Testing & Surveillance: Uganda

This research and analysis was conducted by research partners at the Makerere University School of Public Health.

Introduction and Key Takeaways

Between March 21, 2020, and June 30, 2021, over 1.3 million COVID-19 tests were conducted in Uganda, with nearly 80,000 people testing positive. The country also recorded 1,023 confirmed COVID-19 deaths.¹ Substantial challenges in Uganda’s testing and surveillance systems persist, ranging from inadequate laboratory capacity and long test turnaround times to limited mortality and genomic surveillance. Despite these, Uganda leveraged the laboratory and surveillance capacity that it had developed for previous epidemics as well as innovative COVID-19-specific testing and surveillance strategies for its COVID-19 response. Since the start of the pandemic, Uganda has increased its testing capacity, partially through the scale up of rapid diagnostic tests (RDTs), introduced genotyping and serological surveys.

Uganda confronted a second and more deadly wave of COVID-19 in June 2021. The surge in cases was largely attributed to the spread of the more transmissible Delta variant (which was first identified in Uganda at the end of April 2021),³ the relaxation of mobility restrictions, and low COVID-19 vaccination coverage (fewer than 2 percent of Ugandans had been vaccinated).⁴ The country responded to this surge by implementing a 42-day complete lockdown and travel restrictions.⁵

The following findings are organized according to the Testing & Surveillance framework.

What was Uganda's Pre-Pandemic Context? How did it Respond to COVID-19?

Disease Outbreak Experience

Between 2000 and 2016, Uganda experienced eight public health emergencies of international concern: five outbreaks of Ebola virus disease, most recently in 2018 and 2019, and three outbreaks of Marburg virus disease. During the most recent Ebola virus disease outbreak, Uganda’s community surveillance program trained more than 10,000 health workers and village health teams on infection prevention and control, epidemic surveillance, and other aspects of outbreak response.⁶ Diagnostic testing and confirmation at the Uganda Virus Research Institute (UVRI) recognized only three cases of the disease and no secondary transmission was observed – a testament to the country’s public health emergency response capacity.

Assessment of Pre-Pandemic Preparedness

Uganda uses the Integrated Disease Surveillance and Response (IDSR) strategy to monitor and report on high-priority diseases—which now includes infectious diseases such as COVID-19. This integrated strategy facilitates the best and most efficient use of scarce resources. Uganda adopted this strategy in 2000 and began implementation in 2001.⁷ In 2011, Uganda replaced the older system for transmitting weekly surveillance data via paper-based reports, paid phone calls and short message system (SMS) messages, radio calls, and emails with a free SMS reporting platform.

According to the World Health Organization’s (WHO’s) 2017 Joint External Evaluation of Uganda’s International Health Regulations (2005) core capacities, Uganda had strengthened its capacity in surveillance, laboratory testing, emergency response operations, and risk communication. The evaluation noted that Uganda stood out as model of collaboration in response to health security threats, with an early warning system in place for both indicator- and event-based surveillance, well-equipped national reference laboratories, an efficient national specimen-transport system, and an active Public Health Emergency Operations Centre linked to all districts. The evaluation noted, however, that Uganda needed to expand multisectoral communication and coordination; finalize and validate standard operating procedures, plans, guidance, and tools in cross-cutting areas for emergency preparedness and response; and implement point-of-entry surveillance. The evaluation also recommended the establishment of an emergency fund to support the immediate investigation of disease outbreaks and comprehensive resource mapping for emergency response.⁸

Although the recommendations from the 2017 Joint External Evaluation were not fully implemented at the outset of the COVID-19 epidemic in Uganda, the Global Health Security Program had been strengthened to support the Ministry of Health improve these capacities. Examples include the launch of the RESOLVE project to provide technical support and funds and a strengthened laboratory network.⁹

What was Uganda's COVID-19 Response Strategy for COVID-19?

Because of its limited resources and constrained response capacity, Uganda focused its testing and surveillance strategy on individuals at high risk of contracting COVID-19: symptomatic people and their contacts, truckers and frequent international travelers, and exposed health workers. Following an Intra-Action Review by WHO in January 2021,¹⁰ health authorities in Uganda developed a resurgence plan for the June 2021–June 2022 period in response to the spread of the Delta variant and the surge of COVID-19 cases beginning in mid-April 2021. As part of that plan, Uganda reintroduced a lockdown in June 2021 and restricted travel from high-risk countries. It strengthened genomic surveillance and scaled up testing capacity by increasing the number of reverse transcription polymerase chain reaction (RT-PCR) labs, establishing GeneXpert systems at regional referral hospitals, and scaled the use of rapid diagnostic tests (RDTs).

