Field investigation: implementing a multi-phase diagnostic scale-up for mpox control in Burundi

¹Department of Public Health, Walter Sisulu University, Mthatha, Eastern Cape, South Africa, ²Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia, ³Ministry of Public Health and the Fight Against AIDS, Bujumbura, Burundi

^&Corresponding author
Jean Paul Muambangu Milambo, Department of Public Health, Walter Sisulu University, Mthatha, Eastern Cape, South Africa

Introduction    

Mpox (formerly known as monkeypox) is a zoonotic viral disease first identified in humans in the 1970s in Central Africa and has remained endemic in several African countries. Historically, the disease has primarily affected rural populations with frequent exposure to wildlife reservoirs. However, the 2022 global outbreak marked an unprecedented expansion of Mpox beyond its traditional endemic regions. By the end of 2023, more than 87,000 confirmed cases had been reported across over 110 countries worldwide, including regions such as Europe, the Americas, Asia, and Oceania that had no previous history of sustained Mpox transmission [1]. Despite Africa being the historical epicenter of the disease, the continent accounted for less than 16% of laboratory-confirmed cases globally, reflecting substantial under-detection due to limited diagnostic capacity and surveillance infrastructure in many African countries [2]. During the global outbreak, several high-income countries rapidly strengthened their response capacities through coordinated surveillance, diagnostic testing, and vaccination programs. In North America, the United States reported more than 30,000 confirmed cases, with response efforts coordinated by the Centers for Disease Control and Prevention, including the expansion of laboratory testing and vaccination campaigns [3]. Canada similarly implemented large-scale testing strategies and targeted risk communication, containing the outbreak with fewer than 1,500 reported cases nationwide [4]. In Asia, countries such as Japan, South Korea, and India reported sporadic outbreaks but faced challenges related to diagnostic infrastructure and public awareness [5]. Australia experienced a limited outbreak that was rapidly controlled through aggressive testing, contact tracing, and access to the JYNNEOS vaccine [6].

In contrast, many African countries experienced significant diagnostic and surveillance limitations during the same period. For example, the Democratic Republic of the Congo reported 5,005 suspected Mpox cases in 2022, yet only 5.5% of these cases were laboratory confirmed, highlighting major gaps in disease detection and reporting systems [7]. Similar challenges were observed across several countries where centralized laboratory structures, limited molecular diagnostic capacity, and weak surveillance networks delayed case confirmation and hindered timely public health interventions. In response to the increasing regional burden of Mpox, the African Union declared Mpox a Public Health Emergency of Continental Significance (PHECS) in August 2024. Between August 2024 and July 2025, more than 37,600 confirmed Mpox cases and 263 deaths were reported across 28 African Union Member States. During this period, continental diagnostic coverage improved to an estimated 53-67%. Among the affected countries, Burundi demonstrated notable progress, achieving diagnostic coverage exceeding 90%, reporting the lowest case fatality rate in the region, and documenting a 78% reduction in the weekly average number of confirmed cases between the outbreak peak in October 2024 and May 2025.

In July 2024, Burundi confirmed its first Mpox cases in the provinces of Bujumbura and Gitega, prompting the Ministry of Public Health and the Fight against AIDS to declare a national health emergency. At the onset of the outbreak, laboratory confirmation of Mpox cases relied exclusively on a single National Reference Laboratory located in Bujumbura. This centralized diagnostic system resulted in several operational challenges, including delays in case confirmation, prolonged turnaround times for test results, limited access to diagnostic services for peripheral districts, and increased logistical costs associated with specimen transportation. Although molecular diagnostic platforms such as the GeneXpert system were available in several district laboratories through tuberculosis control programs, these platforms were not initially integrated into the Mpox diagnostic response.

