Genetic study of malaria-carrying mosquitoes tracks evolution of insecticide resistance

The mosquito Anopheles funestus is one of the most significant carriers of malaria.

Now researchers have mapped the genetics of the insect across Africa and through time. They have found that while there is surprisingly little genetic difference across much of the population, there is evidence in their DNA pointing to the evolution of insecticide resistance.

The latest study, published in the journal Science, will help scientists figure out how to control the prevalence of malaria, which kills an estimated 569,000 people a year.

“A. funestus is genetically complex and evolving fast under pressure from insecticide use,” explains Dr Marilou Boddé, first author and Postdoctoral Fellow formerly at the Wellcome Sanger Institute and now at Institut Pasteur de Madagascar and LIB Bonn, Germany.

“This work is progress in generating a foundational genomic understanding of A. funestus. The insights from this study are crucial for designing future tools that need to work across entire continents for the benefit of those living in countries affected by malaria.”

The work was able to make use of historic mosquito specimens cared for by the Natural History Museum, highlighting how museum collections can help inform current and future public health priorities.

“There are 300 drawers of mosquitoes in the Natural History Museum, and that doesn’t include the slides and those preserved in spirits,” explains Dr Erica McAlister, our curator of flies and fleas who was involved in sampling and sequencing these specimens.

“This has allowed us to go back 100 years to get these amazing genomes, and we’re beginning to ask serious questions from the collection.”

The researchers were able to see how some of the genes related to insecticide resistance only started to appear after different insecticides were used. But even when the use of these chemicals dropped in the decades leading up to the 1990s, scientists could see that the resistance genes remained within the population at a low level.

They suspect this primed the insects for further resistance when insecticide use increased again in the 2000s, hampering our ability to control the disease. This shows the incredible potential of natural history collections in developing new control methods.

“We’re able to look at real-time current populations and then work back with looking at these historic populations,” says Erica. “Using this method and doing these sorts of studies within our collections allows us to understand how other populations are evolving, changing and adapting.”

Making progress to beat malaria

Malaria is often talked about as a single disease, but is actually caused by six different species of single-celled parasites in the genus Plasmodium. These can be spread by different mosquito species, all within the genus Anopheles.

To date, the attempts to reduce the prevalence and presence of malaria have been remarkable. It is estimated that up to two billion cases of the disease have been averted, but in recent years progress has slowed.

The main carrier for the most widespread Plasmodium species across Africa is the mosquito Anopheles gambiae. Because of this, the insect has been of intense interest to researchers to figure out a way to control the spread of the deadly disease. This has included sequencing its genome to identify potential genetic weak spots.

But the mosquito A. gambiae is not alone in being able to transmit the parasite. A related species, called Anopheles funestus, is also a well-known vector. It can be found from Senegal in the west to Madagascar in the east and down into South Africa.

The species is anthropophilic, meaning it is attracted to humans specifically as a source of blood, and has a longer lifespan than other mosquito species. It is also highly adaptive. For example, studies suggest that in some regions the usually nocturnal insect has shifted to be more active during the day in response to the use of mosquito nets at night.

As a result, researchers wanted to analyse the genome of A. funestus across not only its range but also time, to see how the species might be changing in response to control techniques such as insecticides. It then allowed them to compare the DNA to A. gambiae to see where similarities and differences lie between the two species.

“Even if the Gambiae Complex disappeared today, malaria would still rage through Africa until A. funestus is also effectively targeted,” explains Dr Mara Lawniczak, the senior author of this latest paper and Senior Group Leader at the Wellcome Sanger Institute.

“We hope the greater understanding of the high levels of genetic diversity and the complex population structure we uncover here will underpin smarter surveillance and targeted vector control.”

Genetic diversity of African mosquitoes

The researchers were able to sequence the genomes of 656 A. funestus mosquitoes collected from across its African range between 2014 and 2018. These were supplemented with the genomes of 45 historic mosquitoes from the Natural History Museum and the Institut de Recherche pour le Développement that were collected between 1927 and 1967.

They found that despite the huge distances between individual populations of mosquitoes, the genetics of the insects were remarkably similar. This suggests that there is more movement between these populations than thought.

In addition to this, comparisons with the genomes of A. gambiae found that a set of key genetic targets were also similar between the species. This is important, because experiments are already underway in A. gambiae to use these genetic markers for a method known as a gene drive.

This technique aims to introduce genetic mutations into the mosquito populations which, for example, will prevent the insect from passing on the malaria parasite. The fact that the most promising genetic targets are similar across the species raises the potential that the same method being trialled on A. gambiae will also work with A. funestus.

Coupled with the new understanding that there is genetic movement across much of the mosquito’s range, this theoretically means that mutations introduced in one region should be able to spread to other regions.

More work will need to be done on the insects and the malaria they transmit, but the study offers encouraging results that could hopefully be used to prevent further deaths. It also shows the real value of natural history collections.

“The study demonstrates why we need these huge collections and why we still need to maintain and enhance them,” explains Erica. “We have 20 drawers of A. funestus, and even though everyone thinks they’re the same thing this sort of investigation shows you that actually they’re not. They’ve come from different locations, different places in time.”

“It is really important that we need to have these comprehensive collections, and to keep adding to and maintaining them.”