name for non-enveloped viruses:

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Naked viruses

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During the attachment phase of replication in animal cells, the spike proteins of the virus attaches to the host cell receptors in the _________. 


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plasma membrane

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Enveloped viruses can enter the host cell by: 

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 membrane fusion or receptor-mediated endocytosis

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Naked viruses can enter the host cell by:

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membrane fusion or receptor-mediated endocytosis

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_______ involve periods of latent infection alternated with periods of active virus productions. 


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Recurrent infections

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_______  are infections in which there is no replication of virus happening, so the virus barely affects the host cells.


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Failed infections

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The virus responsible for causing small pox is known as _______.

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Smallpox virus

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A virus responsible for causing COVID-19 is an example of a _______________.

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Picornavirus

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Poliovirus is a virus that can cause meningitis and poliomyelitis (limb paralysis), especially in children. Poliovirus is a type of ______________.

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Answer

Picornavirus

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