To address these limitations, Burundi implemented a multi-phase strategy to decentralize Mpox diagnostic services as part of its national outbreak response. Initiated in November 2024 and aligned with the continental response framework supported by the Africa Centres for Disease Control and Prevention, the strategy aimed to expand laboratory testing capacity, improve surveillance coverage, and accelerate case detection. By progressively expanding testing from a single national laboratory to a network of decentralized laboratories and mobile diagnostic units, the initiative sought to reduce turnaround times, improve access to testing, and strengthen outbreak preparedness. This field investigation describes the design and implementation of Burundi´s diagnostic decentralization strategy and evaluates its contribution to improving Mpox surveillance and outbreak response in a resource-limited setting.

Methods     

Study design and setting: this investigation was conducted as an operational field investigation during the Mpox outbreak response in Burundi between July 2024 and July 2025. The purpose of the study was to document and evaluate the implementation of a decentralized laboratory diagnostic strategy designed to improve Mpox case detection, surveillance coverage, and outbreak control. The study used a descriptive epidemiological and operational evaluation design, combining routine surveillance data analysis with an assessment of the progressive expansion of the national laboratory network. The response was coordinated by the Ministry of Public Health and the Fight against AIDS with technical support from the Africa Centres for Disease Control and Prevention following the declaration of Mpox as a Public Health Emergency of Continental Significance by the African Union in August 2024 [1,2].

Case definition and case finding: standardized Mpox case definitions were adopted from national surveillance guidelines and international outbreak response recommendations [1-3]. A suspected case was defined as any individual presenting with an acute onset of fever followed by a vesicular or pustular rash and lymphadenopathy or other symptoms compatible with Mpox infection. A probable case referred to a suspected case with epidemiological linkage to a confirmed case or exposure to a high-risk environment. A confirmed case was defined as a suspected or probable case with laboratory confirmation of Mpox virus infection using polymerase chain reaction (PCR). Case finding relied on both passive and active surveillance mechanisms, including routine reporting through the Integrated Disease Surveillance and Response (IDSR) system, active case searches in health facilities, contact tracing, and community-based reporting by trained health workers.

Data sources and data collection: data were obtained from multiple sources, including health facility registers, laboratory information systems, case investigation forms, and national Mpox surveillance databases. Additional information was gathered through structured case investigation interviews, review of laboratory records, and surveillance reports submitted by district health authorities. Variables collected included demographic characteristics (age, sex, residence), clinical symptoms, dates of symptom onset, exposure history, laboratory results, and geographic location of cases. These data were compiled into the national Mpox surveillance database and used to monitor outbreak trends and evaluate the performance of the decentralized diagnostic system.

Laboratory methods and data analysis: clinical specimens were collected from suspected Mpox cases according to national diagnostic protocols [3,4]. Sample types included lesion swabs, crust samples from skin lesions, and oropharyngeal swabs where appropriate. Specimens were transported under cold chain conditions to designated laboratories for testing. Laboratory confirmation was performed using PCR assays, primarily conducted on the GeneXpert system platform after decentralization of diagnostic services. The diagnostic workflow included sample registration, nucleic acid amplification, detection, and electronic reporting of results through the national laboratory information system. Data were analyzed using descriptive epidemiological methods to assess trends in Mpox detection and laboratory performance. Key indicators included the number of operational testing laboratories, samples collected and tested, confirmed Mpox cases, geographic coverage of testing services, and turnaround time from sample collection to result reporting. Analyses were conducted by time, place, and person to compare surveillance performance before and after the implementation of the decentralized laboratory strategy. Table 1 outlines Burundi´s four-phase Mpox diagnostic strategy, beginning with national planning and risk mapping, followed by a pilot rollout in high-priority sites, regional scale-up to affected districts, and finally peripheral and cross-border expansion to pre-empt outbreaks. Each phase progressively expanded laboratory capacity, deployed GeneXpert platforms and mobile labs, trained personnel, and strengthened surveillance systems, ultimately achieving nationwide district-level coverage and improved outbreak readiness.