Countries that do very few tests per confirmed case are unlikely to be testing widely enough to find all cases. The WHO has suggested around 10 – 30 tests per confirmed case a general benchmark of adequate testing.

What was Uganda's COVID-19 Testing Strategy? How did it Establish Testing Capacity?

Uganda’s testing strategy targets high-risk individuals, especially at points of entry and in border districts; symptomatic cases reported through community alerts; and contacts of confirmed cases, including health workers in COVID-19 isolation and treatment units.¹¹ Through 2020, Uganda relied solely on polymerase chain reaction (PCR) testing, with an emphasis on RT-PCR testing in a lab setting. The country began GeneXpert testing in July 2020 at border points of entry. RDTs were introduced into the country’s official testing strategy in October 2020, and in December 2020, Uganda began to pilot RDTs, as a screening test (for higher-risk people, such as hospitalized patients, symptomatic health workers, and quarantined individuals) in a limited number of facilities.

By June 2021, RDT kits were widely distributed and during the peak of the second wave of cases, all symptomatic cases that tested positive with an RDT were considered a confirmed case. At the time of publication, there were five RDTs in Uganda. Two of the five (Standard Q by SD Bisensor and Abbott Panbio) have been validated by the UVRI (a WHO and Africa CDC reference lab) and approved by the Ministry of Health. These were determined to have met WHO’s performance threshold of ≥ 80% sensitivity and ≥ 97% specificity. The other three (Innova, InTec, and LYHER) have passed the UVRI validation, but had not yet been approved by the Ministry of Health. Read more about the evolving use of RDTs in Uganda below.

Because Uganda has limited quantities of testing supplies, free COVID-19 tests are available only to people who qualify. As of June 2021, health workers qualify for free testing (RDT or PCR), while free RDT testing is provided at public health facilities for persons seeking care. Everyone else, including travelers, pays US$50-$65 for a test at a private laboratory.¹²

At the beginning of the pandemic, the government required isolation for confirmed cases of COVID-19 and quarantine for individuals who were contacts of confirmed cases. Both isolated and quarantined individuals were to be tested at least twice (and had to prove negative test results) before they could end isolation or quarantine. As community spread increased and testing costs grew, Uganda modified its testing strategy. In October 2020, follow-up testing at the end of isolation or quarantine was no longer recommended unless an individual continued to display symptoms of COVID-19.

Because Uganda’s testing strategy targets high-risk groups, case detection is suboptimal and many asymptomatic infections go undetected. The cost of tests (initially introduced at $65 per test in September 2020 before being lowered to $50 in October 2020) further reduced access among people ineligible for free testing, such as teachers and students, leading to underreporting among these populations. Additional data, such as excess mortality and serological surveillance data, help health officials better understand the disease burden in Uganda.

Early Implementation Lessons from the use of Rapid Diagnostic Tests (RDTs) in Uganda RDTs were introduced into the country’s official testing strategy in October 2020, and in December 2020, Uganda began to pilot RDTs, as a screening test (for higher-risk people, such as hospitalized patients, symptomatic health workers, and quarantined individuals) in a limited number of facilities. By June 2021, RDT kits were widely distributed and during the peak of the second wave of cases, all symptomatic cases that tested positive with an RDT were considered a confirmed case. During the initial pilot phases, RDTs were used for screening and results were only reported to the national lab database after confirmation with PCR. The official guidance on this changed on June 2, 2021, asking for positive RDT results to be uploaded to the Ministry of Health electronic Results Dispatch System (eRDS). This change was accompanied with a national-level training of trainers (and was followed by regional-, district-, and health facility- level trainings throughout the month of June 2021). Sixty trainers were deployed and certified over 500 end users across the country. While the scale of RTDs has facilitated faster turnaround times and enables clinicians to make rapid decisions, several challenges have been reported: Information management and real-time reporting has been suboptimal. RDTs were distributed to some health facilities that were not linked to the eRDS system, making real-time reporting a challenge. The investigation forms are complex and labor-intensive and often submitted with incomplete data. To address this, the Ministry of Health introduced an SMS-based reporting tool called mTrac and an internet-based reporting system called eLIF (electronic lab investigation form). Both have advantages and disadvantages (for example, mTrac is easier to use, but the type of data reported is limited; eLIF is more time-consuming and relies on the internet, but has a direct data pipeline with the eRDS, facilitating near real-time reporting). As of August 2021, 140 facilities across 70 districts were reporting RDT results via eLIF, and 450 facilities across 60 districts were reporting via mTrac in Uganda. Other challenges include adherence to eligibility criteria for RDTs, lower levels in trust among patients and health workers (compared to PCR tests), coordination of results with the private sector and quality concerns. For quality assurance, the UVRI plans to add proficiency testing for RDTs for COVID-19 which would involve regular retesting of 20 samples (10 negative and 10 positive).

