Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples.

MalariaGEN is a data-sharing network that enables groups around the world to work together on the genomic epidemiology of malaria. Here we describe a new release of curated genome variation data on 7,000 Plasmodium falciparum samples from MalariaGEN partner studies in 28 malaria-endemic countries. High-quality genotype calls on 3 million single nucleotide polymorphisms (SNPs) and short indels were produced using a standardised analysis pipeline. Copy number variants associated with drug resistance and structural variants that cause failure of rapid diagnostic tests were also analysed.  Almost all samples showed genetic evidence of resistance to at least one antimalarial drug, and some samples from Southeast Asia carried markers of resistance to six commonly-used drugs. Genes expressed during the mosquito stage of the parasite life-cycle are prominent among loci that show strong geographic differentiation. By continuing to enlarge this open data resource we aim to facilitate research into the evolutionary processes affecting malaria control and to accelerate development of the surveillance toolkit required for malaria elimination.

Multi-locus genotyping reveals established endemicity of a geographically distinct Plasmodium vivax population in Mauritania, West Africa.

BACKGROUND: Plasmodium vivax has been recently discovered as a significant cause of malaria in Mauritania, although very rare elsewhere in West Africa. It has not been known if this is a recently introduced or locally remnant parasite population, nor whether the genetic structure reflects epidemic or endemic transmission. METHODOLOGY/PRINCIPAL FINDINGS: To investigate the P. vivax population genetic structure in Mauritania and compare with populations previously analysed elsewhere, multi-locus genotyping was undertaken on 100 clinical isolates, using a genome-wide panel of 38 single nucleotide polymorphisms (SNPs), plus seven SNPs in drug resistance genes. The Mauritanian P. vivax population is shown to be genetically diverse and divergent from populations elsewhere, indicated consistently by genetic distance matrix analysis, principal components analyses, and fixation indices. Only one isolate had a genotype clearly indicating recent importation, from a southeast Asian source. There was no linkage disequilibrium in the local parasite population, and only a small number of infections appeared to be closely genetically related, indicating that there is ongoing genetic recombination consistent with endemic transmission. The P. vivax diversity in a remote mining town was similar to that in the capital Nouakchott, with no indication of local substructure or of epidemic population structure. Drug resistance alleles were virtually absent in Mauritania, in contrast with P. vivax in other areas of the world. CONCLUSIONS/SIGNIFICANCE: The molecular epidemiology indicates that there is long-standing endemic transmission that will be very challenging to eliminate. The virtual absence of drug resistance alleles suggests that most infections have been untreated, and that this endemic infection has been more neglected in comparison to P. vivax elsewhere.

[Seasonal transmission of malaria in the Senegal River Valley: case study of the city of Kaedi-Mauritanie]. / Transmission saisonnière du paludisme au niveau de la vallée du fleuve Sénégal: cas de la ville de Kaédi-Mauritanie.

INTRODUCTION: In the face of environmental and climatic changes both ongoing and planned, the epidemiology of malaria in the city of Kaedi (Mauritania), along the Senegal River Valley, requires special attention. Some cases of malaria have been registered in the health facilities throughout the year, with an average of 150,000 annual suspected cases and climatic and ecological conditions which are now favorable for seasonal transmission. METHODS: We conducted two cross-sectional descriptive surveys in the city of Kaedi in September 2014 (wet season) and in May 2015 (dry season). Our cluster sampling involved 700 households. Microscopic examination was performed in all household members. Furthermore, larval surveys, early morning wildlife spraying and nocturnal traps breaking were performed. RESULTS: During both seasons, 9.313 thick smears were manufactured, 15 were positive, with a plasmodium prevalence rate of 0.16%. Among these, 12 were positive in the dry season and 3 in the rainy season. Plasmodium prevalence rate was 0.26% and 0.06% respectively in the dry season (n = 4642) and in the wet season (n = 4671). In the rainy season, rates were 0.04% (2/4671) and 0.02% (1/4671) respectively for Plasmodium malariae and Plasmodium falciparum. The only species found in the dry season was Plasmodium falciparum. Entomological investigations showed the presence of a single species of Anopheles mosquito, Anopheles gambia (two in the rainy season and six in the dry season). Larval surveys showed that the larval fauna was dominated by Culex larvae (99.6%). Anopheles larvae (0.4%) were collected only during the dry season. CONCLUSION: Despite low malaria transmission in the city of Kaedi, in a context of lack of rainfall, health authorities should implement a strategy for malaria elimination in the wilayas of the Senegal River.

