HIV-burden counties brace for donor transition as Sh66.9bn funding gap looms
The Comprehensive Care Clinic at Homa Bay County Teaching and Referral Hospital.
What you need to know:
- For years, global mechanisms, principally the PEPFAR, underwrote clinical staffing, commodity logistics, and specialised programmes across these regions.
As international health assistance faces sudden pullbacks and funding pauses, Kenya’s highest HIV-burden counties, including Homa Bay, Kisumu, Siaya, Migori, and Mombasa find themselves at a critical crossroads. For years, global mechanisms, principally the US President’s Emergency Plan for AIDS Relief (PEPFAR), underwrote clinical staffing, commodity logistics, and specialised programmes across these regions.
The gap left by international donors is monumental. According to a joint assessment published in April 2025 by Harm Reduction International (HRI) and the Kenya Legal & Ethical Issues Network on HIV and AIDS (KELIN), the countrywide PEPFAR funding pause forced approximately 28 clinics offering HIV services and Opioid Agonist Therapy to either close or drastically reduce operations. The report estimates that the Kenyan government would need to inject roughly Sh66.9 billion (USD 518 million) domestically to fully offset the total funding vacuum.
Addressing the transition from international assistance, primarily under USAID and PEPFAR, Council of Governors Health Committee Chair and Mombasa Governor Abdulswamad Shariff Nassir clarified that initial fears of an immediate collapse were mitigated by a managed, phased-out transition. He maintained that Kenya’s HIV response has avoided catastrophic disruption, attributing stability to a structural pivot toward direct bilateral agreements and local facility revenue retention.
“The support did not cease immediately. There was an initial pause, but following high-level engagements, including agreements signed during President Ruto’s visit to the US, the framework is shifting from subsidiary agency implementations to a direct government-to-government model. While these bilateral entities complete the transition, existing agencies are sustaining operations under a phasing-out approach. Counties are utilising their own Facility Improvement Funds to support ongoing requirements,” Nassir stated.
In Migori County, health leadership has leaned heavily on internal facility generation to keep basic commodity streams flowing. Caleb Opondi, Migori Health executive, explains that the county utilises 30 per cent of the funds generated through Facility Improvement Funds every month to purchase commodities.
“Among the commodities that these people receive, health facilities purchase them based on local need. We also have support from local partners here in Migori County; for instance, Luala Community Alliance has been donating supplies to us. They donate commodities, including those specifically required by individuals living with HIV,” said Opondi.
“Donor funding was not limited to commodities; several donors were also paying the salaries of health staff who were subsequently declared redundant and lost their jobs. Whenever our Public Service Board opens positions for recruitment, we give these affected workers priority. We have already absorbed quite a number because significant resources were spent on building their capacity, and we do not want those skills to go to waste. Additionally, where facilities recruit staff on contractual terms, we prioritise hiring these laid-off health workers,” added Opondi.
The official also noted that the county is fully utilising its 3,400 Community Health Promoters (CHPs), attached to 315 community units, to provide essential community-level support to people living with HIV and refer patients to facility-based experts for further clinical management. “While financial constraints remain an ongoing challenge even with allocations from the national government, we complement our budget using own-source revenue generated through our hospitals via Facility Improvement Funds, which has been our most crucial lifeline,” said Opondi.
In Kisumu County, the local administration established a dedicated County Transition Committee chaired by the Deputy Governor, Dr Matthew Ochieng, to steer preparedness and absorb hundreds of displaced healthcare providers into county employment. Furthermore, Kisumu restructured its funding pipelines via a direct cooperative agreement with the United States Centre for Disease Control and Prevention.
Dr Dickens Onyango, a public health expert and co-investigator for the Child Health and Mortality Prevention Surveillance Network, highlights that under this agreement, funding that previously went directly to partners now flows straight to the county government.
This initiative began by supporting 25 facilities in its first year and expanded to over 100 facilities by its third year. “These healthcare providers were hired with specialised skills they already possessed. Now employed directly by the county government, they are deployed across both HIV clinics and general medical duties. Alongside this workforce transition, we are driving service integration by combining HIV care with general health services so they no longer operate in standalone silos. This ensures that all facility staff can treat patients living with HIV and address other health needs seamlessly, regardless of who originally hired them,” said Dr Onyango.
