COVID-19 & PEPFAR: Implications for the Future

Key Points

  • COVID-19 has the potential to deeply impact PEPFAR countries, especially those in sub-Saharan Africa and, as such, affect PEPFAR’s future trajectory.
  • As the largest U.S. global health program, PEPFAR is in a unique position to respond to COVID-19, but the outbreak also raises urgent new questions for PEPFAR, as well as underscores existing challenges.
  • PEPFAR has moved to respond quickly, accelerating prior strategies that could serve to minimize disruption and promote continuity of HIV care, such as multi-month dispensing of antiretrovirals; implementing new strategies, such as telemedicine; and allowing for some program flexibility in reporting requirements, staffing, and funding re-allocation.
  • Despite these steps, there are likely to be additional disruptions and need for further guidance, flexibilities and, potentially, new resources for PEPFAR which, to date, has not received additional support through the emergency measures passed by the U.S. Congress.


The potential for the COVID-19 pandemic to significantly affect the health and development of low- and middle-income countries (LMICs), particularly those in sub-Saharan Africa, has serious implications for PEPFAR, the President’s Emergency Plan for AIDS Relief. PEPFAR is the U.S. government’s flagship global health effort, credited with saving millions of lives and helping to change the trajectory of the global HIV epidemic. As of May 17, coronavirus cases have been reported in all PEPFAR countries1, with cases rising rapidly in some (see Table 1), and many are in lockdown or have instituted other social distancing measures. Most of these countries lack robust health systems and have limited preparedness and readiness capacity to respond to COVID-19. Given PEPFAR’s large country footprint, expertise and country infrastructure, the program is in a unique position to respond to COVID-19.

However, the outbreak also raises urgent new challenges for the program, as well as amplifies existing ones, given the potential for it to halt or even reverse hard-won HIV-related gains and alter the global health landscape. While PEPFAR has taken steps to respond to the outbreak, it is still unclear if these will be enough or if additional measures will be taken. To date, while emergency funding has been provided for certain global efforts and to domestic HIV programs by the U.S. Congress, no new resources have been provided to PEPFAR. As COVID-19 continues to impact the countries within which PEPFAR operates, this issue brief examines the potential implications for PEPFAR, the steps the program has taken to respond to the outbreak, and issues at stake.

Table 1: COVID-19 Cases in 25 PEPFAR Countries


# of COVID-19 Case
(as of May 17, 2020)

Angola 48
Botswana 25
Burundi 23
Cameroon 3,105
Côte d’Ivoire 2,109
Democratic Rep. of the Congo 1,455
Dominican Republic 12,314
Eswatini 203
Ethiopia 317
Haiti 456
Kenya 887
Lesotho 1
Malawi 70
Mozambique 137
Namibia 16
Nigeria 5,959
Rwanda 292
South Africa 15,515
South Sudan 290
Tanzania 509
Uganda 227
Ukraine 18,291
Vietnam 320
Zambia 753
Zimbabwe 44
Total 63,366
NOTES: Includes 25 countries required to develop PEPFAR Country Operating Plans (COPs). Includes confirmed and presumed positive COVID-19 cases.
SOURCE: KFF. COVID-19 Coronavirus Tracker.

PEPFAR Snapshot

PEPFAR is funded at approximately $5 billion per year (not including contributions to the Global Fund to Fight AIDS, Tuberculosis and Malaria), making it the largest U.S. global health program and largest in the world devoted to a single disease. As of September 2019, PEPFAR is estimated to have provided life-saving antiretroviral medications to more than 15 million people, supported testing services for nearly 80 million, and prevented more than 2.6 million babies from being born with HIV.

While PEPFAR support reaches more than 50 countries, the program focuses most of its efforts on a subset of 25 countries.2 These 25 countries represent nearly 65% of people living with HIV (see Table 2). PEPFAR activities focus on expanding access to HIV prevention, treatment, and care interventions. These include provision of HIV testing, antiretroviral treatment, pre-exposure prophylaxis, voluntary male circumcision (VMMC), condoms, and prevention programming focused on certain populations, including adolescent girls and young women. PEPFAR also provides broader health systems support in countries, including investments in health workforce and laboratory capacity.

