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Molecular data and analysis outputs are being integrated into malaria surveillance efforts to provide valuable programmatic insights for national malaria control programs (NMCPs). A plethora of studies from diverse geographies have demonstrated that malaria parasite genetic data can be an important tool for drug resistance monitoring, species identification, outbreak analysis, and transmission characterization. Despite many successful research efforts, there are still important knowledge gaps hindering practical translation of each of these use cases for NMCPs. Here, we leverage epidemiological modeling and time-series data of 2035 genetic sequences collected in Thiès, Senegal from 2006-2018 to provide a quantitative and setting-specific assessment of the levels, trends, and connectivity of malaria transmission. We also identify the genetic features that are the most informative for inferring transmission in Thiès, such as the fraction of the population with multiple infections and the persistence of parasite lineages across multiple transmission seasons. The model fitting and uncertainty quantification framework also reveals a significant decrease in the level of malaria transmission around 2013. This difference coincides with a large-scale drought and bed net campaign by the NMCP and USAID and is independently corroborated by geo-spatial models of incidence in Thiès. We find that genetically identical samples are more likely to be geographically clustered even at the neighborhood scale; and moreover, these lineages propagate non-randomly around the city. Our approach and results provide quantitative guidance for the interpretation of malaria parasite genetic data from Thiès, Senegal and indicates the value of increased malaria genomic surveillance for NMCPs.

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 in households under different field condition. This study investigated survival of different LLIN brands in Senegal.Methods: 12,608 LLINs were distributed in 5 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 model were allowed to estimate independent survival by net type and by area (rural/urban). The complement of survival, attrition and median survival time of each LLIN brand, was determined as those nets that were missing because they were reported given away, destroyed and thrown, 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 three 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 a weak physical integrity and its median survival due to wear and tear was below three 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. It appears that in Senegal, conical nets may be retained longer. This study suggests that a distribution of preferred LLIN brand, accompanied by good communication on care and repair, could lead to increased effective lifespan, and allow for longer intervals between universal coverage campaigns.

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.

Background Northern Senegal is a zone of very low malaria transmission, with an annual incidence of Methods A modified snowball sampling survey of nomadic pastoralists was conducted in five districts in northern Senegal during September and October 2014. Demographic information and dried blood spots were collected. Multiplex bead-based assays were used to assess antibody responses to merozoite surface protein (MSP-119) antigen of the four primary Plasmodium species, as well as circumsporozoite protein (CSP) and liver stage antigen (LSA-1) of Plasmodium falciparum. Results In the five study districts, 1472 individuals were enrolled, with a median age of 22 years (range 1 to 80 years). Thirty-two percent of subjects were under 14 years and 57% were male. The overall seroprevalence of P. falciparum MSP-119, CSP and LSA-1 antibodies were 45, 12 and 5%, respectively. Plasmodium falciparum MSP-119 antibody responses increased significantly with age in all study areas, and were significantly higher among males. The highest seroprevalence to P. falciparum antigens was observed in the Kanel district (63%) and the lowest observed in Podor (28%). Low seroprevalence was observed for non-falciparum species in all the study sites: 0.4, 0.7 and 1.8%, respectively, for Plasmodium ovale, Plasmodium vivax and Plasmodium malariae MSP-1. Antibody responses to P. vivax were observed in all study sites except Kanel. Conclusion Prevalence of P. falciparum MSP-119 antibodies and increases by study participant age provided data for low levels of exposure among this transient nomadic population. In addition, antibody responses to P. falciparum short half-life markers (CSP and LSA-1) and non-falciparum species were low. Further investigations are needed to understand the exposure of the Fulani population to P. vivax.

