A Q&A with evolutionary, computational biologist Trevor Bedford

'Trying to be useful instead of trying to be clever': An evolutionary biologist-virologist-immunologist-computer-wonk finds his niche
Dr. Trevor Bedford
Evolutionary biologist Dr. Trevor Bedford uses powerful computers and complex statistical methods to study the rapid spread and evolution of viruses. Photo by Bo Jungmeyer / Fred Hutch News Service

In his Twitter account — and as a leading advocate for sharing scientific data to advance lifesaving research, yes, he tweets — Dr. Trevor Bedford describes himself as “a scientist @fredhutch studying viruses, evolution and immunity.”

It’s a little more complicated than that.

An evolutionary biologist trained in infectious-disease dynamics and viral phylogentics, Bedford uses powerful computers and complex statistical methods to study the rapid spread and evolution of viruses. Since joining Fred Hutchinson Cancer Research Center as an assistant member in its Vaccine and Infectious Disease and Public Health Sciences divisions in 2013, he has become known for his work on a software tool for tracking viral disease outbreaks.

Recently, that tool, which he developed with Dr. Richard Neher of the Max Planck Institute for Developmental Biology in Germany, was named a finalist in the first phase of the first-ever international Open Science Prize competition. The public is invited to vote here through Jan. 6, 2017, on which of the six finalists should be shortlisted for the prize. (Bedford and Neher's tool is listed on the ballot as “Real-time evolutionary tracking for pathogen surveillance and epidemiological investigation.”)

Trevor took time away from figuring out how flu strains move around the world and wrangling Zika metadata he gathered on a road trip in Brazil to explain how he came to do what he does — and just what that entails.

How do you explain what you do to the person sitting next to you a plane?

That airplane conversation has gotten a lot easier than it used to be. When I was doing a Ph.D., it was, “I do evolutionary biology,” and it ended up being kind of esoteric. Now I usually talk about flu and why we need a new flu vaccine every year, that this is evolution, and we get to watch it happening and try to use our understanding of that to predict which flu virus to put into the vaccine. That’s usually a conversation people can have some kind of personal relationship to.

The things you work with — genetic sequencing, huge data sets, mathematical modeling — were they even around 10 years ago?

There were some very particular phylogenetic tools — methods to build evolutionary trees based upon sequencing data —  that were developed toward the end of my Ph.D. Those methods have become the basis for a huge amount of what I do. I now use these methods to study how viruses move and evolve using sequence data.

When I started the Ph.D., the genomes of the non-human stuff were coming out — malaria and so forth. After that, around 2007, we were able to do comparative genomics. The computational methods have developed a lot. Data have developed a lot. Some of the mathematical modeling ideas have been around for longer, but they’ve been waiting for data to exist to be tested.

What has been the biggest game-changer?

Genetic sequencing. When the WHO [World Health Organization] is either trying to pick a flu vaccine or to figure out what’s going on when there’s a new Ebola or Zika or whatever, sequencing is just an amazingly powerful analysis tool. It really lets people connect what’s going on. You can see concretely where a mutation arose and spread. For the flu vaccine, the WHO is able to better track emerging mutants and match a vaccine. In the Ebola outbreak, it was better able to track transmission chains and aid field epidemiologists. Even though sequencing viruses existed for a while, routine sequencing and surveillance is something that’s been developed in the last 10 years.

How do you connect the work you do in the lab with the world?

Everyone is doing sequencing, but most people aren’t able to analyze their sequences as well or as quickly as they might want to. We’re trying to fill in this gap so that the WHO or the CDC [U.S. Centers for Disease Control and Prevention] or whoever can have better analysis tools to do what they do. We’re hoping that will get our software in the hands of a lot of people.

Are you able to imagine what you’ll be doing in 10 years?

Ten years is hard. I have this example in one of my talks about forecasting viruses. If you think back five years, it’s 2011. The iPhone exists. The market penetration for smart phones isn’t at 50 percent yet, but you can totally see where things are at and you can project it.

If you go back 10 years, 2006, the iPhone does not yet exist. You can see Facebook taking off, but mobile internet is not a thing on the horizon so much. In the 5-year time scale you can extrapolate. In the 10-year time scale, there will be completely new things.

In five years, I’d like our software to be a standard and useful tool for the WHO and the CDC. In 10 years, I’m hoping there will be whole new fields to be working in.

How did you know that you wanted to do what you’re doing, and when did you know that?

I took longer than some people to figure out something that was really mine, that I could run with. After finishing a Ph.D. [in biology] at Harvard, we moved so my wife could attend the University of Michigan for library information science. So I was looking around for labs there. Mercedes Pascual had just published a paper on neural networks [a computing system modeled on the way the brain and nervous system work] and flu evolution, and I had been doing some neural network stuff.

It seemed at the time like I would continue publishing in evolution journals, but with flu. But what ended up happening is that the evolution people didn’t care nearly as much about viruses as they do about fruit flies, but the virus people do care about what the evolutionary methods can tell them about viruses. So there’s been kind of a steady shift towards more epidemiology ever since then. That’s felt good. It’s like trying to be useful instead of trying to be clever.

How has philanthropic support made a difference in the work you do?

When I arrived here, I got a package to help get the lab going. I didn’t have to immediately hustle for grants. So I spent the first couple of years trying to really think about things. I spent a lot of my time writing this first flu software instead of having to write grants that year. That ended up being a useful foundation. I then wrote grants on that software that have subsequently been successful. Now it’s all supported by National Institutes of Health grants, but I needed that springboard.

What’s the most adventurous thing you’ve ever done?

Getting on board this ZIBRA project — Zika in Brazil Real-time Analysis —was the most adventurous thing in the last five years or so. We drove a bus down the northeast coast of Brazil and stopped at government diagnostic labs to go through their freezers and help them with diagnostics. That was my first time at the bench for quite a while. We took positive samples with us and they are now in São Paulo with collaborators, where lab work is continuing.

What’s the most bizarre thing you’ve ever had to do for your science? Like, holding giant pipe cleaners to illustrate genetic trees?

That might be it.

Dr. Trevor Bedford's blackboard
For all his computer skills, Dr. Trevor Bedford remains a devotee of blackboard and chalk for drawing evolutionary trees. Photo courtesy of Dr. Trevor Bedford

I’ve seen the blackboard in your office. It seems so quaint, given all the software you write. Do you actually use it?

It’s all drawing evolutionary trees. That’s 90 percent of what shows up on the blackboard.

Did you have a scientific bent as a kid?

Kind of. My father and mother are wildlife biologists. They’d go on hikes, nature walks. They’d know every bird and every tree. I’ve since forgotten most of those things. When I was in high school, I was thinking of cosmology or something. Then biology and genetics happened somehow in undergraduate. I don’t quite know when that decision was made. It’s sort of following in those footsteps but a little different.

If you could choose one superpower to have, what would it be?

Oh, man. I think time travel. I like to think about what it would actually be like to be in ancient Rome or in feudal Japan. That kind of observation just seems like it would be a neat thing.

It’s interesting that you think of going back rather than forward.

Oh, yes, I guess that is surprising.

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Mary Engel is a former staff writer at Fred Hutchinson Cancer Center. Previously, she covered medicine and health policy for the Los Angeles Times, where she was part of a team that won a Pulitzer Prize for Public Service. She was also a fellow at the Knight Science Journalism Program at MIT. Follow her on Twitter @Engel140.

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