Host preference patterns in domestic and wild settings: Insights into Anopheles feeding behavior.

The adaptation of Anopheles malaria vectors to domestic settings is directly linked to their ability to feed on humans. The strength of this species-habitat association is unequal across the species within the genus, with the major vectors being particularly dependent on humans. However, our understanding of how blood-feeding behavior interacts with and adapts to environmental settings, including the presence of humans, remains limited. Using a field-based approach, we first investigated Anopheles community structure and feeding behavior patterns in domestic and sylvatic settings in La Lopé National Park in Gabon, Central Africa. We characterized the preference indices using a dual-host choice sampling approach across mosquito species, habitats, and seasons. We then quantified the plastic biting behavior of mosquito species in each habitat. We collected individuals from 16 Anopheles species that exhibited significant differences in species composition and abundance between sylvatic and domestic settings. The host-seeking behavior also varied among the seven most abundant species. The general attractiveness to each host, human or animal, remained relatively constant for each species, but with significant variations between habitats across species. These variations, to more generalist and to more anthropophilic behavior, were related to seasonal changes and distance from the village, respectively. Finally, we pointed out that the host choice of major malaria vectors changed in the absence of humans, revealing a plastic feeding behavior of these species. This study highlights the effect of humans on Anopheles distribution and feeding evolution. The characterization of feeding behavior in wild and domestic settings provides opportunities to better understand the interplay between genetic determinants of host preference and ecological factors. Our findings suggest that protected areas may offer alternative thriving conditions to major malaria vectors.

Dirofilaria sp. and Blood Meal Analysis in Mosquitoes Collected in Vojvodina and Macva, and the First Report of Setaria tundra (Issaitshikoff & Rajewskaya, 1928) in Serbia.

Dirofilaria immitis and D. repens are the two most widespread and important species of mosquito-borne nematodes, posing a significant threat to veterinary health and particularly affecting canines and felines. While D. immitis causes cardiopulmonary dirofilariasis, D. repens causes subcutaneous infections in dogs and other carnivores. Despite the extensive knowledge on these parasites, little is known about their natural vectors in Serbia. The parasite Setaria tundra, known to infect deer, has not yet been detected in Serbia but has been documented in neighboring countries. Thus, the aim of this study was to (i) further map out Dirofilaria sp. hotspots in the Vojvodina Province and detect S. tundra for the first time, (ii) detect positive mosquito species that can provide insights into how the nematodes spread in Serbia, and (iii) analyze the blood-fed female mosquitoes of species found to be infected, in order to identify the potential source of parasite infection. A total of 2902 female mosquitoes were collected across 73 locations during 2021 and 2022. Molecular biology methods, based on conventional PCR, were used to analyze non-blood-fed (2521 specimens) and blood-fed (381 specimens) female mosquitos, in order to detect filarial nematode presence and identify blood-meal sources, respectively. When the parasite genome was detected, the amplicon (cox1 gene, 650 bp fragment) was sent for Sanger sequencing, further confirming the presence of nematodes and species assignation. D. immitis was detected in three Culex pipiens mosquitoes collected in Zrenjanin (August 2021) and Glogonj and Svetozar Miletic (both in July 2021). Additionally, Setaria tundra was detected in Aedes vexans collected in Idos (mid-August 2021) and Aedes caspius, which was collected in Mali Idos (end of July 2021). This work identifies two new locations where D. immitis occurs in Vojvodina, and is the first report of S. tundra in Serbian territory. Blood-meal analysis provided insights into the preferences of mosquitoes that were positive for Dirofilaria sp. and S. tundra.

Genomic Signatures of Microgeographic Adaptation in Anopheles coluzzii Along an Anthropogenic Gradient in Gabon.