Summary Adding low-dose primaquine to malaria treatment reduced gametocyte carriage by 73%. Patients who received primaquine had more frequent hemoglobinuria and there was a greater reduction in haemoglobin concentration in G6PD-deficient patients. One patient who received primaquine developed moderately severe anemia., Introduction More information is needed about the safety of low-dose primaquine in populations where G6PD deficiency is common. Methods Adults with Plasmodium falciparum malaria were randomized to receive 1 of 3 artemisinin combination therapies (ACTs) with or without primaquine (0.25 mg/kg). Glucose-6-phosphate dehydrogenase (G6PD) status was determined using a rapid test. Patients were followed for 28 days to record hemoglobin concentration, adverse events, and gametocyte carriage. The primary end point was the change in Hb at day 7. Results In sum, 274 patients were randomized, 139 received an ACT alone, and 135 received an ACT + primaquine. The mean reduction in Hb at day 7 was similar in each group, a difference in the ACT + PQ versus the ACT alone group of −0.04 g/dL (95% confidence interval [CI] −0.23, 0.31), but the effect of primaquine differed according to G6PD status. In G6PD-deficient patients the drop in Hb was 0.63 g/dL (95% CI 0.03, 1.24) greater in those who received primaquine than in those who received an ACT alone. In G6PD-normal patients, the reduction in Hb was 0.22 g/dL (95% CI −0.08, 0.52) less in those who received primaquine (interaction P = .01). One G6PD normal patient who received primaquine developed moderately severe anaemia (Hb < 8 g/dL). Dark urine was more frequent in patients who received primaquine. Primaquine was associated with a 73% (95% CI 24–90) reduction in gametocyte carriage (P = .013). Conclusion Primaquine substantially reduced gametocyte carriage. However, the fall in Hb concentration at day 7 was greater in G6PD-deficient patients who received primaquine than in those who did not and one patient who received primaquine developed moderately severe anemia. Clinical Trial registration PACTR201411000937373 (www.pactr.org)

To study the effects of malaria-control interventions on parasite population genomics, we examined a set of 1,007 samples of the malaria parasite Plasmodium falciparum collected in Thies, Senegal between 2006 and 2013. The parasite samples were genotyped using a molecular barcode of 24 SNPs. About 35% of the samples grouped into subsets with identical barcodes, varying in size by year and sometimes persisting across years. The barcodes also formed networks of related groups. Analysis of 164 completely sequenced parasites revealed extensive sharing of genomic regions. In at least two cases we found first-generation recombinant offspring of parents whose genomes are similar or identical to genomes also present in the sample. An epidemiological model that tracks parasite genotypes can reproduce the observed pattern of barcode subsets. Quantification of likelihoods in the model strongly suggests a reduction of transmission from 2006–2010 with a significant rebound in 2012–2013. The reduced transmission and rebound were confirmed directly by incidence data from Thies. These findings imply that intensive intervention to control malaria results in rapid and dramatic changes in parasite population genomics. The results also suggest that genomics combined with epidemiological modeling may afford prompt, continuous, and cost-effective tracking of progress toward malaria elimination.

Background Malaria transmission in Senegal is highly stratified, from low in the dry north to moderately high in the moist south. In northern Senegal, along the Senegal River Valley and in the Ferlo semi-desert region, annual incidence is less than five cases per 1000 inhabitants. Many nomadic pastoralists have permanent dwellings in the Ferlo Desert and Senegal River Valley, but spend dry season in the south with their herds, returning north when the rains start, leading to a concern that this population could contribute to ongoing transmission in the north. Methods A modified snowball sampling survey was conducted at six sites in northern Senegal to determine the malaria prevention and treatment seeking practices and parasite prevalence among nomadic pastoralists in the Senegal River Valley and the Ferlo Desert. Nomadic pastoralists aged 6 months and older were surveyed during September and October 2014, and data regarding demographics, access to care and preventive measures were collected. Parasite infection was detected using rapid diagnostic tests (RDTs), microscopy (thin and thick smears) and polymerase chain reaction (PCR). Molecular barcodes were determined by high resolution melting (HRM). Results Of 1800 participants, 61% were male. Sixty-four percent had at least one bed net in the household, and 53% reported using a net the night before. Only 29% had received a net from a mass distribution campaign. Of the 8% (142) who reported having had fever in the last month, 55% sought care, 20% of whom received a diagnostic test, one-third of which (n = 5) were reported to be positive. Parasite prevalence was 0.44% by thick smear and 0.50% by PCR. None of the molecular barcodes identified among the nomadic pastoralists had been previously identified in Senegal. Conclusions While access to and utilization of malaria control interventions among nomadic pastoralists was lower than the general population, parasite prevalence was lower than expected and sheds doubt on the perception that they are a source of ongoing transmission in the north. The National Malaria Control Program is making efforts to improve access to malaria prevention and case management for nomadic populations. Electronic supplementary material The online version of this article (doi:10.1186/s12936-017-2055-x) contains supplementary material, which is available to authorized users.

