Daniel Neafsey, Associate Professor at Harvard T.H. Chan School of of Public Health, as well as Associate Director of the Broad (Brode) Institute's Genomic Center for Infectious Disease, talks about his work combatting malaria in Colombia and Guyana through cutting-edge technologies.
June:
Welcome to Faculty Voices. Today we are talking with Daniel Neafsey. He's Associate Professor at Harvard's T. H. Chan School of Public Health, as well as Associate Director of the Broad Institute's Genomic Center for Infectious Disease. Welcome, Dan.
Daniel Neafsey:
Thank you so much for having me, June.
June:
I understand that you've been working a lot in Columbia and Guyana on the issue of malaria. How bad is malaria in these countries? Why should we care about it?
Daniel Neafsey:
That's a great question, June. My laboratory study genetic and genomic variation in malaria parasites and mosquitoes in many parts of the world, but we have an emphasis on malaria in the Americas. Malaria is not as severe a public health problem in Columbia, Guyana and other countries in the Americas as it is in Sub-Saharan Africa. So it's a very fair question to ask, why study malaria there? The World Health Organization says that more than 95% of malaria cases and mortality are in Sub-Saharan Africa. But there's several important and interesting reasons to study malaria in the Americas as a geographic region, the first of which is that South America turns out to be a hotspot for the evolution of resistance to anti-malarial drugs and medications. So three times in the last half century mutations have arisen in the DNA sequence of malaria parasites that have conferred resistance to the current first line drug therapy to malaria.
The first time was in the 1960s when resistance to chloroquine emerged probably in Columbia. The second time was in the 1970s when resistance to sulfadoxine and pyrimethamine drugs arose. And then most recently in Guyana, mutations were observed that confer resistance to the current first line therapy for malaria around much of the world artemisinin or artemisinin drugs that are given in combination with other drug therapies. So for reasons that are not perfectly well understood, resistance to malarial medications tends to arise in places where transmission is lower. And so there's a good reason to be doing DNA sequencing on malaria parasites in South America so that we can catch those mutations before they make it to Africa and other parts of the world where the disease is more severe. And while malaria is more severe in other parts of the world, it still causes tens of thousands of cases per year in Guyana, hundreds of thousands of cases per year in Columbia. And so it's an important part of public health in those countries as well.
June:
Is this a poor person's disease? Who does it affect?
Daniel Neafsey:
It affects people living in tropical parts of the world. And actually, malaria used to be well-established in more Northern latitudes. So there are species of malaria parasite called falciparum malaria, which is the more virulent malaria, and which is responsible for most of the approximately 600,000 deaths per year around the world that are attributable to the disease. But there's another less virulent form of malaria called vivax malaria, which has figured out how to be transmitted by mosquitoes that live at less tropical latitudes. And in fact, there was transmission of vivax malaria in Massachusetts up until the 1950s. It was not until about a half century ago that vivax was finally eliminated from the United States and Europe where it was well entrenched until the advent of DDT and other interventions.
June:
That's really interesting. So how did you end up working in Columbia and Guyana specifically?
Daniel Neafsey:
Well, good connections with good collaborators. Science is definitely a social enterprise at one level, and so there were opportunities that arose through connection in order to establish this study. But as I mentioned previously, Guyana was also the site where mutation was first observed for conferring resistance to artemisinin drugs. And so there was a compelling reason to do a genetic study in Guyana to understand what the potential of this mutation was to spread and undermine clinical treatment for malaria regionally.
June:
Excuse this really non-scientific question, but especially in the case of Guyana, how do you know when a disease is becoming drug resistance?
Daniel Neafsey:
It's not easy. It takes sometimes a carefully controlled therapeutic efficacy study where you could recruit subjects to the study, you give them medication, you often have to check them into a hotel in the case of malaria drugs because it requires three separate doses of the medicine. And if you want to know that the medicine is actually working as it should, you need to ensure that the study subjects take their proper dosage at the proper times. Otherwise, the results of a study can be complicated to interpret. And so typically, most countries only conduct a therapeutic efficacy study where they look for clinical signs of successful clearance of the disease every few years because it takes a lot of resources and organization to measure directly the efficacy of a drug treatment in infected patients.