Multi-population genomic analysis of malaria parasites indicates local selection and differentiation at the gdv1 locus regulating sexual development.

Parasites infect hosts in widely varying environments, encountering diverse challenges for adaptation. To identify malaria parasite genes under locally divergent selection across a large endemic region with a wide spectrum of transmission intensity, genome sequences were obtained from 284 clinical Plasmodium falciparum infections from four newly sampled locations in Senegal, The Gambia, Mali and Guinea. Combining these with previous data from seven other sites in West Africa enabled a multi-population analysis to identify discrete loci under varying local selection. A genome-wide scan showed the most exceptional geographical divergence to be at the early gametocyte gene locus gdv1 which is essential for parasite sexual development and transmission. We identified a major structural dimorphism with alternative 1.5 kb and 1.0 kb sequence deletions at different positions of the 3'-intergenic region, in tight linkage disequilibrium with the most highly differentiated single nucleotide polymorphism, one of the alleles being very frequent in Senegal and The Gambia but rare in the other locations. Long non-coding RNA transcripts were previously shown to include the entire antisense of the gdv1 coding sequence and the portion of the intergenic region with allelic deletions, suggesting adaptive regulation of parasite sexual development and transmission in response to local conditions.

Distribution of Plasmodium spp. infection in asymptomatic carriers in perennial and low seasonal malaria transmission settings in West Africa.

BACKGROUND: Since 2000, substantial progress has been made in reducing malaria worldwide. However, some countries in West Africa remain a hotspot for malaria with all age groups at risk. Asymptomatic carriers of Plasmodium spp. are important sources of infections for malaria vectors and thus contribute to the anchoring of the disease in favourable eco-epidemiological settings. The objective of this study was to assess the asymptomatic malaria case rates in Korhogo and Kaedi, two urban areas in northern Côte d'Ivoire and southern Mauritania, respectively. METHODS: Cross-sectional surveys were carried out during the rainy season in 2014 and the dry season in 2015 in both settings. During each season, 728 households were randomly selected and a household-based questionnaire was implemented to collect demographic and epidemiological data, including of malaria preventive methods used in communities. Finger-prick blood samples were obtained for biological examination using microscopy and rapid diagnostic tests (RDTs). RESULTS: Overall, 2672 households and 15 858 consenting participants were surveyed. Plasmodium spp. infection was confirmed in 12.4% (n = 832) and 0.3% (n = 22) of the assessed individuals in Korhogo and Kaedi, respectively. In Korhogo, the prevalence of asymptomatic malaria was 10.5% (95% CI: 9.7-11.2) as determined by microscopy and 9.3% (95% CI: 8.6-10.0%) when assessed by RDT. In Kaedi, asymptomatic malaria prevalence was 0.2% (95% CI: 0.1-0.4%) according to microscopy, while all RDTs performed were negative (n = 8372). In Korhogo, asymptomatic malaria infection was significantly associated with age and season, with higher risk within the 5-14 years-old, and during the rainy season. In Kaedi, the risk of asymptomatic malaria infection was associated with season only (higher during the dry season; crude OR (cOR): 6.37, 95% CI: 1.87-21.63). P. falciparum was the predominant species identified in both study sites representing 99.2% (n = 825) in Korhogo and 59.1% (n = 13) in Kaedi. Gametocytes were observed only in Korhogo and only during the rainy season at 1.3% (95% CI: 0.7-2.4%). CONCLUSIONS: Our findings show a low prevalence of clinical malaria episodes with a significant proportion of asymptomatic carriers in both urban areas. National policies for malaria infections are focused on treatment of symptomatic cases. Malaria control strategies should be designed for monitoring and managing malaria infections in asymptomatic carriers. Additional measures, including indoor residual spraying, effective use of long-lasting insecticidal nets is strongly needed to reduce the number of Plasmodium spp. infections in Korhogo and Kaedi.

Prevalence and seasonal transmission of Schistosoma haematobium infection among school-aged children in Kaedi town, southern Mauritania.

