Malaria remains one of the leading causes of morbidity and mortality in sub-Saharan Africa, disproportionately affecting children under five years of age. In 2024, the World Health Organization (WHO) reported an estimated 249 million malaria cases and 608,000 deaths, with more than 94% occurring in Africa [1]. Burkina Faso is among the highest-burden countries, reporting an incidence of approximately 400 cases per 1000 population per year, and malaria continues to be the primary cause of outpatient consultations and childhood mortality [1][2].

Over the past two decades, Burkina Faso has introduced multiple malaria control strategies to reduce transmission. These include the large-scale deployment of long-lasting insecticide-treated nets (LLITNs), expanded access to rapid diagnostic tests (RDTs), artemisinin-based combination therapies (ACTs), and the implementation of seasonal malaria chemoprevention (SMC) for children aged 3 - 59 months since 2014 [3][4]. The latter has demonstrated high protective efficacy, reducing clinical malaria episodes by up to 75% when correctly administered [5]. In addition, malaria vaccination (RTS, S and R21) is now part of the national malaria control tools [6][7]. Importantly, combining the malaria vaccine with SMC has been shown to yield greater protection than either intervention alone, reducing clinical malaria by 62% and severe malaria by 70% in a West African trial [8].

Despite these advances, Plasmodium infections remain widespread. These silent infections, common among young children in the Sahel, can account for 20% - 40% parasite prevalence at the onset of the rainy season [9]-[12]. Children who carry parasites contribute to the sustainability of malaria transmission and may experience breakthrough infections [13] despite the deployment of preventive measures. When SMC is not effective in clearing parasites, either because of poor adherence or non-compliance, these persistent infections may progress to clinical malaria [14][15], which, if not promptly treated, can evolve into severe disease with life-threatening consequences [16][17]. Such residual carriage may ultimately reduce the apparent impact of SMC or vaccination by sustaining the parasite reservoir and enabling progression to illness [16].

Understanding the prevalence and determinants of Plasmodium parasite carriage (Plasmodium infection) prior to SMC campaigns is therefore critical. Baseline parasitemia may be useful for understanding short-term SMC effectiveness, identifying higher-risk groups such as older preschool children, and informing the integration of emerging tools, including malaria vaccines, into national malaria control strategies. In fact, a recent study in Northern Cameroon and southern Senegal reported a high baseline prevalence of RDT-confirmed asymptomatic P. falciparum infections prior to the SMC implementation [18]. In the context of large-scale SMC deployment, the protective impact against clinical malaria was high when coverage was adequate, but real-world constraints may reduce the effectiveness and maintain a reservoir of asymptomatic infections [19].

This study aimed to estimate the prevalence of Plasmodium infection by microscopy among children (6 to 59 months) prior to the first SMC round and to identify demographic and household determinants of Plasmodium infections.

This study shows that the overall prevalence of infections was substantial, and older pre-school children carried a disproportionate burden of asymptomatic parasitemia. Age-related gradients similar to those observed here have been consistently documented across the Sahel region, where parasite carriage typically ranges from 20% to 40% at the start of the rainy season [9]-[12][20]. Infants exhibited the lowest prevalence, likely reflecting protection from residual maternal antibodies, lower mobility, and closer household head/caregiver protection [21]-[23]. In contrast, increased independence, outdoor activity, and cumulative exposure may explain the sharp increase in infection among children older than two years, consistent with longitudinal studies from several sub-Saharan African countries [20][24].

The high prevalence of parasitemia observed nearly before the SMC delivery has important operational implications. The protective efficacy of SP–AQ depends on both clearance of existing parasitemia and short-term chemoprophylaxis [19][25][26]. A large baseline reservoir may reduce the observable impact of SMC if parasites are not fully cleared due to incomplete adherence, suboptimal dosing, vomiting, or chemoprophylactic failure [25]. Persistent parasitemia at the time of SMC administration has been associated with increased risk of breakthrough malaria during the same transmission season [14]. If untreated, such infections may progress from asymptomatic to clinical malaria, and eventually to severe disease, especially in younger children [14][15]. These findings highlight the need for improved adherence monitoring, community counselling, and pharmacovigilance during SMC campaigns.

The detection of gametocytes (2.6%) provides further evidence of sustained transmission potential despite preventive measures. Even low-density gametocytemia is sufficient to infect mosquitoes and perpetuate the transmission between SMC cycles [27]. These results support the need to reinforce integrated vector management, particularly ITN durability, replacement campaigns, and complementary strategies addressing outdoor or early-evening biting, which has been increasingly documented in West Africa [28].

