In this edition of FOCUS In Sound, we meet a quantitative biologist who studies the structure and dynamics of complex biological systems. Most recently, he organized and chaired a two-day, so-called “rapid response” workshop called Modeling the Spread and Control of Ebola in West Africa. The meeting, which drew 180 participants from all over the world, was held in January, 2015 at the Georgia Institute of Technology in Atlanta, where Joshua Weitz is a tenured associate professor of biology.
Transcription of “Interview with Joshua Weitz”
00;00;04;03 – 00;00;34;14
Ernie Hood
Welcome to Focus In Sound, the podcast series from the Focus newsletter published by the Burroughs Wellcome Fund. I’m your host, science writer Ernie Hood. In this edition of Focus In Sound, we meet a quantitative biologist who studies the structure and dynamics of complex biological systems. Most recently, he organized and chaired a two day so-called rapid response workshop called Modeling the Spread and Control of Ebola in West Africa.
00;00;35;01 – 00;01;04;06
Ernie Hood
The meeting, which drew 180 participants from all over the world, was held in January 2015 at the Georgia Institute of Technology in Atlanta, where Joshua Weitz is a tenured associate professor of biology. Joshua received his Ph.D. in physics from M.I.T. in 2003, and from 2003 to 2006, he was an NSF postdoctoral fellow and associate research scholar at Princeton University.
00;01;04;17 – 00;01;26;03
Ernie Hood
He joined the Georgia Tech faculty in 2007. In 2007. Joshua received a half million dollar, five year career award at the Scientific Interface Grant from the Burroughs Wellcome Fund to fund his research on the evolutionary ecology of bacterial viruses. Joshua Weitz, Welcome to Focus In Sound.
00;01;26;25 – 00;01;27;18
Joshua Weitz
Thanks for having me.
00;01;28;08 – 00;01;41;16
Ernie Hood
I’d like to initially focus on the Ebola workshop that you chaired. What exactly is dynamic modeling and how does it relate in practical terms to the Ebola epidemic in West Africa?
00;01;42;17 – 00;02;06;28
Joshua Weitz
Dynamic modeling is an effort by many to try and take the processes on the ground involved in an epidemic, let’s say, and translate those into a mathematical form that we can then predict both the future behavior and in some sense understand the mechanisms by which an epidemic may increase or decrease in number over time with the effective interventions.
00;02;07;13 – 00;02;41;10
Joshua Weitz
This sort of scenarios requires, to some extent, assumptions, approximations, but also really a conceptualization of the epidemic process. And so the word dynamic means that it’s something that describes a process that changes in time and model means that it’s a model. So it’s not perfect. On the other hand, it’s one of the few things we have. It’s a resource that we use along with interventions on the ground to first of all, evaluate the efficacy and also to predict how much of a particular kind of intervention we need over what time scale and what our interpretation should be.
00;02;41;15 – 00;02;55;24
Joshua Weitz
Once we get changes where we see changes in the number of cases that come in through other on the ground reports. So it’s really part of the toolbox of what epidemiologists can use to combat infectious diseases.
00;02;56;08 – 00;03;03;25
Ernie Hood
So how are you and others able to gather the data necessary to conduct that type of modeling? Is that one of the major challenges?
00;03;04;09 – 00;03;45;01
Joshua Weitz
There are different levels of data, and certainly the data problem is a challenge. And the degree to which it’s a challenge I think depends on the circumstances. Frankly, the challenge of Ebola virus disease in West Africa makes the problem of data collection rather acute. First of all, it’s not a disease for which, at least in these particular affected countries in West Africa, which they had much experience with their infrastructure in terms of, let’s say, governmental health organizations, clinics, availability of physicians, as well as monitors to record data, was quite limited, very, very starkly different to what we might expect to be at norms in the United States or Western Europe or elsewhere.
00;03;45;21 – 00;04;12;06
Joshua Weitz
So there is this issue of missing data. In fact, to some extent, that’s where models can shine in helping to understand and predict circumstances, even when the data is poor, and then when data becomes available to try to reconcile and test against the predictions. In the case of Ebola, there are many kinds of data that we might want to have and not always or made available to the modeling community for various reasons, because they’re not accessible or the hard to get, etc..
00;04;12;11 – 00;04;19;19
Joshua Weitz
But certainly this notion of data limitation was one that made the response efforts to Ebola virus disease quite difficult.
00;04;19;27 – 00;04;27;26
Ernie Hood
So how have these recently developed dynamic modeling tools contributed to the response to the Ebola epidemic?
