In 2024, mpox cases surged in the Democratic Republic of the Congo (DRC) with cross-border spread to Burundi. We developed a transmission-dynamic model calibrated against surveillance data to understand drivers in enzootic (Clade Ia) and non-enzootic (Clade Ib) areas, and the potential impact of vaccination. In non-enzootic areas we estimated that 58-84% of transmission occurred within sexual networks. MVA-BN vaccination of sex workers could have averted 91% (95% CrI 81%-98%) of infections in Sud Kivu (DRC) but only 35% (95% CrI 26%-47%) in Bujumbura (Burundi), due to later outbreak detection. In historically enzootic Equateur (DRC), ongoing zoonotic spillover best explained sustained incidence. There, pledged Lc18m8 vaccines could have averted 42% (95% CrI 40%-46%) of infections; prioritising children improved impact. Across all settings, doubling vaccine coverage by using a single dose of MVA-BN outperformed two-dose strategies. Timely detection and tailored vaccination strategies are critical to reducing mpox burden. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement RMc, EK, AH, DOM, VMC, KC, CW, AG, NMF, and LW were funded by the Medical Research Council (MRC) Centre for Global Infectious Disease Analysis (MR/X020258/1), funded by the UK MRC and carried out in the frame of the Global Health EDCTP3 Joint Undertaking supported by the EU. TL acknowledges funding from the Wellcome Trust (grant number 312174/Z/24/Z). AP acknowledges funding from the Wellcome Trust (grant number 220900/Z/20/Z). NMF is funded by the National Institute for Health and Care Research (NIHR) Health Protection Research Unit in Health Analytics and Modelling, a partnership between the UK Health Security Agency, LSHTM and Imperial College, the MRC Centre for Global Infectious Disease Analysis (reference MR/X020258/1), funded by the UK Medical Research Council (MRC). This UK-funded award is carried out in the framework of the Global Health EDCTP3 Joint Undertaking. NMF also acknowledges funding from Community Jameel via the Jameel Institute for Disease and Emergency Analytics, and from Wellcome Trust via the Vaccine Impact Modelling Consortium (226727/Z/22/Z). LW acknowledges funding from the Wellcome Trust (grant number 218669/Z/19/Z). The funders had no involvement in the study design, analysis, or writing of the paper. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes The model is available from https://github.com/mrc-ide/mpoxseir and the analysis from https://github.com/mrc-ide/mpox-clade1-vax-analysis.

Abstract Africa bears a disproportionate burden of infectious disease outbreaks and antimicrobial resistance, compounded by weaknesses in public health laboratory systems. In line with its mandate to safeguard public health, the Africa Centres for Disease Control and Prevention (Africa CDC) supports its Member States in strengthening public health laboratory capacity. However, gaps in laboratory leadership continue to threaten the resilience and sustainability of these systems. To address this need, Africa CDC convened a Laboratory Leadership Workshop under the Africa Pathogen Genomics Initiative (Africa PGI) – DETECT Project from 27–29 August 2025 in Mombasa, Kenya. The meeting brought together 24 heads of public health and reference laboratories and senior technical experts from 15 Member States. Combining expert presentations, country case studies, and roundtable discussions, participants examined system-level challenges affecting laboratory performance. Workshop proceedings were synthesized according to the predefined thematic areas that guided the workshop discussions, drawing on rapporteurs’ reports and validated through participant review. Key issues included overreliance on external funding, fragile procurement and supply chains, limited equipment servicing, weak sample referral networks, fragmented data systems, and inadequate contingency planning. Comparative country experiences showed that stronger domestic financing and institutionalized leadership structures were linked to greater operational continuity. Emerging innovations such as hybrid decentralization of diagnostic services and integrated sample referral networks were discussed, with success contingent on strengthened leadership in strategic planning, resource mobilization, and cross-sector coordination. The workshop identified cross-cutting priorities, including financial independence, sustainable equipment servicing, quality management, One Health-aligned digital interoperability, and leadership networks for building resilient systems. The meeting concluded that beyond infrastructure, Africa’s epidemic preparedness depends on empowered and committed leaders capable of overcoming challenges to steer resilient and sustainable laboratory systems.

Utilizing mpox case data from Burundi between August 2024 and April 2025, we calibrated a mathematical model to quantify the temporal trends of clade Ib monkeypox virus transmission. The model outputs indicated a declining overall transmission trend. Children aged 0-4 and 5-9 years were estimated to be at higher risk of infection compared to older age groups, while sexual contact was inferred to contribute up to 50% of the overall transmission.

