Genomic surveillance of pathogens
Sequences from clinical, animal and environmental samples are assembled, assigned to lineages and placed on phylogenies to identify variants and assess relatedness, with sampling coverage reported beside every tree.
The Global Centre for Risk and Innovation (GCRI)
Molecular and life sciences characterise the pathogens, hosts and vectors behind health threats: their genomes, how they evolve, how they resist drugs and how they move between species. In this field they supply the laboratory and genomic evidence that confirms an event, links cases and tracks resistance across human, animal and environmental samples.
GCRI · Established · service level R0
Genomic surveillance is the routine sequencing and analysis of pathogen genomes to detect, characterise and track infections. With other molecular methods it confirms events, links cases, follows how pathogens evolve and resist drugs, and traces movement between people, animals and the environment, including through wastewater.
Molecular and life sciences study the structure and function of living systems from genes and proteins to cells and organisms. They underpin the understanding of pathogens, resistance, toxicity and biological innovation. In health and biosecurity, life sciences support pathogen characterisation, antimicrobial resistance tracking and biosecurity assessment. They inform how biological threats might spread through health, agriculture and trade. The canonical description is on the STEM Commons.
Sequences from clinical, animal and environmental samples are assembled, assigned to lineages and placed on phylogenies to identify variants and assess relatedness, with sampling coverage reported beside every tree.
Pathogen and resistance-gene sequences from people, livestock and the environment are compared to assess whether they share a source, under agreed sampling and metadata standards.
Nucleic acid targets in wastewater are measured and normalised for flow and population markers to follow community infection trends independently of who seeks testing.
Each term as this page uses it. Where a standard-setting body defines the term, the wording follows that body.
| Term | Definition |
|---|---|
| Phylogenetic analysis | Reconstructing the evolutionary relationships among pathogen genomes to infer how cases are linked. |
| Wastewater surveillance | Testing sewage for pathogen genetic material to track infection trends in the community it drains. |
| Variant | A pathogen lineage with genetic changes that distinguish it from others, which may alter spread or severity. |
How far each division sits from a large city, with the roads and airports that carry patients and supplies, shown for the Caribbean as an example geography for this subject.
Data from the source register feeds the methods; calibration and an independent test gate the estimate and its limits; the decision stays with the competent authority.
Fig. 01Nodes carry their type, metrics and state; connectors show what feeds what; the gates are the validation steps; the timeline is one application. Design of the method's use, not a record of a run.
Datasets and records used by molecular and life sciences on this platform, with the role each plays and the label its values carry. Sources are listed in the source register.
| Data | Role | Label |
|---|---|---|
| INSDC archives (GenBank, ENA, DDBJ) | Reference and outbreak sequences | OBSERVED |
| GISAID | Influenza and coronavirus genomes with metadata | OBSERVED |
| WHO GLASS | Resistance phenotypes from laboratory surveillance | REPORTED |
| Wastewater sampling programmes | Community trend signals | OBSERVED |
Results are confirmed through biological replicates, independent laboratories and orthogonal assays. Reference standards and proficiency testing check analytical accuracy.
| Check | How it is done |
|---|---|
| External quality assessment | Laboratories take part in proficiency testing and use reference materials for each assay |
| Sampling representativeness | How sequenced samples were selected is reported, so lineage shares are not over-read |
| Phylogenetic robustness | Trees are tested with bootstrap or posterior support and alternative models before relatedness is described |
Laboratory findings do not always translate to organisms or populations. Sampling bias in sequence databases limits generalisation.
Biotechnology and Biosecurity stewards molecular and life sciences for the Consortium and reviews how it is applied across platforms.
The current service level is R0: information and enquiries. An enquiry receives a reference and names the next step; applications, payments, compute allocations and registrations open only when their team, terms and review capacity exist.