In a discussion with Malaria No More, Dr. Fredros Okumu, one of Africa’s leading entomologists and Sophia Mwinyi, a Research Scientist at Ifakara Health Institute and a PhD candidate at the University of Glasgow, discuss using genomics to support global disease control efforts. Together, they recently published a new study that used advanced sequencing to uncover a new species of mosquito, which could prove critical to evolving malaria control interventions.

Can you tell us about your malaria work?

OKUMU: I am a public health entomologist, who specializes in mosquito-borne diseases. I initially studied in Kenya and Tanzania, then moved to Europe for advanced training. I started my research career in East Africa, where I worked for 15 years, including seven years as Director of Science at the Ifakara Health Institute in Tanzania. I am currently a professor of vector biology (infectious disease ecology) at the University of Glasgow in Scotland, but I continue my research in Africa, primarily in Tanzania, but also in Kenya, Mozambique, South Africa and a few other places.

Lately, I’ve been working on the biology, control and surveillance of vector-borne diseases. My current research portfolio cuts across several disease vectors, but a significant fraction of our work is focused on East and Southern Africa’s most dominant malaria vector, Anopheles funestus. Additionally, under a program called African Conversations, we have been engaging with hundreds of African stakeholders, and the international community around transformative technologies for malaria control, mostly focused on genetically modified mosquitoes, which can be deployed to either suppress local vector populations or modify them to not transmit malaria.

And Sophia, you have a different background, but your expertise meshes seamlessly in this work. Can you explain?

MWINYI: Yes, Initially, I trained as an economist, I began my career at Deloitte Consulting as a Governance and Technology Risk Business Analyst, where I developed a strong interest in data and its role in driving development projects in health and education This passion led me to pursue a master’s degree in data science, specializing in Financial Technology (FinTech), at the University of Cape Town. After completing my degree, I joined the Ifakara Health Institute, where I was assigned a genomics project involving genetic data—an entirely new type of dataset for me despite my experience with many other data science projects. To support my transition, my supervisor (Dr. Okumu) arranged for me to receive intensive training from experts at the Wellcome Sanger Institute, where I was introduced to genomic data science and analytical methods (malaria entomological surveillance).

Before we go further, what are your thoughts on malaria elimination? Is it possible?

OKUMU: Indeed, elimination, as in, reaching a state of zero malaria cases in a specific locality, is possible. The questions are where, when and how.  Right now, we still have lots of deaths, especially in the poorest communities with limited access to health care. So, while I am excited about the possibility of malaria elimination in some settings, I would rather we were more focused on the question of how we reduce this disease to the levels where it is not a major concern. Malaria still claims more than 600 thousand lives every year, the majority in Africa. So, our focus should really be making sure that people are not dying of a disease for which we know the cure, even if they get sick. We also need to make sure that as few people as possible get sick. So, in other words, you want to accelerate towards zero malaria and in the process have as few deaths as possible.  Again, that’s accelerating towards zero, with as few deaths as possible. It might happen that you never go to zero, but you create a situation where even if you get sick, you can find help. In other words, you build resilience. And, so, in my view, we should be much more focused on building structural resilience in these communities. We want to make as much progress as we can but also ensure that progress is sustained. So yes, we want to go towards zero and I hope we will get there someday. But I don’t think it should be the end goal.

You recently published a new study that used advanced sequencing. Can you tell us more about that kind of technology and how it is being used to control malaria?

OKUMU: Advanced sequencing uses cutting-edge DNA sequencing technologies to study the genetic material of malaria vectors and parasites. For several years now, we have been building local capabilities to master the genetic characteristics of Africa’s most important disease vectors. For example, our group at the Ifakara Health Institute was working jointly with the Wellcome Sanger Institute and University of Glasgow. We looked at mosquito samples previously collected in coastal areas of Kenya and Tanzania.

Sophia, you were the lead author of the study and ended up discovering a new mosquito species as a result. Can you tell us how that came about?  

MWINYI: While I was training, I delved into a project which led to the discovery of a previously unknown mosquito strain and a more complex Anopheles. So, we needed to research whether it would respond to insecticides, for example. This was exciting for us because it showed the potential of using genetic technologies. And it’s crucial for us that we have a good understanding of mosquito populations, as well as their genetic makeup. But already, we’re seeing advanced sequencing revolutionizing how we, as scientists, understand, track, and fight malaria.

Why is this discovery significant in the malaria fight?

OKUMU: This is a species of mosquito that had never been identified, though it is very closely related to Africa’s most notorious malaria vector species, Anopheles gambiae. Today, we refer to this new species as as the Pwani molecular form, and it doesn’t look much different than its cousins in the broader Anopheles gambiae complex, but genetically it’s very different. And this can have a huge impact. The Pwani molecular form has its name derived from the Swahili word for “coast.” We identified it through advanced genomic sequencing techniques which showed us that at the molecular level, it’s very different. We were looking at mosquito populations collected along the coastal regions of Kenya and Tanzania where this species consistently emerged, suggesting a unique evolutionary trajectory shaped by the micro-environments of this specific ecological corridor. Some may say this is just another mosquito. It’s not very big. Just a few millimeters. But in the ecosystem of disease transmission, even the tiniest mosquito can be extraordinarily deadly.