Ethical considerations: this investigation was conducted as part of the national Mpox outbreak response and routine public health surveillance activities led by the Ministry of Public Health and the Fight against AIDS in Burundi. The activities were implemented to support outbreak control and improve diagnostic capacity during a public health emergency. Data were analyzed in aggregated form, and no personal identifiers were included in the analytical dataset to ensure confidentiality. The investigation followed national public health regulations and ethical principles for surveillance and outbreak investigations in accordance with international public health guidelines [2,5].

Results     

Descriptive findings

Response rates and case identification: during the study period (July 2024-July 2025), a total of 8,885 suspected Mpox cases were reported across Burundi. Of these, 3,656 cases met the standardized case definition for probable or confirmed Mpox infection, representing a high response rate for case reporting and investigation due to active community and facility-based surveillance. The overall attack rate (AR) for the outbreak was estimated at 0.25% of the national population. Table 2 summarizes surveillance indicators before and after the decentralization strategy. Before August 2024, the system recorded 210 suspected cases, with 210 samples collected and tested (100% testing rate and coverage), resulting in 80 positive samples and a 38% test positivity rate. After decentralization (Aug-Dec 2024), surveillance expanded dramatically to 5,767 suspected cases, 5,743 samples collected, and 5,710 tested, maintaining 99-100% testing performance while identifying 2,975 positive samples and increasing test positivity to 51%. From Jan-May 2025, high performance continued with 2,908 suspected cases and samples tested, 601 positives, and a 47% positivity rate, indicating sustained surveillance capacity and continued detection of transmission.

Distribution by time: the epidemic curve showed an initial surge of suspected cases following the first confirmed cases in July 2024, peaking in October 2024, followed by a steady decline after implementation of the decentralization strategy and enhanced surveillance measures. The phased laboratory expansion coincided with improved case detection and more timely reporting, highlighting the impact of enhanced diagnostic capacity on outbreak monitoring.

Distribution by place: cases were initially concentrated in the provinces of Bujumbura and Gitega, with subsequent spread to high-mobility districts and cross-border regions. Attack rates were highest in urban centers, reaching 0.5% in Bujumbura compared with 0.1-0.2% in rural districts, reflecting differences in healthcare access and diagnostic availability.

Distribution by person: the median age of confirmed cases was 26 years (range: 2-67), with 55% male cases. Clinical features included fever (100%), vesicular or pustular rash (92%), lymphadenopathy (78%), and malaise (65%). Attack rates were highest among adults aged 20-39 years, consistent with exposure in occupational and social settings.

Laboratory findings: a total of 8,631 clinical samples were collected from suspected cases, with 4,356 testing positive for the Mpox virus by PCR, representing a positivity rate of 50%. Typing and confirmation were performed using GeneXpert platforms and validated at the National Reference Laboratory. Most positive cases were confirmed as Clade II Mpox virus, consistent with regional outbreaks observed in Africa during 2022-2025.

Turnaround time improvements: the decentralization strategy led to substantial reductions in turnaround times for sample collection, laboratory processing, and result reporting. Before August 2024, the average duration from alert to sample collection and from sample collection to result release ranged from 24 to 72 hours. Following decentralization, these durations decreased to 2-4 hours, even as testing volumes increased (Table 3).

Laboratory network expansion: the number of operational Mpox testing laboratories increased rapidly following decentralization, from a single National Reference Laboratory before August 2024, to 41 GeneXpert laboratories by December 2024, and 56 laboratories by May 2025. This scale-up enabled equitable diagnostic access across high-risk, newly affected, and peripheral districts (Table 4).

Environmental study findings: environmental sampling in high-density areas included surface swabs and wildlife reservoir testing. Out of 142 environmental samples, 6 (4%) were positive for Mpox viral DNA, matching sequences from human isolates. These findings suggest possible indirect transmission via contaminated surfaces rather than direct zoonotic exposure.

