Day 4: Outbreak management and health system strengthening…

1Organising the response: incident management

An epidemic is managed as an incident, with an incident management system (or emergency operations centre) under the authority of the Ministry of Health and supported by WHO and the cluster. It brings together clear functions: coordination, surveillance and laboratory, case management, infection prevention and control, WASH, risk communication and community engagement, logistics, vaccination.

The daily meeting follows a fixed order: epidemiological situation, stock status, geographical gaps, decisions and persons responsible. A costed response plan and a dashboard of indicators (cases, deaths, case fatality rate, time between symptom onset and treatment, vaccination coverage) guide decisions and advocacy.

2Reading the data: epidemic curve, attack rate and case fatality

The epidemic curve (cases per day or per week) shows whether the epidemic is in a growth, plateau or decline phase, and whether a common source is likely. The attack rate (cases ÷ population at risk) indicates the most affected areas. The case fatality rate (deaths ÷ cases) measures the quality and accessibility of case management: for cholera, it must remain below 1%; a high case fatality rate in facilities signals a quality problem, while a high proportion of community deaths signals an access problem.

Data are disaggregated by age, sex and location, and shown on a map. An apparent drop in cases may also come from weaker surveillance: always check the completeness of reports before drawing conclusions.

3Preserving essential services

During an epidemic, other causes of death do not disappear. Past outbreaks have shown that the collapse of essential services (assisted deliveries, routine immunisation, treatment of malaria, tuberculosis or HIV) can kill more people than the epidemic itself. Staff must therefore be protected (infection prevention and control, personal protective equipment, regular pay), triage at facility entrances maintained and essential service indicators monitored every month.

HeRAMS and the national health information system (often DHIS2) make it possible to identify facilities that are falling behind. Attacks on health care, which close entire services, are reported to the WHO SSA and included in the cluster's advocacy.

4From recovery to system strengthening

A good response leaves a stronger system behind. In practice: work within public facilities rather than alongside them, align incentives with the rules agreed within the cluster, train ministry staff, integrate EWARN into national surveillance, and gradually transfer procurement to national channels and the essential medicines list.

Preparedness is part of the job: contingency plans by risk season (cholera in the rainy season, measles in the dry season, meningitis in the African belt), prepositioned stocks, trained rapid response teams, simulation exercises and after-action reviews following each epidemic.

In-depth course

Detailed methods, a complete worked example, tools, common mistakes and interview questions.

5Setting up incident management: structure, rhythm and a costed response plan

Incident management is not an organisational chart pinned to the wall. It is a way of working that meets three needs: a single chain of decision-making, clearly assigned functions, and a predictable rhythm of information and decision-making. The WHO Emergency Response Framework and national public health emergency management guidelines draw on it; the Ministry of Health retains leadership, often through a public health emergency operations centre.

Step 1: activating and appointing (first 24 to 72 hours)

The Ministry declares the outbreak and appoints an incident manager, with a written mandate and the authority to commit resources.
WHO assesses the risk and grades the emergency according to its internal grading framework, which determines the level of mobilisation of the organisation and its emergency funds.
Each function is given a named lead, with a deputy. Partners (NGOs, agencies, Red Cross and Red Crescent) are attached to the functions in which they work.

Step 2: the functions and their deliverables

Function	Responsibilities	Daily or weekly deliverables
Incident management	Arbitration, priorities, liaison with authorities and donors	Recorded decisions, response plan
Surveillance and laboratory	Data collection, analysis, investigation, active case finding, confirmation	Daily dashboard, weekly bulletin, line list
Case management	Protocols, treatment facilities, training, quality of care	Number of beds, case fatality rate by facility, needs
Infection prevention and control and WASH	IPC in facilities, water, sanitation, CATI, safe burials	IPC assessments, coverage of WASH interventions
Vaccination	Microplanning, campaigns, cold chain, coverage	Doses administered, coverage, AEFI
Risk communication and community engagement	Messages, listening to communities, rumour tracking, feedback mechanisms	Weekly summary of feedback and rumours, adjustments
Logistics and supply	Stocks, transport, cold chain, infrastructure	Status of stocks and needs, lead times
Planning and information	Situation, maps, reports, tracking of commitments	Situation report (SitRep)
Administration and finance	Budget, human resources, contracts	Monitoring of expenditure and funding