This is an important place where genetic studies can play a role because it takes much less effort to simply take a drop of blood from a person who has the disease and read the DNA sequence of the malaria parasites inside that blood in order to look for genetic mutations that have been previously associated with resistance, sometimes in other therapeutics efficacy studies conducted in other parts of the world or in laboratory studies where it's even easier to understand what DNA mutations are associated with drug resistance of various forms.
June:
So in Guyana, for example, did the government sort of catch on to the fact that there was some drug resistance going on through these tests and then you got called in or what happened?
Daniel Neafsey:
Well, the story goes back to the year 2010 when some investigators at the US CDC had a collaboration with the Ministry of Health in Guyana. As part of that collaboration, they collected blood samples from a number of malaria infected individuals in the country. But at that time, there were no mutations that had been discovered that were known to be associated with resistance to artemisinin, the current first line drug used in most combination therapies. So fast-forward several years and a mutation was discovered, and eventually scientists at the CDC in Atlanta took those samples from Guyana out of the freezer that had been collected in 2010, and lo and behold discovered that that mutation had been hiding there, awaiting to be discovered and observed for the very first time in South America. There have been therapeutic efficacy studies in Guyana as well as in Suriname that have identified, let's say, troubling evidence of incomplete clearance of malaria parasite infections following administration of artemisinin or testing of artemisinin in combination with other drugs.
But those studies have not been quite definitive. So what led to our study was the initial recognition of the presence of this mutation in Guyana by the US CDC, some follow-up confirmation by investigators including Dr. [inaudible] at the Institute, Pasteur and French Guyana, that this mutation was present. And indeed, if you put this mutation into the genome sequence, that full DNA sequence of malaria parasites present in this part of South America, that it could confer resistance to the drug as had been previously observed in parasites from Southeast Asia. So those factors led myself and Dr. Caroline Buckee in the epidemiology department at the Harvard Chan School of Public Health to initiate this study to conduct genetic surveillance, DNA based surveillance for this drug resistance mutation and to generally better understand how malaria is being transmitted so that we can keep an eye on this dangerous mutation and perhaps better understand what are the factors that lead to the evolution of drug resistance so easily in South America and malaria parasites compared to African parasites.
June:
And do you have any answers or tentative answers to that?
Daniel Neafsey:
We've learned a lot from our study. For one thing, we've learned that this mutation has disappeared from Guyana. So the combination of forces that led to the origination of this mutation and its onward transmission from 2010 or earlier up through 2017, something changed. Perhaps the nature of drug pressure on that population has changed a bit, and the mutation has not been observed by us or by others since 2017. So we've learned that these resistance mutations can arise, but they can also go away. And that may be a product of both changes in the medication that is being used by the population as well as changes in the frequency of treatment. So especially during the pandemic and in many parts of South America, anti-malarial drugs were hard to obtain. And so this led to many infections not being treated or treated with secondary medications, perhaps sourced from unofficial places. But the upshot is that the particular artemisinin drug that caused the origin of this mutation may have not been imposing as strong a pressure on the parasite population. And that's our hypothesis for why this mutation has likely disappeared subsequently.
June:
And is this in a wide [inaudible] of Latin America, or is this just in Guyana?
Daniel Neafsey:
Well, that was part of the reason to conduct our study in Columbia was to be able to look to see if this mutation had left the neighborhood and had moved across to other parts of South America, especially given that both Guyana and Columbia border Venezuela, a country that due to recent political instability, has had an unfortunate explosion in malaria cases in the last five years. That malaria epidemic has subsequently been brought under control. But there was a real potential there for malaria infected people who might've been carrying this drug resistance mutation to have brought it to other parts of Latin America because we know a great many Venezuelan people who were having a difficult time in country left Venezuela to find work in other places. So we conducted our study in Columbia in part to detect whether this mutation had spread and fortunately have not yet observed the same mutation that was present in Guyana, in Columbia or in other countries in Latin America where we're conducting genetic studies of malaria parasites.