Testing Value Chain

SOURCING TESTING SUPPLIES

As of June 2021, Uganda does not produce its own testing supplies. The Ugandan Ministry of Health procures testing supplies from all over the world; for instance, it gets personal protective equipment from China and PCR amplification reagents from Europe and the United States. Most testing supplies have been procured using donor funding or were donated.¹³

In March 2020, procurement of test commodities was done under a consortium composed of the WHO, Africa CDC, and Africa Society of Laboratory Medicine (ASLM). While the consortium helped to negotiate prices, there were often delays and countries complained about not receiving quantities ordered. Once manufacturing began to stabilize by September 2020, countries were able to get supplies directly from the manufacturers without going through a consortium.

Uganda has had to ration tests due to limited supply of complete testing kits (both globally, for supply chain reasons, and within Uganda). However, RDTs are under development in Uganda. An antibody RDT, expected to cost about US$1 and to give results in two to five minutes, was launched in March 2021 by Makerere University¹⁴ and will likely arrive on the market in 2022. To produce an initial batch of 2,400 tests, Makerere University partnered with Astel Diagnostics Uganda, a World Health Organization-certified manufacturer. It is important to note that these RDTs do not detect active infection. Furthermore, a “Rapid Airjump and RNA Amplification” (RARA) test developed by the Joint Clinical Research Centre was launched in April 2021 and was undergoing validation as of July 2021, with support from the government through the Presidential Scientific Initiative on Epidemics (PRESIDE). The kit uses saliva as opposed to nasal swabs, can be self-administered, and is minimally invasive. The Joint Clinical Research Centre has capacity to produce 100 kits per day (48 tests per kit) and plans to scale up manufacturing once the test has been approved.

TEST DELIVERY

Uganda leveraged existing commodity distribution systems to order and distribute testing supplies. It used the centrally coordinated electronic laboratory information management system, which supports ordering supplies through an electronic inventory management system, to order COVID-19 testing supplies online. This system also links more than 450 lab facilities (27.8 percent of all facilities), which enables electronic reporting of test results. Uganda distributed testing supplies from the National Medical Stores using the preexisting transportation network for lab samples. However, low production and delayed delivery limited the availability of supplies at the central level, so stockouts remained a challenge.

SAMPLE COLLECTION AND TEST DEMAND

Uganda improved access to testing by decentralizing services, increasing the number of sample-collection and testing sites, and widely publicizing them in the media and through Ministry of Health communications. Government campaigns, particularly through radio, television, billboards, and social media platforms such as Twitter and Facebook, increased community awareness of testing and prevention measures. During the second COVID-19 wave in 2021, Uganda established testing camps in Kampala, placed mobile labs in high-risk areas (such as crowded informal settlements in Kampala and border crossings), and improved testing capacity at Entebbe International Airport for incoming travelers. Testing was made free of charge for select groups (symptomatic cases, contacts of confirmed cases, and health workers) by late 2020. The community notification system and sample pickup from suspected COVID-19 cases improved access to testing and the testing turnaround time.

Despite these improvements, Uganda continued to face challenges related to testing access and demand, including inadequate personal protective equipment, high testing costs (US$65 for people ineligible for free testing), delays in setting up mobile labs, lack of trust in some testing labs (many people wanted their tests processed by UVRI despite a campaign that assured everyone of other labs’ quality), and community stigma due to misinformation.

SAMPLE DELIVERY

Uganda already had a sample-transportation network that it could leverage for the COVID-19 response. The system connects 97 percent of health facilities to testing labs. Over the course of the pandemic, measures were taken to improve the delivery system, such as increasing the number of vehicles and establishing an electronic sample-tracking system (RESTRACK-UG), but there still were not enough vehicles to carry all samples in a timely manner, which increased turnaround time. As the pandemic evolved, Uganda adopted point-of-care testing using GeneXpert and later RDTs, which helped address this problem.

