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Abstract Background Drug resistance in Plasmodium falciparum is a major threat to malaria control efforts. Pathogen genomic surveillance could be invaluable for monitoring current and emerging parasite drug resistance. Methods Data from two decades (2000–2020) of continuous molecular surveillance of P. falciparum parasites from Senegal were retrospectively examined to assess historical changes in malaria drug resistance mutations. Several known drug resistance markers and their surrounding haplotypes were profiled using a combination of single nucleotide polymorphism (SNP) molecular surveillance and whole genome sequence based population genomics. Results This dataset was used to track temporal changes in drug resistance markers whose timing correspond to historically significant events such as the withdrawal of chloroquine (CQ) and the introduction of sulfadoxine-pyrimethamine (SP) in 2003. Changes in the mutation frequency at Pfcrt K76T and Pfdhps A437G coinciding with the 2014 introduction of seasonal malaria chemoprevention (SMC) in Senegal were observed. In 2014, the frequency of Pfcrt K76T increased while the frequency of Pfdhps A437G declined. Haplotype-based analyses of Pfcrt K76T showed that this rapid increase was due to a recent selective sweep that started after 2014. Discussion (Conclusion) The rapid increase in Pfcrt K76T is troubling and could be a sign of emerging amodiaquine (AQ) resistance in Senegal. Emerging AQ resistance may threaten the future clinical efficacy of artesunate-amodiaquine (ASAQ) and AQ-dependent SMC chemoprevention. These results highlight the potential of molecular surveillance for detecting rapid changes in parasite populations and stress the need to monitor the effectiveness of AQ as a partner drug for artemisinin-based combination therapy (ACT) and for chemoprevention.

Abstract Background Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Methods This study examined parasites from 3147 clinical infections sampled between the years 2012–2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. Results Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence ( 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was

Abstract The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.

In sub-Saharan Africa, temperatures are generally conducive to malaria transmission, and rainfall provides mosquitoes with optimal breeding conditions. The objective of this study is to assess the impact of future climate change on malaria transmission in West Africa using community-based vector-borne disease models, TRIeste (VECTRI). This VECTRI model, based on bias-corrected data from the Phase 6 Coupled Model Intercomparison Project (CMIP6), was used to simulate malaria parameters, such as the entomological inoculation rate (EIR). Due to the lack of data on confirmed malaria cases throughout West Africa, we first validated the forced VECTRI model with CMIP6 data in Senegal. This comparative study between observed malaria data from the National Malaria Control Program in Senegal (Programme National de Lutte contre le Paludisme, PNLP, PNLP) and malaria simulation data with the VECTRI (EIR) model has shown the ability of the biological model to simulate malaria transmission in Senegal. We then used the VECTRI model to reproduce the historical characteristics of malaria in West Africa and quantify the projected changes with two Shared Socio-economic Pathways (SSPs). The method adopted consists of first studying the climate in West Africa for a historical period (1950–2014), then evaluating the performance of VECTRI to simulate malaria over the same period (1950–2014), and finally studying the impact of projected climate change on malaria in a future period (2015–2100) according to the ssp245 ssp585 scenario. The results showed that low-latitude (southern) regions with abundant rainfall are the areas most affected by malaria transmission. Two transmission peaks are observed in June and October, with a period of high transmission extending from May to November. In contrast to regions with high latitudes in the north, semi-arid zones experience a relatively brief transmission period that occurs between August, September, and October, with the peak observed in September. Regarding projections based on the ssp585 scenario, the results indicate that, in general, malaria prevalence will gradually decrease in West Africa in the distant future. But the period of high transmission will tend to expand in the future. In addition, the shift of malaria prevalence from already affected areas to more suitable areas due to climate change is observed. Similar results were also observed with the ssp245 scenario regarding the projection of malaria prevalence. In contrast, the ssp245 scenario predicts an increase in malaria prevalence in the distant future, while the ssp585 scenario predicts a decrease. These findings are valuable for decision makers in developing public health initiatives in West Africa to mitigate the impact of this disease in the region in the context of climate change.

