Biology subjects

Donnelly, M. J.

Publications and source records attributed to Donnelly, M. J..

At least 19 recordsLinked to original sources

bioRxiv2025

A genomic toolkit for surveillance and elimination of the principal malaria vectors in Southeast Asia.

While substantial progress has been made toward malaria elimination in Southeast Asia, major challenges remain. The principal mosquito vectors, Anopheles dirus and Anopheles minimus, inhabit diverse ecological niches and exhibit a wide range of behavioural and physiological insecticide resistance phenotypes, complicating vector control efforts. In Africa, genomic surveillance has transformed our understanding of vector evolution and resistance, supported by open-access tools and data. Comparable resources for Southeast Asian vectors remain limited. Here, we release Adir1.0, a curated, analysis-ready catalog of 540 An. dirus whole-genome sequences, accessible for interactive cloud-based analysis via the malariagen-data-python application programming interface (API). Alongside, we provide an updated Amin1.0 API to enhance functionality and usability, enabling integrated analyses across historical and new datasets. We demonstrate these resources by performing the first exploratory population genomic analysis of An. dirus from Bangladesh, Thailand, and Cambodia, revealing population structure, candidate regions of physiological resistance, and genomic structural variation. Together, these resources provide a foundation for genomic surveillance studies to inform vector control and malaria elimination strategies in Southeast Asia.

genetics↗

bioRxiv2025

An atlas of positive selection in the genomes of major malaria vectors

Insecticide resistance poses a major threat to malaria control efforts in Africa, yet our understanding of the genomic basis of adaptation in malaria vectors remains incomplete. Here we present a comprehensive atlas of recent positive selection in natural populations of the major African malaria vectors; the An. gambiae species complex and An. funestus. By analyzing whole-genome sequence data from 4,306 mosquitoes collected across twenty-one countries, we identify and characterize both known and novel genomic regions under strong positive selection. We develop an innovative approach for identifying and localising selection signals, and find extensive evidence for parallel evolution between species, with all important loci in An. funestus also under selection in An. gambiae s.l. We confirm intense selection at established resistance loci including known target site proteins (Vgsc, Rdl, Ace1) and metabolic enzymes (Cyp6p, Cyp9k1, Gste, Coeaexf) and describe novel signals at a diacylglycerol kinase on the X chromosome, and in An. gambiae s.l, at the metabolic regulator Keap1. To support real-time monitoring of emerging variants threatening vector control, we present an open-source web resource containing detailed selection scan results for all cohorts. The resource is driven by an automated computational workflow, which enables continuous updates as new whole-genome data are generated. The selection atlas provides a foundation for understanding vector adaptation to insecticide-based interventions and we hope will inform evidence-based resistance management strategies that are critical for sustaining malaria control.

genomics↗

bioRxiv2025

Signatures of selection and mechanisms of insecticide resistance in Ugandan Anopheles funestus: Insights from embedding translational genomics into the LLINEUP cluster randomised trial.