Step 3: the working rhythm

In the acute phase, the coordination meeting is daily, short (60 minutes maximum) and follows a fixed order: epidemiological situation over the last 24 hours; case management (bed occupancy, case fatality, problems); control interventions (coverage, geographical gaps); stocks and logistics; communication and community feedback; decisions, people responsible, deadlines. The one-page minutes, with the list of decisions, are circulated within two hours. A situation report is published once or twice a week for partners and donors.

Step 4: the costed response plan

The response plan is drafted in the first week for a period of 30 to 90 days, then revised. It includes: the situation and risk analysis; scenarios (most likely and reasonable worst case); objectives; activities by function, with areas, targets and people responsible; human resource, supply and logistics needs; the budget; and monitoring indicators.

Budget line	Basis of calculation	Example method
Case management	Number of cases expected according to the scenario, cost per case	Severe cases × consumables per case + staff per bed
Vaccination	Target population × operational cost per person vaccinated + vaccines	Operational cost often separate from the cost of the vaccine, to be checked with UNICEF and the national programme
Surveillance and laboratory	Number of active case-finding teams, samples, transports	Teams × days × cost per day
WASH and IPC	Number of CATIs, water points, hygiene kits	Expected cases × average cost of a CATI
Communication and community engagement	Volunteers, media, tools	Volunteers × months × harmonised incentive
Coordination and logistics	Staff, transport, communications	Percentage of the total or detailed calculation

A response plan that is not costed cannot be funded. Emergency funds (the Central Emergency Response Fund, the WHO Contingency Fund for Emergencies, the IFRC Disaster Response Emergency Fund, country-based pooled funds, donors' crisis envelopes) require a budget, a scenario and indicators within a few days.

6Reading outbreak data without getting it wrong

Response decisions rely on a few simple indicators, but each one has known pitfalls. An experienced epidemiologist always asks what the figure actually measures before interpreting it.

The epidemic curve

Date of symptom onset, not date of notification: the notification date shifts the curve and creates false peaks when a batch of late reports arrives.
Time interval: an interval of about a quarter to a third of the average incubation period is generally chosen (hours or a day for cholera, days or a week for measles).
Reporting delay: the last days of the curve are always incomplete. An apparent drop in cases over the last three days is often an artefact; these days are greyed out on the graph.
Shape: a point common source produces a single rapid peak; a continuous source produces a plateau; person-to-person transmission produces successive waves spaced one incubation period apart.

Rates and their pitfalls

Indicator	Calculation	Pitfall	Correction
Attack rate	Cases ÷ population at risk	Wrong denominator or mobile population	Use the most recent site or health area denominator; compare areas with one another
Case fatality rate	Deaths ÷ cases	Recent cases do not yet have an outcome: the case fatality rate is underestimated at the start of a wave	Also calculate the case fatality rate among cases with a known outcome; present facility and overall case fatality rates
Test positivity rate	Positive tests ÷ tests performed	Depends on the testing strategy (fewer tests are done when tests are short)	Monitor the number of tests together with the positivity rate
Weekly incidence	New cases ÷ population × 1,000 or 100,000	Variation in report completeness	Always show completeness alongside
Time to treatment	Date of treatment minus date of symptom onset	Missing or approximate dates	Median rather than mean, proportion of cases with a recorded date
Vaccination coverage	People vaccinated ÷ target	Outdated denominator, vaccinations of people from outside the area	Rapid convenience monitoring, survey