Species distributed across heterogeneous environments often evolve locally adapted populations, but understanding how these persist in the presence of homogenizing gene flow remains puzzling. In Gabon, Anopheles coluzzii, a major African malaria mosquito is found along an ecological gradient, including a sylvatic population, away of any human presence. This study identifies into the genomic signatures of local adaptation in populations from distinct environments including the urban area of Libreville, and two proximate sites 10km apart in the La Lopé National Park (LLP), a village and its sylvatic neighborhood. Whole genome re-sequencing of 96 mosquitoes unveiled ∼ 5.7millions high-quality single nucleotide polymorphisms. Coalescent-based demographic analyses suggest an ∼ 8,000-year-old divergence between Libreville and La Lopé populations, followed by a secondary contact ( ∼ 4,000 ybp) resulting in asymmetric effective gene flow. The urban population displayed reduced effective size, evidence of inbreeding, and strong selection pressures for adaptation to urban settings, as suggested by the hard selective sweeps associated with genes involved in detoxification and insecticide resistance. In contrast, the two geographically proximate LLP populations showed larger effective sizes, and distinctive genomic differences in selective signals, notably soft-selective sweeps on the standing genetic variation. Although neutral loci and chromosomal inversions failed to discriminate between LLP populations, our findings support that microgeographic adaptation can swiftly emerge through selection on standing genetic variation despite high gene flow. This study contributes to the growing understanding of evolution of populations in heterogeneous environments amid ongoing gene flow and how major malaria mosquitoes adapt to human. Significance: Anopheles coluzzii , a major African malaria vector, thrives from humid rainforests to dry savannahs and coastal areas. This ecological success is linked to its close association with domestic settings, with human playing significant roles in driving the recent urban evolution of this mosquito. Our research explores the assumption that these mosquitoes are strictly dependent on human habitats, by conducting whole-genome sequencing on An. coluzzii specimens from urban, rural, and sylvatic sites in Gabon. We found that urban mosquitoes show de novo genetic signatures of human-driven vector control, while rural and sylvatic mosquitoes exhibit distinctive genetic evidence of local adaptations derived from standing genetic variation. Understanding adaptation mechanisms of this mosquito is therefore crucial to predict evolution of vector control strategies.

Evidence for circulation of Rift Valley fever virus in wildlife and domestic animals in a forest environment in Gabon, Central Africa.

Rift Valley fever (RVF) is a mosquito-borne viral zoonosis caused by the Rift Valley fever virus (RVFV) that can infect domestic and wild animals. Although the RVFV transmission cycle has been well documented across Africa in savanna ecosystems, little is known about its transmission in tropical rainforest settings, particularly in Central Africa. We therefore conducted a survey in northeastern Gabon to assess RVFV circulation among wild and domestic animals. Among 163 wildlife samples tested using RVFV-specific RT-qPCR, four ruminants belonging to subfamily Cephalophinae were detected positive. The phylogenetic analysis revealed that the four RVFV sequences clustered together with a virus isolated in Namibia within the well-structured Egyptian clade. A cross-sectional survey conducted on sheep, goats and dogs living in villages within the same area determined the IgG RVFV-specific antibody prevalence using cELISA. Out of the 306 small ruminants tested (214 goats, 92 sheep), an overall antibody prevalence of 15.4% (95% CI [11.5-19.9]) was observed with a higher rate in goats than in sheep (20.1% versus 3.3%). RVFV-specific antibodies were detected in a single dog out of the 26 tested. Neither age, sex of domestic animals nor season was found to be significant risk factors of RVFV occurrence. Our findings highlight sylvatic circulation of RVFV for the first time in Gabon. These results stress the need to develop adequate surveillance plan measures to better control the public health threat of RVFV.

Extensive variation and strain-specificity in dengue virus susceptibility among African Aedes aegypti populations.