00;04;28;05 – 00;05;02;07
Joshua Weitz
I think we have to kind of go back a little bit in time to understand the ways in which dynamic models in particular have contributed to the effort. And frankly, we should also point out that they remain controversial. So moving back to August or September, when there were increasing news reports that Ebola was spreading, unlike in prior epidemics, meaning it was not limited to a few hundred at most cases in an isolated rural area, but rather affecting hundreds, if not thousands of people in increasingly urban areas and mixing between rural and urban zones.
00;05;02;27 – 00;05;29;17
Joshua Weitz
And so models at the outset were meant I think if we look retrospectively to some extent in a way to raise alarm, to point out the fact that the current trajectory of the epidemic was not something in which the international response community could say, well, yes, this is a very bad disease if you get it, because the mortality rate is approximately 70%, but rather at a population scale.
00;05;29;17 – 00;05;50;22
Joshua Weitz
This epidemic is going to be something that if we don’t stop now, it’s going to get worse. The numbers will increase. And this could lead to systemic problems, not just to those affected because they’re infested, but rather even for those who are infected by other things like malaria or just for governmental institutions, for the overall health of many individuals affected by war and otherwise and the economy.
00;05;51;00 – 00;06;27;29
Joshua Weitz
For all of these reasons, I think the early dynamic models were able to say, let’s take the data. We have these trajectories, these case counts that were coming out of Liberia, Guinea and Sierra Leone and say if this continues unabated, how many people will be affected and over what time scale? And so the early dynamic models are able to take this limited data and say what mechanisms produced this trajectory up to this point, in some sense, training the model on the data we have and then projecting out into the future what the future caseload might be, but also not such a in such a negative view.
00;06;27;29 – 00;06;51;21
Joshua Weitz
It’s such a hopeless view, but rather also in a hopeful view to say what would be the benefits of intervention. And so those early models also pointed out the values of intervention and the value of intervening early, the earliest models, and these are really, I’d say, produced largely by one group from the CDC, but there are other academic workers involved, too, and also from the W.H.O. aligned with Imperial College in London.
00;06;52;02 – 00;07;11;02
Joshua Weitz
So there was a number of groups that around the same time, August, September, were starting to say, look, we need to do something. We need to act quickly. It’s not this is going to get worse. And in fact, it did. But one could also at least give some credit to these models for alerting the community that large scale on the ground interventions, not just models, need to take place.
00;07;12;04 – 00;07;33;22
Joshua Weitz
There’s also a critique of these models because their forecasts said that in September, if no interventions took place, the CDC reported up to a million infected cumulatively by January. That obviously did not take place. The W.H.O. predicted tens of thousands by November and more beyond that. So these sort of dire predictions did not take place. There are many reasons for that.
00;07;33;22 – 00;07;57;05
Joshua Weitz
Models are part I think that they’re frankly a small part. There’s a lot of changes in behavior, but they were part of that effort to raise awareness that specific the kinds of interventions that governments could do. But maybe they need a justification explanation of why such intervention is a necessary part of the diagnosis of the situation has to do with this concept of exponentials, which we may want to talk about as well.
00;07;57;16 – 00;08;00;11
Ernie Hood
Sure. Could you describe that aspect?
00;08;00;18 – 00;08;22;29
Joshua Weitz
So when I say exponential, I think there’s one can hear this sometimes in the popular press, this notion of exponential growth, and this is commonly attributed to bacteria growing inside of you or a virus multiplying inside of you where you have one, then two, then four, then eight. And that doesn’t seem so bad. But soon 1632 and after a few doublings you get quite a lot of whatever the pathogen is.
00;08;23;20 – 00;08;48;22
Joshua Weitz
The same concept applies to the spread of an infectious disease amongst individuals that each individual who’s infected can give rise to a number of new individuals who are newly infected. And when each infected individual basically causes or transmits forward the disease that they have to someone else and an additional person or two, then you can see how that could have a multiplicative effect.
00;08;48;22 – 00;09;10;22
Joshua Weitz
If, for example, one person infects three other people, then you get 1 to 3. If that happens to the next three people to 9 to 27 and soon you have hundreds, if not thousands of individuals who are infected. This is very different than a kind of steady growth, a linear growth in the number of infected cases. And so the concern in August-September is that these early trends looked exponential.
00;09;11;08 – 00;09;26;20
Joshua Weitz
There was a rapid, early expanding epidemic, and that’s something that the modeling community and obviously the Center for Disease Control, W.H.O., many groups for various reasons, realized needed to stop if we were going to avoid these dire, dire scenarios.