Faced with constrained exchequer allocations, high-burden counties have universally turned to service integration, dissolving vertical, standalone HIV clinics, often referred to as Comprehensive Care Centres (CCCs), into mainstream outpatient departments. In Homa Bay County, where HIV and TB burdens remain among the highest nationally, health authorities view integration as an essential maturity milestone for the primary healthcare network.
Grace Osewe, Homa Bay Health executive, noted that while donor withdrawal left significant gaps, it challenged the county to take greater ownership by integrating HIV and TB services into broader county health planning and budgets.
“We are strengthening our healthcare workforce through continuous mentorship, supportive supervision, and capacity building while ensuring that HIV and TB priorities are reflected in our county planning and budget processes. We have also expanded our efforts to take services closer to communities through mobile diagnostic services, including chest X-ray for TB screening and sample networking from lower-level facilities to the hubs, which is particularly important for active TB case finding and early diagnosis,” said Osewe.
“Our message is clear: donor transition should not translate into interruption of services or loss of the gains Homa Bay has made in HIV and TB control. Counties must increasingly own, finance and integrate these services into sustainable primary healthcare systems and encourage the populations to enrol in SHA.”
Dr Osuri Kevin, Homa Bay’s chief officer for medical services, emphasised that physical layout changes match this operational shift. He explains that there is no longer a standalone department called a CCC or HIV clinic; instead, services and staff are fully integrated into a single outpatient department. “We have also trained our officers to keep pace with the evolving demands of HIV and TB care and increased exchequer allocations from our own-source revenue specifically dedicated to the HIV and TB programmes.
Beyond these main interventions, we have invested in facility infrastructure upgrades. For example, at Tom Mboya Memorial Level 4 Hospital, we constructed a new outpatient wing to create additional space and accommodate integrated care, allowing HIV patients and general outpatient clients to be seen seamlessly in the same location,” said Dr Osuri.
“We have also enacted local legislation through our county assembly to mainstream HIV services into law, ensuring guaranteed funding follows the policy. This legislative backing allows the county assembly to directly allocate domestic resources specifically for HIV and TB care. Simultaneously, we have expanded the role of our 2,954 CHPs. They are trained to deliver HIV, TB, and malaria services, assist with HPV vaccination drives, and trace mothers for clinical follow-up,” said Dr Osuri.
Addressing concerns that service integration might erode patient-clinician rapport or compromise care for issues like medication adherence and gender-based violence, which were solely covered under specialised HIV clinics, Dr Osuri stated that this has not been a problem. Patients continue to receive adequate consultation time because the county hired additional healthcare personnel, prioritising experienced workers previously deployed under partner organisations like MSF and LVCT Health. Absorbing these clinicians maintains continuity of care and ensures people living with HIV continue to see familiar faces.
In Siaya County, integration serves a parallel purpose of shielding patients from societal stigma. Dr Bob Awino, Siaya County’s HIV, AIDS, and STI activities coordinator, notes that transitioning from vertical, standalone clinics to a one-stop-shop chronic care model means all clients are seen by the same healthcare worker in one room, effectively eliminating the public identification of HIV patients.
With specialised link assistants and peer counsellors dropped by international partners due to financial cuts, counties are heavily delegating community-level tracking and mobilisation to community health promoters. Siaya County employs its promoters for door-to-door case identification and links patients to community-based organisations to drive economic self-reliance.
“We have conducted expanded capacity-building programmes for healthcare personnel. Previously, training was largely restricted to partner-funded programme staff, but we have now trained Ministry of Health healthcare workers directly so they can manage facility-level care. To sustain this, we established a cadre of county Trainers of Trainers comprised of MOH staff rather than partner-dependent trainers. Additionally, the county has absorbed a significant number of healthcare workers who were previously under the partner payroll,” said Dr Awino.
