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Multiple-strain (polygenomic) infections are a ubiquitous feature of Plasmodium falciparum parasite population genetics. Under simple assumptions of superinfection, polygenomic infections are hypothesized to be the result of multiple infectious bites. As a result, polygenomic infections have been used as evidence of repeat exposure and used to derive genetic metrics associated with high transmission intensity. However, not all polygenomic infections are the result of multiple infectious bites. Some result from the transmission of multiple, genetically related strains during a single infectious bite (cotransmission). Superinfection and cotransmission represent two distinct transmission processes, and distinguishing between the two could improve inferences regarding parasite transmission intensity. Here, we describe a new metric, RH, that utilizes the correlation in allelic state (heterozygosity) within polygenomic infections to estimate the likelihood that the observed complexity resulted from either superinfection or cotransmission. RH is flexible and can be applied to any type of genetic data. As a proof of concept, we used RH to quantify polygenomic relatedness and estimate cotransmission and superinfection rates from a set of 1,758 malaria infections genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode. Contrary to expectation, we found that cotransmission was responsible for a significant fraction of 43% to 53% of the polygenomic infections collected in three distinct epidemiological regions in Senegal. The prediction that polygenomic infections frequently result from cotransmission stresses the need to incorporate estimates of relatedness within polygenomic infections to ensure the accuracy of genomic epidemiology surveillance data for informing public health activities.

Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we report complete viral genomes from 17 previously undetected DENV cases from the city of Thiès. In total we identified 19 cases of DENV in a cohort of 198 individuals with fever collected in October and November 2018. We detected 3 co-circulating serotypes; DENV 3 was the most frequent accounting for 11/17 sequences (65%), 4 (23%) were DENV2 and 2 (12%) were DENV1. Sequences were most similar to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

Dengue virus is a major and rapidly growing public health concern in tropic and subtropic regions across the globe. In late 2018, Senegal experienced its largest dengue virus outbreak to date, covering several regions. However, little is known about the genetic diversity of dengue virus (DENV) in Senegal. Here we used molecular tools including metagenomic sequencing to identify 19 previously undetected dengue virus cases from the city of Thiès and assemble 17 complete virus genomes. DENV3 was the most frequent serotype; 11 sequences (65%) were DENV3, 4 sequences were DENV2 and 2 were DENV1. Sequences were closest to recent sequences from West Africa, suggesting ongoing local circulation of viral populations; however, detailed inference is limited by the scarcity of available genomic data. We did not find clear associations with reported clinical signs or symptoms, highlighting the importance of testing for diagnosing febrile diseases. Overall, these findings expand the known range of DENV in Senegal, and underscore the need for better genomic characterization of DENV in West Africa.

While investigating a signal of adaptive evolution in humans at the gene LARGE, we encountered an intriguing finding by Dr. Stefan Kunz that the gene plays a critical role in Lassa virus binding and entry. This led us to pursue field work to test our hypothesis that natural selection acting on LARGE—detected in the Yoruba population of Nigeria—conferred resistance to Lassa Fever in some West African populations. As we delved further, we conjectured that the “emerging” nature of recently discovered diseases like Lassa fever is related to a newfound capacity for detection, rather than a novel viral presence, and that humans have in fact been exposed to the viruses that cause such diseases for much longer than previously suspected. Dr. Stefan Kunz’s critical efforts not only laid the groundwork for this discovery, but also inspired and catalyzed a series of events that birthed Sentinel, an ambitious and large-scale pandemic prevention effort in West Africa. Sentinel aims to detect and characterize deadly pathogens before they spread across the globe, through implementation of its three fundamental pillars: Detect, Connect, and Empower. More specifically, Sentinel is designed to detect known and novel infections rapidly, connect and share information in real time to identify emerging threats, and empower the public health community to improve pandemic preparedness and response anywhere in the world. We are proud to dedicate this work to Stefan Kunz, and eagerly invite new collaborators, experts, and others to join us in our efforts.