June:
Okay. So for the non-scientists among us, and I would include myself, when you say that you're conducting a study in Columbia, where in Columbia and how do you go about this? What does that actually physically mean that you're conducting a study?
Daniel Neafsey:
Well, it means when I say we, it actually means the collaboration. We're very fortunate to have wonderful collaborators in Columbia, including in the Institute [inaudible], the National Health Institute in Bogota. We work with Dr. [inaudible]. We also work with academic investigators in Colombia, including Dr. Vladimir [inaudible] at University [inaudible]. And Dr. Socrates [inaudible] at the [inaudible] Private Health Institute in Cali. And so working with those teams of investigators who have networks and opportunities to collect blood samples from malaria infected persons in various parts of the country, we've been able to genetically analyze DNA samples from malaria infected people from all across Columbia in order to look for this mutation. And so with that partnership, you asked, how does this actually work? Well, this partnership unfortunately began just before the COVID pandemic hit. And so we'd actually hoped to do much more of the initial genetic screening of malaria infected blood samples in Columbia and in Guyana.
But our travel plans to kind of create that genetic screening capacity in our partner countries were delayed because it just wasn't possible to create that laboratory capacity during the pandemic. But subsequently, what happened was our partners were collecting samples and then sending them to us at our laboratory in Boston in order to extract the DNA from the little pieces of paper on which dried blood samples could be collected, and then we could perform our genetic assays on the extracted DNA here in Boston and sequence that DNA. Since travel has become more practical, again, we've held workshops with our partners in Guyana and in Columbia where we have set up DNA sequencers in laboratories in those countries and conducted workshops to train local teams of investigators on how to generate these data themselves. And it's our hope that these activities continue locally in those countries beyond the lifespan of our project.
June:
What actually does this workshop consist of?
Daniel Neafsey:
Oh, it consists of a combination of lectures. I'm a professor and professors love to lecture, so they usually begin by me giving a few lectures on just the basics, a primer on how you can learn about an infectious disease by studying its DNA. I think during the COVID pandemic, a lot of us have gotten used to hearing about new strains, and we certainly all heard about the Omicron strain that emerged in December and January of 2022. So there's the general paradigm for understanding infectious disease transmission from studying its DNA, and we usually begin workshops by me giving some examples of things that you can learn about malaria and how you can inform local malaria control decisions, how to allocate resources, whether to be using bed nets or whether to change one's drug for treatment. I usually give an initial lecture on the general rationale for doing this work in the first place.
And then individuals from my lab and the lab of Caroline Buckee will give talks on the actual protocol for making the data in a genetics laboratory and how to analyze the data. And these workshops, of course, feature a hands-on component. And so we bring down DNA samples and chemical reagents to perform the genetic assays. And by the end of the workshop, our participants have usually generated DNA sequencing data locally on the DNA sequencer that was already present or that we've been able to install. And then we usually end with a concluding set of presentations from all of the participants where they each explain an aspect of the laboratory protocol and offer some commentary on the data that they've been able to generate. And the whole process of a workshop usually takes about a full week to execute.
June:
About a full week. And the participants, are these doctors, are they lab workers? What level of education do you need to be able to perform this work?
Daniel Neafsey:
Well, they come from a variety of backgrounds. Some of them are MDs, some of them are PhDs, some of them are laboratory technicians who are already doing similar genetic assays in a lab setting. And I think the skills for being able to work with DNA and RNA genetic material and conduct these types of assays, I think have become actually much more common following the COVID pandemic because of the requirement to set up local PCR testing for COVID. And so these skills are actually becoming much more common, and you certainly don't need a PhD or an MD in order to be able to do the genetic assays themselves. Some familiarity with molecular biology goes a long way, and we're hopeful that these assays become easier and easier to use over time because we think there's a real value in being able to perform them routinely to keep tabs on diseases like malaria.