The response dashboard

Area	Indicator	Target or benchmark	Frequency
Epidemiology	New cases and deaths, by area	Downward trend over 2 incubation periods	Daily
Epidemiology	Proportion of new cases known to be contacts or coming from already affected areas	Rising: the response is keeping up with the outbreak	Weekly
Case management	Facility and overall case fatality rates	Depending on the disease (cholera: less than 1%)	Weekly
Access	Median time from symptom onset to treatment	Depending on the disease (cholera: less than 24 hours)	Weekly
Control	Coverage of interventions (CATI, vaccination, chlorination)	At least 80 to 95% depending on the intervention	Weekly
Surveillance	Completeness and timeliness	At least 80%	Weekly
Resources	Days of stock of critical supplies	Above the safety stock	Daily in the acute phase
Community engagement	Main rumours and concerns, responses provided	Every major concern addressed within the week	Weekly

Declaring the end of an outbreak

The end is declared according to criteria set for each disease and by the Ministry, generally after a period with no new cases equal to a multiple of the maximum incubation period (for example two incubation periods), with functioning surveillance. For some diseases (Ebola, for example), WHO sets precise criteria and a period of enhanced surveillance after the end.

Before concluding that an outbreak is declining, ask three questions: is report completeness stable? Is the number of tests or active case-finding efforts stable? Are newly affected areas properly covered by surveillance? If any answer is no, the decline may be an artefact.

7Maintaining essential services during an outbreak: method and indicators

WHO's operational guidance on maintaining essential health services, published during the COVID-19 pandemic, applies to any major outbreak. It is based on a finding documented during the Ebola virus disease epidemic in West Africa: the fall in service attendance, skilled birth attendance and vaccination, and the interruption of malaria, HIV and tuberculosis treatment, caused a number of indirect deaths comparable to, or according to some estimates higher than, the direct deaths from the epidemic.

Step 1: defining the essential services to protect

A list of priority services is drawn up with the Ministry, for example: emergency obstetric and newborn care, routine immunisation, management of malaria, pneumonia and diarrhoea in children, management of severe acute malnutrition, continuity of HIV, tuberculosis and non-communicable disease treatment, clinical management of rape, blood transfusion, emergency care.

Step 2: choosing tracer indicators and an alert rule

Tracer indicator	Source	Example alert rule
Number of curative consultations	Health information system (DHIS2)	A drop of more than 20% compared with the same period of the previous year or with the average of the three months before the outbreak
Facility-based deliveries	Maternity registers	Same rule
Pentavalent 3 doses administered	EPI reports	Same rule
Confirmed malaria cases treated	Monthly reports	Unexplained drop during the transmission season
Patients on antiretrovirals who collected their treatment	Facility registers	Increase in missed appointments
Admissions for severe acute malnutrition	Nutrition programme reports	Drop while prevalence is stable or rising

The 20% rule is a working convention used by many ministries and partners; it must be adapted and validated locally.

Step 3: protecting staff and patients

Comply with the WHO minimum requirements for infection prevention and control programmes: a trained IPC focal point in each facility, protocols, hand hygiene, supply of personal protective equipment, waste management.
Set up triage and screening at the entrance to every facility, with a temporary isolation area, so that non-suspected patients can continue to attend safely.
Pay staff regularly, including harmonised hazard pay; plan for the care of infected staff and psychosocial support.
Where possible, physically separate the outbreak patient flow from that of essential services (opening hours, entrances, dedicated facilities).

Step 4: adapting service delivery

Multi-month dispensing of treatment to stable chronic patients.
Task shifting to community health workers (malaria, diarrhoea, pneumonia, nutrition screening, family planning) in line with national policies.
Vaccination catch-up campaigns as soon as the situation allows, with outreach strategies in affected areas.
Community communication explaining that facilities remain open and safe, and responses to rumours that "going to the health centre means catching the disease".

