Finding children missed by immunization
How embedding short-cycle research within programme structures generates evidence that implementers act on in real time.
A vaccinator's view of community life in Sindh province, Pakistan.*
Across six countries, 25 embedded research teams worked with immunization programmes to generate and apply evidence in real time. This led to measurable improvements in programme implementation at subnational level, including increased adherence to vaccination schedules in Ebolowa district, Cameroon (from 64% to 85%), reduced response times to zero-dose alerts in a union council in Lahore, Pakistan (from 10 days to 3), and improved acceptability of vaccine services in Toamasina I and Mahanoro districts, Madagascar (from 56% to 86%). Additional studies informed more targeted outreach through geospatial mapping in Malawi and identified missed opportunities for human papillomavirus (HPV) vaccination within routine service delivery.
The challenge
Millions of children in Cameroon, Ghana, Madagascar, Malawi, Mozambique and Pakistan are missing routine vaccinations because immunization programmes face persistent challenges in finding and reaching zero-dose and under-immunized children, understanding the barriers they face, and adapting delivery strategies in real time.
The reasons are context-specific. In Madagascar, many caregivers of unvaccinated children were not opposed to vaccination, but were unable to attend clinics due to working patterns in agriculture and informal markets.
“If the schedule is adapted to our rhythm of life, we come without hesitation. It is the organization that blocks us, not the vaccination.”
In Malawi, unvaccinated children were found to be concentrated in specific locations that routine data systems could not identify.
Missed opportunities for vaccination also present challenges. In Dowa district, Malawi, adolescent girls were attending health facilities but were not consistently sensitized for HPV vaccination. In Pakistan, a large proportion of births in Quetta district take place in private facilities participating in government-supported schemes, while routine immunization services are primarily delivered through public-sector clinics, leading to missed opportunities for vaccination at birth.
These challenges are longstanding. However, the tools to analyse them with sufficient precision – and to translate that understanding into timely programme adjustments – have been limited. Routine data are often incomplete or insufficient for local planning. Researchers and programme managers frequently operate separately. Conventional research timelines do not align with operational decision-making cycles.
The Alliance's contribution
Through the Institutionalizing learning by mainstreaming embedded implementation research in country immunization programmes (MAINSTREAM) programme (2023–2025), the Alliance supported a shift in how evidence is generated and used within immunization programmes. The approach focused on embedding short-cycle, locally led implementation research within routine programme structures.
This was operationalized with six national mentor institutes across the participating countries (Cameroon, Ghana, Madagascar, Malawi, Mozambique and Pakistan) – including universities, public health institutes and non-profit research organizations. These institutes were already established within national health systems and had existing relationships with ministries of health and immunization programmes.
Each country began with a multistakeholder priority-setting process, involving national and subnational programme staff, researchers, civil society and community representatives. This ensured that research questions reflected operational needs rather than externally defined agendas. Open calls were used to identify 25 local teams of researchers and implementers, with a requirement for joint design and implementation.
Mentor institutes provided technical support to the local teams across the research cycle, including protocol development, ethics review, data collection and dissemination. They also supported teams to adapt to contextual disruptions, such as elections, insecurity and extreme weather events.
The approach also addressed gaps in communication between different levels of the system. Community health workers in Madagascar noted that they were only engaged during campaigns but had limited opportunities to contribute to problem identification and solution development between campaigns.
The results
Within the participating countries, the research generated findings that could be applied within ongoing programme cycles, as well as insights that reframed how key challenges were understood.
Cameroon: digital tools and appointment reminders
In Ebolowa district, a pilot across 15 health facilities combining SMS appointment reminders with digitalized vaccination schedules increased adherence from 64% to 85%, reaching 3330 children who had previously missed some or all vaccinations.
Adherence to vaccination schedules
Madagascar: clinic hours and caregiver rhythms
In Toamasina I and Mahanoro districts, adjusting clinic hours to align with caregivers' daily routines increased acceptability of vaccination services from 56% to 86%. This simple shift removed the structural barrier that was blocking engagement.