June:
As we're talking, I keep hearing you mention the pandemic in very different contexts from the unavailability of drugs in Venezuela to the way that people have been trained in new fashions. And I'm just wondering if you could [inaudible] overall on the effect of the pandemic in treating diseases like malaria.
Daniel Neafsey:
The pandemic was definitely very disruptive, but it affects, I think are complex. So overall, across the world, the World Health Organization has noted that the annual number of cases and deaths from malaria actually spiked up a little bit in 2020 and 2021. They may be coming back down again in 2022, but the general disruption to healthcare systems and the functioning of public health programs, I think had a deleterious effect on malaria and other diseases. On the flip side, the pandemic also disrupted some of the activities that expose individuals to malaria. So in Guyana, in parts of Columbia and Venezuela, one of the activities that's most associated with malaria infection is mining. So mining for gold, mining for diamonds, mining for other natural resources, which is an activity that takes miners often out into the forest or in places where there's a juxtaposition between a clearing and intact forest.
And that's exactly the habitat that's favored by the mosquitoes that transmit malaria. So during the pandemic, some of the supplies needed for mining, for example, diesel fuel, were in short supply. And so in some parts of South America mining activity decreased and that likely led to a consequent decrease in some malaria transmission in different sites. And so I think it'll take us a bit of time to fully understand all of the different effects of the pandemic on diseases like malaria and other diseases. But I can say certainly there were impacts. I think the pandemic touched every aspect of life in all parts of the world in one way or another.
June:
You didn't get to travel very much.
Daniel Neafsey:
We didn't get to travel. We were sad. We did not suffice with Zoom calls to connect with our collaborators and FedEx shipments to move samples and reagents and supplies back and forth. So I can say that our first trip to South America after the pandemic was in January 2022. It was right in the height actually of the Omicron surge. We planned this trip before Omicron came along, and we just decided to carry through with it. We held a workshop in Georgetown Guyana to develop the local capacity to sequence malaria DNA there. And I'm happy to say we didn't have any transmission during the course of the workshop, and it was a fantastic opportunity to reconnect in person with our partners down there. So we're happily moving past that phase of work where travel was not possible because it's so important to be able to connect in person, especially to be able to transfer these capacities from Harvard to these other sites.
June:
What do you get out of being in person in the workshop?
Daniel Neafsey:
Well, there's really no substitute for being able to perform these laboratory protocols hands-on. You can read a very detailed document about how to do step one, step two, step three. At one level it's kind of like a recipe in a cookbook. So you can intellectually understand how to perform a protocol in order to generate DNA sequence data from malaria infected patient samples. But doing it in real life, doing it in person is a very valuable activity. And so I would say it's essential to have some in-person interaction to successfully make sure that these capacities, that these protocols take root in new laboratories.
June:
So is what you're learning about malaria applicable to other diseases? When you talk about drug resistant, the first thing that comes to mind for me is tuberculosis.
Daniel Neafsey:
Yeah, malaria parasites are great at evolving resistance to drugs, but of course, this is not a problem limited to malaria. There are important resistance concerns, of course for antibiotics with many bacterial infections. There is resistance emerging in several fungal pathogens to some of the common antifungal medications that are used. We lack drugs for certain important diseases, but even understanding whether resistance emerges to vaccines studying the changes in the genetic sequence of the SARS-CoV-2 virus or other pathogens for which there are, we're fortunate to have vaccines is important because if an intervention against an infectious disease is successful, if it's curing people, if it's blocking transmission, by definition, that intervention is imposing a strong evolutionary pressure. And so we can expect resistance to emerge to any effective disease intervention, and that means that studying DNA or RNA sequence is going to be helpful to stay one step ahead of evolution.
June:
I'm really curious as to how you got interested in this whole subject to begin with.