LABORATORY ANALYSIS

To expand its testing capacity and reduce turnaround time at its centralized labs, Uganda engaged the private sector and established new labs. In March 2020, Uganda had one laboratory that could process 2,500 COVID-19 PCR tests per day. By December, 16 labs had the capacity to perform 8,800 daily tests.¹⁵ By June 2021, the country had 25 accredited PCR labs. Most of these, including academic research labs, are privately owned.¹⁶

To quickly increase the country’s testing capacity while minimizing the burden on the government, health officials activated private-sector laboratories with preexisting capacity. Some lab sites (such as the Central Public Health Laboratories and Makerere University) implemented pooled testing which involves mixing several samples together in a “batch” or pooled sample, then testing the pooled sample with a diagnostic test. Two major laboratories that provide 90 percent of the country’s PCR testing services (UVRI and Central Public Health Laboratories) already were supporting disease surveillance (UVRI) and HIV care services (Central Public Health Laboratories) through centralized viral load and early infant diagnosis testing. This “multiplexing” (multiple disease pathogen testing) strategy boosted the rapid ramp-up of testing in Uganda.

Testing using the GeneXpert platform began in July 2020 at three mobile point-of-entry sites designed to test truckers along the trade routes that had carried the majority of the early COVID-19 confirmed cases.¹⁷Shortly after WHO approved the use of RDTs for COVID-19 testing in September 2020, the Ugandan Ministry of Health incorporated them into the country’s official testing algorithm as a screening test. RDT pilots began in December 2020 and countrywide rollout began June 2021, with RDTs distributed to select public health facilities. Private facilities are expected to procure their own.

Building Testing Capacity at Uganda Virus Research Institute In the early stages of the pandemic, the Uganda Virus Research Institute had the only COVID-19 testing lab in the country. The lab usually conducts influenza testing, research on hemorrhagic fever, and research to support Uganda’s Expanded Program on Immunization. As the pandemic progressed and samples reached over 3,000 per day, the lab’s staffing and equipment capacity was overwhelmed. To meet the acute need, the Uganda Virus Research Institute took several measures to expand capacity: Repurposed some of the lab resources used for Uganda’s Expanded Program on Immunization and other virus research Upgraded software for machines, including the GeneXpert and Cobas, to allow COVID-19 testing Procured additional PCR machines Augmented the lab staff with personnel from other departments

Limited staff capacity was initially a major barrier to achieving timely test results, so Ugandan health officials added shifts and deployed volunteer staff at private-sector lab facilities. Turnaround times (from sample collection to result delivery) improved from an average of two to seven days in March 2020 to 8–24 hours in October 2020, although it varied across labs and locations; labs in districts furthest from the central labs have reported turnaround times as long as two weeks. Turnaround time has been shortest where point-of-care testing was introduced. The expanded adoption of RDTs is expected to further reduce the average turnaround time.

All labs go through an accreditation process to conduct COVID-19 testing, which involves the submission of an assessment, training of staff at UVRI, and site visits. On an ongoing basis, labs undergo a quality assurance panel with UVRI as the reference lab.

RESULTS COMMUNICATION

Uganda leveraged the existing electronic results dispatch system (typically used for HIV viral load, early infant diagnosis, hepatitis, and tuberculosis test results) to transmit COVID-19 test results from laboratories to emergency operations centers, districts, and facilities. This has improved communication of results, which took two to seven days (or longer for samples collected at rural sites) early in the pandemic. In this system, the central lab uploads results and testing facilities and lab hubs download and print them. However, not all labs are linked to the electronic laboratory information management system, and some facilities that received RDTs do not have the capacity (such as electronic equipment, internet connection, and skilled personnel) to upload test results. This has led to the underreporting of RDT results and can stretch turnaround times from days to weeks. See case study on the use of digital tools like mTrac and eLIF.

What was Uganda's Surveillance Strategy? How were these data used to Guide Public Health Actions?