BACKGROUND: Mauritania is at the fringe of transmission of human schistosomiasis, which mainly occurs in the southern and southeastern parts of the country. This study aimed to assess the influence of rainfall seasonality on the prevalence of Schistosoma haematobium infection among school-aged children in Kaedi, southern Mauritania. METHODS: Cross-sectional surveys (i.e. parasitological, malacological and observations on water-related human activities) were carried out in Kaedi between September 2014 and May 2015, during both the wet and dry seasons. A total of 2162 children aged 5-15 years provided a single urine sample that was subjected to S. haematobium diagnosis. Snails were sampled and checked for cercarial shedding. Water contact patterns of the local population were recorded by direct observation. RESULTS: The prevalence of S. haematobium was 4.0% (86/2162, 95% confidence interval (CI): 3.2-4.9%) with a geometric mean egg count per 10 ml of urine of 3.7 (95% CI: 2.8-4.3). Being male (adjusted odds ratio (aOR) 1.78, 95% CI: 1.13-2.80), being at primary school (aOR 1.73, 95% CI: 1.04-2.87) and dry season (aOR 0.56, 95% CI: 0.35-0.89) were significantly associated with S. haematobium. Among 284 potential intermediate host snail specimens collected over the rainy and dry seasons, three species were identified: Bulinus senegalensis (n = 13) and B. forskalii (n = 161) in the rainy season, and B. truncatus (n = 157) in the wet season. No snail was shedding cercariae. On average, seven human water contacts were recorded per hour per observer over a 28-day observation period. Twelve types of water contact activities were identified among which, swimming/bathing was predominant (n = 3788, 36.9%), followed by washing clothes (n = 2016, 19.7%) and washing dishes (n = 1322, 12.9%). Females (n = 5270, 51.4%) were slightly more in contact with water than males (n = 4983, 48.6%). The average time spent in the water per person per day was 14.2 min (95% CI: 13.8-14.6 min). The frequency and duration of water contact followed a seasonal pattern. CONCLUSION: Our findings demonstrate a low prevalence and intensity of S. haematobium among school-aged children in Kaedi. Appropriate integrated control measures, including health education among at-risk communities and snail control may help to interrupt transmission of S. haematobium in Kaedi.

Detection of the Northeastern African Rift Valley Fever Virus Lineage During the 2015 Outbreak in Mauritania.

BACKGROUND: Rift Valley fever (RVF) is an acute viral anthropozoonosis that causes epizootics and epidemics among livestock population and humans. Multiple emergences and reemergences of the virus have occurred in Mauritania over the last decade. This article describes the outbreak that occurred in 2015 in Mauritania and reports the results of serological and molecular investigations of blood samples collected from suspected RVF patients. METHODS: An RVF outbreak was reported from 14 September to 26 November 2015 in Mauritania. Overall, 184 suspected cases from different localities were identified by 26 health facilities. Blood samples were collected and tested by enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) at the Institut Pasteur de Dakar (IPD). Sequencing of partial genomes and phylogenetic analyses were performed on RT-PCR-positive samples. As part of routine surveillance at IPD, samples were also screened for dengue, yellow fever, West Nile, Crimean Congo hemorrhagic fever, Zika, and Chikungunya viruses by ELISA and RT-PCR. RESULTS: Of the 184 suspected cases, there were 57 confirmed cases and 12 deaths. Phylogenetic analysis of the sequences indicated an emergence of a virus that originated from Northeastern Africa. Our results show co-circulation of other arboviruses in Mauritania-dengue, Crimean Congo hemorrhagic fever, and West Nile viruses. CONCLUSION: The Northeastern Africa lineage of RVF was responsible for the outbreak in Mauritania in 2015. Co-circulation of multiples arboviruses was detected. This calls for systematic differential diagnosis and highlights the need to strengthen arbovirus surveillance in Africa.

Population genetic structure and adaptation of malaria parasites on the edge of endemic distribution.