Daniel Neafsey:
Well, I did my PhD at Harvard in the Department of Organism and Evolutionary Biology, and I originally studied the genome sequence, not of an infectious bacterium or virus or parasite, but I was studying the genome of puffer fish. And this is because back when I was doing my PhD a little bit more than 20 years ago, puffer fish were the first vertebrate organism to have their genome. A genome is the sum total of all the DNA in a cell. So for our humans, it's all 23 chromosomes. The puffer fish was the first vertebrate animal to have its genome fully sequenced. It came out, it was done before human, before mouse. And you might ask why the full DNA sequence of a puffer fish before you sequence the full DNA sequence of people or an important model organism for understanding disease like mice?
And the answer is because puffer fish have a genome size that's eight times smaller than the human or mouse genome. So puffer fish have the same number of genes, approximately 20,000 genes as you or me or a mouse, but they've cut out a lot of the intervening DNA. Our genomes are composed of DNA that encodes genes, which gets turned into proteins, but it also encodes a lot of DNA that's sometimes disparagingly referred to as junk DNA. It's kind of filler DNA that takes up the space in between genes. Some of that filler. DNA does an important job of telling our cells when to turn genes on or off, when to make a protein or stop making a protein. But much of it is dispensable and puffer fish have figured out how to get rid of most of that dispensable filler DNA.
So I spent my PhD working on puffer fish and trying to understand how they succeeded in getting rid of all this dispensable DNA from their genome sequences. And I loved my PhD thesis, but I knew that I did not want to work on puffer fish for my entire career. And at the time, it was exciting because the first genome sequences, the first completely read out DNA sequences of the genomes of many pathogens were emerging. And the first malaria parasite genome came out just a couple of years before I finished my PhD thesis. So I was excited to transition to studying the genomes of infectious pathogens from puffer fish. And I was really fortunate to find an opportunity at the Broad Institute after I finished my PhD to conduct those types of studies.
June:
And malaria?
Daniel Neafsey:
And including on malaria. So at the Broad Institute, I focused on studying the DNA sequence of malaria parasites of a few fungal pathogens, as well as the anomalies, mosquitoes that transmit malaria. And so I became focused on studying the genomes of malaria, parasites and anomalies, mosquitoes.
June:
So are you turning into a Latin Americanist?
Daniel Neafsey:
I will say that I think there are interesting things to be learned from malaria in Latin America, even though the burden of disease is so much lower there than it is in Africa. And I think there are other important lessons that we can learn from studying malaria in Latin America beyond just trying to understand this propensity for drug resistance to emerge there. For one, I think studying malaria in Latin America tells us that eliminating the disease is possible. So a number of countries in Latin America have completely eliminated malaria in recent years, including Argentina, El Salvador, and Paraguay. Belize is getting pretty close to eliminating malaria, and so it's a part of the world where transmission in many countries is low enough that this incredible prospect of complete elimination of the disease is actually possible. I think Latin America can also teach us about what can happen when a disease is nearly eliminated, but a little trickle of transmission is allowed to continue or continues despite best efforts of public health authorities to stop it.
A number of countries in Latin America have gotten very close to eliminating malaria, but haven't quite gotten all the way, cases have gotten very low in countries like Panama and Honduras. But in recent years, they've gone up. There's been another spike perhaps in part due to disruptions from COVID, and of course Venezuela is one of the most tragic stories. Transmission in Venezuela, as I mentioned, went up sharply in tandem with the political and economic instability there. And Venezuela came very close to eliminating malaria in the 1960s. It went up, but it was maintained at a moderate level and subsequently saw a big explosion. So I think Latin America also offers some lessons about the importance of completely eliminating a disease and trying to muster resources to do that in cases where it's a feasible goal.
June:
So how do you relate the work that you do in your lab with the sociological public health aspect of these infectious diseases?
Daniel Neafsey:
Well, I find it really interesting and fascinating to think about the applied public health aspects of the work that we do. So in my laboratory and in other laboratories that study malaria at the Harvard Chan School of Public Health, there's a lot of work that's invested in understanding the basic biology of the parasites and the mosquitoes, and doing experiments to understand how gene A and gene B interact in order to produce a certain behavior or outcome or aspect of the biology of the disease.
