Kenya’s Immunization System in the Post-Covid World

Report by Michaela Simoneau and Katherine E. Bliss

The Covid-19 pandemic risks undermining the successes of immunization programs in the Republic of Kenya, which has been on track to begin transitioning from support from Gavi, the Vaccine Alliance, and begin fully self-financing vaccine purchases by 2027. With attention to critical health system reforms and assistance from key partners, including the United States, Kenya can continue strengthening its immunization programs, respond effectively to the pandemic, and play an important role in protecting regional health security.

Staff members of the Kenyan Red Cross deliver hand disinfectants to residents to curb the spread of the COVID-19 coronavirus at Mathare slum in Nairobi, Kenya, on May 1, 2020.  | PATRICK MEINHARDT/AFP via Getty Images

A Platform Beyond Pandemic Recovery

At the start of 2020, the Republic of Kenya’s immunization program was on a positive trajectory. After several years of sustained economic growth, Kenya was preparing to begin reducing its support from Gavi, the Vaccine Alliance, and fully self-financing its domestic vaccine purchases by 2027. This long-anticipated transition was expected to mark an important step for Kenya in reducing its reliance on foreign aid and cementing its status as a growing economic power in East Africa

But then the first cases of Covid-19 were reported in Kenya on March 12, with more than 33,000 confirmed cases at the time of publication. Due to economic dislocations resulting from the suspension of trade and shelter-in-place orders, along with disruptions to health services, including routine immunizations, Kenya’s Gavi transition timeline is facing uncertainty.

Trucks wait in a line on the road to enter Uganda in Malaba, a city bordering with Uganda, western Kenya, on April 29, 2020.

Trucks wait in the town of Malaba on the Kenya-Uganda border on April 29, 2020.

| BRIAN ONGORO/AFP via Getty Images

Despite years of progress in improving immunization coverage nationwide, Kenya still faces enduring subnational disparities. These gaps may be exacerbated by the disruption of some vaccination services under the pandemic. And as the government seeks to mobilize resources to respond to the pressures of a plunging global economy, once secure domestic funding for immunization programs may be at risk.

A strong immunization system will be essential in any successful Covid-19 vaccine introduction and pandemic recovery, but it is also vital for ensuring Kenya’s successful Gavi transition and health security. With long-standing technical, economic, and diplomatic relationships with Kenya, the United States has the opportunity and strategic interest to help achieve these objectives and aid Kenya as it navigates the pandemic crisis and the path to vaccine self-sufficiency.

Women waiting in a clinic in Kenya's Western Province in September 2015. | Sala Lewis / CSIS

A Strategic Investment

Immunization is one of the most cost-effective investments in global health, saving $54 for every $1 spent and protecting millions of lives by preventing the spread of many of the world’s most deadly diseases.

Gavi, the Vaccine Alliance, is a public-private partnership launched in 2000. Engaging donor governments, the world’s lowest income countries, vaccine manufacturers, and philanthropic groups, Gavi helps countries purchase and distribute vaccines at low cost. 

Gavi promotes a model of sustainable development in which eligible countries gradually “transition” to fully self-financing their vaccine programs as they grow economically and move past the eligibility threshold, currently an annual gross national income (GNI) per capita of $1,630. To date, 16 countries have fully transitioned from Gavi support.

A woman receives a vaccination in Kenya's Easter province. | Sala Lewis / CSIS

A woman receives a vaccination in Kenya's Easter province.

| Sala Lewis / CSIS

The United States has supported Gavi since its inception, recognizing the important role vaccines play in promoting health security, strengthening economic development, and contributing to regional political stability. With the U.S. government’s recent pledge of $1.16 billion to the Alliance for 2020 to 2023, the United States has reaffirmed its commitment to Gavi’s mission.

U.S. engagement with Gavi complements long-standing bilateral support for immunization programs, channeled primarily through the U.S. Agency for International Development (USAID) and the U.S. Centers for Disease Control and Prevention (CDC), as well as multilateral institutions such as the World Health Organization (WHO) and UNICEF.