Abstract We here analyze data from the first year of an ongoing nationwide program of genetic surveillance of Plasmodium falciparum parasites in Senegal. The analysis is based on 1097 samples collected at health facilities during passive malaria case detection in 2019; it provides a baseline for analyzing parasite genetic metrics as they vary over time and geographic space. The study’s goal was to identify genetic metrics that were informative about transmission intensity and other aspects of transmission dynamics, focusing on measures of genetic relatedness between parasites. We found the best genetic proxy for local malaria incidence to be the proportion of polygenomic infections (those with multiple genetically distinct parasites), although this relationship broke down at low incidence. The proportion of related parasites was less correlated with incidence while local genetic diversity was uninformative. The type of relatedness could discriminate local transmission patterns: two nearby areas had similarly high fractions of relatives, but one was dominated by clones and the other by outcrossed relatives. Throughout Senegal, 58% of related parasites belonged to a single network of relatives, within which parasites were enriched for shared haplotypes at known and suspected drug resistance loci and at one novel locus, reflective of ongoing selection pressure.

Abstract Background The overlap in the epidemiology of malaria and helminths has been identified as a potential area to exploit for the development of an integrated control strategy that may help to achieve elimination of malaria and helminths. A randomized, controlled, observer-blind trial was conducted to assess the feasibility and safety of combining mass drug administration (MDA) for schistosomiasis and soil transmitted helminths (STH) with seasonal malaria chemoprevention (SMC) among children living in Senegal. Methods Female and male children aged 1–14 years were randomized 1:1:1, to receive Vitamin A and Zinc on Day 0, followed by SMC drugs (sulfadoxine-pyrimethamine and amodiaquine) on Days 1–3 (control group); or praziquantel and Vitamin A on Day 0, followed by SMC drugs on Days 1–3 (treatment group 1); or albendazole and praziquantel on Day 0, followed by SMC drugs on Days 1–3 (treatment group 2). Safety assessment was performed by collecting adverse events from all children for six subsequent days following administration of the study drugs. Pre- and post-intervention, blood samples were collected for determination of haemoglobin concentration, malaria microscopy, and PCR assays. Stool samples were analyzed using Kato-Katz, Merthiolate-iodine-formalin and PCR methods. Urine filtration, PCR and circulating cathodic antigen tests were also performed. Results From 9 to 22 June 2022, 627 children aged 1–14 years were randomized into the three groups described above. Mild, transient vomiting was observed in 12.6% (26/206) of children in treatment group 2, in 10.6% (22/207) in group 1, and in 4.2% (9/214) in the control group (p = 0.005). Pre-intervention, the geometric mean value of Plasmodium falciparum parasite density was highest among children who received albendazole, praziquantel with SMC drugs. Post-intervention, the parasite density was highest among children who received SMC drugs only. Children who received praziquantel and SMC drugs had a lower risk of developing severe anaemia than their counterparts who received SMC drugs alone (OR = 0.81, 95% CI 0.13–5.00, p = 0.63). Conclusions Integration of MDA for helminths with SMC drugs was safe and feasible among Senegalese children. These findings support further evaluation of the integrated control model. Trial registration: The study is registered at Clinical Trial.gov NCT05354258.

