Rift Valley fever virus (RVFV; Phlebovirus, Bunyaviridae) is a mosquito–borne, zoonotic pathogen. In Senegal, RVFV was first isolated in 1974 from Aedes dalzieli (Theobald) and thereafter from Ae. fowleri (de Charmoy), Ae. ochraceus Theobald, Ae. vexans (Meigen), Culex poicilipes (Theobald), Mansonia africana (Theobald) and Ma. uniformis (Theobald). However, the vector competence of these local species has never been demonstrated making hypothetical the transmission cycle proposed for West Africa based on serological data and mosquito isolates. Aedes vexans and Cx. poicilipes, two common mosquito species most frequently associated with RVFV in Senegal, and Cx. quinquefasciatus, the most common domestic species, were assessed after oral feeding with three RVFV strains of the West and East/central African lineages. Fully engorged mosquitoes (420 Ae. vexans, 563 Cx. quinquefasciatus and 380 Cx. poicilipes) were maintained at 27 ± 1 °C and 70–80 % relative humidity. The saliva, legs/wings and bodies were tested individually for the RVFV genome using real-time RT-PCR at 5, 10, 15 and 20 days post exposure (dpe) to estimate the infection, dissemination, and transmission rates. Genotypic characterisation of the 3 strains used were performed to identify factors underlying the different patterns of transmission. The infection rates varied between 30.0–85.0 % for Ae. vexans, 3.3–27 % for Cx. quinquefasciatus and 8.3–46.7 % for Cx. poicilipes, and the dissemination rates varied between 10.5–37 % for Ae. vexans, 9.5–28.6 % for Cx. quinquefasciatus and 3.0–40.9 % for Cx. poicilipes. However only the East African lineage was transmitted, with transmission rates varying between 13.3–33.3 % in Ae. vexans, 50 % in Cx. quinquefasciatus and 11.1 % in Cx. poicilipes. Culex mosquitoes were less susceptible to infection than Ae. vexans. Compared to other strains, amino acid variation in the NSs M segment proteins of the East African RVFV lineage human-derived strain SH172805, might explain the differences in transmission potential. Our findings revealed that all the species tested were competent for RVFV with a significant more important role of Ae. vexans compared to Culex species and a highest potential of the East African lineage to be transmitted.

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.

Climatic and environmental variables were used successfully by using models to predict Rift Valley fever (RVF) virus outbreaks in East Africa. However, these models are not replicable in the West African context due to a likely difference of the dynamic of the virus emergence. For these reasons specific models mainly oriented to the risk mapping have been developed. Hence, the areas of high vector pressure or virus activity are commonly predicted. However, the factors impacting their occurrence are poorly investigated and still unknown. In this study, we examine the impact of climate and environmental factors on the likelihood of occurrence of the two main vectors of RVF in West Africa (Aedes vexans and Culex poicilipes) hotspots. We used generalized linear mixed models taking into account spatial autocorrelation, in order to overcome the default threshold for areas with high mosquito abundance identified by these models. Getis’ Gi*(d) index was used to define local adult mosquito abundance clusters (hotspot). For Culex poicilipes, a decrease of the minimum temperature promotes the occurrence of hotspots, whereas, for Aedes vexans, the likelihood of hotspot occurrence is negatively correlated with relative humidity, maximum and minimum temperatures. However, for the two vectors, proximity to ponds would increase the risk of being in an hotspot area. These results may be useful in the improvement of RVF monitoring and vector control management in the Barkedji area.