In response to the emerging threat of insecticide resistance in malaria vectors, insecticides are being repurposed for vector control or developed de novo. Good stewardship of these finite new resources is essential if disease control programmes are to remain effective. This is dependent on timely data to help guide evidence-based decision-making for National Malaria Control programmes (NMCPs). By embedding genomics into cluster randomized control trials (cRCTs), we can perform surveillance and early detection of insecticide resistance variants to new and repurposed chemicals in natural field conditions, supporting effective stewardship. The LLIN Evaluation Uganda Project (LLINEUP) trial evaluated the efficacy of pyrethroid-piperonyl butoxide (PBO) and pyrethroids-only long-lasting insecticidal nets (LLINs). It was conducted in Uganda between 2017-2020 and was the largest cRCT to date, covering 40% of the country in 104 health sub-districts. We embedded genomic surveillance within LLINEUP to detect and track insecticide resistance variants. At baseline and throughout the trial, we sampled Anopheles mosquitoes with Prokopack aspirators and performed Illumina whole-genome sequencing. We show that An. funestus populations were relatively unaffected by the interventions, compared to An. gambiae s.l., which were markedly reduced six months following LLIN deployment. Standard approaches for describing genetic diversity and population structure e.g. fixation index (FST), Principal Component Analysis (PCA) and Neighbour-Joining (NJ) trees, were consistent with the density observations and suggestive of a single large An. funestus population in Uganda with little genetic differentiation. Genome-wide selection scans revealed strong signals of selection at the Resistance to pyrethroid-1 (RP1) locus and Cyp9k1, both loci previously implicated in pyrethroid resistance. We report two additional loci, eye diacylglycerol kinase (Dgk) ({cong}13.5Mb on the X chromosome) and O-mannosyl-transferase (TMC-like) ({cong}67.9Mb on 3RL) that showed signals of selection. Known DDT and permethrin resistance-associated variants at the Gste2 locus, L119F and L119V, were also identified. Over the trial period, changes in haplotype frequencies were observed in regions under selection, with more pronounced shifts in the PBO arm. Notably, there were significant reductions in the frequencies of swept haplotypes (measured by delta ({Delta}) H12) in the Dgk and Cyp6p9a regions, while significant increases in haplotype frequency were observed at Gste2 and Cyp9k1 loci. Our findings reveal the differential impact of the trial on An. gambiae s.l. and An. funestus densities and the differing responses of An. funestus populations to pyrethroid and pyrethroid-PBO selection pressure. These insights underscore the potential value of tailored, species- and region-specific vector control strategies, supported by regional genetic surveillance, to better control insecticide resistance evolution and spread. By embedding genomic surveillance in cRCTs we can facilitate the discovery of putative resistance variants and can provide evidence of their impact on vector control tool efficacy; both of crucial importance to evidence-based deployment of vector control tools by NMCPs.

genomics↗

bioRxiv2025

Spatially-explicit genomics of An. gambiae s.l uncovers fine-scale population structure and mechanisms of insecticide resistance

Progress in malaria control in sub-Saharan Africa is stalling, partly due to the spread of insecticide resistance in Anopheles vectors. Monitoring the evolution of insecticide resistance alleles and their spatial heterogeneity is important for malaria control programmes, and genomic surveillance has emerged as a pivotal tool for this purpose. Earlier genomics research has typically employed convenience-based sampling, and research has yet to be performed to optimise sampling regimens for malaria vector genomics. In an earlier study, we developed a spatially explicit sampling framework that considers the underlying ecology to enable sampling mosquitoes with reduced bias. We applied this framework to sample and perform whole-genome sequencing on 485 individual specimens of An. gambiae s.l mosquitoes from Obuasi, central Ghana, an area with extensive gold mining activities. In this region, An. gambiae s.l have been documented as highly resistant to multiple insecticides, including pyrethroids used for the treatment of bed-nets. High resolution of fine-scale population structure enabled the detection of isolation-by-distance in An. coluzzii in Obuasi, whilst finding that at this scale, geographic distance, rather than the underlying habitat, drives population structure. We examine methods to estimate mosquito kinship, demonstrating that polymorphic chromosomal inversions significantly confound established analytical tools, while revealing how the mosquitos chromosome architecture generates high variance in genetic relatedness among kin. Using genome-wide selection scans and clustering, we discover the novel mutations Gste2-F120L and Cyp9K1-N224I in detoxification enzymes that are driving selective sweeps, likely in response to insecticidal pressure. We find that the frequencies of some resistance variants are associated with artisanal-gold mines, and elucidate the continued evolution of the Voltage-gated sodium channel, the target of pyrethroid insecticides. Overall, we show that sampling vectors strategically may enhance our ability to perform effective genomic surveillance.

genomics↗

bioRxiv2025

Genetic Surveillance Reveals Differential Evolutionary Dynamic of Anopheles gambiae Under Contrasting Insecticidal Tools used in Malaria control

