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Dengue is the leading mosquito-borne viral cause of human illness and death. More than four billion people globally are at risk of dengue virus (DENV) infection, and most infections are asymptomatic or present with a non-specific febrile illness. We characterise the first complete DENV-2 genome from Sierra Leone, recovered from a febrile adult who tested RT-PCR–positive. The sequence was identified as DENV-2 genotype II, lineage F.1.1. Phylogenetically, the Sierra Leone genome formed a well-supported sister lineage with a 2024 USA DENV-2 genome; both were nested within but clearly diverged from Indian DENV-2 sequences (2021–2022) and were distinct from the Réunion DENV-2 clade. The degree of genetic divergence was incompatible with a recent or direct import of a South Asian lineage and was more consistent with diversification in an under-sampled Indian Ocean/South Asia network or outside this region in Africa. With a single Sierra Leone genome, the source and extent of local transmission remain unresolved. These findings underscore the benefits of integrating differential diagnostics and genomics into routine care for febrile illness and sustaining regional arboviral surveillance.

In 2020, a sylvatic dengue virus serotype 2 infection outbreak resulted in 59 confirmed dengue cases in Kedougou, Senegal, suggesting those strains might not require adaptation to reemerge into urban transmission cycles. Large-scale genomic surveillance and updated molecular diagnostic tools are needed to effectively prevent dengue virus infections in Senegal.

Background Chikungunya virus (CHIKV) is a mosquito-borne Alphavirus that has caused several epidemics around the world in recent years. CHIKV is endemic in eastern Senegal, particularly in Kédougou, where epidemiological and virological surveillance is implemented in combination with the 4S network. In August 2023, an outbreak was reported in Kédougou, which rapidly spread to Tambacounda. Epidemiological and virological investigations were carried out in both regions by teams from the Institut Pasteur de Dakar, the WHO, the Africa CDC and the Senegalese Ministry of Health. Methods The team first visited residential areas of confirmed cases, then a definition of suspected cases including socio-demographic aspects and clinical signs was used in an active door-to-door search for other cases. The blood samples were tested for CHIKV infection by real-time RT-PCR and anti-CHIKV IgM ELISA. Continuous variables were described using mean ± SD or median (IQR), and categorical variables as percentages with 95% confidence intervals, with group comparisons via Pearson’s χ 2 or Fisher’s exact test. Kruskal–Wallis tests assessed differences in age across case categories. A multivariate logistic regression (variables with p  < 0.25 in bivariate analysis, manual topdown stepwise selection) was fitted, and model fit evaluated using the Hosmer–Lemeshow test with interaction terms retained at p  < 0.05. Results Out of 1070 blood samples tested, 315 confirmed cases were identified, resulting in an infection rate of 29.4%. There were no deaths. Under 15 and 15–30 age groups, male gender, headache, myalgia, joint pain, asthenia, and retro-orbital pain were among the factors associated with these cases. Conclusions The present study provides clinical and epidemiological characteristics of CHIKV-positive cases, emphasizing the large geographical extension of the epidemic. It outlines the largest chikungunya outbreak documented in Senegal to date, hypothesizes sylvatic transmission, and describes the changing epidemiologic profile of CHIKV. It also stresses that a One-Health strategy is of primary importance in effectively controlling zoonoses.

Chikungunya virus has caused millions of cases worldwide over the last twenty years, with recent outbreaks in Kedougou region in the southeastern Senegal, West Africa. Genomic characterization highlights that an ongoing epidemic in Kedougou in 2023 is not due to an introduction event but caused by the re-emergence of an endemic strain evolving linearly in a sylvatic context.

Senegal is hyperendemic for dengue. Since 2017, outbreaks have been noticed annually in many regions around the country, marked by the co-circulation of DENV1-3. On 8 October 2021, a Dengue virus outbreak in the Rosso health post (sentinel site of the syndromic surveillance network) located in the north of the country was notified to the WHO Collaborating Center for arboviruses and hemorrhagic fever viruses at Institut Pasteur de Dakar. A multidisciplinary team was then sent for epidemiological and virologic investigations. This study describes the results from investigations during an outbreak in Senegal using a rapid diagnostic test (RDT) for the combined detection of dengue virus non-structural protein 1 (NS1) and IgM/IgG. For confirmation, samples were also tested by real-time RT-PCR and IgM ELISA at the reference lab in Dakar. qRT-PCR positive samples were subjected to whole genome sequencing using nanopore technology. Virologic analysis scored 102 positives cases (RT-PCR, NS1 antigen detection and/or IgM) out of 173 enrolled patients; interestingly, virus serotyping showed that the outbreak was caused by the DENV-1, a serotype different from DENV-2 involved during the outbreak in Rosso three years earlier, indicating a serotype replacement. Nearly all field-tested NS1 positives samples were confirmed by qRT-PCR with a concordance of 92.3%. Whole genome sequencing and phylogenetic analysis of strains suggested a re-introduction in Rosso of a DENV-1 strain different to the one responsible for the outbreak in the Louga area five years before. Findings call for improved dengue virus surveillance in Senegal, with a wide deployment of DENV antigenic tests, which allow easy on-site diagnosis of suspected cases and early detection of outbreaks. This work highlights the need for continuous monitoring of circulating serotypes which is crucial for a better understanding of viral epidemiology around the country.