A USAID sign on a wall in Kiberia, Kenya.  | Kalyan Neelamraju via Flickr

U.S. Support for Kenya’s Health Security

Kenya consistently ranks among the largest recipients of bilateral U.S. aid, with investment from the Departments of State, Agriculture, and Defense, USAID, CDC, and other agencies totaling $11.7 billion over the last 20 years. PEPFAR alone has invested $6.5 billion since 2004, supporting life-saving antiretroviral treatment for nearly 1 million people.

USAID’s annual commitments supporting Kenya’s reproductive, maternal, and child health programs, including routine immunizations, have steadily increased in recent years, reaching $40 million in 2018. And the decades-long partnerships between Kenya’s Ministry of Health and Kenya Medical Research Institute (KEMRI) with the U.S. Army Medical Research Directorate-Kenya (USAMRU), the CDC, and USAID, via their affiliated implementing partners, all play a role in strengthening Kenya’s immunization system.

U.S. Army Medical Research Unit – Kenya: supporting efforts to improve malaria diagnosis. | Rick Scavetta, U.S. Army Africa via Flickr

U.S. Army Medical Research Unit – Kenya: supporting efforts to improve malaria diagnosis.

| Rick Scavetta, U.S. Army Africa via Flickr

Beyond direct investments in health and development, the United States and Kenya share long-standing relations across a host of other strategic objectives, including trade, democracy, counterterrorism operations, and security. These partnerships are mutually reinforcing and can be used to further support Kenya as it prepares to transition from Gavi assistance.

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A Trajectory Toward Gavi Transition

Since 2001, Kenya has received over $500 million from Gavi, introducing almost every vaccine the Alliance supports.

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With its annual GNI per capita reaching $1,750 in 2019, Kenya has been preparing to enter the accelerated phase of Gavi transition in 2022, at which point it is expected to begin assuming a greater proportion of co-financing for Gavi-supported vaccines. To anticipate Kenya’s immunization needs and costs over this next period, the Ministry of Health has been working with Gavi and non-governmental organizations such as Jhpiego on a full portfolio planning process.

Recently, the Ministry of Finance established a formal working group to forecast its expected multiyear budget increases across Gavi, the Global Fund, and other multilateral partners that all require increasing co-financing requirements that are linked to annual GNI per capita-based eligibility thresholds. Accurately anticipating spending needs for vaccines and program costs is especially important, as Kenya’s persistently large birth cohorts mean the government will need to ensure a budget sufficient to immunize an increasing number of children each year as the population grows.

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In alignment with Gavi’s focus on equity in its 2021-2025 strategy, Kenya’s portfolio planning process will identify enduring gaps in coverage, particularly among frequently missed urban populations, to recommend where Gavi can provide additional support to strengthen the country’s immunization system and help ensure a successful transition.

The Ministry of Health has set up several technical working groups to benefit from the expertise of in-country partners, which include civil society organizations such as KANCO, inSupply, and PATH; bilateral partners such as the CDC and USAID; and multilateral organizations such as the WHO and UNICEF. This process is intended to help Kenya avoid the post-transition challenges of falling immunization coverage that some other countries have faced after moving away from Gavi financing.

A health care worker writes on a sample of a specimen bottle while a resident of Eastleigh waits in the queue to be tested during a mass testing exercise for the COVID-19 coronavirus in Nairobi on May 20, 2020. | SIMON MAINA/AFP via Getty Images

Immunization in the Time of the Pandemic

Universal Health Coverage (UHC) has emerged as a priority for Kenya over the past decade. It is a key element of the 2008 “Kenya Vision 2030” development strategy, and one of four pillars in President Uhuru Kenyatta’s flagship “Big Four” initiative. While Kenya still remains heavily reliant on donor funding for health programs, high-level interest in UHC has provided an opportunity to cement primary health care and routine immunization as core political priorities, prompting the government to double the immunization budget line item in 2020.