Background The monitoring of Plasmodium falciparum sensitivity to anti-malarial drugs is a necessity for effective case management of malaria. This species is characterized by a strong resistance to anti-malarial drugs. In Senegal, the first cases of chloroquine resistance were reported in the Dakar region in 1988 with nearly 7% population prevalence, reaching 47% by 1990. It is in this context that sulfadoxine–pyrimethamine temporarily replaced chloroquine as first line treatment in 2003, pending the introduction of artemisinin-based combination therapy in 2006. The purpose of this study is to assess the ex vivo sensitivity to different anti-malarial drugs of the P. falciparum population from Pikine. Methods Fifty-four samples were collected from patients with non-complicated malaria and aged between 2 and 20 years in the Deggo health centre in Pikine in 2014. An assay in which parasites are stained with 4′, 6-di-amidino-2-phenylindole (DAPI), was used to study the ex vivo sensitivity of isolates to chloroquine, amodiaquine, piperaquine, pyrimethamine, and dihydroartemisinin. High resolution melting was used for genotyping of pfdhps, pfdhfr, pfmdr1, and pfcrt genes. Results The mean IC50s of chloroquine, amodiaquine, piperaquine, dihydroartemisinin, and pyrimethamine were, respectively, 39.44, 54.02, 15.28, 2.23, and 64.70 nM. Resistance mutations in pfdhfr gene, in codon 437 of pfdhps gene, and an absence of mutation at position 540 of pfdhps were observed. Mutations in codons K76T of pfcrt and N86Y of pfmdr1 were observed at 51 and 11% population prevalence, respectively. A relationship was found between the K76T and N86Y mutations and ex vivo resistance to chloroquine. Conclusion An increase in sensitivity of isolates to chloroquine was observed. A high sensitivity to dihydroartemisinin was observed; whereas, a decrease in sensitivity to pyrimethamine was observed in the parasite population from Pikine.

Understanding genetic causes and effects of speciation in sympatric populations of sexually reproducing eukaryotes is challenging, controversial, and of practical importance for controlling rapidly evolving pests and pathogens. The major African malaria vector mosquito Anopheles gambiae sensu stricto (s.s.) is considered to contain two incipient species with strong reproductive isolation, hybrids between the M and S molecular forms being very rare. Following recent observations of higher proportions of hybrid forms at a few sites in West Africa, we conducted new surveys of 12 sites in four contiguous countries (The Gambia, Senegal, Guinea-Bissau, and Republic of Guinea). Identification and genotyping of 3499 A. gambiae s.s. revealed high frequencies of M/S hybrid forms at each site, ranging from 5 to 42%, and a large spectrum of inbreeding coefficient values from 0.11 to 0.76, spanning most of the range expected between the alternative extremes of panmixia and assortative mating. Year-round sampling over 2 years at one of the sites in The Gambia showed that M/S hybrid forms had similar relative frequencies throughout periods of marked seasonal variation in mosquito breeding and abundance. Genome-wide scans with an Affymetrix high-density single-nucleotide polymorphism (SNP) microarray enabled replicate comparisons of pools of different molecular forms, in three separate populations. These showed strong differentiation between M and S forms only in the pericentromeric region of the X chromosome that contains the molecular form-specific marker locus, with only a few other loci showing minor differences. In the X chromosome, the M/S hybrid forms were more differentiated from M than from S forms, supporting a hypothesis of asymmetric introgression and backcrossing.

In Africa, onchocerciasis and lymphatic filariasis (LF) are co-endemic in many areas. Current efforts to eliminate both diseases are through ivermectin-based mass drug administration (MDA). Years of ivermectin distribution for onchocerciasis may have interrupted LF transmission in certain areas. The Kédougou region, Senegal, is co-endemic for LF and onchocerciasis. Though MDA for onchocerciasis started in 1988, in 2014 albendazole had not yet been added for LF. The objective of this study was to assess in an integrated manner the LF and onchocerciasis status in the three districts of the Kédougou region after ≥10 years of ivermectin-based MDA. The study employed an African Programme for Onchocerciasis Control (APOC) onchocerciasis-related methodology. In the three districts, 14 villages close to three rivers that have Simulium damnosum breeding sites were surveyed. Convenience sampling of residents ≥5 years old was performed. Assessment for LF antigenemia by immunochromatographic testing (ICT) was added to skin snip microscopy for onchocerciasis. Participants were also tested for antibodies against Wb123 (LF) and Ov16 (onchocerciasis) antigens. In two districts, no participants were ICT or skin snip positive. In the third district, 3.5% were ICT positive and 0.7% were skin snip positive. In all the three districts, Wb123 prevalence was 0.6%. Overall, Ov16 prevalence was 6.9%. Ov16 prevalence among children 5–9 years old in the study was 2.5%. LF antigenemia prevalence was still above treatment threshold in one district despite ≥10 years of ivermectin-based MDA. The presence of Ov16 positive children suggested recent transmission of Onchocerca volvulus. This study showed the feasibility of integrated evaluation of onchocerciasis and LF but development of integrated robust methods for assessing transmission of both LF and onchocerciasis are needed to determine where MDA can be stopped safely in co-endemic areas., Author Summary Onchocerciasis and lymphatic filariasis (LF) are neglected tropical diseases caused by infection with filarial parasites, Onchocerca volvulus and Wuchereria bancrofti or Brugia species respectively. Efforts to eliminate both diseases are through ivermectin-based mass drug administration (MDA) for onchocerciasis and MDA with albendazole and ivermectin or diethylcarbamazine for LF. Both diseases overlap significantly in Africa and years of ivermectin-based MDA for onchocerciasis in co-endemic areas may have decreased or interrupted W. bancrofti transmission. Senegal is co-endemic for both diseases. As of 2014, 37 LF endemic districts had not received specific treatment for LF; however, eight of these districts had been receiving ivermectin-based MDA for onchocerciasis for more than 10 years. Here we estimated, using an APOC onchocerciasis-related methodology, the status of LF and onchocerciasis in three districts of Senegal after more than 10 years of ivermectin-based MDA for onchocerciasis. We demonstrated the feasibility of integrated evaluation of LF and onchocerciasis. The results showed that W. bancrofti antigenemia prevalence in one district was ≥1%. In the districts where we did not detect LF antigenemia among the participants a more robust evaluation like a transmission assessment survey among children is still needed to determine if the infection rate for W. bancrofti is below the transmission threshold and MDAs for LF are not needed. Despite the small sample of children included in this study, the onchocerciasis antibody prevalence among them was above the threshold recommended to stop MDA. This study provides another example of the complexities that encompass stop MDA decision-making in onchocerciasis and LF co-endemic areas.