Abstract The recent MPXV epidemic across Africa revealed extensive viral diversity and complex transmission dynamics, prompting a continent-wide genomic investigation. We analysed 3,450 high-quality MPXV virus whole genomes from 24 African Union Member States, revealing the complex and concurrent circulation of Sub-clades Ia, Ib, IIa, and IIb. Subclade Ia showed high levels of virus diversity in reservoir hosts in Central Africa, detected through zoonotic transmission and some sustained human outbreak lastly detected. In contrast, Clade Ib exhibited signatures of sustained human-to-human transmission across Eastern and Southern Africa. Clade IIa remains largely zoonotic in West Africa. Like Ia, IIb shows continued zoonotic transmission, and sustained human outbreak linked to lineage G1 and G2 circulation. Phylogeographic analyses revealed frequent cross-border transmission and interconnectedness, which was aligned with both human mobility corridors and international boundaries. For instance, the Democratic Republic of the Congo or Sierra Leone seems to emerge as a source of regional exportation, while the Cameroon–Nigeria, CAR-Cameroon or CAR-DRC interfaces reflected ongoing cross-border zoonotic spillovers. These findings underscore the need for harmonised genomic surveillance, APOBEC3-aware triage, and integrated One Health strategies to prevent local outbreaks from escalating into regional epidemics and to inform vaccine deployment and public health preparedness.

Genomic surveillance has become an indispensable tool for the identification of pathogens and tracking of transmission chains. Building upon the global sequencing and surveillance infrastructure developed and expanded during the COVID-19 pandemic, these capacities are now being adapted to track other pathogens in low- and middle-income countries which remain disproportionately affected by infectious diseases. This is evident in the recent and unprecedented spread of mpox virus in regions experiencing multiple concurrent infectious disease outbreaks, highlighting the need for broad, adaptable diagnostic detection and sequencing capacity. In this Perspective, we describe the applications, insights, and challenges encountered during ongoing capacity building efforts for the characterization of the mpox outbreak and other emerging pathogens in the African Great Lakes Region.

Despite remarkable progress towards measles elimination in Burundi, the country has seen a resurge in cases since 2019. Epidemiological investigations have been performed; however, it remained unclear if all measles cases involved in recent outbreaks were linked or caused by multiple independent events including introductions from other countries. Therefore, the objective of this study is to investigate the genetic diversity and evolution of measles virus (MeV) during the last large MeV outbreak in Burundi in 2024. The study was carried out on oropharyngeal swab samples collected from four neighboring health districts. Amplicon-based MeV sequencing was performed on the MinION Mk1D. Consensus sequences were generated from 18 isolates and phylogenetic and Bayesian evolution analysis including 152 closely related public genomes were performed. Results showed that all 18 newly generated whole-genome sequences belonged to the genotype B3. Phylogenetic analysis revealed a diverse population of MeV circulating in Burundi, with sequences divided into two separate clusters. The first cluster consisted of two sequences and was most closely related to Italian sequences, while the second cluster was more related to local transmission in the Great-Lakes region based on the N450 region. Based on whole-genome sequences, the remaining 16 whole-genome sequences from Burundi clustered with one sequence from the Netherlands. The most recent common ancestor of the sequences in the second cluster was estimated to be around the beginning of 2023 (between the end of 2022 and the end of 2023 using the 95% confidence intervals) by using Bayesian evolutionary analysis. Here, we provide the first batch of MeV whole-genome sequences generated on the African continent of the ongoing MeV outbreak in the Great Lakes region of Africa. Using these whole genome sequences, we demonstrated that measles viruses genotype B3 were already circulating in Burundi since the beginning of 2023 well before the outbreak in 2024 was noted. We also showed that the recurrent measles outbreaks in Burundi are ignited from different sources, showing that measles in Burundi is sustained by multiple introductions and emphasizing the importance of ongoing molecular surveillance for elimination efforts.

To evaluated artemisinin partial resistance (ART-R) in malaria in Burundi, during December 2023-June 2024, we studied 423 children <5 years of age with uncomplicated Plasmodium falciparum malaria in 8 health facilities in the northern part of the country. After artemether/lumefantrine treatment with only the first dose directly observed, 4.5% remained parasitemic on day 3. No pfkelch13 mutations, validated or candidate markers of ART-R, were detected. However, markers of antifolate and 4-aminoquinoline resistance were widespread: the dhfr triple mutant N51I/C59R/S108N was nearly fixed (92%), dhps double and triple mutants were common (41% and 47%), and pfcrt CVIET, associated with chloroquine and amodiaquine resistance, predominated (84%). Geographic differences occurred in day-3 positivity and haplotype frequencies. Although ART-R markers were absent, delayed parasite clearance and near fixation of multidrug-resistant haplotypes serve as a warning. Strengthened efficacy monitoring and regional molecular surveillance are urgently needed to prevent drug-resistant P. falciparum from becoming established in Burundi.

