Q & A with Daniel Streicker

TEDMED: In your 2018 TEDMED Talk, you impart the importance of trying to stop pandemics before they start. You posit one way to begin to do this is to find patterns and test out new solutions for “everyday killer viruses” that can jump from animals to people, like rabies, but are not necessarily pandemics. What led you to choose to study rabies over another virus?

Daniel Streicker: In short, I followed the data and it led to rabies. Just consider the numbers— whereas many viruses jump into people or domestic animals only every few years or every few decades, rabies is transmitted from wild animals into new species every single day, probably hundreds of times over and governments around the world routinely carry out diagnostics on these cases. That means we get a high-resolution glimpse into the host jumping process: which hosts are involved, where it happens and when. The other thing that struck me about rabies was that we already knew so much about its basic biology. The decades of work done before me meant that I didn’t need to waste much time working out the fundamentals and could jump straight into what for me were the most exciting questions about anticipating and blocking transmission between species.

Photo Credit: Daniel Streicker

TM: Your research took you to the Peruvian Amazon to study rabies in vampire bats. You mention mudslides, power outages and stomach bugs among the challenges you encountered. What was the most difficult part of working in the field?

DS: I never worried too much about the uncontrollable things like getting sick or natural disasters. It was the things I thought I could control, but couldn’t and the things that seemed straightforward, but weren’t, that pushed me to the limit. In the first two years of the project in Peru, I tried to pack much more in than was humanly possible. Every time a key person arrived late, or our transportation didn’t show up, or bats were mysteriously difficult to catch, the realization that the day was lost stressed me out to no end. My solution was to work harder on less and less sleep. Looking back, I’m surprised the field team didn’t mutiny. After about 6 months, I remember walking down a street in Lima feeling like a sleep-deprived zombie, and suddenly realizing that no matter how much planning and wishful thinking I did, things would almost always go wrong in ways that I couldn’t predict. The only solution was to give myself a few extra weeks on both ends of every trip and go with the flow. That seems blindingly obvious now, but it took a lot of pain and frustration for me to get there.

Photo Credit: Daniel Streicker

TM: What impact has your research had on the communities you worked in that were facing a high prevalence of rabies transmittal?

DS: My longer term vision of preventing human and animal rabies by vaccinating bats is still a ways off, but I believe the road to getting there does provide tangible benefits. We have already made some progress with models that forecast rabies risk so this can potentially enable anticipatory vaccination before outbreaks begin, which would save lives. Beyond that, the nature of the work means we get exceptional access to remote communities in the Andes and Amazon that are typically underserved with respect to health access and education. This provides constant opportunities to talk to communities about the research we are doing and what actions they can take now to protect themselves and their animals (for example, using bed nets to prevent human bites or vaccinating livestock). I’d also like to think seeing us capture, handle and collect samples from mysterious animals like bats inspires some natural curiosity in younger generations and might even let them see science as a career possibility.

Photo Credit: Daniel Streicker (Goat with bat bite wound seen in upper left)

TM: You shared that you and your team have used genomics to forecast outbreaks and are working on an edible self-spreading vaccine that can “get rid of viruses at their source before they have a chance to jump to people”. What other creative or innovative tactics have you and your team employed in your efforts?

DS: One of my favorite things about science is that you occasionally get the chance to chase unconventional ideas. One of those was a recent project where a few colleagues and I became convinced that it might be possible to use machine learning to mine the genome sequences of viruses to predict what host they came from. This was a major challenge since when new viruses emerge, it’s almost always from a non-human animal, but it can take years or even decades of experiments and surveillance to find the culprit and while all that research is happening, the disease is free to emerge again. Although there’s still a lot of work to do in this area, we ended up developing algorithms published in Science that when provided, just a single viral genome can instantaneously predict which kinds of animals the virus came from. That effectively narrows the short list of animals for researchers to consider and in some cases could even guide how outbreaks are managed in real time to limit onward transmission.

TM: What do you see for the future of virus control/eradication?

