Much remains unknown about the origin of viruses and how they evolve — but hunting for answers has been the focus of Portland State biology professor Ken Stedman's eXtreme Virus Lab for the past 25 years.
DNA viruses, like monkeypox, were long thought to evolve completely separately from RNA viruses, like the flu. But in 2012, Stedman's lab was the first to publish findings on a newly discovered group called cruciviruses, which appear to have evolved through an unprecedented recombination between RNA and DNA viruses. Since then, hundreds of cruciviruses have been identified from environmental samples ranging from Antarctic lake water to the soil on PSU's own campus. The eXtreme Virus Lab is one of the few, if not the only, in the world dedicated to studying cruciviruses.
"The more we looked into it, the more complicated it got," Stedman said. "We all thought RNA and DNA viruses had completely different origins, but with cruciviruses, we have evidence that they're interacting with each other. We want to try and figure out how frequently this bouncing back-and-forth between different viruses happens and can we catch it in the act."
That's the focus of a new three-year $1 million grant from the National Science Foundation: a targeted discovery of cruciviruses, related RNA viruses and their elusive host microorganisms. By assessing patterns of horizontal gene transfer, the team hopes to shed light not only on the origin of cruciviruses and their host organisms but also on broader patterns of virus emergence and evolution.
"If we could understand how RNA and DNA viruses are interacting with each other, this might also help us think about potential new pandemics," Stedman said. "Having a combination between the two would be really scary, so we want to know something about how it happens in a non-medical context so that we could then think about whether it's likely that something like this could happen."
Nacho de la Higuera, left, and doctoral researcher David Noeckel look at a "protein gel" used to separate proteins by size in the eXtreme Virus Lab at PSU. (Photo by Patric Simon)
Ignacio "Nacho" de la Higuera, a research associate who first joined the lab in 2016 as a postdoctoral researcher, says one of their biggest limitations is that they only have the viruses' genetic sequences — not physical viral particles.
"We have many sequences, but they are so different from each other that there's still a lot that we don't know," he said. "How close can we get to know what's happening at the environmental level? We want to study the population of DNA viruses, cruciviruses and the related RNA viruses within the same sample and see if we can find some recent transfer event."
De la Higuera said the team also doesn't know what the cruciviruses infect. The group is developing new techniques to be able to go to an environment with known cruciviruses and hunt for the host cells, which they suspect are eukaryotic microbes — single-celled organisms that contain a nucleus.
"Having a host means you can then look at the virus and what the virus is doing inside the host, and actually start to learn a lot more about how it's working," Stedman said.
The group will build evolutionary trees from the sequences as well as use more novel machine learning algorithms to model the evolutionary history of cruciviruses. A former high school intern in the lab developed an AI algorithm that distinguishes between the type of capsids — the outer protein shell of a virus that encloses and protects its genetic material — found in RNA viruses compared to those in cruciviruses.
De la Higuera said cruciviruses present the only known example of a capsid protein that can enclose both RNA and DNA viral genomes.
"One of the things that we have learned from these machine learning experiments is that there are different ways that nature has shaped these capsids to either package DNA or RNA," he said. "Capsids are used in biomedicine to deliver gene therapy and vaccines to cells in our body, so this research could potentially help us design better tools to efficiently package DNA or RNA."
The grant will engage high school, undergraduate and graduate researchers in the lab. The group also regularly collaborates with Oregon Museum of Science and Industry (OMSI) and plans to expand their outreach on virus evolution to rural communities through virtual programs — a topic of interest in light of the recent COVID-19 pandemic. De la Higuera is also developing a course-based undergraduate research experience that would bring this research into more classrooms.