Malaria, a febrile disease caused by the Plasmodium parasites and transmitted by mosquitoes, is a leading cause of mortality in children under 5 in endemic countries. The widespread deployment of insecticide-treated bed nets (ITNs) has significantly reduced malaria transmission, but rising levels of insecticide resistance threatens to halt the progress. Monitoring insecticide resistance is vital for effective vector control, particularly when deploying new tools. Understanding mosquito population responses to these interventions is crucial for guiding control programmes in making informed decisions about the selection, timing, and geographic deployment of tools. This genomic study investigates the demographic and evolutionary consequences on the malaria vector Anopheles gambiae of deploying standard ITNs (containing only pyrethroids) and pyrethroid-PBO nets (containing pyrethroids plus the synergist piperonyl butoxide) during a clinical trial in Uganda. Despite substantial reductions in indoor mosquito densities in the clinical trial, estimates of nucleotide diversity ({pi}) and linkage disequilibrium revealed no significant decline in effective population size, reflecting continued large population size even after effective control. Marked allele frequency shifts at resistance-associated loci indicated strong selection pressures driven by the interventions, with distinct selective dynamics between the two net types, highlighting alternative pyrethroid detoxification pathways in the presence of PBO. A duplication in the Cyp9k1 gene significantly increased in frequency in populations exposed to pyrethroid-only nets but decreased in populations exposed to PBO-treated nets, suggesting that selection for over-expression of this gene is removed when this resistance mechanism is impacted by PBO. An alternative potential detoxification mechanism was selected within a region of the 2La chromosomal inversion on chromosome 2L, which encompasses the UDP-glucose 6-dehydrogenase gene. This variant consistently increased in frequency when exposed to PBO-treated nets. Additionally, pyrethroid-only nets selected for a novel locus on the X chromosome containing the diacylglycerol kinase gene, which is potentially linked to behavioural adaptations through its role in neurotransmission modulation. Our findings underscore the importance of genomic surveillance in vector control, revealing distinct evolutionary dynamics of insecticide resistance mechanisms in the presence of PBO. While ITNs remain effective, the persistence and evolution of resistance-associated alleles highlight the need for adaptive and dynamic resistance management strategies. By integrating high-resolution genomic data with epidemiological and entomological monitoring, this study offers actionable insights to sustain malaria control efforts amid the ongoing challenge of insecticide resistance.

genomics↗

bioRxiv2025

The origin, invasion history and resistance architecture of Anopheles stephensi in Africa.

The invasion of Africa by the Asian urban malaria vector, Anopheles stephensi, endangers 126 million people across a rapidly urbanising continent where malaria is primarily a rural disease. Control of An. stephensi requires greater understanding of its origin, invasion dynamics, and mechanisms of widespread resistance to vector control insecticides. We present a genomic surveillance study of 551 An. stephensi sampled across the invasive and native ranges in Africa and Asia. Our findings support a hypothesis that an initial invasion from Asia to Djibouti seeded separate incursions to Sudan, Ethiopia, and Yemen before spreading inland, aided by favourable temperature, vegetation cover, and human transit conditions. Insecticide resistance in invasive An. stephensi is conferred by detoxification genes introduced from Asia. These findings, and a companion genomic data catalogue, will form the foundation of an evidence base for surveillance and management strategies for An. stephensi.

genomics↗

bioRxiv2025

Significant variations in tolerance to clothianidin and pirimiphos-methyl in Anopheles gambiae and Anopheles funestus populations during a dramatic malaria resurgence despite sustained indoor residual spraying in Uganda