To determine whether the major human malaria parasite Plasmodium falciparum exhibits fragmented population structure or local adaptation at the northern limit of its African distribution where the dry Sahel zone meets the Sahara, samples were collected from diverse locations within Mauritania over a range of ~1000 km. Microsatellite genotypes were obtained for 203 clinical infection samples from eight locations, and Illumina paired-end sequences were obtained to yield high coverage genomewide single nucleotide polymorphism (SNP) data for 65 clinical infection samples from four locations. Most infections contained single parasite genotypes, reflecting low rates of transmission and superinfection locally, in contrast to the situation seen in population samples from countries further south. A minority of infections shared related or identical genotypes locally, indicating some repeated transmission of parasite clones without recombination. This caused some multilocus linkage disequilibrium and local divergence, but aside from the effect of repeated genotypes there was minimal differentiation between locations. Several chromosomal regions had elevated integrated haplotype scores (|iHS|) indicating recent selection, including those containing drug resistance genes. A genomewide FST scan comparison with previous sequence data from an area in West Africa with higher infection endemicity indicates that regional gene flow prevents genetic isolation, but revealed allele frequency differentiation at three drug resistance loci and an erythrocyte invasion ligand gene. Contrast of extended haplotype signatures revealed none to be unique to Mauritania. Discrete foci of infection on the edge of the Sahara are genetically highly connected to the wider continental parasite population, and local elimination would be difficult to achieve without very substantial reduction in malaria throughout the region.

Severe Human Illness Caused by Rift Valley Fever Virus in Mauritania, 2015.

BACKGROUND: Rift Valley Fever epizootics are characterized by numerous abortions and mortality among young animals. In humans, the illness is usually characterized by a mild self-limited febrile illness, which could progress to more serious complications.Objectives. The aim of the present prospective study was to describe severe clinical signs and symptoms of Rift Valley Fever in southern Mauritania. PATIENTS AND METHODS: Suspected cases were enrolled in Kiffa (Assaba) and Aleg (Brakna) Hospital Centers from September 1 to November 7, 2015, based on the presence of fever, hemorrhagic or meningoencephalitic syndromes, and probable contact with sick animals. Suspected cases were confirmed by enzyme-linked immunosorbent assay (ELISA) and reverse transcriptase-polymerase chain reaction (RT-PCR). RESULTS: There were thirty-one confirmed cases. The sex ratio M/F and the average age were 2.9 and 25 years old [range, 4-70 years old], respectively. Mosquito bites, direct contact with aborted or dead animals, and frequent ingestion of milk from these animals were risk factors observed in all patients. Hemorrhagic and neurological manifestations were observed in 81% and 13% of cases, respectively. The results of laboratory analysis showed high levels of transaminases, creatinine, and urea associated with thrombocytopenia, anemia, and leukopenia. All patients who died (42%) had a hemorrhagic syndrome and 3 of them had a neurological complication. Among the cured patients, none had neurologic sequelae. CONCLUSION: The hemorrhagic form was the most common clinical manifestation of RVF found in southern Mauritania and was responsible for a high mortality rate. Our results justify the implementation of a continuous epidemiological surveillance.

Malaria in three epidemiological strata in Mauritania.

BACKGROUND: Malaria epidemiology in Mauritania has been characterized on the basis of epidemiological strata, defined by climatic and geographic features, which divide the country into three zones: Sahelian zone, Sahelo-Saharan transition zone, and Saharan zone. The association between geographic stratification and malaria transmission was assessed through a series of parasitological and entomological surveys. METHODS: Surveys were conducted during the 'cool' dry season in 2011, 'hot' dry season in 2012, and rainy season in 2013 in a total of 12 sentinel sites. Finger-prick capillary blood samples were collected from children aged 2-9 years old in randomly selected households for microscopic examination and rapid diagnostic test for malaria. Adult mosquitoes were sampled by pyrethrum spray catch and CDC light traps and identified using morphological keys and molecular tools. RESULTS: Of 3445 children included, 143 (4.15 %) were infected with malaria parasites including Plasmodium falciparum (n = 71, 2.06 %), Plasmodium vivax (57, 1.65 %), P. falciparum-P. vivax (2, 0.06 %), Plasmodium ovale (12, 0.35 %), and Plasmodium malariae (1, 0.03 %). A large majority of P. falciparum infections were observed in the Sahelo-Saharan zone. Malaria prevalence (P < 0.01) and parasite density (P < 0.001) were higher during the rainy season (2013), compared to cool dry season (2011). Plasmodium vivax was mainly observed in the Saharan region [43 of 59 (73 %) P. vivax infections], mostly in Nouakchott districts, with no significant seasonal variation. Of 3577 mosquitoes captured, 1014 (28.3 %) belonged to Anopheles spp. Anopheles gambiae was the predominant species in all three epidemiological strata during the 'cool' dry season in 2011 but was absent in all study sites, except for Teyarett district in Nouakchott, during the 'hot' dry season in 2012. During the rainy season in 2013, An. gambiae, Anopheles arabiensis, Anopheles pharoensis, and Anopheles rufipes were abundant in different zones. CONCLUSIONS: The results of the present study support the stratification of malaria in Mauritania. However, the Sahelian zone had the lowest malaria prevalence, while the Sahelo-Saharan zone had the highest malaria burden. Local changes due to anthropogenic factors (i.e., human migration, urbanization, malaria interventions) should be considered in order to optimize the control strategy.

