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Biodiversity Blog


Some Virus History and Origins

 cell or bust highway small
 Illustration: Nicole Elmer

The history of viruses is difficult to trace because they don’t exist in the fossil record. Unlike our beloved dinosaurs, viruses don’t have bones that can be fossilized, and they are just too small and fragile.

However, there is another way viruses can make their mark in the fossil record, and that’s through the DNA of the host they infected.

But first, to understand how that works, we have to look at what the heck a virus is.

Viruses are basically some genetic information, RNA or DNA, wrapped up in a protein capsule. In order to survive and reproduce, they must infect a host, specifically, the host’s cells. Once a virus accesses a cell, it replicates its DNA and reproduces. The host cell, now hijacked, then manufactures new viruses which then go out and infect other cells to repeat this process.

It’s believed viruses have been around as long as life itself as they can infect all forms of life: bacteria, eukarya, and archaea. Because of their simplicity, they’ve evolved along with the earliest of cells. 

When it comes to looking at viruses in the fossil record, this is how it happens. Sometimes, the virus’ genome becomes integrated into the host’s DNA. If this doesn’t cause a mutation in the host, this bit of viral information may stay there indefinitely. In fact, eight percent of the human genome contains sequences that originally came from viruses.

If the integration of the virus' genome happens in a cell that forms sperm or eggs, the viral gene can then be passed on to the host’s offspring. When the DNA is integrated into the host, it can only mutate as quickly as the host does, which is much slower than the rates viruses normally mutate on their own. (Viruses mutate very quickly over time, which is why, for example, people need to get new flu shots each year.) So, if the conditions are right when the host dies and it becomes part of the fossil record, the viral gene at this stage will also become preserved.

The study of viruses of the past is paleovirology. It’s a relatively young field, built on another field: Genomics. To determine the age of viruses in fossils, researchers will examine the preserved gene. They line up comparable sequences from different organisms and compare. If a sequence of viral DNA in two organisms matches, then they probably got it from a common ancestor. So, the virus is as old as that ancestor.

What are some of the oldest evidence of viruses we know about? Bracoviruses, which infect wasps in specific, could be as old as the insects themselves, meaning about 310 million years. A gene found in mammals called CGIN1 has been dated to the early days of mammal evolution, or 125-180 million years ago. This gene is thought to have come from a virus as parts of it resemble a retrovirus, a virus that is comprised of RNA not DNA.

 cowvirusbackground small
 Illustration: Nicole Elmer

For humans, our relationship with viruses changed dramatically when we became an agricultural society about 10,000 years ago. This was when humans began to domesticate animals, and the contact we made with them often became a source of viruses we still deal with today. Our population dynamics shifted around this time. The nomadic lifestyle of small groups of people would become larger centers of settled populations. With denser human populations coming into contact with large groups of domestic animals, epidemics were able to have a much more profound and sometimes devastating effect. For example, measles is a cattle disease that crossed over to humans. The H1N1 flu (“Swine flu”) of 2009 originated from pig herds. There are many subtypes of avian flu viruses from domesticated birds, and some have infected humans. And of course, there is the origin of the virus on everyone’s minds: the novel SARS-CoV-2 coronavirus.

Research has not yet been conclusive on its origins. Some have suggested that pangolins (Manis javanica) which are scaly anteater-like animals, are the missing link between the virus jump from bats to humans. Bats are a natural reservoir of SARS-CoV-2, but a host is required for it to make its way to humans. Pangolins are often smuggled into China for their meat and scales, which puts them into human contact. However, some researchers are not sure pangolins are the source as their coronavirus is different than SARS-CoV-2. What many do agree upon, however, is that the gradual removal of habitat for these wild animals has caused them to come into closer contact with human populations, and thus increasing the likelihood of the jump of animal-to-human pathogens.

In the next blog post on viruses, we'll take a look at the many theories out there about where viruses came from.


Breiman, Robert. “The COVID-19 culprit is us, not pangolins.” March 27, 2020. CNN (accessed online: (https://www.cnn.com/2020/03/27/opinions/pangolin-coronavirus-pandemic-breiman/index.html)

Garcia de Jesus, Erin. “There’s no evidence the coronavirus jumped from pangolins to people.” March 26, 2020. Science Daily (accessed online: https://www.sciencenews.org/article/covid-19-no-evidence-coronavirus-jumped-pangolin-people)

“Information on Avian Influenza,” Centers for Disease Control. (accessed online: https://www.cdc.gov/flu/avianflu/index.htm)

Langer, Andy. “Geneticist Spencer Wells on COVID-19 as ‘Evolution in Action’ Texas Monthly podcast, March 9, 2020 (accessed online: https://www.texasmonthly.com/podcast/geneticist-spencer-wells-covid-19-sxsw/?utm_source=Twitter&utm_medium=Social&utm_campaign=Web+Social&utm_content=SpencerWells)

“Missing link in coronavirus jump from bats to humans could be pangolins, not snakes” March 26, 2020. Science Daily (accessed online: https://www.sciencedaily.com/releases/2020/03/200326144342.htm)

“Origin of 2009 Swine Flu: Questions and Answers” November 9, 2009. Centers for Disease Control (accessed online: https://www.cdc.gov/h1n1flu/information_h1n1_virus_qa.htm)

“Where did viruses come from?” PBS Eons. (accessed online: https://www.youtube.com/watch?v=X31g5TB-MRo)

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