00;09;27;21 – 00;09;40;03
Ernie Hood
Absolutely. Well, Joshua, is is that where the dynamic aspect of dynamic modeling comes in as the models affect outcomes and change on an ongoing basis and vice versa?
00;09;40;05 – 00;10;09;19
Joshua Weitz
That’s right. So the models themselves don’t treat the current trend as being a static trend. They also account for the fact that when a disease spreads in intrinsically modifies the rate of growth of the dynamic for other diseases, there’s this concept of susceptible depletion that as a disease spreads, there are less people to spread to because many people, one could infect disease like the common cold or may be temporarily mute or for flu or could be immune.
00;10;10;07 – 00;10;33;09
Joshua Weitz
In the case of Ebola, we don’t think we got to a point of some dispute there of susceptible depletion, at least at a population scale, but maybe locally. But there still is an issue of how an intervention might change the spread, how changes in behavior might change the spread, how local populations, structure, networks of contacts, and people begin to change their behavior.
00;10;33;26 – 00;10;58;19
Joshua Weitz
Hospitals are starting to be built. It’s user built which isolate people. People get word that in their village there’s a burial, but they shouldn’t touch the body. So there’s many different ways in which the rate of transmission, which is not just a factor of of the virus, but rather a confluence of the virus and behavior which itself has socioeconomic factors as well.
00;10;59;00 – 00;11;21;22
Joshua Weitz
And all of those determine how many new cases occur per infected individual. And that itself changes over time so that dynamic models try to capture that infection process, the recovery process, but also the intervention process and make reasoned predictions over what would happen without certain interventions and the value of the interventions themselves.
00;11;22;25 – 00;11;29;21
Ernie Hood
Well, Joshua, what were some of the most significant findings that emerged from the recent workshop?
00;11;29;22 – 00;11;55;16
Joshua Weitz
The workshop to put in context was hosted here at Georgia Tech in January 2015, and the objective was to bring together modelers, decision makers, policymakers from different fields, from different backgrounds who usually don’t communicate with each other on a regular basis. But certainly because of the epidemic and the crisis in West Africa, all had common cause of concern and wanted to communicate.
00;11;55;18 – 00;12;22;16
Joshua Weitz
We needed a venue in a setting to do so. Our objective was to try and facilitate having academics as well as government officials and even monitors the different spheres from institutions like the CDC and elsewhere. Communicate the principles by which they made their predictions, why certain types of outcomes may or may not be expected to hurt and also potentially influence ongoing decisions like vaccine trial design.
00;12;23;08 – 00;12;59;07
Joshua Weitz
So I think there were a number of conclusions that came out of the meeting, though our objective was not to reach consensus, but rather to communicate. In fact, a lot of different views on the right way or right ways, I should say, to try to intervene. One of the things, though, that did come out at the outset was the importance of thinking about Ebola in terms of local population structure, the nature of the disease transmission process, requiring contact with bodily fluids suggests that very close contact is necessary and therefore social change.
00;12;59;25 – 00;13;19;13
Joshua Weitz
Funeral events, anything that puts people into close contact with bodily fluids would be a mechanism by which there could be a fourth transmission event. And because of that, some of these dynamic models assumed what is called a well-mixed population, one in which many people interact with essentially everyone. They keep a common cold. You’re on the bus, you sneeze.
00;13;19;24 – 00;13;47;24
Joshua Weitz
That’s not the mechanism by which Ebola spreads. And therefore, one of the major conclusions was that in responding and building dynamic models, we need to think very carefully whether it’s Ebola or the next emerging infectious disease, about the nature of transmission and how to build the appropriate model that reflects population structure and the transmission process. Because conclusions about how fast the disease spread depends critically on the nature of the transmission.
00;13;48;20 – 00;14;26;12
Joshua Weitz
The other thing that I think arose was in fact an issue of communication that what a modeler wants to communicate and how they commute is often different than what a policymaker needs in the timescale over which they need that information. And so the modeling community, to the extent that we are often waiting to kind of do things in a good sense and quite rigorously over long timescales, we were told by many in fact that there’s a value to giving an incomplete answer as long as the uncertainty in our predictions is also communicated that even some information would be important to report back.