During preparedness activities in Senegal to the 2024 Mpox Public Health Emergency of International Concern, a study was conducted to assess the prevalence of Varicella-Zoster virus among patients suspected of having Mpox. Samples, including skin swabs, serum, and nasopharyngeal swabs, were collected from 103 patients who presented with Mpox-like symptoms. Molecular testing via qPCR revealed that 30.1% of patients tested positive for herpesviruses, whereas no Mpox cases were detected. Common symptoms include fever, skin rash, headache, and myalgia, which closely resemble Mpox symptoms, increasing the risk of misdiagnosis. The most affected group was children under 15 years of age (50% of herpesvirus cases), followed by adults over 30 years of age (30.8%). The male/female sex ratio among herpesvirus-positive patients was 2.1, indicating a higher prevalence in males. Phylogenetic analysis of 14 newly characterized Varicella-Zoster virus genomes from metagenomic sequencing revealed that the strains circulating in Senegal were closely related to those from Guinea-Bissau, suggesting possible regional transmission. In addition, viral and bacterial coinfections were identified in Mpox-negative patients, which may have contributed to some skin lesions initially suspected to be Mpox. Our data highlight the importance of differential diagnostic testing to distinguish between Mpox and other infections, such as Chickenpox. The unexpectedly high prevalence of herpesviruses among suspected Mpox cases underscores the need for improved laboratory diagnostics, enhanced epidemiological surveillance, and targeted public health interventions to prevent misdiagnosis and improve patient management.

Statistical arbitrage is becoming increasingly important as a technique for short-term trading. The widespread access to real-time data provides means for tracking spreads between correlated prices, and the deviation of spreads from their long-term value. This study proposes and examines a new approach to statistical arbitrage in which the correlations between stocks are modeled using copulas. Kendall's τ of a copula provides a means to capture the dependence of assets. Since assets returns distributions exhibit fat tails corresponding to extreme market movement, correlation and auto-correlation are modelled by mixing GARCH model, extreme value theory and general Pareto distribution. Upon calibrating a t-copula between pairs, simulated returns are constructed, and trading signal is generated. The strategies of interest are pairs trading of stocks and ETFs and a strategy based on principal components analysis (PCA). Sector-based portfolios are constructed, and beta-hedged. Trading signals are derived from empirical and simulated returns using a mean-reverting Ornstein-Uhlenbeck process to define entry and exit trading points. The tick data used in this study came from the NYSE (2007–2010). It is sampled at five-minute intervals and is comprised of three sector Exchange Traded Funds (ETFs) energy, financials and technology along with their major components. A comparative analysis between the Gaussian model using empirical returns and the t-copula model using simulated returns is conducted for both trading strategies. Corresponding beta, number of trades and annual PNL are compared for both methods. Kendall's τ statistics show that dependence between ETFs and their components is directly related to market capitalization. The t-copula model for simulated returns provides a beta that is more stable and less significant in amplitude. The t-copula model presents a genuine interest for risk management, and beta-hedging does not provide a comparative advantage for either model. Overall, pairs trading favors the Gaussian model whereas principal component analysis favors the t-copula model. However, further study should be conducted. Moreover, results vary by model, year and sector; therefore, combining the two models provides a new risk management and trading tool. Keywords: Statistical arbitrage, GARCH, EVT, MLE, GP, copula, survival copula, beta, tail index, Kendall τ, s-scores, residuals, Ornstein-Uhlenbeck process.