A dramatic malaria resurgence occurred in areas of Uganda between 2020 and 2022 coincident with the switch to clothianidin-based formulations for indoor residual spraying. During the resurgence, Anopheles funestus numbers increased but when an alternative insecticide, pirimiphos methyl, was reintroduced in 2023, both malaria cases and An. funestus mosquito density fell. In this study, we investigated possible causes of the resurgence by assessing; 1) whether sufficient quantities of insecticide were sprayed; 2) the residual insecticide bioefficacy against wild mosquitoes and; 3) the insecticide susceptibility of vector populations using standard test tube assays and wall cone assays. In 2023, after adjusting for extraction efficiency, 70-80% of the houses had optimal residual concentrations of insecticides (clothianidin >0.3g/m2; pirimiphos methyl >0.5g/m2) with significant variations between sampling rounds and wall types. Mud walls had the lowest residual concentration of insecticides, and the lowest observed mortality in wall cone assays, compared to fired bricks with plaster/cement/paint. In the studies of residual bio efficacy, by World Health Organization (WHO) definitions, An. funestus showed resistance to clothianidin (<80% mortality) up to 11 months and susceptibility to pirimiphos methyl (>90% mortality) when exposed to wall surfaces up to 7 months post-spray. In WHO tube tests, variations were observed in susceptibility to clothianidin in An. funestus populations using dose- and time-response assays (80-98% mortality). In 2022, An. gambiae was largely susceptible to the clothianidin-based formulation Sumishield (85-90% mortality) although the levels dropped slightly in 2023 (60-85% mortality) mainly in mud and pole houses. In contrast, An. gambiae was mildly susceptible to the pirimiphos methyl-based formulation Actellic ([~]80% mortality) and time response assays showed An. gambiae populations had very low knockdown and mortality at lower exposure time compared to An. funestus. Regression models showed a positive association between residual insecticide concentration (RIC) and mortality in houses sprayed with Sumishield but not Actellic houses. Despite the possible variations observed in spray operations, the study revealed that An. funestus exhibited a higher tolerance to clothianidin-based formulations compared to An. gambiae, and this might have driven the malaria resurgence observed in Uganda. However, there are signals of An. gambiae resistance to pirimiphos-methyl which will require further investigation and monitoring.

zoology↗

bioRxiv2025

Targeted genomic surveillance of insecticide resistance in African malaria vectors

The emergence of insecticide resistance is threatening the efforts of malaria control programmes, which rely heavily on a limited arsenal of insecticidal tools, such as insecticide-treated bed nets. Importantly, genomic surveillance of malaria vectors can provide critical, policy-relevant insights into the presence and evolution of insecticide resistance, allowing us to maintain and extend the shelf life of these interventions. Yet the complex genetic architecture of resistance, combined with resource constraints in malaria-endemic settings, have thus far precluded the widespread use of genomics in routine surveillance. Meanwhile, stakeholders in sub-Saharan Africa are moving towards locally driven, decentralised generation of genomic data, underscoring the need for standardised and robust genomics workflows. To address this need, we demonstrate an approach to targeted genomic surveillance in Anopheles gambiae s.l with Illumina sequencing. We target 90 genomic loci in the Anopheles gambiae s.l genome, including 55 resistance-associated mutations and 35 ancestry informative markers. This protocol is coupled with advanced, automated software for accurate and reproducible variant analysis. We are able to elucidate population structure and ancestry in our cohorts and accurately identify most species in the An. gambiae species complex. We report frequencies of variants at insecticide-resistance loci and explore the continued evolution of the pyrethroid target site, the Voltage-gated sodium channel. Applying the platform to a recently established colony of field-caught resistant mosquitoes (Siaya, Kenya), we identified seven independent resistance-associated variants contributing to reduced efficacy of insecticide-treated nets in East Africa. Additionally, we leverage a machine learning algorithm (XGBoost) to demonstrate the possibility of predicting bioassay mortality using genotypes alone. This achieved high accuracy (75%), demonstrating the potential of targeted genomics to predictively monitor insecticide resistance. Together these tools provide a practical, scalable solution for resistance monitoring while advancing the goal of building local genomic surveillance capacity in sub-Saharan Africa.