Uganda built its COVID-19 surveillance system on the existing national Integrated Disease Surveillance and Response framework that officials designed for earlier epidemics. This system draws primarily from reports from community village health teams, health facility staff, and trained immigration and port health staff at border points of entry.^18,19,20

Surveillance strategies included monitoring:

• The intensity, geographic spread, and severity of disease in the population to estimate disease burden, assess trends, and inform appropriate mitigation measures
• High-risk groups to better target prevention efforts
• The epidemic’s trajectory and impact on the health care system to inform resource allocation and mobilization of surge capacity and external emergency support
• The impact of mitigation measures to adjust them accordingly

Surveillance Modalities

ALERT MANAGEMENT

Uganda established a national COVID-19 call center at the Public Health Emergency Operations Centre. This center collected alerts (calls and messages) of suspected cases from individuals, verified that reported cases met the COVID-19 case definition, and coordinated district-level surveillance teams to conduct contact tracing for the validated alerts. Districts subsequently established their own alert management desk, staffed by volunteers trained to recognize COVID-19 cases. These volunteers can then quickly verify alerts for follow-up action in their localities rather than relying on the national operation center.

COMMUNITY-BASED SURVEILLANCE

Community reports of suspected cases were verified by rapid response teams with support from Village Health Teams. Village Health Teams and local council leaders were critical surveillance partners, using local tools (such as the Ministry of Health’s printed contact tracing and case identification information sheets) to support case identification, linkage, and reporting.

POINT-OF-ENTRY SURVEILLANCE

Beginning in April 2020, health staff at international points of entry implemented a COVID-19 screening protocol that included mandatory symptom and temperature checks for all arriving travelers. To support surveillance at the border, officials drew health workers from local health facilities, which created staffing shortages and some disruption of non-COVID-19 health services in those facilities. It is worth noting that symptom screens and temperature checks have limited impact in the context of asymptomatic transmission.

Challenges in Screening at Border Early in the pandemic, Uganda classified travelers and truckers as high-risk groups for COVID-19 exposure. To minimize transmission, Uganda introduced mandatory testing for incoming truckers in April 2020. The East African Community reached a regional agreement in May 2020, which mandated COVID-19 negative test results for cross-border travelers in the region. The testing protocol soon faced challenges—backups at the border of up to four days and increased transmission risk due to inability to enforce distancing. This was partially attributable to centralized testing and high costs of test kits, as well as inconsistent policies between countries There was significant intercountry coordination to reduce border wait times. This included a resolution to require testing in a traveler’s country of origin, development of a test certificate that would be valid for two weeks, establishment of an electronic system to track and share results, and use of mobile labs at points of entry to reduce turnaround time of test results.

COMMUNITY SURVEYS

Uganda conducted two community surveys using PCR tests to assess the prevalence of active COVID-19 infection. The first survey, conducted in April 2020, covered specific populations and areas, which included: markets; border crossing points and communities living in these areas; truck drivers and communities along their routes; factory workers; health workers; and security forces. The survey covered eight districts across the country, which were deemed to be at higher risk of COVID-19 transmission and minimal community transmission (0.028 percent) was found. The second survey, in August 2020, targeted 11 districts and found a fourfold increase in prevalence.

A third community survey took place starting March 2021. This was a serological survey and as of June 2021 the findings have not yet been released, though a presentation of the findings at the World Health Summit revealed an infection prevalence of 20.7 percent. Officials used the results of these surveys to adjust lockdowns and modulate the intensity of nonpharmaceutical interventions. These assessments covered eight districts across the country, with a total sample of 10,000 people.¹⁸

GENOMIC SEQUENCING

With support from the UK Medical Research Council, UVRI is conducting genetic sequencing (genotyping) on a selection of confirmed COVID-19 laboratory samples. By February 2021, researchers reported two, newly emerging variant-A sublineages with unclear clinical implications. One of these (A.23.1) became the predominant virus lineage in Kampala.²¹ By the end of April 2021, five variants were identified, including the first case of Delta. By mid-June, barely six weeks later, 97 percent of tested samples were of the Delta variant.² The Delta variant’s increased transmissibility and increases in cases and deaths prompted the national lockdown on June 18.

