Meet the 2024 Microbiology Society Fleming Prize Winner, Professor Daniel Streicker

04 April 2024

Each year, the Microbiology Society awards the Fleming Prize to an individual who has made a distinct contribution to microbiology early in their career.

Ahead of the Fleming Prize Lecture, Federico De Angelis interviewed Professor Daniel Streicker to learn more about his career and how it feels to win a Microbiology Society prize.

Congratulations on winning the 2024 Fleming Prize! Were you expecting this and how did you feel when you found out?

It was not entirely out of the blue! I knew I had been nominated for the prize, but it was a welcome surprise to be selected among such a competitive field of people deserving of these sorts of prizes and recognition.

I actually thought I was unlikely to win this prize, as my work is primarily on the ecology and evolution of infectious diseases. I think of it as being related to microbiology, but on the fringe. Therefore, having my work highlighted by the Microbiology Society is really an honour. I think it will be fun and exciting to present to the Society at Annual Conference in April.

How would you explain your research to a member of the public?

It has gotten a lot easier to explain my research after the COVID-19 pandemic, which made it all hit home. In general, I try to understand what drives pathogens to jump between species. I hope to generate fundamental scientific knowledge that helps devise new strategies to prevent pathogens spreading into animal and human populations.

In practice, my research falls into two categories. The first focuses on vampire bats, which are the most important source of human and animal rabies in many Latin American countries. This includes studies where my team and I are out catching bats in the field, sampling them, and studying their viruses in the laboratory. We also analyse epidemiological data, for example, patterns of rabies mortality in livestock, and try to bring it all together through computer modelling to answer questions like, 'can we anticipate, and when and where is the risk going to be highest?'. 'Are current strategies working?' and 'If not, what might work better?'. We want to generate the data to implement current control strategies more efficiently and to justify the innovation of new biotechnologies.

The second stream of my research takes a much broader approach that looks across hundreds of viruses and tries to find patterns. We ask questions like 'which kinds of viruses are most likely to jump between species?’ and ‘what are the hosts that they come from?’. We build datasets from public records, then apply tools like machine learning to try to pick out patterns that can help us understand where new viral risks are most likely to come from.

What is the most challenging part of your work?

My lab does a lot of international work and that inevitably creates logistical complexity: whether it is materials or equipment that get stuck in customs, samples that get lost or payments that are delayed so that field work cannot start. Those things I find frustrating. How do you deal with a customs agent that wants a bribe? It is the lack of training in dealing with these situations, combined with knowing that the delays are really having an impact on other people's research that is challenging. These delays can generate a lot of anxiety for myself and for others on the team.

What part of work do you enjoy the most?

What I enjoy the most is doing the research, all parts of it. Being out in the field, catching bats and sampling them, analysing data, writing, all those things that are the core of knowledge generation. I like these because it is what you are trained to do when you decide to become a scientist. It is also what helps me focus the best on new ideas. I think most scientists live for that light bulb turning on in your head moment of a new idea or a new way of thinking about your problem. You stop whatever you are doing to write it down. That usually happens when I am really engaged with the research.

Are you excited about presenting your Prize Lecture at Annual Conference?

Of course! It is a great honour to have the chance to present to such a broad and large audience. I am a little bit nervous about it, of course, because it is somewhat outside of the core of my field. However, that has its advantages as well.

I think there is an opportunity here to present, particularly to early career researchers who may have spent their whole scientific career working in a lab and perhaps don't realise that there are parallel career paths that involve things like international field work. Similarly, microbiology is being transformed by the capacity we now have for data generation and sophisticated new analytical techniques. I hope to inspire a few people to think about how they might be able to integrate new activities or analyses into their work. I want to get something out of it too. At the University of Glasgow, I have been part of two institutes, one of which is focused on ecology, evolution, and epidemiology. The other one is focused on virology. I have started to appreciate the interplay of those two much more than I used to, and how working with people with really deep knowledge of a particular virus or process can be really fruitful for thinking about larger-scale processes of transmission and evolution. I am hoping to get new ideas for how to make that bridge again between virological lab work and the ecology/epidemiology side.

Is there an experimental paper or a finished project that you are most proud of and why?

I am going to cheat a little bit and say two things. The first is not a finished project but rather an ongoing one. As a student, I set up a field system in Peru for studying viruses in vampire bats. This was a pretty big risk at the time. My advisors didn't work on bats, nor did they work in Latin America. So, it really felt like I was going off on my own. Additionally, it did not produce much for a long time. It was about five years before the first paper came out of that system. But now it has become integral to so much of the research that I do and is entering a new phase where students and postdocs are branching off within the system, doing their own things with new ideas and technologies. It is super rewarding to see the system evolving beyond my initial vision.

A recent project that I am especially proud of is a paper that we published in 2021 on mammal-infecting deltaviruses. This is a group of viruses I had never published on before, and it was a paper led by a Ph.D. student named Laura Bergner, who transitioned to being a postdoc during the publication of the paper. It was a standout paper for me because it had fascinating biology, but also a nice human story behind it. On the biological side, it was about this bizarre satellite virus called the Hepatitis Delta virus. It is a satellite virus of Hepatitis B, meaning it requires co-infection with that virus to complete its life cycle - at least that was the dogma — for a long-time people thought that it exclusively infected humans that were infected with hepatitis B.

