Sylvie Cornelie

Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data from target-enriched libraries. ViroSeek performs a series of automated steps: quality control, trimming, host and bacterial sequence removal, assembly, taxonomic assignment, read remapping for quantification, and PCR duplicate removal. The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.

Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a lightweight, reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data. ViroSeek performs a series of automated steps: quality control (FastQC), trimming (TrimGalore or fastp), host and bacterial sequence removal (BBduk), assembly (SPAdes), taxonomic assignment (DIAMOND and TaxonKit), read remapping for quantification (minimap2), and PCR duplicate removal (Samtools). The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community. It provides an optimized solution for virome analysis.

Control of invasive species relies partly on permanent surveillance at international points of entry. We report the exceptional trapping of one adult mosquito (Diptera: Culicidae) in the port of Marseille, France, in July 2018, during a routine survey conducted according to International Health Regulations. Morphological and molecular identification classified the specimen as a female Aedes (Stegomyia) aegypti (L.), vector of many arboviruses, absent from Europe and the Mediterranean rim since the 1950s. A world reference panel of approximately 23,000 genome-wide single nucleotide polymorphisms determined that the mosquito originated from Cameroon, west Africa. Cross-reference of this geographic location with boats traveling from Central Africa to Marseille during the trapping period suggests that the mosquito travelled within an identified merchant ship, a vehicles carrier connecting Douala, Cameroon to Marseille, France. This ship left Douala on June 25, 2018 and arrived 20 days later in Marseille on July 15. The mosquito was captured 350 m away from the dock. The interception of a propagule of an invasive species is a rare event that must be considered a priority to prevent its successful establishment.

Background: The implementation of anti-larval strategies in the fight against malaria vectors requires fundamental knowledge of their oviposition sites. The aim of this study was to assess the spatial and temporal distribution of Anopheles breeding sites as well as the influence of abiotic and biotic factors on the proliferation of larvae in urban and non-urban areas of Benin. Methods: Sampling of Anopheles larvae was carried out during the rainy and dry seasons in urbanized and non-urbanized areas of the cities of Cotonou, Bohicon, Parakou, and Natitingou in Benin. The Anopheles larval breeding sites were georeferenced and characterized by their nature, type, physicochemical (pH, temperature, dissolved oxygen, conductivity, turbidity, salinity) and biological attributes (larval density and coliform density). Results: A total of 198 positive breeding sites for Anopheles larvae were identified, comprising 163 (82.3%) in the rainy season and 35 (17.7%) in the dry season. Out of these larval habitats, 61.9% were located in urbanized areas, and were predominantly puddles. Principal component analysis revealed a high positive correlation of larval density with temperature and dissolved oxygen, and with salinity in the coastal zone. In addition, cross-sectional analysis of the microbiological results with larval density showed a significant negative correlation between larval productivity and faecal coliform load. Conclusions: This study indicated the presence of multiple larval habitats of Anopheles in the urban areas which were created through human activities, and associations between larval density and intrinsic factors of the habitats such as temperature, dissolved oxygen and faecal coliform load. This type of information may be useful for the implementation of appropriate control strategies in urban areas, including regulation of the human activities that lead to the creation of breeding sites, proper environmental management and targeted larvicidal use. Graphical

Significance: Transmission of malarial parasites occurs via the bites of Anopheles mosquitoes, whose blood-feeding behavior modulates the risk of infection. In many malaria endemic regions, eradication strategies rely on reducing transmission by targeting nocturnal blood-feeding Anopheles with insecticidal nets. However, a proportion of mosquitoes may naturally feed when humans are not protected by nets, setting a ceiling to the efficacy of massive net-based interventions. In Bangui, Central African Republic, 20 to 30% of daily exposure to indoor bites occurs during daytime, and this fraction may correspond to mosquitoes escaping exposure to current vector control measures. Knowledge about the daily rhythmicity of mosquito biting is therefore crucial to adjust vector control tactics to protect people at places where they spend daytime.

Insecticide-based interventions have averted more than 500 million malaria cases since 2000, but insecticide resistance in mosquitoes could bring about a rebound in disease and mortality. This study investigated whether insecticide resistance was associated with increased incidence of clinical malaria. In an area of southern Benin with insecticide resistance and high use of insecticide-treated nets (ITNs), malaria morbidity and insecticide resistance were measured simultaneously in 30 clusters (villages or collections of villages) multiple times over the course of 2 years. Insecticide resistance frequencies were measured using the standard World Health Organization bioassay test. Malaria morbidity was measured by cases recorded at health facilities both in the whole population using routinely collected data and in a passively followed cohort of children under 5 years old. There was no evidence that incidence of malaria from routinely collected data was higher in clusters with resistance frequencies above the median, either in children aged under 5 (RR = 1.27 (95% CI 0.81–2.00) p = 0.276) or in individuals aged 5 or over (RR = 1.74 (95% CI 0.91–3.34) p = 0.093). There was also no evidence that incidence was higher in clusters with resistance frequencies above the median in the passively followed cohort (RR = 1.11 (0.52–2.35) p = 0.777). This study found no association between frequency of resistance and incidence of clinical malaria in an area where ITNs are the principal form of vector control. This may be because, as other studies have shown, ITNs continue to offer some protection from malaria even in the presence of insecticide resistance. Irrespective of resistance, nets provide only partial protection so the development of improved or supplementary vector control tools is required to reduce Africa’s unacceptably high malaria burden.