HEALTH FACILITY-BASED SURVEILLANCE

Health facilities and isolation units designated for COVID-19 routinely report data on confirmed cases, admissions, discharges, deaths, signs and symptoms, and comorbidities. These data have guided the expansion and distribution of ICU beds, medicine, and supplies and the deployment of health workers. Uganda has provided reliable and consistent oxygen supply and expanded ICU facilities in 14 regional referral hospitals designated to manage COVID-19 cases. As of June 2021, the country had almost three times the number of available ICU beds with life support (nearly 140, up from 55) compared to the beginning of the COVID-19 pandemic.²²

CONTACT TRACING

Contact tracing was conducted intensively from March to September 2020, which identified nearly 18,000 contacts of confirmed cases, including travelers from countries categorized by WHO as high risk.²³  Confirmed cases were referred for isolation at designated centers in districts across the country. As community transmission increased, intensive contact tracing slowed. Linking cases to their source of infection was difficult, and the system was overwhelmed despite the many volunteers recruited to support the task. Contact tracing is still ongoing in areas with manageable caseloads—yet, despite the support of committed partners, these systems have been unable to keep up with the pandemic’s spread.

ISOLATION & QUARANTINE

Initially, all confirmed COVID-19 patients were isolated at designated health care facilities. As cases increased, secondary regional isolation centers (e.g., in the Mandela National Stadium in Namboole, which opened in September 2020) were used to manage non-severe, high-risk patients (e.g., those with comorbidities). Home-based isolation was implemented nationwide for asymptomatic COVID-19 cases or cases with mild symptoms with no known risk or comorbidity. Medical teams instituted by district task forces contacted isolated patients daily to monitor their symptoms. Patients could also contact the medical surveillance team using a national toll-free hotline. Where village health teams were active, they monitored patients through phone calls and reported daily to the attached health facilities. Initially, clinically stable patients could be discharged only after two negative RT-PCR tests performed more than 24 hours apart; follow-up testing at the end of isolation is no longer required.

In March 2020, the government introduced a 14-day quarantine for returning travelers from high-risk countries.²⁴ Initially, all suspects who tested negative were advised to quarantine at home, ²⁵ but due to weak enforcement and low levels of compliance, institutional quarantine was introduced in April. The government then set up 17 quarantine centers around Kampala and Entebbe and additional centers in 21 districts. These were mainly hotels, and quarantined individuals had to meet the costs themselves. Patients could only be discharged after a negative test performed 14 days later without any new risk exposure. Individuals who developed symptoms during quarantine were encouraged to call the Ministry of Health’s toll-free hotline.²⁰ Monitoring was to be conducted by a medical team daily, but this was rarely done.

Reported challenges included the high cost of institutional quarantine (met by the traveler), insufficient space and overcrowding in isolation facilities, risk of repeated exposure that delayed discharge, limited personal protective equipment, and suboptimal health monitoring. The institutional quarantine program was also marred by neglect, dissatisfaction, and mismanagement (which was frequently reported in the media).²⁶  According to an online survey conducted by Ministry of Health in April 2020, health workers checked 59 percent of those in institutional quarantine every day, but only 19.9 percent of those in self-quarantine reported daily checks.²⁷

In September 2020, institutional quarantine was no longer required for returning travelers with negative PCR tests at points of entry. Instead, they were advised to limit contact with other people for two weeks. Testing was also no longer required for asymptomatic people at the end of their quarantine. With community transmission taking place, Uganda implemented home-based care, which is overseen by a new post in the Incident Management Team.

Institutional isolation was reintroduced at the peak of the second wave in May 2021 for incoming travelers who tested positive at points of entry.

Surveillance Activities by Location

Location	Surveillance activities	Data collected
Community	Reporting to PHEOC via alert management system Village Health Team reporting Contact tracing	Potential exposures, alerts, and notifications Demographic information
Health facilities	Screening at outpatient facilities Referrals of suspected cases Health worker reporting via SMS Screening of deaths for evidence of COVID-19	Demographics Hospitalizations Clinical outcomes
Points of entry  (Land crossings & Entebbe Airport)	Mandatory COVID-19 screening protocol Temperature screenings upon entry Testing all truckers	Demographics Symptom data Travel history

Data Management, Reporting, and Use

DATA CAPTURE AND COLLECTION

At the beginning of the COVID-19 pandemic, Ugandan officials built on existing data systems, which enabled the country to quickly scale up new solutions as needed and to use the appropriate data-reporting tools for different aspects of surveillance, though interoperability challenges persist. ²⁸ Examples of these systems are outlined below.