Widespread distribution of Plasmodium vivax malaria in Mauritania on the interface of the Maghreb and West Africa.

BACKGROUND: Plasmodium vivax is very rarely seen in West Africa, although specific detection methods are not widely applied in the region, and it is now considered to be absent from North Africa. However, this parasite species has recently been reported to account for most malaria cases in Nouakchott, the capital of Mauritania, which is a large country at the interface of sub-Saharan West Africa and the Maghreb region in northwest Africa. METHODS: To determine the distribution of malaria parasite species throughout Mauritania, malaria cases were sampled in 2012 and 2013 from health facilities in 12 different areas. These sampling sites were located in eight major administrative regions of the country, within different parts of the Sahara and Sahel zones. Blood spots from finger-prick samples of malaria cases were processed to identify parasite DNA by species-specific PCR. RESULTS: Out of 472 malaria cases examined, 163 (34.5 %) had P. vivax alone, 296 (62.7 %) Plasmodium falciparum alone, and 13 (2.8 %) had mixed P. falciparum and P. vivax infection. All cases were negative for Plasmodium malariae and Plasmodium ovale. The parasite species distribution showed a broad spectrum, P. vivax being detected at six of the different sites, in five of the country's major administrative regions (Tiris Zemmour, Tagant, Brakna, Assaba, and the capital Nouakchott). Most cases in Nouakchott were due to P. vivax, although proportions vary significantly among different health facilities in the city. In the northern town of Zouérat, all cases were due to P. vivax, whereas almost all cases in the south of the country were due to P. falciparum. All P. vivax cases tested were Duffy blood group positive. CONCLUSIONS: It is important that P. vivax is recognized to be a widespread cause of malaria in Mauritania, occurring in diverse regions. This should be noted by the World Health Organization, as it has significant implications for diagnosis, treatment and control of malaria in the northwestern part of Africa.

Spatial air pollution modelling for a West-African town.

Land use regression (LUR) modelling is a common approach used in European and Northern American epidemiological studies to assess urban and traffic related air pollution exposures. Studies applying LUR in Africa are lacking. A need exists to understand if this approach holds for an African setting, where urban features, pollutant exposures and data availability differ considerably from other continents. We developed a parsimonious regression model based on 48-hour nitrogen dioxide (NO2) concentrations measured at 40 sites in Kaédi, a medium sized West-African town, and variables generated in a geographic information system (GIS). Road variables and settlement land use characteristics were found to be important predictors of 48-hour NO2 concentration in the model. About 68% of concentration variability in the town was explained by the model. The model was internally validated by leave-one-out cross-validation and it was found to perform moderately well. Furthermore, its parameters were robust to sampling variation. We applied the model at 100 m pixels to create a map describing the broad spatial pattern of NO2 across Kaédi. In this research, we demonstrated the potential for LUR as a valid, cost-effective approach for air pollution modelling and mapping in an African town. If the methodology were to be adopted by environmental and public health authorities in these regions, it could provide a quick assessment of the local air pollution burden and potentially support air pollution policies and guidelines.

Absence of dry season Plasmodium parasitaemia, but high rates of reported acute respiratory infection and diarrhoea in preschool-aged children in Kaédi, southern Mauritania.