Background Urogenital schistosomiasis is a neglected tropical disease most prevalent in sub-Saharan Africa. In the Senegal river basin, the construction of the Diama dam led to an increase and endemicity of schistosomiasis. Since 2009, praziquantel has frequently been used as preventive chemotherapy in the form of mass administration to Senegalese school-aged children without monitoring of the treatment efficacy and the prevalence after re-infection. This study aims to determine the current prevalence of urogenital schistosomiasis (caused by Schistosoma haematobium ), the efficacy of praziquantel, and the re-infection rates in children from five villages with different water access. Methods The baseline prevalence of S. haematobium was determined in August 2020 in 777 children between 5 and 11 years old and a single dose of praziquantel (40 mg/kg) was administered to those positive. The efficacy of praziquantel and the re-infection rates were monitored 4 weeks and 7 months after treatment, respectively, in 226 children with a high intensity of infection at baseline. Results At the baseline, prevalence was low among children from the village of Mbane who live close to the Lac de Guiers (38%), moderate among those from the villages of Dioundou and Khodit, which neighbor the Doue river (46%), and very high at Khodit (90.6%) and Guia (91.2%) which mainly use an irrigation canal. After treatment, the observed cure rates confirmed the efficacy of praziquantel. The lowest cure rate (88.5%) was obtained in the village using the irrigation canal, while high cure rates were obtained in those using the lake (96.5%) and the river (98%). However, high egg reduction rates (between 96.7 and 99.7%) were obtained in all the villages. The re-infection was significantly higher in the village using the canal (42.5%) than in the villages accessing the Lac de Guiers (18.3%) and the Doue river (14.8%). Conclusion Praziquantel has an impact on reducing the prevalence and intensity of urogenital schistosomiasis. However, in the Senegal river basin, S. haematobium remains a real health problem for children living in the villages near the irrigation canals, despite regular treatment, while prevalence is declining from those frequenting the river and the Lac de Guiers. Trial registration ClinicalTrials.gov, NCT04635553 . Registered 19 November 2020 retrospectively registered, https://www.clinicaltrials.gov/ct2/show/NCT04635553?cntry=SN&draw=2&rank=4

Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (T base) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers. The RIDEV model after genotypic parameter optimization explained 96% of variation in time to flowering for Senegal alone and 91% for Senegal and Madagascar combined. The latter was improved to 94% by including an acclimation parameter reducing T base when the crop experienced low temperatures during early vegetative development. Eighteen significant (P<1.0 × 10−5) quantitative trait loci (QTLs) were identified, namely ten for RIDEV parameters and eight for climatic index variables (difference in time to flowering between key environments). Co-localization of QTLs for different traits were rare. RIDEV parameters gave QTLs that were mostly more significant and distinct from QTLs for index variables. Candidate genes were investigated within the estimated 50% linkage disequilibrium regions of 39 kB. In addition to several known flowering network genes, they included genes related to thermal stress adaptation and epigenetic control mechanisms. The peak SNP for a QTL for the crop parameter Tbase (P=2.0 × 10−7) was located within HD3a, a florigen that was recently identified as implicated in flowering under cool conditions.

Background There have been no major advances in tuberculosis (TB) drug development since the first East African/British Medical Research Council short course chemotherapy trial 35 years ago. Since then, the landscape for conducting TB clinical trials has profoundly changed with the emergence of HIV infection, the spread of resistant TB bacilli strains, recent advances in mycobacteriological capacity, and drug discovery. As a consequence questions have arisen on the most appropriate approach to design and conduct current TB trials. To highlight key issues discussed: Is a superiority, equivalence, or non-inferiority design most appropriate? What should be the primary efficacy outcome? How to consider re-infections in the definition of the outcome? What is the optimal length of patient follow-up? Is blinding appropriate when treatment duration in test arm is shorter? What are the appropriate assumptions for sample size calculation? Methods Various drugs are currently in the development pipeline. We are presenting in this paper the design of the most recently completed phase III TB trial, the OFLOTUB project, which is the pivotal trial of a registration portfolio for a gatifloxacin-containing TB regimen. It is a randomized, open-label, multicenter, controlled trial aiming to evaluate the efficacy and safety of a gatifloxacin-containing 4-month regimen (trial registration: ClinicalTrial.gov database: NCT00216385). Results In the light of the recent scientific and regulatory discussions, we discuss some of the design issues in TB clinical trials and more specifically the reasons that guided our choices, in order to best answer the trial objectives, while at the same time satisfying regulatory authority requirements. Conclusion When shortening TB treatment, we are advocating for a non-inferiority, non-blinded design, with a composite unfavorable endpoint assessed 12 months post treatment completion, and added trial procedures specifically aiming to: (1) minimize endpoint unavailability; and (2) distinguish between relapse and re-infection.