African populations of the mosquito Aedes aegypti are usually considered less susceptible to infection by human-pathogenic flaviviruses than globally invasive populations found outside Africa. Although this contrast has been well documented for Zika virus (ZIKV), it is unclear to what extent it is true for dengue virus (DENV), the most prevalent flavivirus of humans. Addressing this question is complicated by substantial genetic diversity among DENV strains, most notably in the form of four genetic types (DENV1 to DENV4), that can lead to genetically specific interactions with mosquito populations. Here, we carried out a survey of DENV susceptibility using a panel of seven field-derived Ae. aegypti colonies from across the African range of the species and a colony from Guadeloupe, French West Indies as non-African reference. We found considerable variation in the ability of African Ae. aegypti populations to acquire and replicate a panel of six DENV strains spanning the four DENV types. Although African Ae. aegypti populations were generally less susceptible than the reference non-African population from Guadeloupe, in several instances some African populations were equally or more susceptible than the Guadeloupe population. Moreover, the relative level of susceptibility between African mosquito populations depended on the DENV strain, indicating genetically specific interactions. We conclude that unlike ZIKV susceptibility, there is no clear-cut dichotomy in DENV susceptibility between African and non-African Ae. aegypti. DENV susceptibility of African Ae. aegypti populations is highly heterogeneous and largely governed by the specific pairing of mosquito population and DENV strain.

Climate-influenced vector-borne diseases in Africa: a call to empower the next generation of African researchers for sustainable solutions.

We look at the link between climate change and vector-borne diseases in low- and middle-income countries in Africa. The large endemicity and escalating threat of diseases such as malaria and arboviral diseases, intensified by climate change, disproportionately affects vulnerable communities globally. We highlight the urgency of prioritizing research and development, advocating for robust scientific inquiry to promote adaptation strategies, and the vital role that the next generation of African research leaders will play in addressing these challenges. Despite significant challenges such as funding shortages within countries, various pan-African-oriented funding bodies such as the African Academy of Sciences, the Africa Research Excellence Fund, the Wellcome Trust, the U.S. National Institutes of Health, and the Bill and Melinda Gates Foundation as well as initiatives such as the African Research Initiative for Scientific Excellence and the Pan-African Mosquito Control Association, have empowered (or are empowering) these researchers by supporting capacity building activities, including continental and global networking, skill development, mentoring, and African-led research. This article underscores the urgency of increased national investment in research, proposing the establishment of research government agencies to drive evidence-based interventions. Collaboration between governments and scientific communities, sustained by pan-African funding bodies, is crucial. Through these efforts, African nations are likely to enhance the resilience and adaptive capacity of their systems and communities by navigating these challenges effectively, fostering scientific excellence and implementing transformative solutions against climate-sensitive vector-borne diseases.

Towards the invasion of wild and rural forested areas in Gabon (Central Africa) by the Asian tiger mosquito Aedes albopictus: Potential risks from the one health perspective.

BACKGROUND: Since its first record in urban areas of Central-Africa in the 2000s, the invasive mosquito, Aedes albopictus, has spread throughout the region, including in remote villages in forested areas, causing outbreaks of Aedes-borne diseases, such as dengue and chikungunya. Such invasion might enhance Ae. albopictus interactions with wild animals in forest ecosystems and favor the spillover of zoonotic arboviruses to humans. The aim of this study was to monitor Ae. albopictus spread in the wildlife reserve of La Lopé National Park (Gabon), and evaluate the magnitude of the rainforest ecosystem colonization. METHODOLOGY: From 2014 to 2018, we used ovitraps, larval surveys, BG-Sentinel traps, and human landing catches along an anthropization gradient from La Lopé village to the natural forest in the Park. CONCLUSIONS: We detected Ae. albopictus in gallery forest up to 15 km away from La Lopé village. However, Ae. albopictus was significantly more abundant at anthropogenic sites than in less anthropized areas. The number of eggs laid by Ae. albopictus decreased progressively with the distance from the forest fringe up to 200m inside the forest. Our results suggested that in forest ecosystems, high Ae. albopictus density is mainly observed at interfaces between anthropized and natural forested environments. Additionally, our data suggested that Ae. albopictus may act as a bridge vector of zoonotic pathogens between wild and anthropogenic compartments.