Abstract Background Malaria is endemic in Senegal, with seasonal transmission, and the entire population is at risk. In recent years, high malaria incidence has been reported in urban and peri-urban areas of Senegal. An urban landscape analysis was conducted in three cities to identify the malaria transmission indicators and human behavior that may be driving the increasing malaria incidence occurring in urban environments. Specifically, mosquito vector bionomics and human sleeping behaviors including outdoor sleeping habits were assessed to guide the optimal deployment of targeted vector control interventions. Methods Longitudinal entomological monitoring using human landing catches and pyrethrum spray catches was conducted from May to December 2019 in Diourbel, Kaolack, and Touba, the most populous cities in Senegal after the capital Dakar. Additionally, a household survey was conducted in randomly selected houses and residential Koranic schools in the same cities to assess house structures, sleeping spaces, sleeping behavior, and population knowledge about malaria and vector control measures. Results Of the 8240 Anopheles mosquitoes collected from all the surveyed sites, 99.4% (8,191) were An. gambiae s.l., and predominantly An. arabiensis (99%). A higher number of An. gambiae s.l. were collected in Kaolack (77.7%, n = 6496) than in Diourbel and Touba. The overall mean human biting rate was 14.2 bites per person per night (b/p/n) and was higher outdoors (15.9 b/p/n) than indoors (12.5 b/p/n). The overall mean entomological inoculation rates ranged from 3.7 infectious bites per person per year (ib/p/y) in Diourbel to 40.2 ib/p/y in Kaolack. Low anthropophilic rates were recorded at all sites (average 35.7%). Of the 1202 households surveyed, about 24.3% of household members slept outdoors, except during the short rainy season between July and October, despite understanding how malaria is transmitted and the vector control measures used to prevent it. Conclusion Anopheles arabiensis was the primary malaria vector in the three surveyed cities. The species showed an outdoor biting tendency, which represents a risk for the large proportion of the population sleeping outdoors. As all current vector control measures implemented in the country target endophilic vectors, these data highlight potential gaps in population protection and call for complementary tools and approaches targeting outdoor biting malaria vectors. Graphical Abstract

Urban malaria has become a challenge for most African countries due to urbanization, with increasing population sizes, overcrowding, and movement into cities from rural localities. The rapid expansion of cities with inappropriate water drainage systems, abundance of water storage habitats, coupled with recurrent flooding represents a concern for water-associated vector borne diseases, including malaria. This situation could threaten progress made towards malaria elimination in sub-Saharan countries, including Senegal, where urban malaria has presented as a threat to national elimination gains. To assess drivers of urban malaria in Senegal, a 5-month study was carried out from August to December 2019 in three major urban areas and hotspots for malaria incidence (Diourbel, Touba, and Kaolack) including the rainy season (August-October) and partly dry season (November-December). The aim was to characterize malaria vector larval habitats, vector dynamics across both seasons, and to identify the primary eco- environmental entomological factors contributing to observed urban malaria transmission. A total of 145 Anopheles larval habitats were found, mapped, and monitored monthly. This included 32 in Diourbel, 83 in Touba, and 30 in Kaolack. The number of larval habitats fluctuated seasonally, with a decrease during the dry season. In Diourbel, 22 of the 32 monitored larval habitats (68.75%) were dried out by December and considered temporary, while the remaining 10 (31.25%) were classified as permanent. In the city of Touba 28 (33.73%) were temporary habitats, and of those 57%, 71% and 100% dried up respectively by October, November, and December. However, 55 (66.27%) habitats were permanent water storage basins which persisted throughout the study. In Kaolack, 12 (40%) permanent and 18 (60%) temporary Anopheles larval habitats were found and monitored during the study. Three malaria vectors (An. arabiensis, An. pharoensis and An. funestus s.l.) were found across the surveyed larval habitats, and An. arabiensis was found in all three cities and was the only species found in the city of Diourbel, while An. arabiensis, An. pharoensis, and An. funestus s.l. were detected in the cities of Touba and Kaolack. The spatiotemporal observations of immature malaria vectors in Senegal provide evidence of permanent productive malaria vector larval habitats year-round in three major urban centers in Senegal, which may be driving high urban malaria incidence. This study aimed to assess the presence and type of anopheline larvae habitats in urban areas. The preliminary data will better inform subsequent detailed additional studies and seasonally appropriate, cost-effective, and sustainable larval source management (LSM) strategies by the National Malaria Control Programme (NMCP).

