A brief history, and the future of viruses

Viruses are perhaps one of the biggest biological enigmas that scientists have faced. To the general population on earth, the name virus often invokes a feeling of fear. We picture a small repulsive organism that causes disease and death. Along with causing diseases, viruses have contributed massively to the evolution and progression of life on earth which we fail to realize. It is perhaps one of the most powerful “living” organisms on this planet, without which none of us would exist.

The virus originated around 3.5 billion years ago, along with its cousin, the bacterium. It is hypothesized that they both originated from a common ancestor — a fully functioning cell that was able to reproduce independently that lived about 3.4 billion years ago- shortly afterlife had just emerged on earth. From this point onwards we have seen bacteria evolving by becoming increasingly more complex in terms of their cell structure, DNA composition, and function. However, viruses, have gone in the opposite direction. Viruses have evolved in the direction of decreasing complexity. They have shed away genes that they found futile- to the point where they cannot even reproduce independently. They have become so simple that viruses only carry essential genetic material that they can use to slip inside host cells and manipulate it into making more copies of the virus. Viruses, like the influenza virus, carry only 14 protein-coding genes in the form of either single or double-stranded RNA or DNA. Due to their simplicity scientists debate whether it should even be considered as a life form.

Now a question often arises challenging these theories, how do we know what happened 3.5 billion years ago? This same question troubled Gustavo Caetano, a professor of bioinformatics at the University of Illinois. His team of scientists decided to map the ancestry of the virus. The conventional method for tracing back the lineage of a species is to compare their genes to other organisms and pinpoint the one with which they share the most similarities. However, this technique only lets you go back a couple of million years, beyond which the DNA has mutated so much that it is nearly impossible to pinpoint any similarities between the species. This was no easy task as viruses have mutated so rapidly over the years, that it is almost impossible to find any similarities between many viral families. To understand the origins of the virus the scientists also needed to travel billions of years back. So instead of comparing genetics, they compared the shape or folds of proteins. Why proteins? Well, proteins are very high precision molecules, which will cease to function if their shape is changed. While genetics can be molded and changed gently over a continual period of time, proteins cannot change at the same rate as nucleic acids, therefore evolve much more slowly. Retracing the protein shape is the best shot that scientists have at investigating the lineage of the virus. This was no easy task either as viruses have massive genetic diversity.

The researchers developed an algorithm that compares the protein shapes of 3,460 different viruses and 1,620 cells. 442 proteins were found to be common between viruses and regular cells, however, 66 folds were unique to viruses. Now, these 442 proteins were arranged into a tree diagram which the scientists added a new branch to every time a new type of protein fold evolved (the 66 which were unique to viruses). Wherever this evolution happens, the scientists labeled it with a date which they derived from fossil evidence. For example, blue-green algae (cyanobacteria) has a particular protein fold which can be found in every fossil sample of blue-green algae for the past 2 billion years. By comparing protein folds of viruses and bacteria, they have found that they evolved from a common ancestor.

Now that the mystery of the origin of the virus has been “solved”, let's take a look at its contributions to life on earth. I have mentioned earlier in my essay that without viruses none of us would be alive. This was not an exaggeration; it is a fact. Often viruses are only thought of as agents of infection and death, however, life on earth would not be what it is today without viruses. Around 100 million years ago, scientists speculate that a primitive mammal was infected by a virus that uploaded a gene that helped the mammalian placenta evolve. The protein known as syncytin helps the virus fuse cells together in order to transfer from one host to another. In mammals, these are the same proteins that fuse the placenta to the uterus, which allows the fetus to draw nutrients from the mother. As we do know, the length of time that viruses can survive outside the host's body varies hugely. Some survive for seconds, whereas others can remain viable for decades. Temperature affects how quickly viruses die. In hot environments, viruses tend to die quicker, which is why heating is often an effective way to kill viruses. This could even be the reason why humans and other animals have evolved to develop fevers in response to an infection. Viruses have not only contributed to acquiring characteristics that would help us survive but they have also been used in experiments that have led humans to make revolutionary discoveries. The bacteriophage is a type of virus that looks like something out of a science-fiction novel, has helped us discover the role of DNA in passing on characteristics to our offspring. Prior to this experiment, it was believed that proteins are responsible for the passing of genetics from parent to offspring, this was falsified by Hershey- Chase in 1952 who proved that DNA is indeed genetic material.

Viruses are known to mutate and evolve at astonishingly fast rates, unlike any other living species on this planet. In comparison to a human, viruses can evolve a million times faster, this constantly gives them access to new genetic material which enables them to acquire remarkable traits and survival mechanisms. When the host is infected by a virus, they can share these acquired genes with the host in a process known as horizontal gene transfer. This is much like two organisms “trading” their genetics to become more powerful or skilled at surviving. With viruses, these trades can happen rapidly and thus enables the organism to build a more refined set of genes. However, horizontal gene transfer does not occur with individual people directly as our genome is pretty fixed. Horizontal gene transfer does explain the variety and complexity of life on earth. Simple organisms are able to evolve rapidly and trade genes, enabling them to survive in almost any environment. Antibiotic resistance in bacteria was also a result of horizontal gene transfer between bacteriophages and bacteria, this is also the reason why antibiotics are futile against viral infections. This relationship between a virus and its host has helped evolutionary biologists understand the origins of life and its success on our planet.

When outside the host's body, viruses are relatively inert and show no sign of activity. Once they are inside, their behavior has been described as “sophisticated” by many virologists. Viruses are able to communicate with one another by sending peptide-based signaling. This signaling is used by the viruses to establish cooperation between them or competition in the host's body. Viruses that cause polio, flu, and measles have been found to use this communication to coordinate when to attack and when to stay dormant. Bacteriophages which are known for infecting bacteria have secret signals which are special to them. Poliovirus has signals which are unique to them. Every virus has a unique signal of its own. Viruses are not only able to communicate with one another, but there are also able to eavesdrop on other viruses and the host cells as well. These abilities of the virus can be used to combat bacteria such as E. Coli and Salmonella. Researchers at Princeton University have engineered bacteriophages that can sense signals sent between microbes such as E. coli and ultimately zone them in and destroy them. We can use the virus to destroy any bacterium on command, which is far more effective than antibiotics which are becoming increasingly futile against combating bacteria due to antibiotic resistance.

For the majority of human history, research into viruses has primarily been focused on their ability to cause disease and how to terminate them effectively. However, over the past decade, our perception of viruses has changed, we have begun to see how crucial they are to life on earth and how they can be used to benefit humanity. We know little about them and assuming that they are only here to cause disease and harm would be very ignorant of us. We need a more solid understanding of what they actually are before classifying them. The fact that many scientists have disregarded them as a life form, despite their many contributions, shows how limited our knowledge about them is. A deeper understanding of viruses will help humanity not only redefine what life is but also open our eyes to a variety of other possibilities where life can exist. Perhaps the reason life on other planets has not been found, is because humans are looking for evidence which only covers a small area of the enormous bubble under which life can be classified.