What Is Genomic Pathogen Surveillance?
Genomic pathogen surveillance is a powerful complement to public-health infrastructure that can help researchers and public-health officials inform pandemic and epidemic preparedness, drug discovery and management of endemic diseases.
Genomic surveillance is a multi-step process. It begins with a strategy to identify and collect pathogen samples, informed by research and public-health priorities. Researchers or clinical technicians use machines to process these pathogens and yield their genetic code, the sequence. Powerful computational tools must then assemble and analyse this raw sequence data in a standardised manner. Genomic surveillance is the process of using this prepared, whole-genome data, alongside many previously observed pathogen sequences, to identify the emergence and spread of pathogens.
The immediate value of genomic surveillance lies in recognising changes in the genome that indicate the appearance of new lineages – some of concern – and mutations that produce changes in a pathogen’s behaviour, such as resistance to vaccines or therapeutic drugs. These classes of information enable recognising and tracking outbreaks, identifying drug resistance and improving surveillance of infectious diseases. Thus, genomic pathogen surveillance could help enhance the medical management of patients, empower improved local public-health interventions and strengthen global responses to infectious diseases, particularly for epidemics and pandemics.
Pathogen monitoring has traditionally relied on international academic-researcher networks sharing unexpected phenomena within a relatively narrow set of patient samples. In the past two decades, however, developments in both genomic sequencing and data-sharing infrastructure have significantly changed these processes, enabling researchers and clinical technicians to systematically sequence and analyse large sets of samples from the broad population.
These technologies include:
Next-generation sequencers to rapidly generate raw genomic data from a biological sample.
Processing software that cleans and analyses these data sets in a standardised manner.
Cloud-based data-storage systems to store and share data efficiently and securely, at scale.
Data-visualisation tools to aid analysis, identify trends and communicate findings to decision-makers.
Global databases and repositories, such as the Global Initiative on Sharing Avian Influenza Data (GISAID), that allow researchers to share genomic data internationally and identify trends and genomic mutations.
These technologies represent a link in the chain from swab sample to public-health policy decision at both the national and international levels. These advances – coupled with coordination on standard-setting, funding and governance activities at local, national and global levels – will enable the international community to scale and systematise genomic-surveillance capabilities for use in regular public-health monitoring of pandemic, epidemic and endemic diseases.