BACKGROUND:Cholera outbreaks remain a major public-health challenge in sub-Saharan Africa, where diagnostic capacity is limited and clinical case definitions are non-specific and re ly heavily on syndromic diagnosis. Rapid identification of Vibrio cholerae is critical, yet cholera-suspected diarrhoea can have multiple infectious causes not captured by targeted diagnostics. METHODS:We evaluated a mobile, culture-independent metagenomic sequencing workflow for on-site detection of gastrointestinal pathogens directly from faecal samples in Burundi. The offline workflow combined long-read Oxford Nanopore Technologies (ONT) sequencing with rapid, laptop-based taxonomic and antimicrobial resistance (AMR) screening and was deployed across a health centre, a district hospital, and a refugee transit camp. The frontline and real-time results were verified using both conventional culturing and in-depth bioinformatic analyses. RESULTS:V. cholerae signals were only detected in a subset of suspected cholera cases, while many samples were dominated by alternative bacterial taxa, most frequently Escherichia coli. V. cholerae abundance correlated strongly with detection of the C holera T oxin P hage CTXφ, supporting differentiation between toxigenic signal and background exposure. AMR genes were detected across samples, providing early situational insight into resistance determinants among gastrointestinal bacteria. CONCLUSIONS:Mobile, offline metagenomic sequencing enables rapid frontline characterization of gastrointestinal disease, especially cholera-suspected, in resource-limited settings and complements existing diagnostics by improving etiological resolution and outbreak response.

Background In low- and middle-income countries, many challenges hinder achievement of universal health coverage. Among these challenges, the limited availability of information on costs of delivering healthcare services remains a major issue, despite recent progress by many of these countries in digitalizing their health systems. This study was conducted to estimate the annual financial cost of providing healthcare services using electronic medical and financial records. It also aimed to demonstrate that benefits of digitalization extend beyond improving quality of services delivery by supporting health economics analyses. Methods Cost data were collected in a retrospective costing study carried out in 34 health centers, 14 district hospitals, and 3 regional hospitals, covering a one-year time horizon from July 1st, 2024, to June 30th, 2025, from the perspective of the healthcare system. Data were analyzed using Excel 2016 and R version 4.3.2. The median annual total financial costs of delivering health services were estimated, as well as the unit costs of delivering curative, preventive, outpatient, and inpatient services. Results In Burundi, the median total yearly costs of providing services increase as the level of care rises, from €103 372 for a health center to €548 318 for a district hospital and €1,719 902 for a regional hospital. Financial costs at health centers are largely attributed to medicine and consumable costs, which account for 73.3%. In contrast, at district and regional hospitals, the financial costs of service delivery are largely attributed to personnel costs. Personnel costs account for 43% of financial costs at district hospitals and 48.4% at regional hospitals. Conclusions Findings from this study showed that total and unit costs of providing services increase as the level of care rises and suggest that reimbursement tariffs should be fixed according to the health facility level instead of a unique tariff for all health facilities. Findings also suggest that strategies aimed at improving health facility management efficiency should focus on improving medicines management in health centers whereas they should focus on personnel recruitment in hospitals. This study also showed that the benefit of digitalization extends beyond improving quality of health services delivery to support health economics analyses.

The burden of infectious diseases and antimicrobial resistance (AMR) in Africa highlights the critical need for strengthened genomic surveillance capacities that are embedded within the national public health framework. In the East African Community (EAC), this challenge is compounded by limited infrastructure and insufficient workforce capacity in bioinformatics and genomics, particularly within National Public Health Laboratories (NPHLs). This paper describes the implementation of a regional capacity-building initiative based on a multi-phase Training-of-Trainers (ToT) model across six EAC Partner States. Anchored in a One Health framework, the initiative focused on equipping public health professionals within NPHLs with practical skills in pathogen genomics, AMR analysis, and bioinformatics workflows, while also supporting the institutionalization of standardized procedures and tools. Through modular training, in-country cascade sessions, and structured mentorship, the program enabled integration of genomic approaches into public health surveillance activities. Despite infrastructural and operational constraints, the initiative supported measurable gains in applied proficiency, routine use of genomics tools in surveillance tasks, and regional coordination on pathogen data analysis. This case study outlines the program's design, implementation, and observed outcomes, and offers a transferable framework for workforce and systems development in low-resource settings. This experience contributes to ongoing global discussions on equitable genomic surveillance and preparedness by demonstrating how structured, context-specific training can support sustainable adoption of genomics within national public health institutions.