DS: I think right now is an incredibly exciting time for disease control. We have technologies at our fingertips that just a few years ago were almost unimaginable. Transmissible vaccines are the example I discussed in my Talk, but other approaches like engineering pathogen resistance into hosts or using natural enemies or symbionts to control human pathogens like malaria or dengue within the mosquito vectors that transmit them are also taking off and show great promise. More and more the scientific question is not whether these tools work in the lab (we know they do), but how to apply them in the real world. That creates an interesting interdisciplinary challenge that will need to involve collaborations among the laboratory scientists developing the technologies, the field biologists who understand the natural systems, the epidemiologists who can project the outcomes on disease transmission, and the social scientists who can evaluate the economic costs and acceptability to the public. That last challenge is crucial since interventions in natural systems, particularly those involving genetic engineering of hosts or vaccines, are bound to be controversial. My view is that it’s vital to recognize in these situations that inaction costs lives. Rational, evidence-based assessment of the risks and benefits of these technologies will be increasingly important so we can actually realize the potential that new technologies have to transform human and animal health.

Massive Science on Daniel Streicker

Massive Science is a digital science media publication that brings together scientists and the science-curious public. The team at Massive joined us at TEDMED 2018 and covered talks by various speakers including Daniel Streicker. Check out their coverage of Streicker’s 2018 TEDMED Talk below.

Photo by Zdeněk Macháček on Unsplash

Many of the world’s deadliest viruses didn’t originate in humans. Rabies, HIV, and Ebola are just three of the countless illnesses that have jumped from animals to humans. Known as zoonotic diseases, this kind of cross-species transmission is actually not an exception, but a norm. So in order to protect people from dangerous new diseases, we must first understand where and how people might be exposed in the first place.

Tracking the transmission of viruses across species is a monumental task. To do so, scientists conduct field research in far-flung places, often on multiple species—all hopefully without contracting diseases themselves. Take, for example, the deadly rabies virus, which is found in many animal species, including bats. Daniel Streicker is a senior research fellow at the University of Glasgow who has been working with collaborators in Peru to track the spread of rabies. Streicker’s been traveling to different barns and caves across Peru and hoisting nets around the exits, capturing vampire bats in order to tag and sample them. For Streicker and his research team, understanding how rabies is transmitted by bats was the first step toward learning what viral and host characteristics impact disease transmission generally.

While we may be racing against fast-evolving viruses, there’s no doubt human ingenuity is playing defense.

Just as Streicker started this project in Peru, the region began battling a rabies outbreak. Vampire bats typically live south of the United States border with Mexico (at least for now), and are particularly problematic because of their feeding habits: Since they bite other animals to feed, they’re “the perfect vector for this disease,” says Striecker.

Uwe Schmidt

Streicker and his colleagues have been collecting DNA and RNA sequences from vampire bats, as well as other environmental DNA.

While strategies to contain rabies transmission from dogs and bats are well established in North America, Latin America still suffers from widespread outbreaks. The numbers of cases have decreased, but many thousands of animals in Latin America still die of rabies every year. Especially in rural areas, which have limited public health infrastructure, the prevalence of the virus makes it dangerous for humans and animals alike. For farmers in particular, rabid bats are a constant fear. If a rabies outbreak from bats reaches their lands, livestock infections pose not only a health risk, but a problem for their pocketbook. “It doesn’t kill off thousands of livestock at once,” Streicker says, but cumulatively outbreaks are still a substantial public threat.

The researchers have learned that male bats are largely to blame for the virus’ spread, and that bat culling, a strategy used to reduce rabies transmission, may in fact, hurt the effort to stop rabies virus.