Urban Green Spaces and Vector-Borne Disease Risk in Africa: The Case of an Unclean Forested Park in Libreville (Gabon, Central Africa).

In Africa, vector-borne diseases are a major public health issue, especially in cities. Urban greening is increasingly considered to promote inhabitants' well-being. However, the impact of urban green spaces on vector risk remains poorly investigated, particularly urban forests in poor hygienic conditions. Therefore, using larval sampling and human landing catches, this study investigated the mosquito diversity and the vector risk in a forest patch and its inhabited surroundings in Libreville, Gabon, central Africa. Among the 104 water containers explored, 94 (90.4%) were artificial (gutters, used tires, plastic bottles) and 10 (9.6%) were natural (puddles, streams, tree holes). In total, 770 mosquitoes belonging to 14 species were collected from such water containers (73.1% outside the forested area). The mosquito community was dominated by Aedes albopictus (33.5%), Culex quinquefasciatus (30.4%), and Lutzia tigripes (16.5%). Although mosquito diversity was almost double outside compared to inside the forest (Shannon diversity index: 1.3 vs. 0.7, respectively), the species relative abundance (Morisita-Horn index = 0.7) was similar. Ae. albopictus (86.1%) was the most aggressive species, putting people at risk of Aedes-borne viruses. This study highlights the importance of waste pollution in urban forested ecosystems as a potential driver of mosquito-borne diseases.

Monitoring mosquito richness in an understudied area: can environmental DNA metabarcoding be a complementary approach to adult trapping?

Mosquito surveillance programmes are essential to assess the risks of local vector-borne disease outbreaks as well as for early detection of mosquito invasion events. Surveys are usually performed with traditional sampling tools (i.e., ovitraps and dipping method for immature stages or light or decoy traps for adults). Over the past decade, numerous studies have highlighted that environmental DNA (eDNA) sampling can enhance invertebrate species detection and provide community composition metrics. However, the usefulness of eDNA for detection of mosquito species has, to date, been largely neglected. Here, we sampled water from potential larval breeding sites along a gradient of anthropogenic perturbations, from the core of an oil palm plantation to the rainforest on São Tomé Island (Gulf of Guinea, Africa). We showed that (i) species of mosquitoes could be detected via metabarcoding mostly when larvae were visible, (ii) larvae species richness was greater using eDNA than visual identification and (iii) new mosquito species were also detected by the eDNA approach. We provide a critical discussion of the pros and cons of eDNA metabarcoding for monitoring mosquito species diversity and recommendations for future research directions that could facilitate the adoption of eDNA as a tool for assessing insect vector communities.

Climate change and vector-borne diseases: a multi-omics approach of temperature-induced changes in the mosquito.

BACKGROUND: Climate change and globalization contribute to the expansion of mosquito vectors and their associated pathogens. Long spared, temperate regions have had to deal with the emergence of arboviruses traditionally confined to tropical regions. Chikungunya virus (CHIKV) was reported for the first time in Europe in 2007, causing a localized outbreak in Italy, which then recurred repeatedly over the years in other European localities. This raises the question of climate effects, particularly temperature, on the dynamics of vector-borne viruses. The objective of this study is to improve the understanding of the molecular mechanisms set up in the vector in response to temperature. METHODS: We combine three complementary approaches by examining Aedes albopictus mosquito gene expression (transcriptomics), bacterial flora (metagenomics) and CHIKV evolutionary dynamics (genomics) induced by viral infection and temperature changes. RESULTS: We show that temperature alters profoundly mosquito gene expression, bacterial microbiome and viral population diversity. We observe that (i) CHIKV infection upregulated most genes (mainly in immune and stress-related pathways) at 20°C but not at 28°C, (ii) CHIKV infection significantly increased the abundance of Enterobacteriaceae Serratia marcescens at 28°C and (iii) CHIKV evolutionary dynamics were different according to temperature. CONCLUSION: The substantial changes detected in the vectorial system (the vector and its bacterial microbiota, and the arbovirus) lead to temperature-specific adjustments to reach the ultimate goal of arbovirus transmission; at 20°C and 28°C, the Asian tiger mosquito Ae. albopictus was able to transmit CHIKV at the same efficiency. Therefore, CHIKV is likely to continue its expansion in the northern regions and could become a public health problem in more countries than those already affected in Europe.