Introduction: In recent years Africa has been facing epidemics linked to poliovirus derived from the vaccine strain with a predominance of type 2. This situation does not spare Burundi. A case of Acute Flaccid Paralysis was notified on 18 June 2023 from Kayanza district, samples were collected which tested positive for circulating vaccine derived poliovirus type 2 (cVDPV2). We investigated to determine cases' characteristics, to identify possible source of infection, to determine the extent of the outbreak and make recommendations. Methods: This was a cross-sectional study. Data collection was done using Polio investigation form extracted from novel oral polio vaccine type 2 (nVPO2) surveillance guidelines. Review of patient's note, case's household visit, contact tracing and environmental assessment were conducted. Data were analyzed using Excel. A case was defined as any child under 15 years of age with paralytic illness from who poliovirus was isolated and resident of Kayanza district from June to August 2023. Results: The case was a male child living with his parents, aged 18 months, from a family of 2 children of which he is the second, received 4 doses of bivalent oral polio vaccine (bOPV) and one dose of inactivated polio vaccine (IPV). He presented to the clinic on 18 June, 2023 with a sudden paralysis which started on his right leg on June 15, 2023. In the past medical history, the child was on plumpy Nut which is a specific formulated product for the nutritional rehabilitation. The case's household and neighborhood environment were unhygienic. Of 12 contacts found, 67% (8) were male, all (100%) contacts were vaccinated, 75% had vaccination card and 100% of contacts had no symptoms. Conclusion: Our study shows that there could be link between the case and the unhygienic environment he lived in. The child received only one dose of IPV which was inadequate to protect against polio according to CDC. The case was malnourished which could have further predisposed him to getting poliomyelitis. It is necessary to initiate environmental surveillance of polio in the area and introduce one or two more inactivated polio vaccine doses in the routine vaccination schedule.

BACKGROUND:Knowledge of intrahousehold transmission dynamics of clade Ib mpox, especially in recently epidemic African contexts, is scarce. Our study aimed to quantify household transmission patterns of clade Ib mpox in Burundi, with a focus on children. METHODS:We conducted a prospective cohort study in two health districts, Bujumbura and Kayanza, in Burundi from Jan 23 to March 20, 2025, enrolling 88 laboratory-confirmed primary mpox cases and 432 of their household contacts. We estimated household secondary attack rates (SARs), serial intervals, and basic reproduction number (R0), including a sensitivity analysis to assess the effect of potential misclassification of mpox index cases younger than 15 years. The primary outcome was occurrence of a secondary mpox infection within the household, defined as any laboratory-confirmed mpox case identified among contacts during the follow-up period. FINDINGS:Of the 88 households, 18 (20%) experienced secondary transmission, with most primary mpox cases generating a single secondary case. The overall SAR across all households was 6·15% (95% CI 4·02-8·95) and was significantly higher among those younger than 15 years (8·77% [5·44 -13·22]) than among those aged 15 years or older (2·84% [0·92-6·50]). The overall R0 was 0·30 (95% CI 0·17-0·46), and was significantly higher for those younger than 15 years (0·43 [0·21-0·70]) than those aged 15 years or older (0·15 [0·03-0·27]). The sensitivity analysis showed significantly higher estimates (R0 0·9 [0·71-1·09]; SAR 17% [13·57-21·03]). INTERPRETATION:Intrahousehold transmission of clade 1b mpox in Burundi was limited, and unlikely to sustain a broader community spread. The involvement of children in transmission chains within the household underscores their vulnerability, emphasising the need for accurate household investigation, early detection, and strategies to protect them. Our findings suggest that infection outside the household, with adults serving as a source for initial household introductions, might be a primary driver of the outbreak. The mpox outbreak response should adopt a dual approach combining interventions for household settings and targeted prevention strategies for adults at risk where community transmission is more probable. FUNDING:UNICEF Burundi Country Office.