Acceptability of vaccine services
Malawi: geospatial mapping and HPV vaccination gaps
In Ntcheu and Mchinji districts, two projects applied geospatial modelling to identify the location of unvaccinated children at a much finer resolution than previously possible. While national survey data provided estimates at administrative cluster level, the modelling approach generated continuous spatial estimates, revealing localized clusters of zero-dose children that could not be identified through routine data. This provided a more actionable basis for planning and targeting services.
In Dowa district, findings on HPV vaccination showed that all eligible girls in the study area had accessed health services, yet 92% were not sensitized to the vaccine. Once offered the vaccine, 69% of girls were immunized. This indicated a missed opportunity within service delivery rather than a lack of access or demand.
Key finding: Systemic gaps in health worker knowledge about vaccine eligibility were the barrier – not demand or access.
Pakistan: real-time monitoring and vaccinator well-being
Lahore: digital dashboards for zero-dose alerts
A digital monitoring tool piloted in one union council reduced response times to zero-dose alerts from 10 days to 3 through the use of real-time dashboards and action tracking. This systemic change compressed the time between problem identification and implementation response.
Response time to zero-dose alerts
Malir: vaccinator well-being and workload support
Research focused on the working conditions of vaccinators. High workloads, difficult terrain and operational constraints were associated with reduced motivation and performance. An arts-based intervention using structured reflection was associated with improvements across several microplanning indicators, including identification of hard-to-reach communities.
This study reframed the problem: eliminating zero-dose communities requires attending to the health workers who deliver services.
Quetta: private-sector coordination gaps
Engagement with private health providers indicated that facilities delivering a large share of births had both capacity and willingness to provide vaccination services if integrated into programme delivery. The primary constraint was related to coordination and governance, not supply or demand.
Beyond individual studies
MAINSTREAM demonstrated that immunization programmes can strengthen their capacity to generate and use evidence iteratively. Priority-setting processes in all participating countries identified more questions than available resources could support, indicating sustained demand for this approach.
The findings are already informing programme planning, supervision and service delivery in the participating countries. More broadly, MAINSTREAM has shown that embedding research within national immunization programme structures can support more responsive, evidence-informed approaches to reaching children who are currently missed by immunization services.
The 25 country-based research teams represent a generation of implementer-researchers. The institutional relationships built during MAINSTREAM provide a foundation for sustained, iterative learning within national health systems.
Lessons learned
Short research cycles can work – if there is a programme willing to act on findings.
Embedding research within programme structures generates evidence that implementers can use in real time. MAINSTREAM demonstrated that short-cycle implementation research, when designed with operational partners, produces findings that are acted on rather than filed. The structural link between research and decision-making is as important as the evidence itself.
Operational disruptions are predictable – build in flexibility from the start.
Ethics approvals, elections, insecurity and extreme weather events compressed research timelines across multiple countries. The same contextual barriers that make zero-dose communities hard to reach for immunization services also make them harder to reach for research teams. Future programmes need contingency timelines, flexible mentorship arrangements, and the expectation – not the surprise – of disruption.
Mentor institutes are the structural backbone of the model.
Locally embedded institutions provided continuity, brokered trust between researchers and programme staff, and absorbed contextual shocks in ways external technical assistance cannot. The quality of country-level mentorship was the most consistent predictor of research quality and programme uptake. Investing in these institutions – not only in individual research projects – is what made the model function.
Multistakeholder priority-setting is not an administrative step – it is a condition for uptake.
Research questions generated through inclusive, locally led processes reflect operational realities and carry the commitment of programme staff to act on findings. Studies that answer questions nobody asked rarely produce change. The priority-setting process is where research relevance is determined.
Institutionalizing research capacity takes time and requires sustained investment.
MAINSTREAM's 25 country-based research teams represent a generation of implementer-researchers. Sustaining what has been built requires institutional commitment that outlasts any single programme cycle – in national systems, mentor institutes, and funding arrangements alike.