Streicker and his colleagues have been collecting DNA and RNA sequences from vampire bats, as well as other environmental DNA. By tracing and comparing the variations in these sequences, Streicker and his collaborators have learned more about how the rabies virus has moved around Peru. Their phylogenetic analysis works like this: Imagine 100 people start in the center of town for a bar crawl. Groups of people head in the directions of their favorite stops. At the end of the night, by comparing who went to which bar, you have an idea of who drank together. The variation within the sequences Streicker collects from DNA and RNA samples provides the same information about the rabies virus and bat populations. We now know, for example, how far the virus can travel in a year, and what areas may be most at risk. The researchers have learned that male bats are largely to blame for the virus’ spread, and that bat culling, a strategy used to reduce rabies transmission, may in fact, hurt the effort to stop rabies virus, since possibly infected bats typically disperse to new areas after populations are culled

To minimize public health risks, Streicker emphasizes the need to “control rabies in the bats themselves.” Luckily, a United States Geologic Survey researcher, Tonie Rocke has been studying bats in captivity to develop an innovative vaccine. Unlike normal vaccines, which would be unfeasible to deliver to wild populations, Rocke’s invention can be transmitted directly from bat to bat through skin contact. Combined with Streicker’s research, the scientists are hoping to target at-risk populations, like bats who live near a known outbreak. While these strategies may reduce outbreaks within five years, Streicker’s ultimate goal is a long-term solution. “It would be nice to have something to target elimination, more than just localized prevention.”

The insights these scientists are gleaning about rabies transmission may also be useful in understanding other diseases. Streicker, for example, recently published a bold theory about Ebola virus. He was curious if the Ebola virus was now evolving quickly as it spread among primates, reasoning that as the virus replicated within different hosts, it would essentially self-optimize in each. Could researchers use this virus evolution as clues to which animal host new outbreaks sprang from? If so, researchers could learn critical information during early stages of epidemics, helping prevent people’s exposure.

Pictured: Ebola virus particles. NIAID / Flickr

Improving our epidemiological toolkits is important because the future of pandemics doesn’t look great.

In the paper, published in Science, Streicker and his collaborators gathered hundreds of viral sequences, and then used machine learning algorithms to predict what animal host the viruses came from. These machine learning models were able to make predictions with 72 percent accuracy. Next, Streicker and his team hope to improve the model by testing its results in the field, but it’s already a notable step towards being able to predict and respond to Ebola outbreaks. During pandemics, the ability to run genetic sequences from samples through such a model could quickly narrow down potential hosts. Such a tool would benefit many neglected diseases, including Lassa virus, and other devastating illnesses.

Improving our epidemiological toolkits is important because the future of pandemics doesn’t look great. Responding to disease outbreaks requires a complex combination of local, national, and global efforts. Being able to warn a neighboring community of a potential rabies outbreak, intelligently inoculate at-risk bat populations, or predict the host animal of a deadly new virus would give public health officials a critical headstart in combating outbreaks.

Photo by Drew Hays on Unsplash

Researchers are sampling and sequencing diverse viruses across the globe.

As researchers sample and sequence diverse viruses across the globe, their insights can have a direct impact on response plans for pandemics. This is precisely the goal of the Global Virome Project (GVP). Although the international effort is in early stages, an initial project called PREDICT is collecting samples from over 30 countries. The collection of these samples provides efforts like Streicker’s more data to help predict virus behavior. “Everywhere we work, the teams are a resource for public health networks, strengthening capacity for secure and safe field surveillance, as well as laboratory training.” explains Dr. Jonna Mazet, global lead of PREDICT and member of the GVP steering committee.

While we may be racing against fast-evolving viruses, there’s no doubt human ingenuity is playing defense.


About the author: Joshua Peters is a PhD student in Biological Engineering at MIT. Around two billion people in the world are infected with a microscopic bug called Mycobacterium Tuberculosis. Despite this, only a fraction develop tuberculosis. And a fraction of those infected – almost 5,000 a day – die. He puts on Stranger Things-esque protection equipment and probes these bacteria to ask, what allows them bacteria to win this tug-of-war? To understand this variation, he looks at how both human and bacteria cells change on a genetic level in response to each other, as a member of the Blainey Lab, located in the Broad Institute, and Bryson Lab, located in the Ragon Institute and MIT.