Biology subjects

Duchemin, J.-B.

Publications and source records attributed to Duchemin, J.-B..

8 recordsLinked to original sources

bioRxiv2025

Spatio-temporal factors shape mosquito virome diversity and composition in a host and virus phylogeny-dependent manner

Beyond the arboviruses they transmit to humans and animals, mosquitoes harbour diverse viral communities that shape infection and immunity dynamics. Understanding how these communities shift within mosquito populations across time and space has important implications for how we anticipate and manage arboviral disease epidemics. Here, we examined the viromes of rural and sylvatic mosquito species sampled longitudinally across two years from countries representing South America, Africa, and Southeast Asian geographies to quantify the relative contributions of host and ecological factors in shaping their virome dynamics. We found that virus diversity and virome composition are strongly influenced by host phylogeny and spatial factors and show limited temporal variation. By examining virus similarity networks across mosquito species and biogeographies, we observed frequent instances of within- and cross-genus Culex-Anopheles virus sharing in Madagascar. Taken together, these findings inform the development and implementation strategies of any virome-based vector control technology and raise new evolutionary questions on how host generalism shapes the spatial prevalence of viruses and their potential for disease emergence.

microbiology↗

bioRxiv2025

Population genomics of Anopheles darlingi, the principal South American malaria vector mosquito

Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 A. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including thirteen putative segregating inversions, and no evidence for cryptic sympatric taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes, one of which we validated experimentally. Our results will facilitate effective mosquito surveillance and control, while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the western hemisphere.

evolutionary biology↗

bioRxiv2024

A DNA barcode library for Culex mosquitoes (Diptera: Culicidae) of South America with the description of two cryptic species of subgenus Melanoconion

The genus Culex is one of the most diverse in the world and includes numerous known vector species of parasites and viruses to humans. Morphological identification of Culex species is notoriously difficult and rely mostly on the examination of properly dissected male genitalia which largely prevents female and immature identification during entomological, ecological or arboviral surveys. The aims of this study were (i) to establish a DNA barcode library for Culex mosquitoes of French Guiana based on the mitochondrial gene cytochrome c oxidase I (COI) marker, (ii) to compare three approaches of molecular delimitation of species to morphological identification, and (iii) to test the effectiveness of the COI marker at a broader geographical scale across South America. Mosquitoes used in this study were sampled in French Guiana between 2013 and 2023. We provide 246 COI sequences for 90 morphologically identified species of Culex, including five new country records and two newly described species. Overall, congruence between morphological identification and molecular delimitations using the COI barcode were high. The Barcode of Life Data clustering approach into Barcode Index Numbers gives the best result in terms of species delimitation, followed by the muti-rate Poisson Tree Processes and the Assemble Species by Automatic Partitioning methods. Inconsistencies between morphological identification and molecular delimitation can be explained by introgression, incomplete lineage sorting, imperfect taxonomy or the effect of the geographical scale of sampling. This increases by almost two-fold the number of mosquito species for which a DNA barcode is available in French Guiana, including 75% of the species of Culex currently known in the territory. Finally, this study confirms the usefulness of the COI barcode in identifying Culex mosquitoes of South America, but also points the limits of this marker for some groups of species within the subgenera Culex and Melanoconion.

molecular biology↗

bioRxiv2022

Establishment of a colony of Anopheles darlingi from French Guiana for vector competence studies on malaria transmission

Anopheles darlingi is a major vector of both Plasmodium falciparum and Plasmodium vivax in South and Central America. However, vector competence and physiology of this mosquito species have been scarcely studied due to difficulties in rearing it in the laboratory. Here, we report the successful establishment of a robust colony, from mosquito collection in French Guiana. We describe our mosquito colonization procedure with relevant information on environmental conditions, mating ability, larval development and survival, recorded over the first six critical generations. Experimental infection showed that our An. darlingi colony has a moderate permissiveness to in vitro produced gametocytes of the P. falciparum NF54 strain originating from Africa. This colony, that has reached its 20th generation, will allow further characterization of An. darlingi life-history traits and of Plasmodium-mosquito interactions with South American malaria parasites.

microbiology↗

bioRxiv2022

Decoding rRNA Sequences for Improved Metagenomics in Sylvatic Mosquito Species

As mosquito-borne virus epidemics are often preceded by undetected spillover events, surveillance and virus discovery studies in non-urban mosquitoes informs pre-emptive and responsive public health measures. RNA-seq metagenomics is a popular methodology but it is constrained by overabundant rRNA. The lack of reference sequences for most mosquito species is a major impediment against physical and computational removal of rRNA reads. We describe a strategy to assemble novel rRNA sequences from mosquito specimens, producing an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). We also evaluate the utility of rRNA sequences as molecular barcodes relative to the mitochondrial cytochrome c oxidase I (COI) gene. We show that rRNA sequences can be used for species identification when COI sequences are ambiguous or unavailable, revealing evolutionary relationships concordant with contemporary mosquito systematics. This expansion of the rRNA reference library improves mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader species range and streamlined species identification by rRNA barcoding. In addition, rRNA barcodes could serve as an additional tool for mosquito taxonomy and phylogeny.