While significant progress has been made, prior to the outbreak, only a limited number of PEPFAR’s countries were on target to meet global HIV milestones, including the UNAIDS 90-90-90 targets (by 2020, 90% of people with HIV would know their status; 90% of people diagnosed with HIV would be on treatment; and 90% of those on treatment would be virally suppressed), or PEPFAR’s own goal of achieving epidemic control by 2020 (defined by PEPFAR to be when new HIV infections fall below deaths from all causes among people with HIV). Other challenges facing PEPFAR that pre-date the outbreak include:

  • Concern about U.S. funding fatigue amidst a growing global funding gap;
  • Promise versus reality of domestic resource mobilization;
  • Interdependence of PEPFAR’s and the Global Fund’s successes and donor coordination more broadly;
  • How to optimally reach marginalized populations and those most at risk for HIV; and
  • Converging timelines of the expiration of PEPFAR’s current strategy, the next U.S presidential and congressional elections, and the lead-up to PEPFAR’s next reauthorization.
Table 2: HIV Indicators for 25 PEPFAR Countries
Treatment Cascade
Country Number of People Living with HIV
HIV Prevalence
HIV Incidence-to-Prevalence Ratio
HIV Incidence-to-Mortality Ratio
% People living with HIV who know their status
% People living with HIV receiving ART
% People living with HIV who have suppressed viral loads
HIV Incidence per 1000 Population
Angola 330,000 2 8.45 1.71 42 42 1.01
Botswana 370,000 20.3 2.31 1.24 91 83 81 4.36
Burundi 82,000 1 2.03 0.63 80 0.16
Cameroon 540,000 3.6 4.37 1.04 74 52 1.02
Cote d’Ivoire 460,000 2.6 3.67 0.79 63 55 41 0.7
Democratic Rep. of the Congo 450,000 0.8 4.13 1.1 62 57 0.21
Dominican Republic 70,000 0.9 3.92 1.72 82 56 37 0.26
Eswatini 210,000 27.3 3.78 2.03 92 86 81 8.62
Ethiopia 690,000 1 3.28 1.48 79 65 0.24
Haiti 160,000 2 4.63 1.9 67 58 0.69
Kenya 1,600,000 4.7 2.94 1.26 89 68 1.02
Lesotho 340,000 23.6 3.87 1.29 86 61 57 7.8
Malawi 1,000,000 9.2 3.65 2.04 90 78 69 2.28
Mozambique 2,200,000 12.6 6.64 2.05 72 56 5.25
Namibia 200,000 11.8 3.05 1.51 91 92 87 2.82
Nigeria 1,900,000 1.5 6.57 1.73 67 53 42 0.65
Rwanda 220,000 2.5 1.59 0.86 94 87 74 0.29
South Africa 7,700,000 20.4 3.08 1.88 90 62 54 4.94
South Sudan 190,000 2.5 9.93 1.71 24 16 1.56
Tanzania 1,600,000 4.6 4.64 2.13 78 71 62 1.41
Uganda 1,400,000 5.7 3.82 1.56 84 72 64 1.4
Ukraine 240,000 1 5.26 1.69 71 52 48 0.28
Vietnam 230,000 0.3 2.48 1.01 65 0.06
Zambia 1,200,000 11.3 3.89 1.94 87 78 59 2.97
Zimbabwe 1,300,000 12.7 2.93 1.34 90 88 2.79
Global 37,900,000 0.8 4.6 1.71 79 62 53 0.24
Global Target <3.0 <1 90 81 73 <1
# Countries Meeting Target 6 3 7 5 4 10

NOTES: Includes 25 countries required to develop PEPFAR Country Operating Plans (COPs). HIV data is for all ages unless otherwise specified. HIV prevalence data is for adults (ages 15-49). Percentages for the treatment cascade global targets are based on the 90-90-90 global targets.
SOURCES: U.S. Department of State, “Where We Work — PEPFAR” webpage, UNAIDS, AIDSInfo database, accessed May 2020. UNAIDS, Global AIDS Update 2019, December 2019. UNAIDS, “Ratio of new HIV infections to number of people living with HIV improving”, April 2020. UNAIDS, “Making the End of AIDS Real: Consensus building around what we mean by epidemic control”, October 2017.