Importantly, children older than three years had the highest prevalence and parasite densities, suggesting that this age group represents a particularly important reservoir. Although still eligible for SMC, their increasing exposure and waning maternal immunity may reduce the relative protection provided by chemoprevention alone. Evidence from recent West African trials shows that combining SMC with malaria vaccination (RTS, S/AS01 or R21/Matrix-M) yields additive protection and substantially reduces clinical malaria by more than 60% [6][8][29][30]. Vaccination of this older pre-school group may therefore enhance protection during the high-risk period when exposure intensifies.

No socioeconomic or household-level characteristics were associated with infection risk, likely reflecting the relative socioeconomic homogeneity of rural Nanoro. The lack of association with malaria prevention practices, dominated by reported ITN use, probably reflects behavioral and entomological factors rather than absence of effect [31]. In Burkina Faso, substantial outdoor and early evening vector biting could limit ITN protection, which is largely confined to indoor sleeping hours. As a result, an estimated 10 percent of malaria transmission persists despite high ITN coverage, occurring when human activity overlaps with vector exposure outside net use [31]. In addition, self-reported ITN use often overestimates actual protection by 8 to 13.6 percent, potentially biasing assessments of ITN effectiveness [32][33]. These findings highlight the persistence of residual transmission and the need for complementary malaria control strategies.

This study has several strengths. HDSS-linked random sampling ensured strong population representativeness, while data collection conducted immediately prior to the SMC implementation enabled an accurate estimation of baseline infection prevalence. The use of GEE-based modified Poisson regression provided valid population-averaged effect estimates and appropriately accounted for within-village clustering. Nevertheless, some limitations should be considered. Microscopy may have underestimated the true prevalence by missing sub-patent infections detectable only by molecular methods such as PCR. The cross-sectional design captures infection status at a single time point, precluding assessment of temporal dynamics or causality. In addition, malaria prevention practices were self-reported and therefore subject to recall and social desirability bias.

Despite these limitations, the study provides valuable insights into the asymptomatic malaria reservoir in a high-burden Sahelian setting and underscores the need to adapt malaria control strategies, particularly for older pre-school children who remain highly exposed despite their eligibility for seasonal malaria chemoprevention.

Asymptomatic Plasmodium infections were highly prevalent among children under five in Nanoro immediately before the 2025 SMC cycle, with older pre-school children being the main reservoir of infection and transmission. Age was the main determinant of infection risk, whereas socioeconomic and household characteristics showed no meaningful influence. These findings underscore the need to strengthen malaria control strategies for children aged 2 - 4 years, who experience increasing exposure but remain incompletely protected by SMC alone.

Enhanced community-based surveillance, improved adherence monitoring during SMC, and reinforcement of ITN and vector management strategies are essential to reduce the asymptomatic reservoir. Integrating malaria vaccination with SMC could provide additional protection, particularly for older pre-school children who carry the highest burden of the infection. This baseline assessment will be critical for evaluating the impact of the MalNut intervention and guiding future malaria control strategies in Burkina Faso.

The study was approved by the ethic committee of Burkina Faso (Comité d’Ethique pour la Recherche en Santé, n˚2024-10-308). Written informed consent was obtained from parents or legal guardians prior to participation.

The datasets generated and/or analysed during the current manuscript are not publicly available due to ethical and confidentiality restrictions but are available from the corresponding author on reasonable request, subject to institutional approval and applicable data-sharing regulations.

This work was conducted within the framework of the MalNut study and was funded by EDESIA. The funder supported the implementation of the study but had no role in the analysis and interpretation of the data or in the writing of the manuscript, unless otherwise stated.

TR conceived the analysis idea, conducted the statistical analysis, interpreted the data, and drafted the first version of the manuscript. HT, SO, PS and BK contributed to study design and supervision of field implementation. IB, MKS, WEC WGM and KD contributed to data collection and laboratory procedures. HT, PS and BK contributed to data interpretation and critical revision of the manuscript. All authors read and approved the final manuscript.

We sincerely thank the children and their parents or legal guardians for participating in this study. We are also grateful to the field workers, microscopists, data management staff, and community leaders in the Nanoro health district for their valuable support during study implementation. We acknowledge the support of the Clinical Research Unit of Nanoro and all members of the MalNut study team for their contribution to the conduct of this work.

The authors used ChatGPT (OpenAI) solely for English language editing and improvement of writing clarity. All scientific content, interpretation, and conclusions were developed and validated by the authors.