In 2006, artemether-lumefantrine (AL) became the first-line treatment of uncomplicated malaria in Senegal, Mali, and the Gambia. To monitor its efficacy, between August 2011 and November 2014, children with uncomplicated Plasmodium falciparum malaria were treated with AL and followed up for 42 days. A total of 463 subjects were enrolled in three sites (246 in Senegal, 97 in Mali, and 120 in Gambia). No early treatment failure was observed and malaria infection cleared in all patients by day 3. Polymerase chain reaction (PCR)-adjusted adequate clinical and parasitological response (ACPR) was 100% in Mali, and the Gambia, and 98.8% in Senegal. However, without PCR adjustment, ACPR was 89.4% overall; 91.5% in Mali, 98.8% in Senegal, and 64.3% in the Gambia (the lower value in the Gambia attributed to poor compliance of the full antimalarial course). However, pfmdr1 mutations were prevalent in Senegal and a decrease in parasite sensitivity to artesunate and lumefantrine (as measured by ex vivo drug assay) was observed at all sites. Recrudescent parasites did not show Kelch 13 (K13) mutations and AL remains highly efficacious in these west African sites.

Background The use of artemisinin as a monotherapy resulted in the emergence of artemisinin resistance in 2005 in Southeast Asia. Monitoring of artemisinin combination therapy (ACT) is critical in order to detect and prevent the spread of resistance in endemic areas. Ex vivo studies and genotyping of molecular markers of resistance can be used as part of this routine monitoring strategy. One gene that has been associated in some ACT partner drug resistance is the Plasmodium falciparum multidrug resistance protein 1 (pfmdr1) gene. The purpose of this study was to assess the drug susceptibility of P. falciparum populations from Thiès, Senegal by ex vivo assay and typing molecular markers of resistance to drug components of ACT currently used for treatment. Methods The ex vivo susceptibility of 170 P. falciparum isolates to chloroquine, amodiaquine, lumefantrine, artesunate, and artemether was determined using the DAPI ex vivo assay. The high resolution melting technique was used to genotype the pfmdr1 gene at codons 86, 184 and 1246. Results A significant decrease in IC50 values was observed between 2012 and 2013: from 13.84 to 6.484 for amodiaquine, 173.4 to 113.2 for lumefantrine, and 39.72 to 18.29 for chloroquine, respectively. Increase of the wild haplotype NYD and the decrease of the mutant haplotype NFD (79 and 62.26 %) was also observed. A correlation was observed between the wild type allele Y184 in pfmdr1 and higher IC50 for all drugs, except amodiaquine. Conclusion This study has shown an increase in sensitivity over the span of two transmission seasons, marked by an increase in the WT alleles at pfmdr1. Continuous the monitoring of the ACT used for treatment of uncomplicated malaria will be helpful.