bioinformatics↗

bioRxiv2019

Broad Dengue Neutralization in Mosquitoes Expressing an Engineered Antibody

With dengue virus (DENV) becoming endemic in tropical and subtropical regions worldwide, there is a pressing global demand for effective strategies to control the mosquitoes that spread this disease. Recent advances in genetic engineering technologies have made it possible to create mosquitoes with reduced vector competence, limiting their ability to acquire and transmit pathogens. Here we describe the development of Aedes aegypti mosquitoes synthetically engineered to impede vector competence to DENV. These mosquitoes express a gene encoding an engineered single-chain variable fragment derived from a broadly neutralizing DENV human monoclonal antibody and have significantly reduced viral infection, dissemination, and transmission rates for all four major antigenically distinct DENV serotypes. Importantly, this is the first engineered approach that targets all DENV serotypes, which is crucial for effective disease suppression. These results provide a compelling route for developing effective genetic-based DENV control strategies, which could be extended to curtail other arboviruses.\n\nSignificance StatementHere we describe the development of Ae. aegypti mosquitoes synthetically engineered to impede vector competence to multiple serotypes of DENV. Given the global significance of DENV, these mosquitoes may be used to curtail Dengue transmission by this potent vector.

bioengineering↗

bioRxiv2018

Dengue virus infection changes Aedes aegypti oviposition olfactory preferences

Aedes aegypti mosquitoes, main vectors for numerous flaviviruses, have olfactory preferences and are capable of olfactory learning especially when seeking their required environmental conditions to lay their eggs. In this study, we showed that semiochemical conditions during Aedes aegypti larval rearing affected future female choice for oviposition: water-reared mosquitoes preferred to lay eggs in water or p-cresol containers, while skatole reared mosquitoes preferred skatole sites. Using two independent behavioural assays, we showed that this skatole preference was lost in mosquitoes infected with dengue virus. Viral RNA was extracted from infected female mosquito heads, and an increase of virus load was detected from 3 to 10 days post infection, indicating replication in the insect head and possibly in the central nervous system. Expression of selected genes, potentially implied in olfactory learning processes, were also altered during dengue infection. Based on these results, we hypothesise that dengue virus infection alters gene expression in the mosquitos head and is associated with a loss of olfactory preferences, possibly modifying oviposition site choice of female mosquitoes.

animal behavior and cognition↗

bioRxiv2018

RNASeq analysis of Aedes albopictus mosquitoes during chikungunya virus infection

Chikungunya virus (CHIKV), preferentially transmitted by Aedes mosquitoes, is an emerging pathogen around the world and causes significant morbidity in patients. A single amino acid mutation in the envelope protein of CHIKV has led to shift in vector preference towards Aedes albopictus, an invasive mosquito. Previous studies have shown that after infection, mosquitoes mount an antiviral immune response. However, molecular interactions during the course of infection at different tissues and time-points remain largely uncharacterised. Here we performed whole transcriptome analysis on dissected midguts and head/thorax of CHIKV (Indian Ocean strain) infected Aedes albopictus to identify differentially expressed genes compared with uninfected controls. For this, RNA was extracted at two days post-infection (D2) from pooled midguts and eight days post-infection (D8) from heads and the anterior 1/3rd of the thorax. We identified 25 and 96 differentially expressed genes from the D2 and D8 samples respectively (p-value <0.05). Custom de novo transcriptomes were assembled for the reads that did not align with the reference genome and an additional 225 and 4771 differentially expressed genes from D2 and D8, respectively, were identified. Twenty-two of the identified transcripts, possibly involved in immunity, were validated by qRT-PCR. Interestingly, we also detected changes in viral diversity, as shown by number of mutations in the viral genome, with increase in number of mutations in the midgut compared with mammalian host (Vero cell culture), followed by reduction in the number of mutations in head and thorax at D8, indicating a possible genomic bottleneck. Taken together, these results will help in understanding Aedes Albopictus interactions with CHIKV and can be utilised to reduce the impact of this viral infection.\n\nAuthor SummaryChikungunya virus has caused several outbreaks around the world in the last decade. Once a relatively unknown virus, it now causes seasonal infections in tropical and some temperate regions. This change in epidemiology is attributed to vector switch from Aedes aegypti to Aedes albopictus, an invasive pest leading to spread and causing infections in temperate regions. Although recent research has identified mosquito factors influencing infections, our understanding of interaction between chikungunya virus and its vector is limited. Using whole transcriptome sequencing of chikungunya infected mosquitoes, we identified differentially expressed genes in the midgut and head and thorax, over the course of mosquito infection. We also detected changes in the viral genome during mosquito infection and a possible genetic bottleneck event with reduction in viral variants at the head and thorax region of mosquito in the later stages of infection. These results will lead to improving our understanding of mosquito-virus interactions with Aedes albopictus as a vector and in turn lead to development of novel disease control strategies.

microbiology↗