Mosquito vector competence for dengue is modulated by insect-specific viruses.

Aedes aegypti and A. albopictus mosquitoes are the main vectors for dengue virus (DENV) and other arboviruses, including Zika virus (ZIKV). Understanding the factors that affect transmission of arboviruses from mosquitoes to humans is a priority because it could inform public health and targeted interventions. Reasoning that interactions among viruses in the vector insect might affect transmission, we analysed the viromes of 815 urban Aedes mosquitoes collected from 12 countries worldwide. Two mosquito-specific viruses, Phasi Charoen-like virus (PCLV) and Humaita Tubiacanga virus (HTV), were the most abundant in A. aegypti worldwide. Spatiotemporal analyses of virus circulation in an endemic urban area revealed a 200% increase in chances of having DENV in wild A. aegypti mosquitoes when both HTV and PCLV were present. Using a mouse model in the laboratory, we showed that the presence of HTV and PCLV increased the ability of mosquitoes to transmit DENV and ZIKV to a vertebrate host. By transcriptomic analysis, we found that in DENV-infected mosquitoes, HTV and PCLV block the downregulation of histone H4, which we identify as an important proviral host factor in vivo.

Extensive variation and strain-specificity in dengue virus susceptibility among African Aedes aegypti populations.

African populations of the mosquito Aedes aegypti are usually considered less susceptible to infection by human-pathogenic flaviviruses than globally invasive populations found outside Africa. Although this contrast has been well documented for Zika virus (ZIKV), it is unclear to what extent it is true for dengue virus (DENV), the most prevalent flavivirus of humans. Addressing this question is complicated by substantial genetic diversity among DENV strains, most notably in the form of four genetic types (DENV1 to DENV4), that can lead to genetically specific interactions with mosquito populations. Here, we carried out a continent-wide survey of DENV susceptibility using a panel of field-derived Ae. aegypti colonies from across the African range of the species and a colony from Guadeloupe, French West Indies as non-African reference. We found considerable variation in the ability of African Ae. aegypti populations to acquire and replicate a panel of six DENV strains spanning the four DENV types. Although African Ae. aegypti populations were generally less susceptible than the reference non-African population from Guadeloupe, in several instances some African populations were equally or more susceptible than the Guadeloupe population. Moreover, the relative level of susceptibility between African mosquito populations depended on the DENV strain, indicating genetically specific interactions. We conclude that unlike ZIKV susceptibility, there is no clear-cut dichotomy in DENV susceptibility between African and non-African Ae. aegypti. DENV susceptibility of African Ae. aegypti populations is highly heterogeneous and largely governed by the specific pairing of mosquito population and DENV strain.

Zika vector competence data reveals risks of outbreaks: the contribution of the European ZIKAlliance project.

First identified in 1947, Zika virus took roughly 70 years to cause a pandemic unusually associated with virus-induced brain damage in newborns. Zika virus is transmitted by mosquitoes, mainly Aedes aegypti, and secondarily, Aedes albopictus, both colonizing a large strip encompassing tropical and temperate regions. As part of the international project ZIKAlliance initiated in 2016, 50 mosquito populations from six species collected in 12 countries were experimentally infected with different Zika viruses. Here, we show that Ae. aegypti is mainly responsible for Zika virus transmission having the highest susceptibility to viral infections. Other species play a secondary role in transmission while Culex mosquitoes are largely non-susceptible. Zika strain is expected to significantly modulate transmission efficiency with African strains being more likely to cause an outbreak. As the distribution of Ae. aegypti will doubtless expand with climate change and without new marketed vaccines, all the ingredients are in place to relive a new pandemic of Zika.