Abstract Background Routine continuous distribution (CD) of insecticide-treated nets (ITNs) has been an important part of an overall ITN strategy to complement mass campaigns since the early 2000s. The backbone of CD implementation for many sub-Saharan African countries is distribution through antenatal care (ANC) and Expanded Programme for Immunizations (EPI) channels. Performance of these channels is often not monitored closely at the national level, nor is it reviewed globally, unlike the oversight provided to mass campaigns. The question as to why every eligible pregnant woman and child attending these services does not get an ITN remains important and yet, unanswered. Methods ANC and EPI issuing rates from seven countries were reviewed with the aim of conducting a blinded multi-country analysis. Monthly data from January to December 2021 was extracted from each country’s health management information system and analysed jointly with a National Malaria Control Programme (NMCP) focal point. VectorLink CD assessment reports were also reviewed to glean key findings. Results ITN issuing rates varied across countries at ANC (31% to 93%) and EPI (39% to 92%). Across the seven countries, the median ITN issuing rate was 64% at ANC and 78% at EPI. Results varied greatly across months per country at both ANC and EPI. NMCP focal points are aware that mass campaigns often negatively affect implementation of ITN distribution through ANC and EPI, even though global and national guidelines emphasize sustaining CD during campaigns. Concerns were also raised about the standard ITN issuing rate indicator at ANC and even more so at EPI due to the denominator. Findings from CD assessments were similar across countries: ITN stock was inconsistent and sometimes inadequate, and updated guidelines on ITN distribution and utilization and funding for social behaviour change activities were lacking at the facility level. Conclusion The importance of optimizing ANC and EPI routine channels cannot be underscored enough. They are at the frontline to protect the most biologically vulnerable populations, i.e., pregnant women and unborn and young children. Although there are encouraging signs of improvement in issuing rates with some countries reaching optimal rates, further improvements are needed to ensure that every pregnant woman and young child receives the ITN to which they are entitled.

Abstract Background Long lasting insecticidal nets (LLIN) are one of the core components of global malaria prevention and control. The lifespan of LLIN varies widely depending on the population or environment, and randomized studies are required to compare LLIN inaccording to arbitrary thresholds households under different field conditions. This study investigated survival of different LLIN brands in Senegal. Methods Ten thousand six hundred eight LLINs were distributed in five regions, each stratified by rural and urban setting. As part of the longitudinal follow-up, 2222 nets were randomly sampled and monitored from 6 to 36 months. Using random effects for households, Bayesian models were used to estimate independent survival by net type (Interceptor®, Life Net®, MAGNet™, Netprotect®, Olyset® Net, PermaNet® 2.0 R, PermaNet® 2.0 C, Yorkool® LN) and by area (rural/urban). In addition to survival, median survival time and attrition of each LLIN brand was determined. Attrition was defined as nets that were missing because they were reported given away, destroyed and thrown away, or repurposed. Results Three net types had a proportion of survival above 80% after 24 months: Interceptor®87.8% (95% CI 80–93.4); conical PermaNet® 2.0 86.9% (95% CI 79.3–92.4) and Life Net® 85.6% (95% CI 75–93). At 36 months, conical PermaNet® 2.0 maintained a good survival rate, 79.5% (95% CI 65.9–88.8). The attrition due to redistributed nets showed that the two conical net types (PermaNet® 2.0 and Interceptor®) were more often retained by households and their median retention time was well above 3 years (median survival time = 3.5 years for PermaNet® 2.0 and median survival time = 4 years for Interceptor®). Despite this good retention, Interceptor® had weak physical integrity and its median survival due to wear and tear was below 3 years (median survival time = 2.4 years). The odds ratio of survival was 2.5 times higher in rural settings than in urban settings (OR 2.5; 95% CI 1.7–3.7). Conclusions Differences in survival among LLIN may be driven by brand, shape or environmental setting. In this study in Senegal, conical PermaNet® 2.0 were retained in households while rectangular PermaNet® 2.0 had lower retention, suggesting that net shape may play a role in retention and should be further investigated. Distribution of preferred LLIN shape, accompanied by good communication on care and repair, could lead to increased effective lifespan, and allow for longer intervals between universal coverage campaigns.

