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.

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.

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.

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

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?

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. See figure 1 for a visual of common viruses.

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.

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. See figure 2.

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

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.