COVID-19 has introduced particular challenges for the HIV response. First, while there is no evidence that people with HIV are at greater risk of SARS-CoV-2 infection, the virus that causes COVID-19, those with underlying health conditions, including uncontrolled HIV, are at greater risk of developing more severe disease if infected. Second, the very health systems and services that people with and at risk for HIV rely on could be disrupted, potentially affecting access to and continuity of critical medications, care, and other services. Third, lockdowns and other social distancing measures may also affect the ability of those with HIV to access services or exacerbate factors that put people at risk for HIV, including interpersonal and/or gender-based violence (IPV/GBV). New modeling estimates from the WHO and UNAIDS show that there could be half a million additional deaths from AIDS-related illnesses and significant increases in mother-to-child HIV transmission in sub-Saharan Africa if more is not done to mitigate service interruptions.

There are already reports from PEPFAR3 and the Global Fund to Fight AIDS, Tuberculosis and Malaria of interruptions, delays, and other challenges in the HIV service ecosystem in developing countries. These include:

  • Disruptions in supply chains for antiretrovirals, rapid tests, and other key commodities related to HIV services;
  • Reductions in HIV program personnel due to evacuations or redeployment to address COVID-19; and suspension of some prevention services, such as voluntary medical male circumcision;
  • Anticipation of increased use of laboratory facilities and lab staff for SARS-CoV-2 testing, which could impact HIV testing and lab capacity;
  • Lack of personal protective equipment (PPE) for health workers.
  • Concerns that physical distancing measures and health system pressures will prevent people with and at risk for HIV from seeking services, including treatment and testing, and about the potential for clinic closures;
  • Barriers to effective telehealth services, especially for youth; and
  • Concerns about potential food insecurity and resulting poor nutrition, which can negatively affect antiretroviral therapy and can be particularly detrimental to pregnant and breastfeeding women.

PEPFAR’s Response to COVID-19

PEPFAR has identified four key priorities to guide its programming during the outbreak: ensuring continuity of care for people living with HIV, particularly antiretroviral treatment; leveraging PEPFAR’s infrastructure to respond to COVID-19; reducing risk of exposure to staff and clients; and providing program flexibility.

PEPFAR also began providing technical guidance to the field, first released on March 20, and updated regularly. The guidance addresses multiple areas, including: maintenance of antiretroviral treatment; HIV testing; prevention, including provision of PrEP, especially for those who are most vulnerable; particular needs of women, children and families; co-infection/ co-morbidities (e.g., tuberculosis); integration of services, such as HIV and family planning; IPV/GBV; and supply chain challenges and laboratory capacity issues (see Table 3). It provides a number of strategies that can be used by country and regional teams to adapt to the new realities of COVID-19.

Some are strategies PEPFAR has already been working to prioritize and are now being accelerated by the outbreak, such as multi-month dispensing (MMD) of antiretrovirals and health care worker (HCW) task shifting/sharing. These are part of PEPFAR’s larger move to differentiated service delivery, an approach to providing services that aims to meet the diverse needs of clients, while also reducing the burden on health facilities and improving health outcomes. Others are designed to respond to the acute situation of COVID-19 and reduce the risk of transmission, such as encouraging telehealth, cancelation of most in-person activities, and health care worker re-training in Infection Prevention and Control (IPC) and training on COVID-19. The guidance also indicates where flexibilities are permitted, including extensions of reporting periods, and indicates that requests to utilize HIV resources to also respond to COVID-19 can be made.