On the climate-health issue, studies have already attempted to understand the influence of climate change on the transmission of malaria. Extreme weather events such as floods, droughts, or heat waves can alter the course and distribution of malaria. This study aims to understand the impact of future climate change on malaria transmission using, for the first time in Senegal, the ICTP’s community-based vector-borne disease model, TRIeste (VECTRI). This biological model is a dynamic mathematical model for the study of malaria transmission that considers the impact of climate and population variability. A new approach for VECTRI input parameters was also used. A bias correction technique, the cumulative distribution function transform (CDF-t) method, was applied to climate simulations to remove systematic biases in the Coupled Model Intercomparison Project Phase 5 (CMIP5) global climate models (GCMs) that could alter impact predictions. Beforehand, we use reference data for validation such as CPC global unified gauge-based analysis of daily precipitation (CPC for Climate Prediction Center), ERA5-land reanalysis, Climate Hazards InfraRed Precipitation with Station data (CHIRPS), and African Rainfall Climatology 2.0 (ARC2). The results were analyzed for two CMIP5 scenarios for the different time periods: assessment: 1983–2005; near future: 2006–2028; medium term: 2030–2052; and far future: 2077–2099). The validation results show that the models reproduce the annual cycle well. Except for the IPSL-CM5B model, which gives a peak in August, all the other models (ACCESS1–3, CanESM2, CSIRO, CMCC-CM, CMCC-CMS, CNRM-CM5, GFDL-CM3, GFDL-ESM2G, GFDL-ESM2M, inmcm4, and IPSL-CM5B) agree with the validation data on a maximum peak in September with a period of strong transmission in August–October. With spatial variation, the CMIP5 model simulations show more of a difference in the number of malaria cases between the south and the north. Malaria transmission is much higher in the south than in the north. However, the results predicted by the models on the occurrence of malaria by 2100 show differences between the RCP8.5 scenario, considered a high emission scenario, and the RCP4.5 scenario, considered an intermediate mitigation scenario. The CanESM2, CMCC-CM, CMCC-CMS, inmcm4, and IPSL-CM5B models predict decreases with the RCP4.5 scenario. However, ACCESS1–3, CSIRO, NRCM-CM5, GFDL-CM3, GFDL-ESM2G, and GFDL-ESM2M predict increases in malaria under all scenarios (RCP4.5 and RCP8.5). The projected decrease in malaria in the future with these models is much more visible in the RCP8.5 scenario. The results of this study are of paramount importance in the climate-health field. These results will assist in decision-making and will allow for the establishment of preventive surveillance systems for local climate-sensitive diseases, including malaria, in the targeted regions of Senegal.

Abstract Background Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. Methods A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. Results Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. Conclusions These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.

Abstract Background Population-wide interventions using malaria testing and treatment might decrease the reservoir of Plasmodium falciparum infection and accelerate towards elimination. Questions remain about their effectiveness and evidence from different transmission settings is needed. Methods A pilot quasi-experimental study to evaluate a package of population-wide test and treat interventions was conducted in six health facility catchment areas (HFCA) in the districts of Kanel, Linguère, and Ranérou (Senegal). Seven adjacent HFCAs were selected as comparison. Villages within the intervention HFCAs were stratified according to the 2013 incidences of passively detected malaria cases, and those with an incidence ≥ 15 cases/1000/year were targeted for a mass test and treat (MTAT) in September 2014. All households were visited, all consenting individuals were tested with a rapid diagnostic test (RDT), and, if positive, treated with dihydroartemisinin-piperaquine. This was followed by weekly screening, testing and treatment of fever cases (PECADOM++) until the end of the transmission season in January 2015. Villages with lower incidence received only PECADOM++ or case investigation. To evaluate the impact of the interventions over that transmission season, the incidence of passively detected, RDT-confirmed malaria cases was compared between the intervention and comparison groups with a difference-in-difference analysis using negative binomial regression with random effects on HFCA. Results During MTAT, 89% (2225/2503) of households were visited and 86% (18,992/22,170) of individuals were tested, for a combined 77% effective coverage. Among those tested, 291 (1.5%) were RDT positive (range 0–10.8 by village), of whom 82% were