Background Seasonal Malaria Chemoprevention (SMC) with sulfadoxine-pyrimethamine (SP) plus amodiaquine (AQ), given each month during the transmission season, is recommended for children living in areas of the Sahel where malaria transmission is highly seasonal. The recommendation for SMC is currently limited to children under five years of age, but, in many areas of seasonal transmission, the burden in older children may justify extending this age limit. This study was done to determine the effectiveness of SMC in Senegalese children up to ten years of age. Methods and Findings SMC was introduced into three districts over three years in central Senegal using a stepped-wedge cluster-randomised design. A census of the population was undertaken and a surveillance system was established to record all deaths and to record all cases of malaria seen at health facilities. A pharmacovigilance system was put in place to detect adverse drug reactions. Fifty-four health posts were randomised. Nine started implementation of SMC in 2008, 18 in 2009, and a further 18 in 2010, with 9 remaining as controls. In the first year of implementation, SMC was delivered to children aged 3–59 months; the age range was then extended for the latter two years of the study to include children up to 10 years of age. Cluster sample surveys at the end of each transmission season were done to measure coverage of SMC and the prevalence of parasitaemia and anaemia, to monitor molecular markers of drug resistance, and to measure insecticide-treated net (ITN) use. Entomological monitoring and assessment of costs of delivery in each health post and of community attitudes to SMC were also undertaken. About 780,000 treatments were administered over three years. Coverage exceeded 80% each month. Mortality, the primary endpoint, was similar in SMC and control areas (4.6 and 4.5 per 1000 respectively in children under 5 years and 1.3 and 1.2 per 1000 in children 5-9 years of age; the overall mortality rate ratio [SMC: no SMC] was 0.90, 95% CI 0.68–1.2, p = 0.496). A reduction of 60% (95% CI 54%–64%, p < 0.001) in the incidence of malaria cases confirmed by a rapid diagnostic test (RDT) and a reduction of 69% (95% CI 65%–72%, p < 0.001) in the number of treatments for malaria (confirmed and unconfirmed) was observed in children. In areas where SMC was implemented, incidence of confirmed malaria in adults and in children too old to receive SMC was reduced by 26% (95% CI 18%–33%, p < 0.001) and the total number of treatments for malaria (confirmed and unconfirmed) in these older age groups was reduced by 29% (95% CI 21%–35%, p < 0.001). One hundred and twenty-three children were admitted to hospital with a diagnosis of severe malaria, with 64 in control areas and 59 in SMC areas, showing a reduction in the incidence rate of severe disease of 45% (95% CI 5%–68%, p = 0.031). Estimates of the reduction in the prevalence of parasitaemia at the end of the transmission season in SMC areas were 68% (95% CI 35%–85%) p = 0.002 in 2008, 84% (95% CI 58%–94%, p < 0.001) in 2009, and 30% (95% CI -130%–79%, p = 0.56) in 2010. SMC was well tolerated with no serious adverse reactions attributable to SMC drugs. Vomiting was the most commonly reported mild adverse event but was reported in less than 1% of treatments. The average cost of delivery was US$0.50 per child per month, but varied widely depending on the size of the health post. Limitations included the low rate of mortality, which limited our ability to detect an effect on this endpoint. Conclusions SMC substantially reduced the incidence of outpatient cases of malaria and of severe malaria in children, but no difference in all-cause mortality was observed. Introduction of SMC was associated with an overall reduction in malaria incidence in untreated age groups. In many areas of Africa with seasonal malaria, there is a substantial burden in older children that could be prevented by SMC. SMC in older children is well tolerated and effective and can contribute to reducing malaria transmission. Trial Registration ClinicalTrials.gov NCT00712374, In a stepped-wedge cluster-randomized trial, Paul J. Milligan and colleagues determine the effectiveness of SMC in Senegalese children up to ten years of age., Author Summary Why was this study done? SMC was originally intended for children under five years of age. In many areas of the sub-Sahel, there is a substantial burden of malaria in older children; this may justify extending the age range of SMC. This study was done in central Senegal to evaluate the effectiveness of SMC when given to children up to ten years of age. What did the researchers do and find? SMC was introduced into the area served by 54 health posts by district health teams over three years using a randomised stepped-wedge design. Malaria cases were detected at outpatient clinics and in hospitals, and deaths were recorded through a demographic surveillance system. SMC reduced the incidence of malaria in children up to ten years of age by 60%. No reduction in all-cause child deaths was observed, but the incidence of severe malaria was reduced by 45%. SMC administered to children up to ten years of age led to a reduction in malaria incidence in older age groups by 26%. What do these findings mean? SMC given to children up to ten years of age is highly effective in preventing malaria in children and can contribute to reducing overall malaria transmission. SMC programmes have started in 11 countries. In many of these countries, there is a substantial burden of malaria in older children. The findings of this study indicate that a much greater impact could be achieved by extending the age range of SMC.