Table 3: PEPFAR’s COVID-19 Technical Guidance – Summary Of Key Provisions
Program Area/ Activity Key Provisions
General Facilities should minimize patient contact and reduce non-essential visits.
Clinics to consider staggering appointments and streamlining clinic flow; HIV patients should be seen in clinics that are dedicated for HIV treatment.
Telehealth (e.g., phone calls, SMS, WhatsApp, social media, and other digital platforms) should be used to communicate with HIV clients.
Facilities should maximize 6-month refills for ARVs where stock is available.
Clients should preferably receive drug supplies (e.g., ARVs, PrEP, HIV self-tests, other medicines for chronic conditions) outside of the facility setting (e.g., home deliveries, community or private pharmacies, pop-up pharmacies, automated lockers, or community pickups).
Additional steps should be taken to prepare for clinic closures.
Beyond any Chief of Mission directive, involvement in larger U.S. government COVID-19 response should be based on and limited to the intersection of HIV, HIV/TB, and COVID; PEPFAR Coordination Offices should stay abreast of ways in which PEPFAR program investments are being leveraged for the larger U.S. COVID-19 response and potential adaptations necessary to implement the PEPFAR program safely; PEPFAR Coordination Offices are not responsible for coordinating the larger U.S. COVID-19 response.
Human Resources for Health PEPFAR-supported health care workers (HCWs) should be prepared to continue to deliver essential HIV services.
Staff should be prepared for task shifting/sharing of essential services where allowed and be prepared to be repurposed or redeployed, including to enable provision of services outside of facilities; staff should work with local governments to allow emergency task-shifting where formal policies are not in place.
Depending on role, HCWs should be trained to screen HIV patients for COVID-19 and refer for testing and treatment based on in-country guidance for COVID-19 cases.
HCWs should receive refresher training in Infection Prevention and Control (IPC) and steps should be taken to protect their safety (e.g., secure authorization from local authorities for continued work, support staff to avoid public transportation, reduce in-person contact).
Limit home visits to those “absolutely essential.”
Direct HCW-patient interactions for HIV services should not take place where routine adequate PPE is not available (e.g., gloves).
HIV Treatment Accelerate and complete scale up of 3 to 6 multi-month dispensing (MMD) of ARVs, where available.
ARV distribution for all people living with HIV should be decentralized.
Phone or electronic follow-up encouraged to support adherence/assess side effects for those initiating treatment, to continue peer support for youth, and for other purposes related to HIV treatment.
Routine viral load monitoring in stable patients may be delayed.
HIV Prevention Packaging of condoms and lubricants, and at larger than normal quantities, should be supplied to extent possible; distribution points should be modified to reflect social distancing.
PrEP should continue as part of comprehensive prevention; MMD should be allowed.
New VMMCs may be delayed or paused, depending on host government guidance/policies on social distancing; post-operative follow up should continue.
Phone and digital platforms should be utilized for general HIV prevention services, as well as for PrEP and VMMC follow up.
HIV Testing Adapt HIV testing services to host country government directives or policies on social distancing.
Maximize use of self-testing outside of the clinic setting through decentralized distribution approaches (e.g., peer home delivery, private/community pharmacies).
Prioritize clinical-based testing for those most in need (e.g., in antenatal settings, diagnostic testing for individuals presenting with suspected HIV, individuals with TB/STIs/malnutrition; early infant diagnosis (EID) detection, passive partner/index/family testing, in certain key population programs).
Testing should not take place where routine adequate PPE is not available (e.g., gloves).
Recommended recency testing be temporarily paused at health facilities and laboratories.
Shortages of rapid test kits have been reported.
TB Programs should continue to screen and test for TB in high prevalence areas and consider testing for both TB and COVID-19 in people living with HIV, especially in people presenting with fever and cough.
PEPFAR-supported TB contact investigations should make efforts to use mobile/virtual platforms; community-based testing and active TB case-finding strategies among people with HIV should follow local/national COVID-19 guidance on movement restriction/social distance/continuity of operations; if mobile and virtual platforms cannot be used and it is not safe for HCWs to conduct contact investigations in the community, contact-tracing/case-finding for TB may need to be deferred.
People with HIV should be provided with the full or remaining course of their drugs for TB-HIV or drugs for TB prevention.
Phone consultations for people with HIV-TB should be used, where possible.
Women’s Health Voluntary family planning services continue as an essential service.
HIV services integrated with contraceptive services should be streamlined to avoid patient visits to facilities or optimally use time when in clinic.