Instead, our paper showed that there are a bunch of deltaviruses out there in a diversity of mammals, and it's most likely that they're jumping between species and doing so in an unconventional way by harnessing other viruses. Our data also suggest that they  are likely to also switch between the viruses that they exploit to get into the cells in the new species, so they are both switching hosts and their helper viruses. Biologically, that is bizarre. You would think it is already hard enough to jump between species if you're just a regular virus, but then to be dependent on a second virus to do it. What are the chances of that happening and resulting in a pathogen that is actually of great importance for human health?!

There was also this cool human story behind this paper, in how we discovered this bat Delta virus in the first place.

We were analysing metagenomic sequence data that we had generated from vampire bats captured all around Peru. My lab’s primary interest was to understand how ecological conditions affect viral diversity, but we suspected there were probably some novel viruses in there that we would not necessarily pick out as being interesting. So, when Laura, the postdoc leading this work presented it at an internal seminar, she handed out a printout of the viruses we had discovered and asked the audience to make notes on anything they found interesting. The bat deltavirus got all the attention, so we set about studying it in much more detail.

At the same time, we got scooped by a group doing massive scale data mining on a coronavirus that we were also trying to describe from the same metagenomic dataset. We contacted the other lab, and cleared up the coronavirus drama. But at the same time, we were also interested in using the tools that those people developed to screen additional public datasets for animal infecting deltaviruses. And so, we teamed up with them, and found additional mammal-infecting deltaviruses which ended up strengthening our analysis and making for a much stronger paper.

In the end, I thought it was a nice integrative paper that shows how you can go from field to lab to massive scale computational and have it all come together as a nice story through teamwork and collaboration.

What are you looking forward to most as your career proceeds?

I would like to see my work having real-world impacts, and that comes in a couple of different flavours. One is seeing former students and postdocs succeed and diverge so much in their own research that current lab members go to them as collaborators. I feel that that is good for science, but is also rewarding for me. I hope more of that happens because that makes me feel like I have trained people to become independent while also maintaining a research environment that ex-lab members are happy to return to as collaborators.

The other impact that I hope to see is some of the work that we are doing being translated into reducing the burden of human and animal disease. A lot of our work is about improving the way we do surveillance or management of zoonotic viruses. I hope that some of our discoveries become well-supported enough that they can inform how governments manage disease and the risk of pathogen emergence.

It seems like you are sitting at the edge of multiple disciplines. What do you think will be some of the next steps forward in your fields in the next ten years?

I can't predict the future, but I think it's going to be easier and easier to make the movement of ideas and technologies more fluid between subdisciplines of infection biology. Field studies, lab studies, experiments and quantitative methods are poised to become much more integrated than they used to be. They are more accessible and scalable than ever before. You could imagine seeing the effect of a protein in vitro and then predicting its importance at individual and population scales, and then how it might be influenced by environmental changes or human pressures.

There are also potentially transformative biotechnologies being generated right now, from CRISPR-gene editing to self-disseminating vaccines for animals. Most of these things are still in the laboratory research stage, but it will be exciting when some of those things start to become used or at least trialed in the real world. The prospects for these novel interventions to benefit both human health and animal welfare will be really interesting because it will force society to grapple with some long controversial concepts, like GMOs and biotechnology.

You have worked on viral cross-species transmission for 13 years, looking at ecological and evolutionary barriers against host jumps. Have you observed some factors in particular that could play an important role in zoonoses and the establishment of emerging pathogens?

Host phylogenetic relatedness would be on my list, but it is not a perfect predictor. The idea is that pathogens should be more likely to jump between and establish transmission within closely related species compared to distantly related species. This is something that I saw during my PhD when looking at patterns of bat rabies transmission between bat species, and it has now been observed in so many different host-virus systems that it is almost a default expectation. However, there are always going to be exceptions – viruses that emerge between distantly related host species - and those exceptions are often important and interesting, so there remains much to explain.

The other thing that I think about a lot are the context-dependencies of cross-species transmission risk. There's much more appreciation now than there was a decade ago that just having the source of a virus and a human in the same place doesn't equate to a spillover event happening or a virus becoming established in a new host species. That is just too simplistic. So much depends on the context of exposure. What is going on in the reservoir population? Is there a seasonal dynamic to when the reservoir is most infectious? Maybe the virus moves around in a complex way on the landscape, so it's actually absent from any single reservoir population most of the time. We need to begin to understand those processes if we are going to make predictions about spillover risk.

The final thing I think a lot about the human side, how humans are contributing to the risk of disease emergence. There is an increasing appreciation for the idea that environmental changes influence pathogen emergence, but much of the actual evidence is anecdotal. We need to get better at generating mechanistic understanding of how human activities alter risk before we can recommend specific solutions. That is exceptionally difficult to do because most of the time, viruses that emerge into human populations appear just once or twice. There is very little replication. Pathogens like rabies that repeatedly spill over into human or animal populations provide a powerful opportunities to gain actionable understanding and move towards spillover prevention.