During an outbreak, the most telling indicator of how the system is functioning is not the number of outbreak cases, but the number of assisted deliveries and children vaccinated each month. If these fall, the response is costing lives elsewhere.

8Worked example: the measles outbreak in Morinka district

Fictional context: Morinka district has 180,000 inhabitants, including 30,000 displaced people who have been living in a camp for a year (health area 1). The district's administrative measles coverage is 68%, with no follow-up campaign for four years. The malaria transmission season is starting. In week 10, the EWARN reports three cases of fever with rash in the camp; two IgM tests are positive in week 11. The Ministry declares the outbreak.

1. Outbreak data (weeks 10 to 17)

Week	W10	W11	W12	W13	W14	W15	W16	W17	Total
Cases	8	21	54	112	186	240	205	150	976
Deaths	0	1	2	4	6	7	5	3	28

Cumulative case fatality rate: 28 ÷ 976, or 2.9%. Age distribution: 62% of cases among under-5s, 30% among 5- to 14-year-olds, 8% among those aged 15 and over. 81% of cases have no documented dose. Of the deaths, 19 were malnourished children.

Health area	Population	Cases	Attack rate
Area 1 (camp)	30,000	420	1.40%
Area 2 (district capital)	50,000	310	0.62%
Area 3	60,000	180	0.30%
Area 4	40,000	66	0.17%
Total	180,000	976	0.54%

2. Organising the response

The district medical officer is appointed incident manager. WHO supports surveillance, UNICEF supports vaccination and the cold chain, a medical NGO supports case management in the camp and area 2, and a national NGO supports community communication. Daily meeting at 8 a.m. at the district office, SitRep on Tuesdays and Fridays.

3. Key decisions and their rationale

Reactive campaign across the whole district, 6 months to 14 years, not limited to the camp: the attack rate is high in area 2 and routine coverage is low everywhere. Target: 180,000 × 43%, or 77,400 children; doses: 77,400 × 1.18, or 91,332 doses (9,134 10-dose vials); teams: 77,400 ÷ (300 × 6 days), or 43, rounded up to 44 teams and 11 supervisors. Sequence: camp and area 2 first (week 14), areas 3 and 4 the following week, given cold chain capacity.
Case management: vitamin A for all cases (two doses 24 hours apart), systematic nutrition screening, antibiotic treatment of complications, a 20-bed isolation unit for complicated cases in the camp; a home-care protocol for uncomplicated cases with follow-up by community volunteers.
Surveillance: active case finding in areas 3 and 4, line list with vaccination status and nutritional status, sampling limited to 5 per newly affected area.
Communication: messages on the severity of measles and the safety of the vaccine, tracking of a rumour that vaccination sterilises girls, response by religious leaders and mothers of vaccinated children.

4. Essential services slip (week 16 review)

Tracer indicator (monthly)	Pre-outbreak baseline	Outbreak month	Change
Curative consultations	9,000	6,300	Minus 30%
Facility-based deliveries	420	300	Minus 29%
Pentavalent 3 doses	650	470	Minus 28%
Confirmed malaria cases treated (compared with the same month of the previous year)	3,800	2,600	Minus 32%

Analysis: all indicators exceed the 20% alert rule. Health centre vaccination staff were mobilised for the campaign, women are avoiding facilities for fear of contagion, and the drop in treated malaria cases at the height of the transmission season signals untreated children, not a decline in malaria. Decisions: health centre staff return to their posts every other day during the campaign, temporary vaccinators are recruited, a separate patient flow for measles cases in each health centre, community case management of malaria by volunteers in areas 1 and 2, a radio message saying "maternity wards remain open and safe", and integration of these four indicators into the daily meeting dashboard.