Multi-month provision of oral contraceptives and condoms should be provided and optimal schedules for long-acting contraceptives should be developed between client and provider (note: PEPFAR cannot be used to procure contraceptives; they are made available to PEPFAR-supported programs through collaboration with national family planning programs, USAID, and other donors).
Problems with contraceptive supply chains have been noted; country teams advised to include contraceptives on lists of essential drugs allowed into countries while shipments are restricted; integrating FP and HIV supply chain management and distribution may also help ensure contraceptives are available for HIV-affected populations.
Cervical cancer screening outside of same-day/same-site ART clinical services should be limited; screening done as part of routine ART visit may continue; high-grade lesion treatment can continue.
Maternal Child Health Women should follow local/national guidelines for ANC testing; options to limit or reduce time spent in clinic settings should be considered (e.g., providing services in community settings, bundling services); regular retesting for HIV is encouraged, if feasible.
HIV self-testing can be used for pregnant and breastfeeding women; women screening positive should be fast-tracked for confirmatory testing and treatment services.
PrEP should continue to be offered and MMD should be considered.
Consider offering newborn prophylaxis in case of home/community births.
EID should continue as an essential service with proper precautions.
Expand phone/SMS support to mothers and infants.
DREAMS Contact with DREAMS participants should be maintained via phone/SMS/WhatsApp/digital platforms, depending on country and local context.
Group-based activities should follow local guidelines for mass gatherings.
Where feasible, facility-based DREAMS services should be offered in community with appropriate social distancing.
IPV/GBV Teams should advocate with host governments to designate child protection and GBV responders; work with local entities and donors to update directories of response services; ensure that PEPFAR staff have information on resources and can support clients experiencing violence.
Children Many stipulations noted above apply to children and the guidance outlines additional recommendations given the special treatment, testing, and prevention needs of children.
Orphans and Vulnerable Children (OVC) activities can continue and can be conducted virtually, including for treatment literacy and adherence support, linkages to food supplementation/assistance, hygiene supplies, and distance learning opportunities; staff encouraged to incorporate COVID-19 prevention messaging and resources, per host country government guidelines, into virtual support to households; enrollment can continue to extent possible and certain populations should be prioritized, including children and adolescents living with HIV; HIV-exposed infants; and infants, children, and adolescents exposed to abuse, harm, or violence.
Laboratory Some countries are experiencing delays for HIV test kits and consumables; orders should be placed at least one month earlier than usual.
Due to recent WHO and FDA guidance on emergency use authorization for HIV viral load, EID, and TB-related instruments for SARS-CoV-2 testing, there is potential for increased demand on diagnostic networks; teams should anticipate increased use of instruments, facilities, consumables, and PPE for COVID-19, HIV, and TB-related testing and prepare for staff diversions or reductions in lab and other staff.
Laboratories should prioritize testing based on local policies and needs; HIV-related testing should be prioritized for certain populations (e.g., EID, viral load services for children and pregnant and breastfeeding women, non-virally suppressed adults).
If HIV and COVID-19-related testing need to be conducted on same instrument, SOPs for testing prioritization should be developed in collaboration with host country government and other stakeholders.
Use of existing national laboratory capacity, systems, and networks for COVID-related testing encouraged; funding dedicated for HIV and TB testing should not be reallocated for COVID-19; any additional costs for COVID-19 testing should be paid using country-specific COVID-19 supplemental funds from other sources.
Supply Chain/Commodities Country programs advised to assess current stocks of antiretrovirals and develop distribution plans with goal to distribute drugs so each client has enough for at least 3 months; PEPFAR working to ensure HIV commodity supplies; USAID coordinating with Global Fund to Fight AIDS, Tuberculosis and Malaria to prevent stock outs; country teams should work with host country governments to ensure MMD policies communicated to providers, facilities, pharmacies, and supply chain actors.
Delays expected for ARVs due to majority of U.S.-FDA approved ARV manufacturers in India; facilities have experienced interruptions due reduced capacity and logistical challenges during lockdown.
Should additional stock be necessary for acceleration of 6-month MMD, teams should notify proper U.S. government staff.
PEPFAR cannot ensure appropriate and adequate supply of PPE; teams asked to seek alternative sources.
NOTE: This table highlights a selection of issues; see guidance for more detail.
SOURCE: PEPFAR. PEPFAR Technical Guidance in Context of COVID-19 Pandemic (May 13, 2020).