00;14;26;12 – 00;14;57;27
Joshua Weitz
And I think the modeling community, in fact in some sense doing that, there are now journals and venues that one, for example, is called plus current outbreaks that is meant to facilitate reporting academic findings on a rapid timescale in the midst of an epidemic, which is not something that one thinks of academics do. I don’t think that’s the conventional view of the academic timescale, but in the course of a few months and we can do that in this world to build models, make predictions linked to data, and we are finding that this is of value to that community.
00;14;58;11 – 00;15;31;05
Joshua Weitz
And finally, I think another conclusion is that there is also a greater need for the interfacing of models that include epidemic transmission dynamics, but also one of logistics, because in West Africa there really is a problem of logistics and how to bring, whether it’s supplies or people information to affected areas and models for the most part, make certain simplifications or assume certain kinds of processes that may not be taking place, particularly on the ground, particularly these countries with poor infrastructure.
00;15;31;15 – 00;15;45;09
Joshua Weitz
So this really was less of a conclusion that we know the answer to, but rather an area that we need to pursue if we want as modelers to contribute to response efforts in the developing world, particularly in West Africa.
00;15;46;17 – 00;15;59;13
Ernie Hood
So Joshua was the 2014 Ebola epidemic an opportunity, in a sense, for four lessons learned going forward? Will new knowledge emerge from all of this?
00;16;00;09 – 00;16;35;00
Joshua Weitz
Well, I think the answer is yes, to the extent that there’s obviously a lot still to be learned about the best way to integrate dynamic models into the response process. Obviously, we would like to learn these lessons without having to respond. But to the extent that we now know, first of all, for diseases like Ebola, the importance of considering spatial local structure, the importance of coordinating early and there are now, unlike prior epidemics, mechanisms of collaboration and communication, at least in the United States and in other countries as well.
00;16;35;00 – 00;17;07;03
Joshua Weitz
For example, in the United States, there’s a group called BARDA, which is coordinated essentially groups of modelers communicating even pre-publication, so that the information and the predictions we were making could be essentially communicated and trickled up to policymakers. And so to the extent that that is a communication, collaboration, tools, the lessons learned, that’s important in terms of response, I think obviously earlier response is needed and in fact getting information out, particularly in integrating local customs with Ebola.
00;17;07;13 – 00;17;34;11
Joshua Weitz
The notion of the burial transmission was a key factor in many places in the initiation of spread. And so if the next time Ebola appears, especially in urban or rural areas, how we can communicate quickly to people to be cognizant of the risks. And also one of the big issues is how does one build infrastructure to isolate people quickly and distinguish them from people who may have the same symptoms but have very different disease with different ideologies and different transmission risks?
00;17;35;03 – 00;17;47;19
Ernie Hood
Joshua, You and one of your colleagues also recently published a paper about modeling post-death transmission of Ebola. Tell us some of the findings that you report in that article.
00;17;48;10 – 00;18;16;22
Joshua Weitz
Because of the nature of Ebola virus disease, it is possible to contract it even from a dead individual, someone who died due to Ebola. And the reason is, again, in part a combination of the ideology of the virus, the way that the virus persists in an individual as well as cultural practices in these affected countries. It is to some extent common practice to have burial ceremonies in which bodies are physically touched.
00;18;17;08 – 00;18;41;16
Joshua Weitz
Now, that is in some sense we might think of that as a very strange and unusual behavior or cultural practice. But if one takes a look at common burial practices in the United States, we are not so far away from that common practice involved unveilings of bodies being close, maybe not touching, but certainly being close. And bodies are prepared for burial, often by funeral homes.
00;18;42;04 – 00;19;14;21
Joshua Weitz
Yet it’s not a community effort. By and large. So to the extent that this is a community effort to prepare the body as well as touch the body as a form of marking, respect that practice overlapping with the disease for which transmission can be mediated by contact with bodily fluids, leads to the possibility. And in fact, evidence suggests that this happened many times and may be responsible for about a quarter of the transmission of Ebola forward on to previously susceptible, therefore unaffected individuals.
00;19;14;21 – 00;19;35;14
Joshua Weitz
The other risk here is then how do we treat properly Ebola viruses at the population scale? And so my colleague and I, Jonathan Duchamp from McMaster University, asked the question, how much benefit would the response really get in terms of controlling the disease from focusing on funerals in addition to their focus on hospitalization and isolation of people who are alive?
00;19;35;14 – 00;20;01;08
Joshua Weitz
So if post-death transmission is rare, then yes, it’s important, but it’s not going to have major impacts on the spread of the disease. And to the contrary, our analysis suggests that based on the TIME series data at the very start of the outbreak, this is in the summer of 2014 that it was possible to fit the data with models in which a significant portion of the risk could be attributed to post-death transmission.