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The intensification of the Covid-19 pandemic in Kenya, including the diversion of health resources to outbreak response, has disrupted routine immunization services at the local level.

Many health care workers have been reassigned from routine immunization to emergency Covid-19 response. Thousands of health care workers have walked off the job, citing faulty personal protective equipment and unpaid salaries, among other grievances. In some cases, parents have avoided health facilities out of concerns that they or their children may be exposed to the virus. Civil strife and harsh enforcement of lockdowns over the course of the pandemic have also led families to avoid health clinics and other public facilities.

Kevin Gitau's mother (C) wears a mask with her son's name, who was killed by Kenyan Police during a nigh curfew, as she raises her fist in front of the Kenyan Parliament during their protest against police brutality in Nairobi on June 9, 2020.

Kevin Gitau's mother wears a mask with the name of her son, who was killed by Kenyan Police during a night curfew.


As Kenya approaches a presidential election in 2022, it also faces a potential resurgence of election violence, which has historically disrupted health services. Were Kenya to be transitioning from Gavi support and rolling out a novel Covid-19 vaccine amid these shifting power dynamics, that turmoil could exacerbate existing challenges in routine vaccine delivery.

Turkana women and children waiting for supplementary feeding for infants at a relief and health centre in northwestern Kenya. | SIMON MAINA_AFP via Getty Images

Kenya’s Devolution and Disparities

Although Kenya’s national immunization coverage has improved in recent years, there are significant disparities in regional immunization coverage, largely due to the uneven success of the government’s “devolution” of authorities under the 2010 constitution. Under devolution, most political, fiscal, operational, and administrative responsibility was delegated to 47 decentralized counties.

Starting in 2013, devolution also split responsibility for different elements of the immunization system. The federal government has maintained control of nationwide policy, procurement, and financing of vaccines themselves. However, commodities such as syringes and safety boxes are procured nationally but paid for by the counties. Under devolution, immunization operations were also split, with the national government delivering vaccines to regional warehouses but the counties responsible for transporting vaccines to local facilities for delivery.

As county officials’ management experience in implementing immunization programs has varied widely, so has success under devolution. While overall national immunization coverage rates continued to rise after the devolution, there has been backsliding in many of the lowest performing counties, which often prioritize other objectives over investment in health, such that some have not yet risen back to pre-devolution coverage levels.

Immunization Coverage Vs. Covid-19 Cases by County

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The interactive maps above show Kenyan counties' 2018 immunization coverage (left) side-by-side with their Covid-19 caseloads (right) as reported on July 27, 2020. A darker color indicates a higher volume of immunization coverage and reported Covid-19 infections. Vaccination coverage is represented by the third dose of diphtheria toxoid, tetanus toxoid, and pertussis containing vaccine (DTP3). Click on either map to see exact figures for each county¹

Historically underserved populations such as the urban poor, nomadic pastoralists in the arid northern districts, and refugees have been left acutely vulnerable by this devolution process.

Hotspots of regional instability, largely driven by the Al-Shabaab militant group in Somalia, have pushed hundreds of thousands of refugees into Kenya. While Kenya has often decried the burden of its refugee population, it has reliably supported refugee immunization services in official camps serviced by organizations including UNICEF, UNHCR, the International Organization for Migration (IOM), KEMRI, and the CDC. However, refugees are often overlooked by health services when they settle in urban areas.

For example, refugees living in the large, crowded cities of Nairobi, Mombasa, and Kisumu have access to fewer services, are less well documented, and are highly mobile, making them difficult to reach and easily lost by the health system. In fact, the pandemic has caused nearly three times as much disruption to routine immunization in urban areas as the rest of the country.

