The pathogens that cause disease—parasites, viruses, bacteria—are continually evolving to evade the human immune system, and to resist the vaccines and drugs that are used against them. As a result, efforts to control these diseases often lead to the spread of pathogens that are better able to withstand the particular intervention. This can lead to the rebound of disease in the less controllable form. Drug resistance is one well-documented example of this evolutionary process.
Evidence of this biological struggle can be found by studying changes in the pathogens’ DNA. Advances in DNA sequencing technologies allow scientists to assemble the entire DNA sequence—or whole genome—of pathogens quickly and at a relatively low cost. Essential systems are now in place to isolate and sequence pathogens from many thousands of clinical samples per year, generating an unprecedented amount of raw genetic data.
Through detailed statistical analyses of these big data sets, researchers can identify positions in the DNA sequences that vary between pathogens. By studying genetic variation in this way, across the whole genome, scientists are gaining previously unimaginable insights into genetic diversity and evolution amongst pathogen populations.
This is particularly true when researchers working in different parts of the world are generating genetic data according to standard methods, which can then be pooled for statistical analyses—a feat often achieved through multi-institutional, global data-sharing initiatives.
This is a fast-paced, rapidly-expanding area of research. In the past few years, we’ve increasingly seen the potential for genomics to transform our understanding of how infectious pathogens bypass our biological defences and respond to public health interventions. Genomics has a crucial role to play in disease surveillance efforts by helping to understand the origins of drug resistance, mapping hotspots and routes of spread, and providing a cost effective and rapid means of monitoring and evaluating the impact of different interventions.
Four ways genomics can fight infectious disease
Much additional research and development is needed to translate advances in DNA sequencing and genomics into reconnaissance tools for clinicians and public health officials on the frontline of the fight against infectious diseases. However, in the long-term, genomics has the potential to:
- Assist disease control by providing up-to-date geographical information about known and newly-emerging forms of drug resistance, by examining genetic variation in the context of how whole pathogen genomes are evolving rather than as fragmentary information about individual genetic changes or polymorphisms. Mobile technologies can put this information in the hands of public health officials and practitioners on the ground, providing important reconnaissance in real-time.
- Rationalise drug and vaccine development by providing a systematic catalogue of genetic variation in potential drug or vaccine targets, crucial information for assessing the viability and sustainability of a proposed drug or vaccine.
- Catalyse a new generation of research on the genetic basis of drug resistance and of other forms of biological adaptation in pathogen populations, by providing a standard analytical framework for the design and interpretation of genome-wide association studies.
- Revolutionise scientific understanding of the population biology of infectious disease, by providing an unprecedented level of information about genetic diversity, population structure, evolutionary selection, demography and gene flow, and by enabling this to be linked to information about the behaviour and migration patterns of human and pathogen populations.