genomics↗

bioRxiv2024

Cryptic population structure and insecticide resistance in Anopheles gambiae from the southern Democratic Republic of Congo

The Democratic Republic of Congo (DRC) suffers from one of the highest malaria burdens worldwide, but information on its Anopheles vector populations is relatively limited. Preventative malaria control in DRC is reliant on pyrethroid-treated nets, raising concerns over the potential impacts of insecticide resistance. We sampled Anopheles gambiae from three geographically distinct populations (Kimpese, Kapolowe and Mikalayi) in southern DRC, collecting from three sub-sites per population and characterising mosquito collections from each for resistance to pyrethroids using WHO tube bioassays. Resistance to each of three different pyrethroids was generally high in An. gambiae with <92% mortality in all tests, but varied between collections, with mosquitoes from Kimpese being the most resistant. Whole genome sequencing of 165 An. gambiae revealed evidence for genetic differentiation between Kimpese and Kapolowe / Mikalayi, but not between the latter two sample sites despite separation of approximately 800km. Surprisingly, there was evidence of population structure at a small spatial scale between collection subsites in Kimpese, despite separation of just tens of kilometres. Intra-population (H12) and inter-population (FST) genome scans identified multiple peaks corresponding to genes associated with insecticide resistance such as the voltage gated sodium channel (Vgsc) target site on chromosome 2L, a Cyp6 cytochrome P450 cluster on chromosome arm 2R, and the Cyp9k1 P450 gene on chromosome X. In addition, in the Kimpese subsites, the P450 redox partner gene Cpr showed evidence for contemporary selection (H12) and population differentiation (FST) meriting further exploration as a potential resistance associated marker.

evolutionary biology↗

bioRxiv2024

Copy number variants underlie the major selective sweeps in insecticide resistance genes in Anopheles arabiensis from Tanzania.

To keep ahead of the evolution of resistance to insecticides in mosquitoes, national malaria control programmes must make use of a range of insecticides, both old and new, while monitoring resistance mechanisms. Knowledge of the mechanisms of resistance remains limited in Anopheles arabiensis, which in many parts of Africa is of increasing importance because it is apparently less susceptible to many indoor control interventions. Furthermore, comparatively little is known in general about resistance to non-pyrethroid insecticides such as pirimiphos-methyl (PM), which are crucial for effective control in the context of resistance to pyrethroids. We performed a genome-wide association study to determine the molecular mechanisms of resistance to deltamethrin (commonly used in bednets) and PM, in An. arabiensis from two regions in Tanzania. Genomic regions of positive selection in these populations were largely driven by copy number variants (CNVs) in gene families involved in resistance to these two insecticides. We found evidence of a new gene cluster involved in resistance to PM, identifying a strong selective sweep tied to a CNV in the Coeae2g-Coeae6g cluster of carboxylesterase genes. Using complementary data from An. coluzzii in Ghana, we show that copy number at this locus is significantly associated with PM resistance. Similarly, for deltamethrin, resistance was strongly associated with a novel CNV allele in the Cyp6aa / Cyp6p cluster. Against this background of metabolic resistance, target site resistance was very rare or absent for both insecticides. Mutations in the pyrethroid target site Vgsc were at very low frequency in Tanzania, yet combining these samples with three An. arabiensis individuals from West Africa revealed a startling diversity of evolutionary origins of target site resistance, with up to 5 independent origins of Vgsc-995 mutations found within just 8 haplotypes. Thus, despite having been first recorded over 10 years ago, Vgsc resistance mutations in Tanzanian An. arabiensis have remained at stable low frequencies. Overall, our results provide a new copy number marker for monitoring resistance to PM in malaria mosquitoes, and reveal the complex picture of resistance patterns in An. arabiensis.

genomics↗

bioRxiv2024

Parallel evolution in mosquito vectors - a duplicated esterase locus is associated with resistance to pirimiphos-methyl in An. gambiae