Since the first identification of mpox virus (MPXV) clade Ib in Burundi in July 2024, Burundi is one of the most affected countries in this evolving outbreak outside of the DRC. Here we aimed to understand the route(s) of introduction and spread of MPXV throughout the first months of the outbreak in Burundi. In total, 98 genome sequences from cases diagnosed during the first three months of the outbreak were generated. Here we show using phylogenetic analysis that the virus was introduced from the DRC and Bayesian evolutionary analysis shows that different clusters could be identified in Burundi leading to further spread within the country. In summary, we identify sustained circulation of clade Ib MPXV in Burundi, most likely after several different introductions from the bordering province of South Kivu-DRC. The virus has acquired several additional APOBEC-3 mediated mutations, in line with reported evidence of ongoing human-to-human transmission. Mpox is a viral infection caused by the mpox virus (MPXV). A specific MPXV strain called lb, is spreading in the Eastern African region. Here, we aimed to understand how this strain was introduced into Burundi and spread to the rest of the country using genetic sequencing. Using this data, we could track the genetic evolution of the virus and found that there were several different introductions of the virus into Burundi, or that the virus had already been circulating in the country since around May 2024. Additionally, we identified specific mutations in the virus, indicative of human-to-human transmission (APOBEC-3). These findings suggest there is sustained circulation of mpox MPXV Ib in Burundi, largely driven by human-to-human transmission. Nzoyikorera et al. describe the genomic surveillance efforts following introduction of the mpox clade Ib virus into Burundi. They demonstrate sustained circulation of clade Ib in Burundi and discuss the potential routes of introduction from neighbouring regions.

The production of β-lactamases by the Enterobacterales family is currently the leading cause of antibiotic resistance. Urinary tract infections (UTIs) account for 25

Antimalarial resistance, including failure of artemisinin combination therapy, is increasing in Africa. Molecular surveillance of markers of drug resistance is essential to monitoring drug resistance. Plasmodium falciparum isolates from Cibitoke Province, Burundi were sequenced for ten markers of resistance (including potential background markers conferring kelch-13mediated artemisinin partial resistance) by Illumina or Nanopore sequencing. Plasmepsin-2 and mdr1 copy number variations were typed by digital PCR. Among 157 isolates, no validated pfkelch13 mutations linked to artemisinin partial resistance (ART-R) were detected. However, a novel pfkelch13 mutation, A675T, was identified. A mutation in the same position (A675V) had been found and validated in neighboring Rwanda previously. Background mutations were frequent, including pffd D193Y (45.9%) and pfarps10 V127M (11.5%). Sulfadoxine-pyrimethamine (SP) resistance was widespread, with quintuple haplotypes detected in 82.3% and sextuple haplotypes in 12.3% of mono-infections. The pfcrt IET triple mutant haplotype (94.9%) and pfmdr1 N-F-D mutant haplotype (57.9%) indicate sustained CQ resistance and efficacy of artemether-lumefantrine (AL). No pfpm2 duplications but rare pfmdr1 amplifications (1.8%) were identified. These findings indicate substantial SP resistance, posing a threat to the efficacy of IPTp and SMC strategies in Burundi. The findings also show potential ART-R and partner drug resistance in Burundi, highlighting the need for strengthened surveillance and coordinated regional efforts to mitigate resistance and sustain malaria control.

Background:Hepatitis B virus infection is a common cause of viral hepatitis and affects 257 million people worldwide. Hepatitis B virus disease is a potentially life-threatening liver infection and a major global health problem that puts people at high risk of death from cirrhosis and hepatocarcinoma. The present study sought to investigate the proportion of hepatitis B virus (HBV) and associated factors for its transmission among people aged at least 15 years in three selected cities of Burundi attending the HBV screening campaign. Methods:We conducted a cross-sectional design by selecting conveniently 629 consenting participants aged at least 15 years during the screening campaign in three selected cities of Burundi namely Gitega, Rumonge and Cankuzo in June 2022. During the campaign, a structured questionnaire was administered by trained healthcare workers to collect socio-demographic and behavioural characteristics, as well as the history of exposure to HBV. HBV screening tests were performed with Cypress Diagnostics HBsAg Cards (Hulshout, Belgium). Univariate and multivariable logistic regression analyses were used to assess factors associated with HBV infection in the screened participants. Results:The study included 629 participants, 8.43% of whom tested positive for hepatitis B viral infection, with a mean age of 37.84 (SD=13.9) years. The participants were predominantly found in the over 50 years age group (31.1%) and the 18-30 years age group at 26.69%, the married (70.6%), the female (57.71%), and the farmers (60.25%), Rumonge city dwellers (33.39%), and those with a primary school level (36.25%). In this study, the associated factors with viral hepatitis B infection were residence in Cankuzo (OR=2, CI= 1-4, p=.04), and history of sharing sharp materials (OR=1.8, CI=1-3.3, P=.03). Conclusion:HBV infection was significantly associated with residence in Cankuzo and sharing sharp materials. HBV infection is endemic in these three provincial cities namely Cankuzo, Gitega and Rumonge. Given the various ways for HBV infection to occur within a general population, control of hepatitis B and its associated factors is one of the highest priorities in order to mitigate its transmission and monitor continuous exposure among Burundian population. There needs to be more help in the form of screening, immunizations for adults and other preventative measures, as well as treatment for the patients.