From bacteria to humans, each cell that makes up every organism on Earth contains the entire genetic code of that particular individual. The code is written in deoxyribonucleic acid, DNA for short, composed of just four types of proteins (called nucleotides) represented by letters, A, T, C and G. This genetic code, known as the genome, may be billions of nucleotides long. The genome, which is passed down from parents to offspring, contains the instructions required for the synthesis, repair and growth of new cells and this code is ubiquitous across all forms of life.
Though DNA has been known to science as the basis of the genetic code for nearly 100 years, it is only in the last 30 that improvements in technology and techniques enable us to read and decipher it. From these investigations we are able learn much about an individual organism, the population it lives in and about the species to which it belongs. Prior to these advances, studying the attributes of individuals or populations could often be difficult, time consuming and expensive. For example, establishing which species an individual belongs to could require an expert in anatomy with years of experience. However, due to the link between genotype (the DNA code) and phenotype (the organism’s traits e.g. behaviour or morphology), by reading particular regions of DNA and looking for the presence or absence of certain nucleotides, the phenotype may be established. Simple genetic tests now enable fast and cheap identification of genetic variants associated with specific phenotypes. The implications of these techniques for public health are huge and the fight against malaria using vector control has been no exception.
Malaria is vectored (transmitted) only by species of mosquitoes belonging to the Anopheles genus. Though the different species vary greatly in phenotypes important to their ability to transmit malaria (e.g. resistance to the malaria parasite, indoor/outdoor resting, peak biting times) they all look very similar, with some closely related species being practicably identical. Because of this, surveying the species, and therefore the malaria risk in a region, was traditionally a difficult task. However, within the DNA of mosquitoes are regions of the code unique to each species and by using a technique known as a polymerase chain reaction (PCR) test, these regions can be quickly evaluated. Rather than laboriously trying to identify mosquitoes collected from an area using traditional identification keys and microscopes, DNA can be extracted and in a just a few hours the species hundreds of mosquitoes can be established. The PCR test works by replicating a region of genome, chosen because it differs in length between species, millions of times using enzymes and temperature cycling. Though the DNA region of interest is too small to be seen with the naked eye, by making so many copies and then staining them with a fluorescent dye, their length (and therefore the species they belong to) can be measured. Species surveillance can now be quickly achieved allowing advice about malaria risk to be disseminated to communities, saving lives.
One of the most pressing issues in vector control is insecticide resistance. Not long after DDT was first used in attempts to eradicate malaria in the 1950s, resistance was detected and possibly as a result control campaigns started to fail. The same pattern of resistance emergence has been seen for every group of insecticides used since. The problem stems from organisms’ great ability to adapt when put under evolutionary pressures. Insecticides may kill many mosquitoes, but resistance only takes the chance change of a DNA nucleotide through mutation in a region of the genome responsible for insecticide efficacy in one individual. If this individual is better able to survive the insecticide and passes the mutation to it’s offspring the resistance mutation quickly spread in just a few generations. Knowing which insecticides the vectors are resistant to is therefore of major importance in organising a vector control campaign.
Insecticide resistance has historically been measured by biological assays (“bioassays”) where vectors are exposed to insecticides for a fixed period of time, after which the number of dead and alive individuals counted. The problems with this technique are manifold: large numbers of individuals are required, often necessitating an insectary and the time to rear adults mosquitoes from eggs or larvae, and the tests are also very sensitive to environmental conditions. Fortunately the genotype-phenotype link and genetic tests have enabled much more effective techniques. Regions of the genome thought to be involved in insecticide resistance have been sequenced, allowing us to actually read the DNA code and find the mutations linked to resistance. Once the resistance mutation is known, PCR based tests can be designed to indicate its presence or absence in many individuals in just a few hours, with no need for insectaries. These genetic insecticide resistance testing techniques mean that informed decisions about which insecticide is most effective can be made quickly and cheaply.
Recent years have seen sequencing technology improve very quickly, newer methods allowing much more DNA to be sequenced more quickly and for less cost than ever before. These techniques opened the opportunity for sequencing the entire mosquito genome and in 2002 the first Anopheles genome became publicly available, all 278 million nucleotides. The availability of this reference genome allows much easier design of PCR based tests and gave us a much better understanding of which regions of the genome were important to vector control e.g. which were responsible for malaria parasite resistance or targets for insecticides. As advances have continued, more malaria vector species and individuals have been sequenced. A recent project has seen 16 Anopheles reference sequences released and another will make thousands of Anopheles gambiae genomes available (http://www.malariagen.net/projects/vector/ag1000g). These resources will enable us to tailor vector control campaigns even more effectively: chose the correct insecticides to help prevent resistance, determine which areas insecticide spraying should target and monitor changes in vector populations in response to control campaigns. Genetics and genomics has already made huge advances in our understanding of vector control and also more widely in the fight against malaria, it will be an essential tool in the elimination of malaria as a public health problem.
Chris Clarkson is a third year PhD student at the Liverpool School of Tropical Medicine where he uses genomics to investigate speciation and insecticide resistance in Anopheles mosquitoes. He became interested in how genomics can be applied to evolutionary questions while studying grasshopper hybrid zones during his undergraduate degree at Queen Mary, University of London. In a recent paper published in Nature Communications, “Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation”, Chris and colleagues demonstrated that the introgression of an insecticide resistance mutation from important vector species to another also transferred a huge region of genome along with it.