Data science and genomic studies on major mosquito vectors of human and zoonotic diseases

Vector-borne diseases cause over 700,000 deaths each year and account for more than 17% of infectious diseases globally. Most of them are caused by blood-sucking insects, and among them mosquitoes (Diptera: Culicidae) are the most important vectors for global public health. Mosquito species within the genus Anopheles are responsible for transmitting the malaria parasite: Plasmodium. In contrast, some species of Aedes and Culex genera are vectors of human arboviruses (e.g., Yellow Fever, Dengue, Zika, Chikungunya), zoonotic arboviruses (e.g., West Nile, Japanese encephalitis), and filarial nematodes. Mosquito-borne diseases are most prevalent in tropical regions. According to the 2023 World Health Organization (WHO) report on malaria, the disease remains one of the most significant global health challenges, with an estimated 249 million cases and over 608,000 deaths annually. Notably, approximately 233 million of these cases (about 94%) occur within the WHO African Region, underscoring the disproportionate impact of malaria in this area. On the other hand, Dengue incidence has escalated dramatically worldwide, with WHO-reported cases rising from approximately 505,000 in 2000 to 5.2 million in 2019. In 2023, dengue reached an unprecedented peak, affecting over 80 countries and causing more than 6.5 million cases and 7,300 deaths. The disease is now endemic in over 100 countries, with Asia accounting for about 70% of the global disease burden. Key factors driving the epidemic include expanding distribution of dengue vectors due climate change impacts. However, in recent years, some mosquito-borne diseases have become increasingly relevant also in temperate areas previously considered no/low risk. This shift is attributed to climate conditions that favour the transmission of zoonotic arboviruses by native Culex species and to the global spread of invasive Aedes mosquitoes, which are vectors for human arboviruses. Mosquito-borne diseases represent a significant global health challenge, driven by vector species’ ecological diversity and genetic and metabolic resistance to control measures as well as insecticides. Data science is playing an increasingly important role in this field, enhancing epidemiology and mosquito control strategies through genomic surveillance, species distribution modelling, and statistical models to predict mosquito-borne disease transmission. Under the guidance of the Medical Entomology group in the Department of Public Health and Infectious Disease at Sapienza University in Rome, I became familiar with the research field of the mosquito vectors genomics, ecology and their disease that may transmit. Based on my background in bioinformatics and data science, the thesis project was developed in order to contribute to studies on the distribution, bionomics and population genomics of mosquito vectors of malaria and arbovirus by exploitation of large datasets. More in detail, my research objectives are divided into three key topics, addressing different species of public health importance in different geographic regions. The first objective was to assess the distribution of Anopheles gambiae and An. coluzzii - major malaria vectors in Sub-Saharan Africa - by exploiting environmental data to map their present and future distribution and to assess the implications of their ecological divergence and reproductive isolation. To address this objective a systematic review and meta-analysis was conducted using PRISMA 2020 guidelines, gathering species frequency data from 2001 to 2022 across 2118 geolocated sampling sites from 255 studies. Unlike earlier studies, this analysis incorporated fine-scale satellite data to link ecological predictors with An. coluzzii distribution patterns. The study identified key coastal and ecoclimatic variables shaping An. coluzzii spatial range, confirming its predominance in specific regions. Future models predict increasing An. coluzzii presence in Sub-Saharan Africa under several climate, including new previsions in East Africa, outside its known range. The results obtained are valuable to generate an updated map of the two vectors’ distribution and to predict possible variations in malaria transmission in relation to climate changes and other factors that increase species habitat suitability. Second, I investigated on population genomics of An. gambiae and An. coluzzii at the far-western limits of their range. These two species are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as “intermediate” between the two species by WGS data, and as hybrid forms by conventional molecular diagnostics. Results obtained by population genomics analyses of 1,190 individuals from 36 localities across 13 countries in West Africa, allowed to identify a putative taxon (provisionally named Bissau molecular form) in the westernmost region, which did not arise by admixture between An. coluzzii and An. gambiae, but rather appear to be originated at the same time as the split between the two species. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches. Finally, I contributed to three different research projects carried out by the Medical Entomology group at Sapienza University focussing on mosquito vectors of arboviruses in Europe. Firstly, I supported bioinformatic genomic analyses to study pyrethroid resistance mechanisms in Cx. pipiens, with particular reference to mutations in the voltage-gated sodium channel (VGSC) gene - referred to as knock-down resistance (kdr) mutations - which reduce the mosquito sensitivity to pyrethroid by altering the insecticide's interaction with the VGSC, thereby increasing the dose required to incapacitate the mosquito. Specifically, I carried out the bioinformatic analysis of Next Generation Sequencing data in order to genotype the VGSC gene of 82 Cx. pipiens. Results revealed 26 non-synonymous substitutions widespread in the VGSC gene, 3 of which (at positions 253, 1534, and 1879) were detected for the first time in the species. These included the super-kdr haplotype determined by association of kdr-alleles 918T and 1014F, previously identified in M. domestica. These new mutations pose challenges for vector control. Moreover, I participated on the Mosquito Alert Citizen Science project and its outreach, engaging Italian citizens with the aim to monitor Aedes and Culex mosquito species populations via a smartphone app, resulting in over 11,000 reports of both alien and native mosquito species. This project enhanced knowledge of species distribution and public awareness of mosquito-borne diseases and mosquito biology. Lastly, I contributed on interpolate environmental and demographic data to a model that assess dengue and chikungunya transmission risks, based on a cross-sectional mosquito sampling in Rome: results highlighted increased mosquito abundance and prolonged seasons in warmer years, underscoring potential future public health challenges. These results represent a significant advancement in the field with epidemiological and translational implications.