Transition and hypotheses generated: the descriptive and laboratory findings indicate that young adults in urban centers, particularly males, were the highest-risk groups. Transmission appears to have been primarily person-to-person, with household and community contact as key exposure pathways. Environmental detection supports potential fomite-mediated transmission. These observations generated hypotheses for further analytical studies: 1) infection risk is associated with household contact with confirmed cases; 2) attendance at social or occupational gatherings increases susceptibility; 3) decentralized laboratory testing accelerates case detection and isolation, reducing secondary transmission.

Analytical study findings: univariate and bivariate analyses confirmed higher attack rates among males, adults aged 20-39, and urban residents. Bivariate analysis identified household exposure as a significant risk factor (RR = 3.4, 95% CI 2.8-4.1, p <0.001). Multivariable logistic regression, adjusting for age, sex, and district, showed that household contact (adjusted OR = 3.1, 95% CI 2.5-3.8) and attendance at large social gatherings (adjusted OR = 2.2, 95% CI 1.8-2.7) were independently associated with infection. Further studies, including viral genome sequencing of selected isolates and environmental samples, are ongoing.

Discussion     

The decentralization of Mpox virus diagnostic services in Burundi represents a major advancement in strengthening national outbreak preparedness and response capacity. Prior to August 2024, diagnostic testing was centralized within a single national reference laboratory, creating significant delays in case confirmation, contributing to under-detection of infections, and limiting equitable access to testing services, particularly in remote and high-risk areas. Through a structured multi-phase scale-up strategy, Burundi expanded diagnostic capacity from one centralized facility to 56 GeneXpert-equipped laboratories within less than one year. This rapid expansion improved geographic accessibility to testing and enabled more timely identification of cases, reflected by a 496% increase in case detection and improved surveillance sensitivity across multiple provinces [1,3]. A critical factor contributing to the success of this diagnostic expansion was the strategic repurposing of existing GeneXpert platforms initially established for tuberculosis control. Rather than investing in entirely new diagnostic infrastructure, Burundi leveraged available laboratory assets and adapted them for Mpox molecular testing, allowing rapid deployment while minimizing additional costs and implementation delays. The introduction of multiplex PCR testing enabled efficient confirmation of suspected cases, with turnaround times reduced to approximately 2-4 hours following sample collection. Faster diagnostic confirmation supported early isolation of cases, reduced the risk of healthcare-associated transmission, and strengthened key outbreak control interventions, including contact tracing and ring vaccination strategies [2,4].

The incorporation of mobile laboratory units further enhanced the effectiveness of the decentralized diagnostic network by extending testing capacity to rural, underserved, and border areas. These mobile platforms improved outbreak responsiveness by enabling testing closer to affected communities, reducing dependency on central laboratories, and minimizing delays associated with specimen transportation. Beyond operational improvements, the presence of decentralized and mobile testing services contributed to increased community confidence in public health interventions by demonstrating improved accessibility and responsiveness of the health system. This strengthened response capacity contributed to improved outbreak management and a lower case fatality rate compared with experiences reported in several comparable settings [3,5]. Despite the substantial achievements of Burundi´s decentralized diagnostic model, several operational and systemic challenges require attention to ensure long-term sustainability. Maintaining a network of 56 diagnostic sites requires continuous investment in laboratory consumables, equipment maintenance, supply chain management, and skilled human resources. In addition, variations in laboratory performance, staff competencies, and adherence to quality standards may affect consistency of diagnostic accuracy across facilities. Strengthening national quality assurance and quality control systems, including routine proficiency testing, external assessments, and supportive supervision, will be essential to maintain reliable diagnostic performance across the decentralized network [1,3].