Kenya is a diverse, multilingual, multireligious country, and confidence in the government and the health system varies widely. Historically, some Kenyan people’s mistrust of vaccines has spanned from mild confusion, such as when parents questioned why polio vaccinators were making so many successive home visits, to aggressive opposition, as when the Catholic Church in Kenya claimed the HPV and tetanus vaccines were forced contraception. As the world looks forward to an eventual Covid-19 vaccine, many Kenyans still deny the existence of the coronavirus.

Samson Waithaka, (C) chats with a man by the road side as he rides his bicycle.

Samson Waithaka, (C) chats with a man by the road side as he rides his bicycle.

| SIMON MAINA/AFP via Getty Images

Kenya’s National Vaccine and Immunization Program is well equipped to respond to the realities of introducing a new Covid-19 vaccine, having conducted introductions of the pneumococcal and rotavirus vaccines and pilots of the yellow fever, meningitis, HPV, and malaria vaccines. It can also rely on key lessons learned from the Global Polio Eradication Initiative, including the importance of listening to community concerns and clearly communicating the risks and benefits of vaccines to instill community confidence, and can utilize the vast infrastructure that program has built over the past three decades.

Cultural performers from the Maasai tribe shelter in the shadow of a traditional building in the Maasai Mara National Reserve where their work of performing for visiting tourists has dwindled since the pandemic.  | TONY KARUMBA/AFP via Getty Images

Charting the Way Forward

Kenya’s network of in-country immunization partners has worked to coordinate their efforts as they adjust to the reality of devolution. Some players, such as the CDC, continue to work exclusively on national-level technical assistance. Others, including Gavi and USAID, focus their health systems support on select low-performing counties, working with the Ministry of Health with the support of partners such as UNICEF, John Snow Inc., Jhpiego, and KANCO.

During Kenya’s ongoing immunization portfolio planning process, the Ministry of Health will map out the types of activities for which it will request Gavi support during the 2021-2025 strategic period and beyond, including the introduction of a Covid-19 vaccine. Leading up to this, it will be important for U.S. partners to directly engage local officials in assessing where development partners are overlapping or where there are gaps in technical assistance, to better coordinate and rectify inequities in nationwide service delivery.

A nurse (R) talks with mothers at their home about polio vaccines.A nurse (R) talks with mothers at their home about polio vaccines. | YASUYOSHI CHIBA/AFP via Getty Images

A nurse (R) talks with mothers at their home about polio vaccines.

| YASUYOSHI CHIBA/AFP via Getty Images

Even if delivery capacity is in place, accessing and distributing an eventual Covid-19 vaccine will be critical for facilitating Kenya’s pandemic recovery. The Access to Covid Tools (ACT) Accelerator—through its vaccine pillar, COVAX, and the COVAX Facility—is one effort to pool resources from a global consortium of states and organizations to fast-track the development of Covid-19 vaccines and provide equitable access for all countries. The Gavi Advance Market Commitment (AMC) is intended to secure doses at low cost for dissemination in 92 low- and lower-middle-income countries (LMICs), including Kenya.

These cooperative global mechanisms build on the successes of past Gavi initiatives, such as the AMC for the pneumococcal vaccine, but they are still unproven, operating in a more competitive space and currently facing a significant gap in donor financing.

Therefore, LMICs such as Kenya are also hedging their bets by pursuing other solutions, such as a nascent bilateral deal with Russia and the African Union (AU) and Africa Centers for Disease Control and Prevention’s plan to scale up late-stage vaccine trials on the continent. In hosting local, reputable trials, Kenya would secure committed doses from manufacturers and help combat fears that the population’s vulnerabilities are being exploited by Western interests.

U.S. agencies and implementing partners can support Gavi and the Kenyan Ministry of Health during this period. The CDC could support future pilots of an electronic immunization registry and use of sub-county data in targeted jurisdictions to better track coverage among traditionally marginalized communities, as it did in one county in 2018. The long-standing U.S. Army-CDC-KEMRI partnership could also be mobilized to coordinate clinical trials and mass vaccination efforts.