5. After action review (two months after the end)

What was planned	What happened	Why	Recommendation, person responsible, deadline
Reactive vaccination within 14 days of confirmation	21 days	Insufficient ice-pack freezing capacity at district level	Two additional freezers prepositioned, national EPI programme, before the next dry season
Case fatality rate below 3%	2.9%, but 6% among malnourished children	Late nutrition screening of cases	MUAC screening built into the case management protocol, nutrition partner, immediately
Maintenance of essential services	Drop of 28 to 32%	Staff reassigned, fear of contagion	Continuity plan integrated into the district contingency plan, district manager, within three months

The after action review is not an assessment of individual performance. It takes place in a no-blame climate, compares what was planned with what was achieved, and produces a small number of recommendations, each with a person responsible and a deadline, which are followed up at subsequent meetings.

9From recovery to strengthening: transition, preparedness and accountability

The exit from an emergency phase is prepared from its very beginning. The six building blocks of the health system described by WHO (service delivery, health workforce, information, medical products, financing, governance) provide a framework for checking that the intervention leaves something sustainable behind.

Transition framework by building block

Building block	Risk when exiting the emergency	Transition actions	Readiness indicator
Service delivery	Parallel facilities that close overnight	Integration into the health facility map, gradual handover to the Ministry, accompaniment period	Facility included in the district plan and staffed by public personnel
Health workforce	Sudden loss of incentives, staff leaving	Harmonised and gradually decreasing incentive scale, negotiation with the Ministry and development donors, continuing education	Proportion of staff paid by the State
Information	EWARN and NGO reports not integrated	Integration into the national system (DHIS2), training of district data managers	Proportion of facilities reporting in the national system
Medical products	Stock-outs when NGO supplies stop	Gradual shift to the national central medical store, strengthening of stock management at district level	Stock-out days for tracer medicines after handover
Financing	Return of out-of-pocket payments, drop in attendance	Advocacy for fee exemptions for vulnerable groups, performance-based financing or grants, coordination with development donors	Utilisation rate after free care ends
Governance	District team bypassed during the emergency	Joint planning, joint supervision, co-chairing of coordination meetings	Coordination meetings chaired by the district

The humanitarian-development nexus

In protracted crises, transition does not mean humanitarian actors leaving but a different division of roles. The aim is collective outcomes shared with development actors (for example, reducing maternal mortality in the province), multi-year planning and longer-term funding. The OECD DAC Recommendation on the Humanitarian-Development-Peace Nexus (2019) serves as the donors' reference for this approach.

Preparedness for future outbreaks

Contingency plan for each risk season: scenarios, triggers, roles, stocks, funds that can be mobilised; updated every year before the season.
Prepositioned stocks: cholera modules, rapid diagnostic tests, ORS, Ringer's lactate, personal protective equipment, sampling materials, at district level and in high-risk facilities.
Multidisciplinary rapid response teams (epidemiology, clinical care, laboratory, WASH, communication), trained and listed with their deputies.
Simulation exercises: half-day tabletop exercise, functional exercise or full-scale exercise, following the WHO simulation exercise manual, at least once a year.
Intra-action and after action reviews: the intra-action review takes place during the response to adjust course; the after action review within three months of the end.
International Health Regulations capacities: district preparedness contributes to the assessment of national capacities (IHR Monitoring and Evaluation Framework, Joint External Evaluations).

Accountability to affected populations during an outbreak

A response that ignores community trust fails: vaccine refusal, hidden cases, clandestine burials. The Core Humanitarian Standard requires that affected people have access to information, participate in decisions and have safe complaints mechanisms. In practice: community committees involved in planning, weekly collection and analysis of feedback and rumours, visible responses to concerns, and mechanisms for reporting sexual exploitation and abuse that everyone knows about, including in treatment centres and during campaigns.

A good test of the quality of a transition: six months after the NGO has left, is the facility still functioning, with the same level of attendance and no medicine stock-outs? If nobody has planned to measure this, the transition has not been planned.