Another important challenge is the need for stronger integration of laboratory-generated data into national surveillance systems. Although decentralization improved access to diagnostic services, incomplete interoperability between peripheral laboratories and centralized health information platforms limits the ability to conduct real-time epidemiological analysis and rapid decision-making. Developing an integrated digital surveillance system that links decentralized laboratories with national response structures would improve data visibility, outbreak forecasting, and resource allocation. Such investments are critical for sustaining preparedness beyond the current Mpox response and strengthening compliance with International Health Regulations (IHR 2005) core capacities [1,2]. Burundi´s experience provides valuable lessons for other low-resource settings seeking to strengthen epidemic preparedness. Compared with countries facing limited diagnostic capacity, Burundi demonstrated that strategic adaptation of existing infrastructure can rapidly improve outbreak detection. For example, the Democratic Republic of Congo confirmed fewer than 5.5% of suspected cases in 2022, largely due to insufficient laboratory capacity and limited diagnostic access [2]. Conversely, high-income countries such as Canada, the United States, and Australia benefited from pre-established decentralized laboratory networks and advanced real-time surveillance systems that enabled rapid outbreak response [4,5]. Burundi´s approach illustrates that phased implementation, efficient use of available resources, and targeted investments can significantly narrow diagnostic capacity gaps between resource-limited and high-income settings.

To maintain and expand the benefits achieved through Mpox diagnostic decentralization, several strategic actions are recommended. Sustainable financing mechanisms should be established through national health budgets and international partnerships to ensure continuous availability of reagents, equipment maintenance, and retention of trained personnel. Nationally standardized quality assurance frameworks should be implemented across all decentralized laboratories, supported by regular supervision and competency assessments. In parallel, investments in workforce development, including laboratory training, data management capacity, and retention strategies, will be essential for maintaining a skilled diagnostic workforce. Furthermore, the development of interoperable real-time laboratory information systems should be prioritized to support integrated surveillance and outbreak analytics. Finally, Burundi´s decentralized diagnostic model should be considered for adaptation to other epidemic-prone diseases, including Lassa fever, Marburg virus disease, and Ebola virus disease, supporting the development of a sustainable multi-pathogen diagnostic network aligned with IHR (2005) requirements [1,2].

Conclusion     

Burundi´s multi-phase decentralization strategy for Mpox diagnostics demonstrates how innovative approaches can rapidly transform epidemic response capacity in resource-constrained settings. By leveraging existing GeneXpert infrastructure, deploying mobile laboratories, and implementing risk-based expansion strategies, the country substantially improved testing coverage, case identification, and response timelines. These achievements highlight the value of decentralized diagnostic systems as a foundation for resilient public health preparedness. However, sustained impact will depend on continued financing, robust quality assurance mechanisms, workforce strengthening, and full integration of laboratory data into national surveillance systems. Burundi´s experience offers a practical and scalable model for strengthening laboratory networks and improving epidemic resilience in alignment with IHR (2005) core capacities.

Competing interests     

The authors declare no competing interests.

Authors' contributions     

Jean Paul Muambangu Milambo: conceptualization, study design, field investigation, data analysis, interpretation of findings, literature review, and manuscript preparation. Joseph Nyombe Tshimbuka: technical guidance, methodological review, interpretation of diagnostic scale-up strategies, critical revision of the manuscript, and public health response coordination. Marie Noelle Uwineza: field coordination, data validation, implementation oversight, contextual interpretation of national Mpox response activities, and critical review of the manuscript. All authors contributed to manuscript development, reviewed the final version, and approved the submitted manuscript.

Acknowledgments     

The authors acknowledge the Ministry of Public Health and the Fight against AIDS of Burundi for coordinating the national Mpox response and facilitating access to surveillance and laboratory data. We thank the Africa Centres for Disease Control and Prevention for technical support, as well as Prof. Andre Bulabula for valuable technical guidance during the investigation and manuscript preparation. We also recognize the dedication of frontline healthcare workers, laboratory staff, surveillance officers, and community health workers across Burundi, whose efforts were essential in implementing the decentralized diagnostic strategy. Finally, we acknowledge the academic support provided by Walter Sisulu University and University of South Africa.

Tables and figure     

Table 1: Mpox diagnostic strategy summary table by phase

Table 2: surveillance indicators pre- and post-decentralization strategy

Table 3: laboratory timeline indicators

Table 4: laboratory network expansion by phase

References