The primary control methods for the African malaria mosquito, Anopheles gambiae, are based on insecticidal interventions. Emerging resistance to these compounds is therefore of major concern to malaria control programmes. The organophosphate, pirimiphos-methyl, is a relatively new chemical in the vector control armoury but is now widely used in indoor residual spray campaigns. Whilst generally effective, phenotypic resistance has developed in some areas in malaria vectors. Here, we used a population genomic approach to identify novel mechanisms of resistance to pirimiphos-methyl in Anopheles gambiae s.l mosquitoes. In multiple populations, we found large and repeated signals of selection at a locus containing a cluster of detoxification enzymes, some of whose orthologs are known to confer resistance to organophosphates in Culex pipiens. Close examination revealed a pair of alpha-esterases, Coeae1f and Coeae2f, and a complex and diverse pattern of haplotypes under selection in An. gambiae, An. coluzzii and An. arabiensis. As in Cx. pipiens, copy number variation seems to play a role in the evolution of insecticide resistance at this locus. We used diplotype clustering to examine whether these signals arise from parallel evolution or adaptive introgression. Using whole-genome sequenced phenotyped samples, we found that in West Africa, a copy number variant in Anopheles gambiae is associated with resistance to pirimiphos-methyl. Overall, we demonstrate a striking example of contemporary parallel evolution which has important implications for malaria control programmes.

evolutionary biology↗

bioRxiv2023

Mechanisms of transcriptional regulation in Anopheles gambiae revealed by allele specific expression

Malaria control relies on insecticides targeting the mosquito vector, but this is increasingly compromised by insecticide resistance, which can be achieved by elevated expression of detoxifying enzymes that metabolize the insecticide. In diploid organisms, gene expression is regulated both in cis, by regulatory sequences on the same chromosome, and by trans acting factors, affecting both alleles equally. Differing levels of transcription can be caused by mutations in cis-regulatory modules (CRM), but few of these have been identified in mosquitoes. We crossed bendiocarb resistant and susceptible Anopheles gambiae strains to identify cis-regulated genes that might be responsible for the resistant phenotype using RNAseq, and cis-regulatory module sequences controlling gene expression in insecticide resistance relevant tissues were predicted using machine learning. We found 115 genes showing allele specific expression in hybrids of insecticide susceptible and resistant strains, suggesting cis regulation is an important mechanism of gene expression regulation in Anopheles gambiae. The genes showing allele specific expression included a higher proportion of Anopheles specific genes on average younger than genes those with balanced allelic expression. Author SummaryThe evolution of insecticide resistance, including resistance that is due to changes in the expression levels of certain resistance associated genes is threatening progress in malaria control. We investigated how the expression of genes in the malaria vector Anopheles gambiae is controlled, by implementing a method for the first time in this species. Each mosquito inherits a set of chromosomes from both parents, so has a maternal and paternal copy of most genes. When a gene is expressed, the DNA encoding that gene is transcribed into messenger RNA. This process is controlled by the cellular environment and by other DNA sequences on the same chromosome as each gene. We crossed mosquitoes from insecticide resistant and susceptible strains to equalize the cellular environment and then measured the levels of messenger RNA from both gene copies. 115 genes showed consistently different messenger RNA levels between gene copies in most crosses, suggesting these genes are regulated by factors on the same chromosome. There were relatively more Anopheles specific genes with imbalanced expression. Using machine learning we identified DNA sequences that may be responsible for controlling gene expression in mosquito tissues; several of these sequences were close to genes with imbalanced expression.

genetics↗

bioRxiv2023

Spatially explicit sampling frameworks to identify regions of increased mosquito abundance