With the paradigm shift from the reduction of morbidity and mortality to the interruption of transmission, the focus of malaria control broadens from symptomatic infections in children ≤ 5 years of age to include asymptomatic infections in older children and adults. In addition, as control efforts intensify and the number of interventions increases, there will be decreases in prevalence, incidence and transmission with additional decreases in morbidity and mortality. Expected secondary consequences of these changes include upward shifts in the peak ages for infection (parasitemia) and disease, increases in the ages for acquisition of antiparasite humoral and cellular immune responses and increases in false-negative blood smears and rapid diagnostic tests. Strategies to monitor these changes must include: 1] studies of the entire population (that are not restricted to children ≤ 5 or ≤ 10 years of age), 2] study sites in both cities and rural areas (because of increasing urbanization across sub-Saharan Africa) and 3] innovative strategies for surveillance as the prevalence of infection decreases and the frequency of false-negative smears and rapid diagnostic tests increases.

L'origine des repas sanguins des femelles d'Anopheles gambiae s.l., d'An. funestus , d'An. pharoensis et d'An. rufipes a ete determinee par tests enzymatiques (precipitines ou ELISA) dans les differentes zones bioclimatiques du Senegal, les especes du complexe An. gambiae se sont montrees tres polyphages, mais se nourrissent preferentiellement sur homme dans toutes les localites prospectees. Des 4597 femelles endophiles d'An, gambiae s.l. collectees, 29 % etaient gorgees sur animal avec 7,5 % de repas mixtes dont principalement des repas homme-bovin et homme-equin. Une importante deviation animale a ete observee dans les localites proches des amenagements agricoles irrigues de la moyenne vallee du fleuve Senegal. La presence d'animaux, hotes alternatifs, la densite des populations culicidiennes et l'inaccessibilite des hotes humains semblent etre les facteurs les plus determinants de cette deviation animale. Le sang des differents animaux domestiques a ete retrouve dans l'estomac des moustiques recoltes, mais les bovides et equides ont ete les principaux hotes pour les femelles zoophages. An. funestus , moins repandu que An. gambiae s.l., a ete significativement plus zoophage dans le sud-est que dans le centre-ouest du pays. An. pharoensis , particulierement abondant dans le delta du fleuve Senegal, se nourrit essentiellement sur homme dans toutes les regions prospectees. An. rufipes , espece tres endophile, est strictement zoophage dans toutes les localites ou il est rencontre.

The study sites for the West African ICEMR are in three countries (The Gambia, Senegal, Mali) and are located within 750 km of each other. In addition, the National Malaria Control Programmes of these countries have virtually identical policies: (1) Artemisinin Combination Therapies (ACTs) for the treatment of symptomatic Plasmodium falciparum infection, (2) Long-Lasting Insecticide-treated bed Nets (LLINs) to reduce the Entomololgic Inoculation Rate (EIR), and (3) sulfadoxine-pyrimethamine for the Intermittent Preventive Treatment of malaria during pregnancy (IPTp). However, the prevalence of P. falciparum malaria and the status of malaria control vary markedly across the four sites with differences in the duration of the transmission season (from 4-5 to 10-11 months), the intensity of transmission (with EIRs from unmeasurably low to 4-5 per person per month), multiplicity of infection (from a mean of 1.0 to means of 2-5) and the status of malaria control (from areas which have virtually no control to areas that are at the threshold of malaria elimination). The most important priority is the need to obtain comparable data on the population-based prevalence, incidence and transmission of malaria before new candidate interventions or combinations of interventions are introduced for malaria control.

Three villages in the Senegal River basin were selected to study the biting and resting behavior of #Anopheles gambiae$ s.l. in relation to human habits, rainfalls, and rice culture irrigation. All inhabitants sleep outside throughout the year, mainly under poor quality bednets. Mosquitoes were collected host-seeking during the night on human bait outside and resting during the day inside and outside in pit shelters. #An. gambiae$ s.s. and #An. arabiensis$ fed mainly outside, the only place where hosts are available ; fed and gravid females resting indoors fed outside. The proportions of #An. gambiae$ s.s. and #An. arabiensis$ in outdoor biting catches and in indoor spray catches were not significantly different, but they differed from year to year with the latter sampling method. #An. gambiae$ s.s. predominated in 1990, a more wet and humid year, whereas #An. arabiensis$ was more common in 1991, which was an arid year. Both species are highly endophilic in this arid area where outdoor-resting places are limited. (Résumé d'auteur)

The classical cytological technique and a new PCR technique were compared for the identification of mosquito species of the Anopheles gambiae complex. Fifty seven specimens, caught in three different bioclimatic senegalese regions, were tested. Thirty two An. gambiae and 25 An. arabiensis were determined by both methods. All the results were similar. The advantages of each method are discussed.