Using haematophagous fly blood meals to study the diversity of blood-borne pathogens infecting wild mammals.

Many emerging infectious diseases originate from wild animals, so there is a profound need for surveillance and monitoring of their pathogens. However, the practical difficulty of sample acquisition from wild animals tends to limit the feasibility and effectiveness of such surveys. Xenosurveillance, using blood-feeding invertebrates to obtain tissue samples from wild animals and then detect their pathogens, is a promising method to do so. Here, we describe the use of tsetse fly blood meals to determine (directly through molecular diagnostic and indirectly through serology), the diversity of circulating blood-borne pathogens (including bacteria, viruses and protozoa) in a natural mammalian community of Tanzania. Molecular analyses of captured tsetse flies (182 pools of flies totalizing 1728 flies) revealed that the blood meals obtained came from 18 different vertebrate species including 16 non-human mammals, representing approximately 25% of the large mammal species present in the study area. Molecular diagnostic demonstrated the presence of different protozoa parasites and bacteria of medical and/or veterinary interest. None of the six virus species searched for by molecular methods were detected but an ELISA test detected antibodies against African swine fever virus among warthogs, indicating that the virus had been circulating in the area. Sampling of blood-feeding insects represents an efficient and practical approach to tracking a diversity of pathogens from multiple mammalian species, directly through molecular diagnostic or indirectly through serology, which could readily expand and enhance our understanding of the ecology and evolution of infectious agents and their interactions with their hosts in wild animal communities.

Experimental infections with Zika virus strains reveal high vector competence of Aedes albopictus and Aedes aegypti populations from Gabon (Central Africa) for the African virus lineage.

ABSTRACTThe two main Zika virus (ZIKV) vectors, Aedes albopictus and Aedes aegypti (invasive and native species, respectively), are present in Gabon (Central Africa). The aim of this study was to determine the entomological ZIKV risk associated with these mosquito species in Gabon by evaluating their vector competence for an African (i.e. representative of the endemic strains circulating in sub-Saharan Africa) and two Asian (i.e. representatives of exogenous epidemic strains that could be introduced) ZIKV strains. The transmission efficiency of one Ae. aegypti and two Ae. albopictus field-collected populations from Libreville and Franceville was assayed at day 7, 14 and 21 after experimental oral infection. The two mosquito species could transmit all three ZIKV strains already at day 7 post-infection, but transmission efficiency was higher for the African strain than the non-African strains (>60% versus <14%; incubation period of 14-21 days). The two mosquito species exhibited comparable vector competence for ZIKV, although the amount of viral particles (African strain) in saliva was significantly higher in Ae. albopictus than Ae. aegypti at day 14 post-infection. These findings suggest that overall, ZIKV risk in Gabon is mainly related to virus strains that circulate endemically across sub-Saharan Africa, although the transmission of non-African strains remain possible in case of introduction. Due to its high infestation indexes and ecological/geographical ranges, this risk appears mainly associated with Ae. albopictus. Vector surveillance and control methods against this invasive mosquito must be strengthened in the region to limit the risk of future outbreaks.

Population genomics in the arboviral vector Aedes aegypti reveals the genomic architecture and evolution of endogenous viral elements.

Horizontal gene transfer from viruses to eukaryotic cells is a pervasive phenomenon. Somatic viral integrations are linked to persistent viral infection whereas integrations into germline cells are maintained in host genomes by vertical transmission and may be co-opted for host functions. In the arboviral vector Aedes aegypti, an endogenous viral element from a nonretroviral RNA virus (nrEVE) was shown to produce PIWI-interacting RNAs (piRNAs) to limit infection with a cognate virus. Thus, nrEVEs may constitute a heritable, sequence-specific mechanism for antiviral immunity, analogous to piRNA-mediated silencing of transposable elements. Here, we combine population genomics and evolutionary approaches to analyse the genomic architecture of nrEVEs in A. aegypti. We conducted a genome-wide screen for adaptive nrEVEs and searched for novel population-specific nrEVEs in the genomes of 80 individual wild-caught mosquitoes from five geographical populations. We show a dynamic landscape of nrEVEs in mosquito genomes and identified five novel nrEVEs derived from two currently circulating viruses, providing evidence of the environmental-dependent modification of a piRNA cluster. Overall, our results show that virus endogenization events are complex with only a few nrEVEs contributing to adaptive evolution in A. aegypti.