While the guidance is being regularly updated to address emerging issues, there are potential gaps or questions that exist. For instance, the guidance calls for an acceleration of antiretroviral MMD and, while it notes the challenges in achieving MMD goals for people with HIV in an expedited timeframe, it will be important to monitor how supply chain disruptions, lockdowns/restrictions in movement, and the rapid scale-up will impact MMD across populations and countries. Additionally, the extent to which decentralization and telehealth can be implemented in all settings, especially those with hard-to-reach populations, will be important to assess as well and may require other measures to support continuity of care. The guidance also calls for staff in health care settings to have proper personal protective equipment (PPE), although it does not indicate these can be secured amid shortages and restrictions on purchasing with U.S. assistance dollars.

PEPFAR’s responses also will depend upon host government approaches to COVID-19 mitigation and ensuring the continuity of HIV services during the outbreak. To date, the governments of several PEPFAR countries have issued their own guidance for HIV services amid the pandemic. Further, while PEPFAR has stated that program flexibility is a key goal at this time, there may be a need for more specificity about what is permitted. Finally, as PEPFAR works to maintain its current levels of service, particularly antiretroviral treatment, amid the new challenges of COVID-19, there could be considerable resource implications. While Congress has provided emergency COVID-19 funding to domestic HIV programs, it has not yet provided such funding to PEPFAR.

Questions Ahead

Despite the ongoing uncertainties regarding COVID-19’s impact in PEPFAR countries, it is highly likely that there will be significant implications for PEPFAR in both the short- and long-term. Some of these pre-date COVID-19 but are exacerbated by the outbreak; others are new concerns and challenges. Key questions to consider include:

  • What guardrails and warning systems can be put in place to help ensure the needs of people with HIV, particularly for antiretroviral treatment, are being met in real time as the COVID-19 outbreak worsens?
  • Will additional flexibilities, or clarification about existing flexibilities, be provided, including around the ability to reallocate current budgets?
  • Will additional resources be provided and how far will they go in meeting needs? How will those resource needs be quantified?
  • How will the decentralization of services and responses to COVID-19, including telehealth, carry forward after the pandemic?
  • How can the PEPFAR platform be leveraged to respond to COVID-19 without affecting HIV services? Can marginal investments be made in PEPFAR’s infrastructure, such as its laboratory networks and equipment, that are more cost-effective than building new systems to respond to COVID-19?
  • Will HIV trajectories in PEPFAR countries be impacted? Will ground be lost?
  • Will the larger landscape of HIV donor funding, which was already strained, be further impacted?
  • What does this mean for shifts to domestic HIV funding (which has been an increasing priority for PEPFAR and the U.S. government more broadly)? Are transitions away from PEPFAR funding by countries even more unlikely now, depending on the economic damage done by COVID?
  • How will COVID-19 contribute to and shape PEPFAR’s future role, including tensions between a laser focus on HIV and a broader focus on building health systems in PEPFAR-supported countries?

As the pandemic continues to unfold and health systems are tested and pushed further than most countries have experienced in modern history, the impact of COVID-19 on people with and at risk for HIV, and the programs and systems that serve them, will come into focus, as will the implications for PEPFAR. Should PEPFAR’s early response to COVID-19 be sustained, leveraged, and adequately resourced, it could help to bolster protections for people with HIV during the pandemic and contribute to the broader response in countries. On the other hand, the pandemic could potentially reshape PEPFAR and the broader HIV policy landscape for the years to come.

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