An employee washes is hands and face inside a bicycle shop in Nairobi. | KABIR DHANJI/AFP via Getty Images

An Uncertain Economic Outlook

Recognizing the economic pressures of the pandemic, the Gavi Board moved in May 2020 to freeze countries’ eligibility statuses for 2020 and 2021. This decision may allow Kenya, and all countries benefitting from Gavi support, the time and flexibility to recover from the pandemic. However, if Kenya’s GNI per capita drops significantly in this next phase, the country’s entry into accelerated transition in 2022 could be postponed.

Africa as a whole is projected to suffer its first recession in 25 years, and the International Monetary Fund (IMF) predicts that Kenya’s GDP growth will drop from 5.6 percent in 2019 to just 1.0 percent in 2020. The tourism industry has seen its revenues cut in half, and the informal jobs sector, making up 80 percent of the workforce, has been devastated by lockdowns.

An electronics shop assistant watches on television Kenya's President Uhuru Kenyatta giving a state of the nation address on the coronavirus (COVID-19) pandemic.

An electronics shop assistant watches on television as Kenya's President Uhuru Kenyatta gives a state of the nation address on the coronavirus (COVID-19) pandemic.

| SIMON MAINA/AFP via Getty Images

In addition to the pandemic, Kenya is dealing with several compounding challenges. East Africa faces its worst desert locust outbreak in 70 years, forecast to cost $1.5 billion in damages by the end of 2020. The government, still reeling from recent corruption scandals, has been accused of misusing millions in pandemic relief funds. Furthermore, the government is struggling with its considerable debt service—nearly a third of the budget—leaving very little fiscal room for a social safety net, even if the global economy rebounds quickly in 2021.

While Kenya has thus far resisted asking international creditors for complete debt forgiveness, a decision by the G20 countries to extend debt relief beyond the end of 2020 could give LMICs the space to respond to and recover from the pandemic. The United States has an opportunity to support such flexibility through its participation in multilateral commitments by the G7 and the G20.

A vaccination is received in the Eastern province of Kenya. | Sala Lewis, CSIS

Strengthening U.S. Partners for a Post-Covid World

Although Kenya’s Covid-19 caseload remains comparatively low at present, the number of reported cases across sub-Saharan Africa is rising, and the threat of surging cases, particularly among health care workers and senior health officials, remains ever-present.

A sustained, strategic response to the pandemic over the next three years will be critical to Kenya’s ability to both navigate the Covid-19 crisis and realize its Gavi transition. As Kenya works to address gaps in its immunization system, build community confidence in vaccines, and mitigate the risk of further political and economic turmoil, a strong routine immunization system can serve as the backbone that supports it through pandemic recovery and growth beyond Covid-19. While the impact of Covid-19 will be uneven across Gavi-eligible countries, Kenya’s efforts to proactively plan for its transition, despite these challenges, could provide guideposts for other countries anticipating transition from Gavi support in the future.

Child refugees receive their vaccination certificates after they were immunized at Dadaab refugee camp in northeastern Kenya. | ROBERTO SCHMIDT/AFP via Getty Images

Child refugees receive their vaccination certificates after they were immunized at Dadaab refugee camp in northeastern Kenya.

| ROBERTO SCHMIDT/AFP via Getty Images

The United States has a unique opportunity to muster its global technical, economic, and diplomatic relationships to support Kenya’s immunization program through this uncertain period. Three critical ways to do this are:

  1. Supporting the technical review of subnational capacities to identify and better serve frequently missed populations;
  2. Working through multilateral platforms to support financial flexibility for emergency response; and
  3. Contributing to efforts by the COVAX Facility, AU, and Africa CDC to help Kenya secure access to an eventual Covid-19 vaccine and facilitating its introduction.