Vector control interventions often lack comprehensive information on vector population distribution and dynamics. This knowledge gap poses challenges in targeting interventions effectively, especially in areas with heterogeneous transmission and where complementary vector control tools may be required to achieve sustained impact on disease transmission. In this study, we implemented a spatially explicit sampling framework for improved vector surveillance in coastal Kenya. Our stratified lattice with close pair sampling design aimed to characterise the vector dynamics of the primary malaria-transmitting species in the area and assess the ecotype classifications effectiveness at identifying clear population patterns. The study collected 3,621 mosquitoes, with An. funestus s.l. being the most abundant malaria vector. The inclusion of the ecotype classification significantly improved spatial abundance model estimates for An. gambiae and Culex spp. Wetlands, topographic wetness index, and proximity to rivers were associated with increased mosquito abundance. Spatial modelling revealed high abundance regions near the Galana-Sabaki River. Our study demonstrates the applicability of a reproducible spatial sampling approach to identify areas with high vector abundance and inform targeted vector control strategies. The study highlights the importance of ecological stratification and a spatial explicit sampling approach for predicting mosquito presence when prior data is limited and underscores the potential for refining future sampling for control efforts.

ecology↗

bioRxiv2023

Hypnotic treatment reverses NREM sleep disruption and EEG desynchronization in a mouse model of Fragile X syndrome to rescue memory consolidation deficits.

Fragile X syndrome (FXS) is a highly-prevalent genetic cause of intellectual disability, associated with disrupted cognition and sleep abnormalities. Sleep loss itself negatively impacts cognitive function, yet the contribution of sleep loss to impaired cognition in FXS is vastly understudied. One untested possibility is that disrupted cognition in FXS is exacerbated by abnormal sleep. We hypothesized that restoration of sleep-dependent mechanisms could improve functions such as memory consolidation in FXS. We examined whether administration of ML297, a hypnotic drug acting on G-protein-activated inward-rectifying potassium channels, could restore sleep phenotypes and improve disrupted memory consolidation in Fmr1-/y mice. Using 24-h polysomnographic recordings, we found that Fmr1-/y mice exhibit reduced non-rapid eye movement (NREM) sleep and fragmented NREM sleep architecture, alterations in NREM EEG spectral power (including reductions in sleep spindles), and reduced EEG coherence between cortical areas. These alterations were reversed in the hours following ML297 administration. Hypnotic treatment following contextual fear or spatial learning also ameliorated disrupted memory consolidation in Fmr1-/y mice. Hippocampal activation patterns during memory recall was altered in Fmr1-/y mice, reflecting an altered balance of activity among principal neurons vs. parvalbumin-expressing (PV+) interneurons. This phenotype was partially reversed by post-learning ML297 administration. These studies suggest that sleep disruption could have a major impact on neurophysiological and behavioral phenotypes in FXS, and that hypnotic therapy may significantly improve disrupted cognition in this disorder.

neuroscience↗

bioRxiv2023

Development and deployment of improved Anopheles gambiae s.l. field surveillance by adaptive spatial sampling design

Accurate assessments of vector occurrence and abundance, particularly in widespread vector-borne diseases such as malaria, is essential for efficient deployment of disease surveillance and control interventions. This study emphasizes the need for flexible spatial sampling designs that can capture the dynamic relationships between disease vector species and the environment. Although previous studies have examined the benefits of adaptive sampling for disease hotspot identification (mostly by simulations), limited research has been conducted on field surveillance of malaria vectors. Here, an adaptive spatial sampling design targeting potential and uncertain An. gambiae hotspots, a major malaria vector in sub-Saharan Africa, is presented. The first phase of the proposed design involved ecological zone delineation and a proportional lattice with close pairs sampling design to maximise spatial coverage, representativeness of ecological zones and vector spatial autocorrelation (by the employment of close pairs). In the second phase, a spatial adaptive sampling design targeted high-risk areas with the largest uncertainty. For the second phase, the sample size was reduced compared to the first phase, but predictions improved for out-of-sample and training data. However, the overall model uncertainty increased, highlighting the trade-off in multi-criteria adaptive sampling designs. It is important that future research focuses on these trade-offs to reduce the timescale for effective malaria control and elimination efforts.

ecology↗

bioRxiv2023

Molecular archaeology: individual human DNA and infection profiles from 100 year old mosquitoes