Background: The National Malaria Control Programme in Senegal, introduced since 2006, artemisinin-based combination therapy (ACT administration) for the treatment of uncomplicated malaria cases. In this framework, an anti-malarial pharmacovigilance plan was developed and implemented in all public health services. This study investigated the occurrence of Adverse Drug Events (ADEs) after ACT. Methods: The study was conducted between January 2007 and December 2009. It was based on spontaneous reports of ADEs in public health facilities. Data on patient demographic characteristics, dispensing facility, adverse signs and symptoms and causality were collected from a total of 123 patients. Results: The age range of these patients was six months to 93 years with a mean of 25.9 years. Of the reported symptoms, 46.7% were related to the abdomen and the digestive system. Symptoms related to the nervous system, skin and subcutaneous tissue, circulatory and respiratory systems and general symptoms and signs were 7%, 9.7%, 3.5% and 31.3%, respectively. Causality results linked 14.3% of symptoms to Falcimon W (Artesunate-Amodiaquine) with certainty. Effects were classified as mild and severe in 69.1% and 7.3% of cases respectively while 23.6% were serious. All patients with serious ADEs were hospitalized. One death was reported in a patient who had taken 24 pills at once. Conclusion: These results confirm the need to develop and implement pharmacovigilance systems in malaria endemic countries in order to monitor the safety of anti-malarial treatments.

Background Effective case management of malaria requires prompt diagnosis and treatment within 24 hours. Home-based management of malaria (HMM) improves access to treatment for populations with limited access to health facilities. In Senegal, an HMM pilot study in 2008 demonstrated the feasibility of integrated use of RDTs and ACT in remote villages by volunteer Home Care Providers (HCP). Scale-up of the strategy began in 2009, reaching 408 villages in 2009 and 861 villages in 2010. This paper reports the results of the scale-up in the targeted communities and the impact of the strategy on malaria in the formal health sector. Methods Data reported by the HCPs were used to assess their performance in 2009 and 2010, while routine malaria morbidity and mortality data were used to assess the impact of the HMM programme. Two high transmission regions where HMM was not implemented until 2010 were used as a comparison. Results and discussion From July 2009 through May 2010, 12582 suspected cases were managed by HCPs, 93% (11672) of whom were tested with an RDT. Among those tested, 37% (4270) had a positive RDT, 97% (4126) of whom were reported treated and cured. Home care providers referred 6871 patients to health posts for management: 6486 with a negative RDT, 119 infants Conclusion Home-based management of malaria including diagnosis with RDT and treatment based on test results is a promising strategy to improve the access of remote populations to prompt and effective management of uncomplicated malaria and to decrease mortality due to malaria. When scaled-up to serve remote village communities in the regions of Senegal with the highest malaria prevalence, home care providers demonstrated excellent adherence to guidelines, potentially contributing to a decrease in hospital deaths attributed to malaria.

Background While WHO recently recommended universal parasitological confirmation of suspected malaria prior to treatment, debate has continued as to whether wide-scale use of rapid diagnostic tests (RDTs) can achieve this goal. Adherence of health service personnel to RDT results has been poor in some settings, with little impact on anti-malarial drug consumption. The Senegal national malaria control programme introduced universal parasite-based diagnosis using malaria RDTs from late 2007 in all public health facilities. This paper assesses the impact of this programme on anti-malarial drug consumption and disease reporting. Methods and Findings Nationally-collated programme data from 2007 to 2009 including malaria diagnostic outcomes, prescription of artemisinin-based combination therapy (ACT) and consumption of RDTs in public health facilities, were reviewed and compared. Against a marked seasonal variation in all-cause out-patient visits, non-malarial fever and confirmed malaria, parasite-based diagnosis increased nationally from 3.9% of reported malaria-like febrile illness to 86.0% over a 3 year period. The prescription of ACT dropped throughout this period from 72.9% of malaria-like febrile illness to 31.5%, reaching close equivalence to confirmed malaria (29.9% of 584873 suspect fever cases). An estimated 516576 courses of inappropriate ACT prescription were averted. Conclusions The data indicate high adherence of anti-malarial prescribing practice to RDT results after an initial run-in period. The large reduction in ACT consumption enabled by the move from symptom-based to parasite-based diagnosis demonstrates that effective roll-out and use of malaria RDTs is achievable on a national scale through well planned and structured implementation. While more detailed information on management of parasite-negative cases is required at point of care level to assess overall cost-benefits to the health sector, considerable cost-savings were achieved in ACT procurement. Programmes need to be allowed flexibility in management of these funds to address increases in other programmatic costs that may accrue from improved diagnosis of febrile disease.