Objectives: A nationwide cross-sectional epidemiological survey was conducted to capture the true extent of COVID-19 exposure in Senegal. Methods: Multi-stage random cluster sampling of households was carried out between October and November, 2020, at the end of the first wave of COVID-19 transmission. Anti-SARS-CoV-2 antibodies were screened using three distinct ELISA assays. Adjusted prevalence for the survey design were calculated for each test separately, and thereafter combined. Crude, adjusted prevalence based on tests performances were estimated to assess the seroprevalence. As some samples were collected in high malaria endemic areas, we also investigated the relationship between SARS-CoV-2 seroreactivity and antimalarial humoral immunity. Results: Of the 1,463 participants included in this study, 58•8% were women and the mean age of participants was 29•2 years (range 0.25–82.0). The national seroprevalence was estimated at 28.4% (95% CI: 26.1-30.8). There was substantial regional variability. All age groups were impacted and the prevalence of SARS-CoV-2 was comparable in symptomatic and asymptomatic groups. We estimated 4,744,392 SARS-CoV-2 (95% CI: 4,360,164 – 5,145,327) potential infected in Senegal compared to 16,089 COVID-19 RT-PCR laboratory-confirmed cases reported by the national surveillance. No correlation was found between SARS-CoV-2 and plasmodial seroreactivities. Conclusions: These results provide a better estimate of SARS-CoV-2 virus dissemination in the Senegalese population. Preventive and control measures need to be reinforced in the country and especially in the south border regions.

Rift Valley Fever and Crimean-Congo Hemorrhagic Fever are two infections classified among the emerging diseases to be monitored with highest priority. Studies undertaken in human and animals have shown endemicity of these two arboviruses in several African countries. However, most of the investigations were carried out on domestic cattle and the studies conducted on human populations are either outdated or limited to a small number of well-known endemic areas. It is then critical to better evaluate the burden of these viruses in Senegal at a national scale. This work relies on a previous seroprevalence survey undertaken in all regions of Senegal at the end of 2020. The existing biobank was used to determine the immunoglobulin G [IgG] Rift Valley Fever and Crimean-Congo Hemorrhagic Fever seroprevalences by indirect enzyme-linked immunosorbent assay. The crude seroprevalences of Rift Valley Fever and Crimean-Congo Hemorrhagic Fever were 3.94% and 0.7% respectively, with the northern and central part of the countries as the main exposed areas. However, acute infections reported in both high and low exposed regions suggest sporadic introductions. This study gives updated information and could be of interest to support the stakeholders in the management of these zoonoses.

Dengue fever is the most prevalent arboviral disease worldwide. Dengue virus (DENV), the etiological agent, is known to have been circulating in Senegal since 1970, though for a long time, virus epidemiology was restricted to the circulation of sylvatic DENV−2 in south-eastern Senegal (the Kedougou region). In 2009 a major shift was noticed with the first urban epidemic, which occurred in the Dakar region and was caused by DENV−3. Following the notification by Senegal, many other West African countries reported DENV−3 epidemics. Despite these notifications, there are scarce studies and data about the genetic diversity and molecular evolution of DENV−3 in West Africa. Using nanopore sequencing, phylogenetic, and phylogeographic approaches on historic strains and 36 newly sequenced strains, we studied the molecular evolution of DENV−3 in Senegal between 2009 and 2022. We then assessed the impact of the observed genetic diversity on the efficacy of preventive countermeasures and vaccination by mapping amino acid changes against vaccine strains. The results showed that the DENV−3 strains circulating in Senegal belong to genotype III, similarly to strains from other West African countries, while belonging to different clades. Phylogeographic analysis based on nearly complete genomes revealed three independent introduction events from Asia and Burkina Faso. Comparison of the amino acids in the CprM-E regions of genomes from the Senegalese strains against the vaccine strains revealed the presence of 22 substitutions (7 within the PrM and 15 within the E gene) when compared to CYD-3, while 23 changes were observed when compared to TV003 (6 within the PrM and 17 within the E gene). Within the E gene, most of the changes compared to the vaccine strains were located in the ED-III domain, which is known to be crucial in neutralizing antibody production. Altogether, these data give up-to-date insight into DENV−3 genomic evolution in Senegal which needs to be taken into account in future vaccination strategies. Additionally, they highlight the importance of the genomic epidemiology of emerging pathogens in Africa and call for the implementation of a pan-African network for genomic surveillance of dengue virus.