Enhanced Zika virus susceptibility of globally invasive Aedes aegypti populations.

The drivers and patterns of zoonotic virus emergence in the human population are poorly understood. The mosquito Aedes aegypti is a major arbovirus vector native to Africa that invaded most of the world's tropical belt over the past four centuries, after the evolution of a "domestic" form that specialized in biting humans and breeding in water storage containers. Here, we show that human specialization and subsequent spread of A. aegypti out of Africa were accompanied by an increase in its intrinsic ability to acquire and transmit the emerging human pathogen Zika virus. Thus, the recent evolution and global expansion of A. aegypti promoted arbovirus emergence not solely through increased vector-host contact but also as a result of enhanced vector susceptibility.

The COVID-19 pandemic should not jeopardize dengue control.

The concurrent circulation of dengue and coronavirus disease 2019 (COVID-19) may produce many unfavourable outcomes-such as co-infections; delays in diagnosis, treatment, and mitigation measures; overwhelming of the healthcare system; underreporting of cases; deterioration in surveillance and control interventions; and exacerbation of social inequalities. Indeed, lockdown is greatly compromising the effectiveness of vector control, especially social mobilization campaigns and preventive insecticide spraying in private spaces (indoor and peridomestic spraying). Thus, failure to appropriately implement the full range of vector control interventions can lead to a reduction in their overall effectiveness and an increasing risk of vector-borne diseases circulating. Consequently, the health community and policy makers should develop proactive policies and allocate adequate resources to prevent and manage the resurgence of dengue and other vector-borne diseases in the new era of COVID-19.

Author Correction: Genomes of all known members of a Plasmodium subgenus reveal paths to virulent human malaria.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti.

Although specific interactions between host and pathogen genotypes have been well documented in invertebrates, the identification of host genes involved in discriminating pathogen genotypes remains a challenge. In the mosquito Aedes aegypti, the main dengue virus (DENV) vector worldwide, statistical associations between host genetic markers and DENV types or strains were previously detected, but the host genes underlying this genetic specificity have not been identified. In particular, it is unknown whether DENV type- or strain-specific resistance relies on allelic variants of the same genes or on distinct gene sets. Here, we investigated the genetic architecture of DENV resistance in a population of Ae. aegypti from Bakoumba, Gabon, which displays a stronger resistance phenotype to DENV type 1 (DENV-1) than to DENV type 3 (DENV-3) infection. Following experimental exposure to either DENV-1 or DENV-3, we sequenced the exomes of large phenotypic pools of mosquitoes that are either resistant or susceptible to each DENV type. Using variation in single-nucleotide polymorphism (SNP) frequencies among the pools, we computed empirical p values based on average gene scores adjusted for the differences in SNP counts, to identify genes associated with infection in a DENV type-specific manner. Among the top 5% most significant genes, 263 genes were significantly associated with resistance to both DENV-1 and DENV-3, 287 genes were only associated with DENV-1 resistance and 290 were only associated with DENV-3 resistance. The shared significant genes were enriched in genes with ATP binding activity and sulfur compound transmembrane transporter activity, whereas the genes uniquely associated with DENV-3 resistance were enriched in genes with zinc ion binding activity. Together, these results indicate that specific resistance to different DENV types relies on largely non-overlapping sets of genes in this Ae. aegypti population and pave the way for further mechanistic studies.