“Siaya is also aggressively pushing HIV clients to register with the Social Health Authority. By empowering clients economically through localised group training, patients can secure the financial stability required to pay upfront contributions for SHA. As a result, they can not only access basic HIV tests but also benefit from a wide spectrum of services,” said Dr Awino. He also noted that the county is currently using CHPs as community mobilisers to refer clients for malaria testing since regulatory frameworks still restrict them from performing direct rapid HIV diagnostic testing.
As international donors scale back direct financial support, Nairobi County has put a transition strategy into action guided by a formal roadmap approved by the governor’s office. A primary driver involves funding daily clinical operations through domestic healthcare revenue. By collecting 1.8 billion shillings in SHA payments since October last year, the county is deploying these local funds to cover daily operational expenses as donor agencies step out.
Dr Carol Ngunu, director of preventive and promotive health at Nairobi County, noted that high-volume centres serving up to 3,000 clients continue operating as standalone, dedicated HIV clinics, while smaller facilities have integrated HIV care directly into routine outpatient departments. “To support this integrated setup, regular hospital clinicians have undergone upskilling to manage multiple conditions in one place, eliminating parallel treatment systems,” said Dr Ngunu.
Following a decline in the donor-supported health workforce, the county upskilled existing county staff and absorbed nearly 600 health workers previously attached to partner-funded clinics. While these workers are not yet on the permanent county payroll, they have been transitioned into a county-managed, U.S. government-funded bilateral programme. “We continue to engage the U.S. government to sustain this arrangement while updating our official staff establishment to map personnel gaps and finalise a transition plan for their eventual absorption onto the county payroll,” said Dr Ngunu.
To safeguard commodity management and laboratory networks, the county launched an integrated sample referral system using facility-assigned motorbikes to transport patient specimens directly to testing facilities. Most receiving sites are government-run, including upgraded Level 5 county laboratories.
“There was a lot of support for EMR systems. However, Nairobi County has been able to work with DHA to get onto the TAIFA care platform and to take advantage of the hardware given by the national government. So we have been able to digitise the data, and we are in the process of making sure that we fully digitise the HIV data and have the cloud systems hosted under the DHA system and also under the county ICT servers,” she added.
While mainstream clinical care has largely survived through structural absorption and integration, specialised services for key populations such as harm reduction and opioid substitution therapy (OST) are experiencing profound operational fractures. OST is a medical treatment for opioid dependence that replaces short-acting illicit drugs like heroin with longer-acting, safer prescription medications, which lowers the frequency of injecting drugs and halves the risk of acquiring HIV. According to the HRI and KELIN findings, Kenya hosts an estimated 27,056 people who inject drugs, with an 11.3 per cent HIV prevalence rate within this demographic. While the Global Fund has continued support for needle and syringe programmes, PEPFAR historically shouldered the bulk of OST financing.
The withdrawal fallout is starkly evident. In Nairobi, the Ngara Methadone Clinic has maintained uninterrupted services thanks to healthcare workers supplied directly by the county government. On the other hand, the nationally managed Mathari MAT Clinic has faced severe disruptions due to stop-work directives, resulting in critical shortages of psychosocial counsellors and a complete absence of defaulter re-enrolment. In Kawangware, the NOSET drop-in centre, funded by PEPFAR through the Centre for International
Health Education and Biosecurity-Kenya, was forced to shut down entirely, leaving six peer educators on leave. With NOSET closed, the sole remaining operational drop-in centre in the immediate area is Support for Addictions Prevention and Treatment in Africa (SAPTA), backed by the Global Fund. Although SAPTA turns no one away, it has grappled with family planning commodity shortages, while HIV clients have faced nerve-wracking reductions in drug refills; slashing supplies from three-month windows down to a single month, alongside initial treatment interruptions for vulnerable tuberculosis patients.
The transition from donor-funded HIV programmes to domestically sustained services marks a pivotal moment for Kenya’s health system. While counties have demonstrated remarkable resilience through service integration, workforce absorption, and innovative use of local revenue, the path ahead remains uncertain. The success of this transition will ultimately depend on sustained political commitment, adequate domestic financing, and the continued strengthening of primary healthcare systems to ensure that the gains made in HIV control over the past two decades are not reversed.