But what makes this discovery especially interesting is the mosquito’s insecticide resistance profile. It doesn’t have the common molecular markers which possibly indicate that the Pwani form could be resisting insecticides through a completely different, and currently unknown, genetic pathway. However, it could also be more resistant. We just don’t know yet. But either way, this presents a challenge. If it’s more susceptible, why are we seeing higher cases of malaria in places where we’ve been finding it? And if it’s more resistant, the tools we have today would be ineffective. Either way, this is a blind spot in our current public health strategy. But the Pwani form’s unique genetic traits suggest it may be thriving even when other vectors go away – meaning it’s possibly sustaining malaria transmission even during off-peak seasons.

MWINYI: Our research used whole-genome sequencing. What we found was that the Pwani mosquito had undergone significant genetic divergence. It has a unique combination of genes that suggest distinct ecological and possibly behavioral traits, including how it finds hosts, where it breeds, and when it is most active. For us, understanding these unique behavioral patterns is crucial, since these changes in behavior could explain why certain communities continue to experience high rates of malaria despite the widespread use of nets and sprays. But this tells us that our standard toolbox of interventions, such as long-lasting insecticide-treated nets and indoor residual spraying, may need to be reevaluated or expanded to deal with this latest challenge.

How will this information be used?

OKUMU: As malaria adapts, science must too. We wouldn’t have been able to detect the Pwani mosquito without these latest genomic technologies. Advanced sequencing allows us to look for subtle variations that would have been undetectable a decade ago. This discovery underscores the power of genomic tools to reveal hidden factors in disease transmission. It’s exciting that our research has already led to follow-up studies in Tanzania and Kenya, with entomologists collecting more specimens, conducting transmission experiments and monitoring genetic shifts. By using genomics, we can help stay ahead of the game in the fight against malaria. Understanding the DNA of mosquito populations helps us as scientists and other public health officials to design better interventions to ultimately stop malaria transmission. Surveillance systems must evolve to look for genetic diversity within mosquito populations. At this point, we must also point out the value of partnerships with established institutions, such as Wellcome Sanger Institute, where Sophia initially received her technical training to undertake this analysis.

What needs to happen next?

MWINYI: Following the discovery of the Pwani form mosquito, the next and most urgent step must involve determining whether this mosquito can transmit malaria parasites, understanding its ecological and biting behavior, and since it lacks known resistance markers, laboratory and field studies are needed to confirm its vulnerability to the current vector control tools. Surveillance systems must also be updated to detect and track this cryptic species, which could otherwise be misidentified. Regional collaboration, particularly with neighboring countries like Kenya, will be critical to ensure a coordinated response and to prevent this potentially hidden vector from undermining malaria control efforts along the East African coast.

In addition, genomics and data science are revolutionizing public health surveillance by enabling the rapid and robust detection of emerging disease threats and the ability to monitor them in real time. In malaria control, we have seen genomic tools help to identify hidden mosquito species, track insecticide resistance, and capable in detecting parasite changes that could compromise diagnostics tools or treatments. When combined with data science, these insights can power predictive models to guide targeted interventions and anticipate future outbreaks. To fully realize this potential, countries need to invest in local genomic surveillance infrastructure, build capacity in bioinformatics and data analysis, and integrate these tools into national and sub-national disease control programs. Additionally, regional data-sharing frameworks and collaborative networks should be strengthened to ensure coordinated responses across borders.

OKUMU: I just want a better world for our kids and communities. I believe that is true for most people. But time is of the essence. The discovery of the Pwani mosquito only underscores the need for more entomological and epidemiological interventions. We don’t know whether this specific finding will negatively impact disease control, but it signals the complexity of malaria control, and the areas that we must investigate even as we anticipate potential new technologies in future, such as gene drives.

As Sophia explained in our publication, we need to determine if it’s a malaria vector, and if so, how it behaves and interacts with humans. That means tracking its biting habits, reproductive cycles, seasonal patterns and susceptibility to insecticides. But by refining and enhancing our malaria control efforts, that could translate into saving thousands of lives.  

Besides your malaria work, what are you doing to help scale these efforts?

OKUMU: Well, perhaps most importantly, my colleagues and I participate actively in training young people; and also creating enabling environments for early-career African scientists, like my colleague, here Sophia, who is herself an excellent scientist and also a PhD candidate with us, working between Glasgow & Ifakara. Last year alone, there were 7 new PhDs from the group in Ifakara, alongside several masters fellows. This is important for the sustainability of global health R&D in Africa. And on the international scene, I serve on a number of advisory bodies, notably the WHO’s Malaria Policy Advisory Group (MPAG), the Gates Foundation’s Malaria Strategic Advisory Panel, and the Advisory Board of the Malaria Elimination Initiative. I have also recently started as an advisor on a new initiative by the African Diaspora Network to engage and channel the global community of the African diaspora towards addressing Africa’s priority challenges, including, of course Malaria. The idea here that you to link African scientists based abroad with their counterparts on the continent so that they can collectively, and more effectively tackle specific health problems.

###