• Uganda has a District Health Information Software 2 (DHIS2) system that is integrated with the electronic integrated disease surveillance and reporting system for real-time data collection. It also has an associated Android app, which is used extensively at points of entry.
• Uganda uses Go.Data for field data collection (a platform focused on case data from the lab, hospitalization, and other variables collected through the case investigation form, and contact data including contact follow-up information),²⁹ Open Data Kit for district-level reporting,³⁰ and U-Report for community engagement and messaging.³¹
• A regional tool to support smooth border crossing, the Regional Electronic Cargo and Driver Tracking System, launched in September 2020. The government provided funds for this technology via the Makerere University and Innovations Fund (Mak-RIF), which supports the scale-up of surveillance tools.
• As of June 2021, all 22 COVID-19-accredited laboratories upload their results into an online electronic laboratory information management system. The system has an electronic results dispatch system (eRDS), which can produce print reports that are accessible by key stakeholders in a lab or clinic.³²  The results go through the emergency operations center to the incident commander, facilitating epidemic response updates for risk communication and also guiding public health action.
• For RDT data management in Uganda, the Ministry of Health introduced two systems for healthcare workers to send data from facilities to the central level: the SMS-based reporting tool called mTrac and an internet-based reporting system called eLIF (electronic lab investigation form) which has a direct data pipeline to the eRDS mentioned above.
• Uganda also established a public, web-based information dashboard on COVID-19 that provides pandemic data in real time to support rapid, evidence-based decision making for a wide range of stakeholders. The dashboard is updated daily with information on test results, recoveries, active cases, deaths, and cases by district.³³  Officials use these data to monitor high-burden areas, shape each pillar of the country’s pandemic response, and identify the groups and individuals at highest risk.

How Did Uganda Coordinate Its Testing and Surveillance Efforts?

Immediately after WHO declared COVID-19 a public health emergency of international concern at the end of January 2020, the Ugandan Ministry of Health immediately activated the Public Health Emergency Operations Centre and National Task Force to support and coordinate COVID-19 preparedness and response. The multisectoral and multidisciplinary National Task Force, chaired by the Prime Minister and composed of political and technical leaders from key government sectors, was responsible for coordinating Uganda’s COVID-19 response.

The National Task Force’s Incident Management Team developed a COVID-19 preparedness and response plan with an emphasis on risk communication and community engagement to promote good public health practices. The Incident Management Team managed six key pillars of direct response, including management of the surveillance and lab systems and logistics for supplies and transport. It also set up rapid response teams.

After Uganda registered its first case of COVID-19 on March 21, 2020, the National Task Force turned its focus from preparedness to emergency response.³⁴ It activated district task forces to coordinate subnational and local COVID-19 response activities, such as surveillance, contact tracing, and isolation. It also established a scientific advisory committee composed of public health specialists, physicians, epidemiologists, immunologists, and statisticians from Makerere University’s schools of public health, medicine, and statistics, the Medical Research Council, and the Uganda Virus Research Institute. It developed and disseminated a resurgence plan in June 2021, covering the 12 months ending in June 2022, which divided the surveillance and laboratory pillar into two—the surveillance and laboratory pillar and the new home-based care pillar. It is planning to establish regional emergency operations centers, but the four in existence are not yet fully functional due to resource constraints.

What Are the Key Lessons from Uganda’s Response to COVID-19?

Uganda had existing surveillance and laboratory infrastructure, developed to respond to other infectious diseases, that it could leverage to rapidly respond to COVID-19. However, lack of resources and supplies, and communication breakdowns (between the national and local levels), continue to limit the country’s ability to roll out comprehensive testing and surveillance solutions to the entire population.

Conclusion

Because Uganda leveraged its previous epidemic experience, preexisting surveillance and testing infrastructure, and ongoing relationships with funding partners, it was able to respond rapidly to the COVID-19 pandemic. It quickly ramped up testing capacity and strategy and employed multiple surveillance approaches and digital health tools.

However, as the pandemic progressed and community spread increased, Uganda’s response system was overwhelmed, which led to gaps in subnational surveillance capacities, suboptimal case detection, and reductions in contact tracing, institutional quarantine, and isolation. To improve testing access and turnaround times, Uganda began to scale the roll out RDTs beginning in June 2021. The system continues to be challenged by inadequate supplies, quality concerns, and underreporting of test results.

While Uganda has experienced challenges with their COVID-19 response, there are lessons that can be learned from how the country innovated and adapted strategies to address these challenges. Documenting the country’s response may also inform improvements for future pandemic preparedness and response efforts.

AUTHORS Alice Namale, Suzanne N. Kiwanuka, Fred Monje, Rawlance Ndejjo, Susan Kizito, Rhoda K. Wanyenze