Malaria control is heavily reliant on insecticides, especially pyrethroids. Resistance of mosquitoes to insecticides may threaten the effectiveness of insecticide-based vector control and lead to a resurgence of malaria in Africa. In 21 villages in Southern Benin with high levels of insecticide resistance, the resistance status of local vectors was measured at the same time as the prevalence of malaria infection in resident children. Children who used LLINs had lower levels of malaria infection [odds ratio = 0.76 (95% CI 0.59, 0.98, p = 0.033)]. There was no evidence that the effectiveness of nets was different in high and low resistance locations (p = 0.513). There was no association between village level resistance and village level malaria prevalence (p = 0.999). LLINs continue to offer individual protection against malaria infection in an area of high resistance. Insecticide resistance is not a reason to stop efforts to increase coverage of LLINs in Africa.

Arboviral diseases are an important public health concerns. Vector control remains the sole strategy to fight against these diseases. Because of the important limits of methods currently used to assess human exposure to Aedes mosquito bites, much effort is being devoted to develop new indicators. Recent studies have reported that human antibody (Ab) responses to Aedes aegypti Nterm-34kDa salivary peptide represent a promising biomarker tool to evaluate the human-Aedes contact. The present study aims investigate whether such biomarker could be used for assessing the efficacy of vector control against Aedes. Specific human IgG response to the Nterm-34kDa peptide was assessed from 102 individuals living in urban area of Saint-Denis at La Reunion Island, Indian Ocean, before and after the implementation of vector control against Aedes mosquitoes. IgG response decreased after 2 weeks (P < 0.0001), and remained low for 4 weeks post-intervention (P = 0.0002). The specific IgG decrease was associated with the decline of Aedes mosquito density, as estimated by entomological parameters and closely correlated to vector control implementation and was not associated with the use of individual protection, daily commuting outside of the house, sex and age. Our findings indicate a probable short-term decrease of human exposure to Aedes bites just after vector control implementation. Results provided in the present study indicate that IgG Ab response to Aedes aegypti Nterm-34kDa salivary peptide could be a relevant short-time indicator for evaluating the efficacy of vector control interventions against Aedes species. In absence of effective treatment and vaccine, vector control is the main strategy against arboviral diseases such as dengue, Zika and chikungunya. Given the limitation of entomologic tool currently used, news tools are urgently needed to assess the efficacy of vector control against arboviral diseases. The present study aimed to investigate whether human IgG antibody specific response to only one Aedes salivary peptide could be useful for assessing the efficacy of vector control against arboviral diseases. For this purpose, IgG response to Nterm-34kDa peptide was assessed from 102 individuals living in urban area at La Reunion Island, Indian Ocean, before and after the implementation of vector control against Aedes albopictus mosquito species. A significant decrease of this specific IgG level was noticed after vector control implementation. The decrease was associated to the decline in Aedes mosquito density estimated by entomological parameters, such as adult mosquito density, House and Breteau indices. The results of the present study indicated that human IgG response to the Aedes Nterm-34kDa salivary peptide could be a useful tool to evaluate the efficacy of vector control strategies against arboviruses.

Large-scale implementation of Indoor Residual Spraying and Insecticide Treated Nets has been implemented in Plateau Department, Benin between 2011 and 2014. The purpose of this study was to monitor the frequency and mechanisms of pyrethroid resistance in malaria vectors following the implementation of vector control tools for malaria prevention. Anopheles larvae were collected in 13 villages twice a year from 2012 to 2014. WHO tube tests were used to assess the phenotypic resistance of each population to 0.05 % deltamethrin. Sibling species within Anopheles gambiae complex were identified by PCR techniques. Taqman and biochemical assays were performed to identify the presence of kdr mutations in individual mosquitoes and to detect any increase in the activity of enzymes putatively involved in insecticide metabolism (oxidases, esterase and glutathione-S-transferases). Quantitative real time PCR was used to measure the expression of three metabolic genes involved in pyrethroid resistance (CYP6P3, CYP6M2 and GSTD3). Anopheles populations showed < 90 % mortality to deltamethrin in all villages and at all time points. The 1014 F kdr allele frequency was close to fixation (> 0.9) over the sampling periods in both An. gambiae and An. coluzzii. Biochemical assays showed higher activities of alpha esterase and GST in field malaria vector populations compared to susceptible mosquitoes. qPCR assays showed a significant increase of CYP6P3, CYP6M2 GSTD3 expression in An. gambiae after a three-year implementation of LLINs. The study confirmed that deltamethrin resistance is widespread in malaria vectors in Southern Benin. We suspect that the increase in deltamethrin resistance between 2012 and 2014 resulted from an increased expression of metabolic detoxification genes (CYP6M2 and CYP6P3) rather than from kdr mutations. It is urgent to evaluate further the impact of metabolic resistance on the efficacy of vector control interventions using pyrethroid insecticides.