However, I think it's fascinating and it's important to relate that biology back to public health in a translational manner, and that requires engaging with public health personnel and getting a different audience to appreciate the value of a different type of data and teaching, creating tools and capacity to not only generate the data, but to understand it and react to it. There's been a long tradition, especially the lab of Dyann Wirth in my department at the Harvard School of Public Health in trying to do this in Africa. So my group is trying to achieve this and get good engagement to inform public health malaria decisions with some of the latest cutting edge scientific knowledge and scientific tools.
June:
That's really interesting. On the website, it mentions he meaning you is excited by the potential for new technology and data. Is that referring only to the DNA sequencing or does that new technology go beyond that?
Daniel Neafsey:
The description of my research probably was written mostly with DNA sequencing in mind, but I think DNA sequencing is helping support the development of lots of new technologies that have exciting prospects for application to combat malaria. I'll cite just one example, which is the advent of monoclonal antibodies, which are being developed in multiple different infectious disease contexts. Early in the COVID pandemic, before there were efficacious vaccines, monoclonal antibodies were being used to treat severe clinical cases, and monoclonal antibodies work kind of like a silver bullet. They're special little proteins that are produced by human immune cells that can bind very specifically to a part of a pathogen and neutralize it or call in recruits from other cells in your immune system to take care of that pathogen and knock it out. In recent years, there's been some exciting progress in developing effective monoclonal antibodies for malaria that have been observed in some clinical trials to give very high protection for as long as six months.
The malaria field has been working to develop a highly protective vaccine for over 30 years, and the very first vaccine was fully approved and licensed just a few years ago. The RTS,S vaccine manufactured by GSK. It's exciting to have that tool, but it doesn't provide as much protection against disease as I think the field would really want. And so the quest continues for an even more efficacious vaccine, even while RTS,S, I think is going to really reduce the burden of disease in many settings where it's already been rolled out in Africa.
June:
So Dan, what's your holy grail?
Daniel Neafsey:
Oh, I think I probably speak for the whole field when I say that a vaccine that could provide very high protection against malaria infection for a period of at least a year, and where that protection could be conferred by just a single vaccination as opposed to a vaccination and then two boosters would do wonders for eliminating malaria. So I think the field with encouragement from the Bill and Melinda Gates Foundation has reoriented around the goal of not just reducing the burden of malaria as a disease, but trying to eliminate it, to completely get rid of it from various geographies and with an ultimate goal of eradicating the disease, of stopping its transmission anywhere in the world.
To get to that point, I think we need some powerful new tools. We need monoclonal antibodies or vaccines or drugs that are going to give really high levels of protection and that will be practical to implement in lots of settings. And I hope we get there. I think there are some exciting developments, and I am hopeful that DNA sequencing and other new technologies that the field didn't have during previous pushes to eliminate or eradicate the disease, for example, in the 1960s. There are lots of new tools we have at our disposal, so I think there's good reason to be optimistic that some of these holy grails may actually be realized in the next couple of decades.
June:
Well, I think that's a wonderful place to stop asking you questions. Is there anything that you would like to add?
Daniel Neafsey:
Well, just that I'm so grateful to have had these opportunities to work with partners in Guyana, Dr. Horace Cox and Dr. Reza Niles, and our partners in Columbia, whom I've already mentioned. Dr. Buckee and I have been just extremely fortunate to have wonderful collaborators and to be able to perform these studies. I'm grateful to the families and the patients who've consented to participate in our studies, and I'm hopeful that the knowledge that we've been able to produce will help to inform the control of disease in Latin America and elsewhere.
June:
Thank you. You've been listening to Daniel Neafsey. He's associate professor at the Harvard Chan School of Public Health, as well as his associate director of the Broad Institute's Genomic Center for Infectious Disease. Thank you for being with us, Dan.
Daniel Neafsey:
Thank you very much, June.