Implementing the reforms necessary for Kenya to strengthen its routine immunization services and move toward fully self-financing vaccine procurement and distribution will help avert outbreaks of vaccine preventable disease and build toward a successful transition from Gavi support. These efforts, while helping to improve Kenya’s health outcomes, will also contribute to health emergency preparedness and regional resilience.

The Nursing Council of Kenya organizes dance sessions for health care providers to re-energize and uplift their sprits during this pandemic. | YASUYOSHI CHIBA:AFP via Getty Images

About the Authors

Michaela Simoneau

Program Manager, Global Health Policy Center
Photo of Michaela Simoneau
Michaela Simoneau is the program manager for the CSIS Global Health Policy Center, where she supports the polio, immunization, and nutrition portfolios. Prior to joining CSIS, she worked as an intern on projects concerning antimicrobial stewardship, conflict resolution, and human rights, and managed her university partnership with a grassroots non-profit organization in Coimbatore, India. Ms. Simoneau holds a B.S. in Biology and International Studies from Boston College, where she wrote her senior thesis on the Rohingya refugee crisis.

Katherine E. Bliss

Senior Fellow, Global Health Policy Center
Photo of Katherine E. Bliss

Katherine E. Bliss brings her expertise in the social sciences, Latin American studies, and international relations to her work analyzing U.S. government support for health programs in low- and middle-income countries. She is particularly interested in how political and cultural perspectives shape approaches to such global health challenges as HIV/AIDS; vaccine-preventable diseases; and access to safe drinking water and sanitation. Trained as a historian, Katherine spent the early part of her career teaching at the university level and publishing books and articles on gender relations and public health in twentieth-century Mexico. A Council on Foreign Relations International Affairs Fellowship enabled her to shift her focus to global health policy, placing her at the U.S. Department of State, where she worked on environmental health issues and the development of foreign policy approaches to pandemic preparedness. At CSIS, Katherine has previously served as deputy director and senior fellow within both the Americas Program and Global Health Policy Center, where she oversaw a multi-program project on the influence of the BRICS countries on the global health agenda and directed the Project on Global Water Policy. Her recent work has examined the health situation in the context of the Venezuelan political crisis and the challenges facing immunization programs within fragile or disordered settings. Katherine received her A.B. in history and literature, magna cum laude, from Harvard College and her Ph.D. in history from the University of Chicago. She completed a David E. Bell Fellowship at the Harvard Center for Population and Development Studies.

The authors would like to thank the following individuals for their generous contributions to this project:

  • Amb. Mark Bellamy, Senior Associate, CSIS Africa Program
  • Rachel Belt, Senior Country Manager, Kenya, Gavi, the Vaccine Alliance
  • Amos Chweya, Kenyan Senior Immunization Technical Officer, John Snow, Inc.
  • Sarah Grace, Producer and Multimedia Content Lead, iDeas Lab, CSIS
  • Gerald Macharia, Vice President, Regional Director for East and Southern Africa, and Country Director, Kenya, Clinton Health Access Initiative (CHAI)
  • Sheila Macharia, Director, Family Health Center of Excellence, and Senior Health Advisor, USAID Kenya
  • Thomas Mampilly, Center for Global Health, U.S. Centers for Disease Control and Prevention
  • Isaac Mugoya, Kenya Logistics Officer, John Snow, Inc
  • Stephen Mutwiwa, Country Director, Kenya, Jhpiego
  • Lizzie Noonan, Immunization Advisor, Bureau for Global Health, U.S. Agency for International Development
  • Christie M. Reed, Former Senior Immunization Advisor in Kenya, Global Immunization Division, Center for Global Health, U.S. Centers for Disease Control and Prevention
  • Angela Shen, (Capt, Ret, USPHS), Visiting Professor, Children’s Hospital of Philadelphia, and Drexel Dornsife School of Public Health
  • Lora Shimp, Technical Director, Immunization Center, John Snow, Inc.


A product of the Andreas C. Dracopoulos iDeas Lab, the in-house digital, multimedia, and design agency at the Center for Strategic and International Studies.