The Global Centre for Risk and Innovation (GCRI)
An outbreak becomes an emergency when a pathogen spreads faster than the systems that detect, characterise and contain it. Readiness depends on surveillance that sees early, laboratories that confirm, and evidence that is honest about what is not yet known. This page sets out how infectious threats emerge and spread, how they are detected and assessed, and how uncertainty is carried into the decisions of public health authorities.
GCRI · Established · service level R0
An infectious disease outbreak is an occurrence of cases above what is normally expected in a place and time. It becomes an emergency when the pathogen spreads faster than surveillance, laboratories and response can detect and contain it. Early figures change as reporting catches up, so estimates carry their delays and uncertainty.
How far each division sits from a large city, with the roads and airports that carry patients and supplies, shown for the Horn of Africa as an example geography for this subject.
The working screen behind this subject: its structure, terms and states. Names are placeholders and values illustrative.
Outbreak readiness, surveillance and uncertainty. The dossier below sets out how the risk develops, what is measured, where the data come from, how it is modelled and who decides.
Cases appear in surveillance only after infection, symptoms, care-seeking, testing and reporting. Each step adds delay and loses cases, so early counts describe the past and undercount the present.
Spread depends on the pathogen's transmissibility, the timing of infectiousness, population immunity and contact patterns. Mobility, crowding and mass gatherings connect local chains of transmission into regional and international ones.
Variants with altered transmissibility, severity or immune escape arise and are selected. Genomic surveillance detects them, but only where sequencing capacity exists and samples and data are shared promptly.
Surges strain hospitals and staff, travel and trade restrictions disrupt supply chains, and absenteeism reaches food, energy and transport. Public trust and the quality of information shape behaviour, and so the course of the outbreak itself.
Each term as this page uses it. Where a standard-setting body defines the term, the wording follows that body.
| Term | Definition |
|---|---|
| Reproduction number | The average number of people one case infects; the time-varying value reflects current immunity and control measures. |
| Public health emergency of international concern | An extraordinary event that may spread internationally and need a coordinated response, declared by the WHO Director-General under the IHR. |
| Nowcasting | Estimating current case numbers by correcting recent counts for reporting delays. |
| Case fatality risk | The proportion of confirmed cases who die of the disease, which depends heavily on testing and case definitions. |
Each indicator carries its unit, its cadence, the kind of source behind it and the evidence label a value would carry. No values are shown: a programme supplies them under its own authority.
| Indicator | Unit | Cadence | Source type | Label |
|---|---|---|---|---|
| Notified cases by date of onset | cases | daily or weekly | Indicator-based surveillance | REPORTED |
| Time-varying reproduction number | dimensionless | weekly | Transmission models on onset and case data | ESTIMATED |
| Test positivity | percent of tests positive | weekly | Laboratory reporting | OBSERVED |
| Sequencing coverage | percent of confirmed cases sequenced | weekly | Genomic surveillance and public repositories | OBSERVED |
| Timeliness of detection, notification and response | days between emergence, detection, notification and response | per event | Event records against national timeliness targets | REPORTED |
| Influenza-like illness and severe acute respiratory infection | consultations or admissions per hundred thousand population | weekly | Sentinel surveillance in GISRS | OBSERVED |
| Case fatality risk | percent of confirmed cases with known outcome | per event | Line lists with outcome follow-up | ESTIMATED |
| Excess mortality | deaths above expected | weekly or monthly | Vital registration against modelled baselines | ESTIMATED |
The topic as a computational graph: named sources feed the methods, an evidence review gates the outputs, and the decisions stay with the authorities that hold them.
Fig. 02Nodes carry their type, two metric rows and a state; connectors show what feeds what; dashed frames name the owners; the timeline is the cadence. Design of the pipeline, not a record of a run.
Named public datasets and institutional records, each with its licence class. Sources by agreement are used only under their terms and never republished.
| Source | What it gives | Licence class |
|---|---|---|
| WHO Disease Outbreak News | Official public reports on acute public health events | Public records, WHO terms of use |
| WHO GISRS: FluNet and FluID | Virological and epidemiological influenza surveillance from national influenza centres | Open, attribution, WHO terms of use |
| GISAID | Influenza and coronavirus genomes with sampling metadata | Registered access under the GISAID database access agreement |
| INSDC sequence archives and Nextstrain | Open pathogen sequences and phylogenetic analyses | Free and unrestricted; open, attribution |
| ECDC Surveillance Atlas and Africa CDC epidemic intelligence reports | Regional surveillance data and weekly event reports | Open, attribution, terms per agency |
| ProMED and HealthMap | Event-based signals from media, professional networks and informal reports | Terms per service |
| Global.health | De-identified case line lists for selected outbreaks | Open, attribution (CC BY 4.0) |
Health Nexus prepares evidence. The decisions below are taken by the authorities named, under their own rules, and never by the platform.
| Who decides | The question | Evidence this page serves |
|---|---|---|
| National public health institutes | Whether a signal is a true event, and what investigation and response it warrants | Signal verification trail; line lists; nowcasts with their uncertainty |
| IHR National Focal Points | Whether an event meets the criteria for notification to WHO under the IHR decision instrument | Event assessments with the evidence for each criterion labelled |
| Hospital systems | How much surge capacity to activate, and when | Admission scenarios by region with confidence bands |
| Ministries of health and cabinets | Which public health and social measures to apply, adjust or lift, and for how long | Transmission estimates; evidence on the effects of measures with its limits; cascade scenarios |
Most decisions about outbreaks are made before the facts are settled.
Transmission depends on the pathogen's biology, contact patterns between people, immunity in the population and the environment. The reproduction number summarizes how many people each case infects on average; when it stays above one, case numbers grow. Mobility, crowding, seasonality and human behaviour change the reproduction number over time.
Severity depends on age, underlying conditions, access to care and how stretched the health system is. A pathogen of moderate severity can still overwhelm hospitals if it spreads widely, which is why the indirect harm from disrupted services can rival the direct harm of the infection.
| Method or data | What it shows | Limits |
|---|---|---|
| Indicator and event-based surveillance | Unusual clusters and trends from reports, laboratories and media | Reporting delays, under-ascertainment and changing testing practice |
| Genomic surveillance | Variants, transmission chains and introductions | Uneven sequencing capacity and sampling bias |
| Compartmental and agent-based models | Scenarios of spread and the effect of interventions | Highly sensitive to uncertain parameters early in an outbreak |
| Nowcasting and short-term forecasting | Current and near-future trends corrected for reporting delay | Reliable only over short horizons |
| Serological surveys | How many people have been infected | Antibody waning and test performance complicate interpretation |
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.