Natural history collections represent a vast biological and genetic resource, which has remained largely untapped. We revisit mosquito collections of varying ages; some made by early tropical medicine pioneers over 100 years ago. By applying species-specific primers, a panel of forensic short tandem repeat (STR) markers, and Plasmodium diagnostics, we were able to obtain the unique genetic profile and Plasmodium infection status of the individual from whom each mosquito obtained their final bloodmeal. We show evidence of long-dead mosquitoes feeding on multiple individuals in the same gonotrophic cycle, and how the human hosts are likely to have been infected with malaria at the time of blood-feeding. This approach may be used to track the host-fidelity of vectors over an evolutionary time scale.

genetics↗

bioRxiv2023

Genome-wide association studies reveal novel loci associated with pyrethroid and organophosphate resistance in Anopheles gambiae s.l.

Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of the most widespread tools currently used to control malaria. The genetic underpinnings of resistance are still only partially understood, with much of the variance in resistance phenotype left unexplained. We performed a multi-country large scale genome-wide association study of resistance to two insecticides widely used in malaria control: deltamethrin and pirimiphos-methyl. Using a bioassay methodology designed to maximise the phenotypic difference between resistant and susceptible samples, we sequenced 969 phenotyped female An. gambiae and An. coluzzii from ten locations across four countries in West Africa (Benin, Cote dIvoire, Ghana and Togo), identifying single nucleotide polymorphisms (SNPs) and copy number variants (CNVs) segregating in the populations. The patterns of resistance association were highly multiallelic and variable between populations, with different genomic regions contributing to resistance, as well as different mutations within a given region. While the strongest and most consistent association with deltamethrin resistance came from the region around Cyp6aa1, this resistance was based on a combination of several independent CNVs in An. coluzzii, and on a non-CNV bearing haplotype in An. gambiae. Further signals involved a range of cytochrome P450, mitochondrial, and immunity genes. Similarly, for pirimiphos-methyl, while the strongest signal came from the region of Ace1, more widespread signals included cytochrome P450s, glutathione S-transferases, and a subunit of the nAChR target site of neonicotinoid insecticides. The regions around Cyp9k1 and the Tep family of immune genes were associated with resistance to both insecticide classes, suggesting possible cross-resistance mechanisms. These locally-varying, multigenic and multiallelic patterns highlight the challenges involved in genomic monitoring and surveillance of resistance, and form the basis for improvement of methods used to detect and predict resistance. Based on simulations of resistance variants, we recommend that yet larger scale studies, exceeding 500 phenotyped samples per population, are required to better identify associated genomic regions.

genomics↗

bioRxiv2023

AgamPrimer: Primer Design in Anopheles gambiae informed by range-wide genomic variation

The major malaria mosquito, Anopheles gambiae s.l, is one of the most studied organisms in medical research and also one of the most genetically diverse. When designing polymerase chain reaction (PCR) or hybridisation-based molecular assays, reliable primer and probe design is crucial. However, single nucleotide polymorphisms (SNPs) in primer binding sites can prevent primer binding, leading to null alleles, or bind suboptimally, leading to preferential amplification of specific alleles. Given the extreme genetic diversity of An. gambiae, researchers need to consider this genetic variation when designing primers and probes to avoid amplification problems. In this note, we present a python package, AgamPrimer, which exploits the AG1000G dataset and allows users to rapidly design primers in An. gambiae, whilst summarising genetic variation in the primer binding sites and visualising the position of primer pairs. AgamPrimer allows the design of both genomic DNA and cDNA primers and hybridisation probes. By coupling this python package with Google Colaboratory, AgamPrimer is an open and accessible platform for primer and probe design, hosted in the cloud for free. AgamPrimer is available here https://github.com/sanjaynagi/AgamPrimer and we hope it will be a useful resource for the community to design probe and primer sets that can be reliably deployed across the An. gambiae species range.

genomics↗