10Common mistakes, contextual variations, interview questions and references

Common mistakes

Mistake	Consequence	Good practice
Multiple, competing coordination structures (Ministry, WHO, cluster, NGOs)	Contradictory decisions, endless meetings	A single incident management system under the authority of the Ministry, to which the cluster and partners are attached
Response plan with no scenario or budget	Late or refused funding	Most likely and reasonable worst-case scenarios, budget by function, revision every 30 days
Curve plotted by notification date	False peaks, false decline	Date of symptom onset, last days greyed out
All staff reassigned to the outbreak	Collapse of essential services, indirect excess mortality	Tracer indicators monitored, temporary staff, separate patient flows
End of the outbreak announced too early	Resurgence, loss of credibility	End criteria defined in advance, surveillance maintained
After action review never carried out or never followed up	Same mistakes in the next outbreak	Review scheduled in the response plan from the outset, recommendations followed up in the contingency plan
NGO exit without transition	Services close, gains lost	Transition plan from the design stage, readiness indicators

Variations by context

Context	Adaptations
Sudden-onset crisis	Incident management activated within a few days, support from emergency medical teams and rapid response teams, initial 30-day response plan
Protracted crisis	Recurrent outbreaks: seasonal contingency plans, integration into the national system, multi-year funding
Camp	Rapid and exhaustive response, but pay attention to the surrounding host population, which is often forgotten
Urban settings	Coordination with municipal authorities and the private sector, high mobility, communication through the media and social networks
Remote management	Incident management in the capital or a neighbouring country, local teams on site, simplified indicators, third-party monitoring
Insecurity or areas controlled by armed groups	Negotiating access for campaigns, use of actors accepted by all parties, rapid and targeted campaigns
Local partners with low capacity	Clear roles within a single function, mentoring, simplified tools, lasting capacity strengthening

What donors and evaluators look at

Speed: time between alert, confirmation, decision and the start of control measures.
Results: case fatality rate, duration of the outbreak, coverage of interventions, and not just the activities carried out.
Indirect effects: monitoring and protection of essential services.
The quality of coordination and the place of the Ministry.
Accountability to communities and protection from sexual exploitation and abuse.
Lessons learned: whether an after action review took place and was followed up.

Interview questions and elements of a strong answer

"Describe how you would organise the daily response meeting." Fixed order, limited duration, data prepared in advance, decisions with people responsible and deadlines, rapid minutes, role of the Ministry.
"Cases have been falling for three days. Is the outbreak under control?" Reporting delay, date of symptom onset, completeness, case-finding effort, new areas; conclude only after several incubation periods and with stable surveillance.
"How do you protect essential services during an outbreak?" List of priority services, tracer indicators with an alert rule, IPC, triage, separate patient flows, temporary staff, communication, adaptations to service delivery.
"How do you prepare the exit from an emergency programme?" Framework by health system building block, harmonised and gradually decreasing incentives, integration of data and procurement, advocacy on financing, readiness indicators, follow-up after departure.
"What makes a good after action review?" No-blame climate, comparison of planned and achieved, causes, a few recommendations with people responsible and deadlines, follow-up in the contingency plan.

Key references

WHO, Emergency Response Framework (ERF), current edition.
WHO, Maintaining essential health services: operational guidance for the COVID-19 context (2020), applicable by analogy to other outbreaks.
WHO, Minimum requirements for infection prevention and control programmes (2019).
WHO, Guidance for after action review (AAR) (2019) and the simulation exercise manual.
WHO, International Health Regulations (2005) and the IHR Monitoring and Evaluation Framework.
WHO, guidance on measles outbreak response and measles surveillance.
WHO, Everybody's business: strengthening health systems to improve health outcomes (2007), the six building blocks framework for health systems.
OECD, DAC Recommendation on the Humanitarian-Development-Peace Nexus (2019).
Global Health Cluster, Health Cluster Guide (2020).
CHS Alliance, Groupe URD and Sphere Association, Core Humanitarian Standard on Quality and Accountability (2024 revision).