Several vector-borne diseases, such as malaria, are sensitive to climate and weather conditions. When unusual conditions prevail, for example, during periods of heavy rainfall, mosquito populations can multiply and trigger epidemics. This study, which consists of better understanding the link between malaria transmission and climate factors at a national level, aims to validate the VECTRI model (VECtor borne disease community model of ICTP, TRIeste) in Senegal. The VECTRI model is a grid-distributed dynamical model that couples a biological model for the vector and parasite life cycles to a simple compartmental Susceptible-Exposed-Infectious-Recovered (SEIR) representation of the disease progression in the human host. In this study, a VECTRI model driven by reanalysis data (ERA-5) was used to simulate malaria parameters, such as the entomological inoculation rate (EIR) in Senegal. In addition to the ERA5-Land daily reanalysis rainfall, other daily rainfall data come from different meteorological products, including the CPC Global Unified Gauge-Based Analysis of Daily Precipitation (CPC for Climate Prediction Center), satellite data from the African Rainfall Climatology 2.0 (ARC2), and the Climate Hazards InfraRed Precipitation with Station data (CHIRPS). Observed malaria data from the National Malaria Control Program in Senegal (PNLP/Programme National de Lutte contre le Paludisme au Senegal) and outputs from the climate data used in this study were compared. The findings highlight the unimodal shape of temporal malaria occurrence, and the seasonal malaria transmission contrast is closely linked to the latitudinal variation of the rainfall, showing a south–north gradient over Senegal. This study showed that the peak of malaria takes place from September to October, with a lag of about one month from the peak of rainfall in Senegal. There is an agreement between observations and simulations about decreasing malaria cases on time. These results indicate that the southern area of Senegal is at the highest risk of malaria spread outbreaks. The findings in the paper are expected to guide community-based early-warning systems and adaptation strategies in Senegal, which will feed into the national malaria prevention, response, and care strategies adapted to the needs of local communities.

An amendment to this paper has been published and can be accessed via the original article.

Abstract Background The diagnosis of malaria cases in regions where the malaria burden has decreased significantly and prevalence is very low is more challenging, in part because of reduced clinical presumption of malaria. The appearance of a cluster of malaria cases with atypical symptoms in Mbounguiel, a village in northern Senegal where malaria transmission is low, in September 2018 exemplifies this scenario. The collaboration between the National Malaria Control Programme (NMCP) at the Senegal Ministry of Health and the Laboratory of Parasitology and Mycology at Cheikh Anta Diop University worked together to evaluate this cluster of malaria cases using molecular and serological tools. Methods Malaria cases were diagnosed primarily by rapid diagnostic test (RDT), and confirmed by photo-induced electron transfer-polymerase chain reaction (PET-PCR). 24 single nucleotide polymorphisms (SNPs) barcoding was used for Plasmodium falciparum genotyping. Unbiased metagenomic sequencing and Luminex-based multi-pathogen antibody and antigen profiling were used to assess exposure to other pathogens. Results Nine patients, of 15 suspected cases, were evaluated, and all nine samples were found to be positive for P. falciparum only. The 24 SNPs molecular barcode showed the predominance of polygenomic infections, with identifiable strains being different from one another. All patients tested positive for the P. falciparum antigens. No other pathogenic infection was detected by either the serological panel or metagenomic sequencing. Conclusions This work, undertaken locally within Senegal as a collaboration between the NMCP and a research laboratory at University of Cheikh Anta Diop (UCAD) revealed that a cluster of malaria cases were caused by different strains of P. falciparum. The public health response in real time demonstrates the value of local molecular and genomics capacity in affected countries for disease control and elimination.