00;20;01;19 – 00;20;29;03
Joshua Weitz
And therefore, we speculated that controlling post-death transmission could lead to the reduction of before transmission. About one half of that that which is necessary to lead as a population scale to stopping the epidemic. We release this on what is called the archive. It’s a public server that academics use to share information in advance of publications. Our hope was to try to get this information out to the policymakers early.
00;20;29;15 – 00;20;56;13
Joshua Weitz
In fact, in October and November, December, this sort of response was ongoing in West Africa. There were extensive efforts to have burial teams, safe burial teams, to make them culturally sensitive, to explain why these burials needed to be safe and to try to reconcile norms, whether religious or cultural norms with the key public health need to stop for transmission of Ebola during funeral ceremonies.
00;20;56;18 – 00;21;05;02
Ernie Hood
Do you think that increased attention to the extreme danger of post death transmissions contributed to getting the outbreak under control?
00;21;05;03 – 00;21;31;09
Joshua Weitz
I think the answer to that is yes. There are multiple lines of evidence for it. The CDC has released one of its case study reports basis here where they reported the number of safe burials that took place in counties. And this was substantial. If each one of those safe burials reduced by three or four or five and there are cases of dozens of people in Mali, there was an initiation of, I think about a dozen new effective cases from a burial ceremony.
00;21;31;17 – 00;21;56;16
Joshua Weitz
So if each one of these burial ceremonies became a safe burial, you can imagine that at a population scale, you have a substantial impact on the transmission of the disease. Fewer people were infected, therefore, in fact, fewer people moving forward. And you move more quickly to an endgame scenario, we hope, rather than a continued epidemic crisis. So to summarize, yes, I think that these safe burial teams were a key part.
00;21;56;17 – 00;22;27;04
Joshua Weitz
The other issue there is that you can implement a safe burial team on a much more rapid timescale than one can build and staff any two you or a hospital given circumstances, meeting the requirements from a materials and personnel and training perspective are significant less. And yet, you know, a person who’s not infected is still a person who’s not infected either, because you’ve moved them out of the community, isolated them when they’re live, or because after death you treat them with dignity and respect that also gave them a safe burial.
00;22;27;14 – 00;22;46;20
Ernie Hood
Joshua, I know we’ve spent much of our time discussing the workshop and dynamic modeling, but you and your lab group also conduct very valuable research in other aspects of quantitative biology and theoretical ecology. Would you give us just a quick thumbnail sketch of some of your other work?
00;22;46;24 – 00;23;23;21
Joshua Weitz
Sure. The focus of our research is on the interactions of viruses and their hosts. Ebola is an example where the virus infects humans, but in fact, much of our work focuses on viruses and their microbial hosts. Microbes, whether they’re bacteria or archaea, or even small eukaryotic meaning small organisms, get diseases. These diseases are often viral diseases. And my group is interested in the effect that these viral diseases have on the fate of an individual microbe, whether it lives or dies or enters a new state in which the virus in some sense takes over.
00;23;24;05 – 00;24;10;03
Joshua Weitz
The let’s call it the nano brain of the microbe meaning alters its physiology and behavior. And we’re also interested in how viruses affect the structure of entire populations and communities. How many microbes are there? Which kind? What genes do they have? And what sort of functions they perform at larger ecosystem scales? We are a theory group, meaning we build models, we interact with experimentalists and empiricists, and we work in very different environments, ranging from funded research on the viruses of archaea living in hot Springs in Yellowstone National Park, to studies of viruses that in fact ubiquitous bacteria that live in the surface ocean in the North Pacific Ocean in Hawaii.
00;24;10;16 – 00;24;30;27
Joshua Weitz
So common to these studies is really our effort to bring a nonlinear dynamic perspective similar to that which we we try to to bring to bear on Ebola epidemic dynamics, but also on the epidemic dynamics and the interactions that take place between viruses and their microbial hosts.
00;24;31;24 – 00;24;46;25
Ernie Hood
Joshua, you’re making some very significant contributions to understanding and controlling epidemics large and small, such as Ebola. And we wish you the best of luck for continued success. Thanks for joining us today on Focus In Sound.
00;24;46;27 – 00;24;47;15
Joshua Weitz
Thank you, Ernie.
00;24;47;27 – 00;24;55;24
Ernie Hood
We hope you’ve enjoyed this edition of the Focus In Sound podcast. Until next time, this is Ernie Hood. Thanks for listening.