BACKGROUND: The epidemiology of malaria in the Senegal River Gorgol valley, southern Mauritania, requires particular attention in the face of ongoing and predicted environmental and climate changes. While "malaria cases" are reported in health facilities throughout the year, past and current climatic and ecological conditions do not favour transmission in the dry season (lack of rainfall and very high temperatures). Moreover, entomological investigations in neighbouring regions point to an absence of malaria transmission in mosquito vectors in the dry season. Because the clinical signs of malaria are non-specific and overlap with those of other diseases (e.g. acute respiratory infections and diarrhoea), new research is needed to better understand malaria transmission patterns in this region to improve adaptive, preventive and curative measures. METHODS: We conducted a multipurpose cross-sectional survey in the city of Kaédi in April 2011 (dry season), assessing three major disease patterns, including malaria. Plasmodium spp. parasite rates were tested among children aged 6-59 months who were recruited from a random selection of households using a rapid diagnostic test and microscopic examination of Giemsa-stained thick and thin blood films. Acute respiratory infection and diarrhoea were the two other diseases investigated, administering a parental questionnaire to determine the reported prevalence among participating children. FINDINGS: No Plasmodium infection was found in any of the 371 surveyed preschool-aged children using two different diagnostic methods. Acute respiratory infections and diarrhoea were reported in 43.4% and 35.0% of the participants, respectively. About two thirds of the children with acute respiratory infections and diarrhoea required medical follow-up by a health worker. CONCLUSIONS: Malaria was absent in the present dry season survey in the capital of the Gorgol valley of Mauritania, while acute respiratory infections and diarrhea were highly prevalent. Surveys should be repeated towards the end of rainy season, which will enhance our understanding of the potential changes in malaria transmission in a region known as 'hot spot' of predicted climate change.

Distribution, host preference and infection rates of malaria vectors in Mauritania.

This study reports for the first time on the distribution, host preference and infection rates of malaria vectors in Mauritania. It was conducted during an outbreak of Rift valley fever. Three anopheline species were reported. An. arabiensis was the predominant species observed in all regions whereas An. pharoensis and An. funestus were observed along the south border in the Senegal River valley where extensive irrigation schemes are present. The distribution limits of anopheline species were observed from the Senegal River basin in the Trarza region up to the south limit of the Saharan desert in Tidjikja city. Overall, all An. funestus and An. pharoensis were fed respectively on human and ovine hosts whereas the mean anthropophilic rate of An. gambiae s.l. was 53%. A low Plasmodium falciparum infection rate was observed for species of the An. gambiae complex (0.17%) represented mainly by An. arabiensis. Because of the specific nature of this investigation, longitudinal studies are essential to better characterize the malaria vectors and their respective role in malaria transmission.

Preliminary study of malaria incidence in Nouakchott, Mauritania.

BACKGROUND: Malaria is one of the main motives for outpatient consultation and hospitalization in Mauritania. However, its incidence remains unclear because of diagnostic problems and insufficient epidemiological data. METHODS: Between April and August 2007, a study on malaria incidence was carried out in Nouakchott city. A total of 237 febrile outpatients, from all Nouakchott districts, attending the two main hospitals of the city were investigated. Finger prick and blood dried filter paper samples were performed to prepare thick and thin films and nested-PCR for malaria parasite species identification and density. The accuracy of diagnosis of 'presumptive malaria', assigned by clinicians and based on fever and other malaria suggestive symptoms, was assessed. Entomological investigations based on morphological and molecular characterization of Anopheline species were conducted in Dar Naïm district. RESULTS: Malaria prevalence rate was 25.7% (61/237), the majority of positive blood slides as well as nested-PCR products were due to Plasmodium vivax 70.5% (43/61) and Plasmodium ovale 24.6% (15/61). Two malaria patients, both with P. vivax, have never travelled out of Nouakchott and seem likely to have been autochthonous (3.3%). Of the 237 individuals included in the survey, 231(97.5%) were clinically diagnosed and treated as malaria cases. 26.4% of clinically diagnosed cases were positive for Plasmodium using microscopic examination and PCR. Thus, false positive cases constituted 73.6% (170/231) of the clinically diagnosed malaria cases. The search for mosquito vectors in Dar Naïm district allowed morphological and molecular identification of Anopheles arabiensis and Anopheles pharoensis. CONCLUSION: This study demonstrates that, during the hot and dry season, Plasmodium species responsible of recurrent malaria (P. vivax and P. ovale) are the dominant species in Nouakchott city and autochthonous malaria cases exist but are rare. Clinical diagnosis of malaria has a very low positive predicted value. The systematic use of microscopy-based diagnosis and/or rapid diagnostic tests should be considered to appropriately manage malaria and non-malaria cases.