Heterogeneous genetic invasions of three insecticide resistance mutations in Indo-Pacific populations of Aedes aegypti (L.)

Parallel Signatures of Diet Adaptation in the Invasive Common Myna Genome

Invasive species offer uniquely replicated model systems to study rapid adaptation. The common myna (Acridotheres tristis) has been introduced to over a dozen countries and is classified as one of the most invasive birds in the world. Their multiple invasions provide an opportunity to identify repeated adaptation, as invasive populations originated from multiple source populations. We compared whole-genome resequencing data from 80 individuals from four native and seven invasive populations, representing two independent introduction pathways. Results from two different selection scan methods were combined and identified a strongly selected region on chromosome 8 that spans two copies of AMY2A, part of the alpha-amylase gene family, a putative ncRNA and an insertion-deletion structural variant (SV) that contains an ERVK transposable element (TE). Outlier SNPs and the SV are polymorphic in native populations, but fixed or close-to-fixed in the two invasive pathways, with the fixation of the same alleles in two independent lineages providing evidence for parallel selection on standing variation. Intriguingly, the second copy of AMY2A has a non-conservative missense mutation at a phylogenetically conserved site. This mutation, alongside variation in the SV, TE and ncRNA, provide possible routes for changes to protein function or expression. AMY2A has been associated with human commensalism in house sparrows, and genes in this family have been linked to adaptation to high-starch diets in humans and dogs. This study illustrates the value of replicated analyses within and across species to understand rapid adaptation at the molecular level.

Widespread geographic distribution of Aedes aegypti (Diptera: Culicidae) kdr variants in Panama

We searched for evidence of knockdown resistance (kdr) mutations in the voltage-gated sodium channel gene of Aedes aegypti (Linnaeus) (Diptera: Culicidae) and Aedes albopictus (Skuse) (Diptera: Culicidae) mosquitoes from Panama. Conventional PCR was performed on 469 Ae. aegypti and 349 Ae. albopictus. We did not discover kdr mutations in Ae. albopictus, but 2 nonsynonymous kdr mutations, V1016I (found in 101 mosquitoes) and F1534C (found in 29 of the mosquitoes with the V1016I), were detected in Ae. aegypti. These kdr mutations were present in all specimens that were successfully sequenced for both IIS5-S6 and IIIS6 regions, which included samples collected from 8 of the 10 provinces of Panama. No other kdr mutations were found in Ae. aegypti, including V1016G, which has already been reported in Panama. Findings suggest that the V1016I-F1534C variant is prevalent in Panama, which might be related to the introduction and passive movement of mosquitoes as part of the used-tire trade. However, we cannot rule out the possibility that selection on de novo replacement of kdr mutations also partially explains the widespread distribution pattern of these mutations. These 2 ecological and evolutionary processes are not mutually exclusive, though, as they can occur in tandem. Research in Panama needs to calculate the genotypic and allelic frequencies of kdr alleles in local Ae. aegypti populations and to test whether some combinations confer phenotypic resistance or not. Finally, future studies will have to track the introduction and spreading of new kdr mutations in both Aedes species.

Detection of the 1016Gly and 989Pro Knockdown Resistance Mutations in Florida, USA Aedes aegypti

Aedes aegypti is a major arboviral disease vector and is therefore a critical target for control by public health programs. Early eradication efforts have shown that Ae. aegypti can rapidly build insecticide resistance, and, now, resistance to pyrethroids, the major class of adulticides used for operational control, is common in many populations. A major contributor to this resistance is a group of knockdown resistance (kdr) SNPs that normally exist in distinct ensembles in the Western Hemisphere and the Indopacific with little known mixing. In this study, we detected, and confirmed, using multiple methods, the Indopacific kdr SNPs, both V1016G and S989P, in three recent collections from Osceola County, Florida. This represents a large expansion of the geographic range of the Indopacific kdr SNPs. We consider the implications of this finding on future insecticide resistance surveillance studies, including assessing the ability of our current screening tools to detect these SNPs. We find that the presence of the Indopacific SNPs requires the modification of existing resistance screening protocols and requires further work to understand the operational implications for mosquito control.

Global, asynchronous partial sweeps at multiple insecticide resistance genes in Aedes mosquitoes

Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are globally invasive pests that confer the world's dengue burden. Insecticide-based management has led to the evolution of insecticide resistance in both species, though the genetic architecture and geographical spread of resistance remains incompletely understood. This study investigates partial selective sweeps at resistance genes on two chromosomes and characterises their spread across populations. Sweeps at the voltage-sensitive sodium channel (VSSC) gene on chromosome 3 correspond to one resistance-associated nucleotide substitution in Ae. albopictus and three in Ae. aegypti, including two substitutions at the same nucleotide position (F1534C) that have evolved and spread independently. In Ae. aegypti, we also identify partial sweeps at a second locus on chromosome 2. This locus contains 15 glutathione S-transferase (GST) epsilon class genes with significant copy number variation among populations and where three distinct genetic backgrounds have spread across the Indo-Pacific region, the Americas, and Australia. Local geographical patterns and linkage networks indicate VSSC and GST backgrounds probably spread at different times and interact locally with different genes to produce resistance phenotypes. These findings highlight the rapid global spread of resistance and are evidence for the critical importance of GST genes in resistance evolution.

Robustness in population-structure and demographic-inference results derived from the Aedes aegypti genotyping chip and whole-genome sequencing data

The mosquito Aedes aegypti is the primary vector of many human arboviruses such as dengue, yellow fever, chikungunya, and Zika, which affect millions of people worldwide. Population genetic studies on this mosquito have been important in understanding its invasion pathways and success as a vector of human disease. The Axiom aegypti1 SNP chip was developed from a sample of geographically diverse A. aegypti populations to facilitate genomic studies on this species. We evaluate the utility of the Axiom aegypti1 SNP chip for population genetics and compare it with a low-depth shotgun sequencing approach using mosquitoes from the native (Africa) and invasive ranges (outside Africa). These analyses indicate that results from the SNP chip are highly reproducible and have a higher sensitivity to capture alternative alleles than a low-coverage whole-genome sequencing approach. Although the SNP chip suffers from ascertainment bias, results from population structure, ancestry, demographic, and phylogenetic analyses using the SNP chip were congruent with those derived from low-coverage whole-genome sequencing, and consistent with previous reports on Africa and outside Africa populations using microsatellites. More importantly, we identified a subset of SNPs that can be reliably used to generate merged databases, opening the door to combined analyses. We conclude that the Axiom aegypti1 SNP chip is a convenient, more accurate, low-cost alternative to low-depth whole-genome sequencing for population genetic studies of A. aegypti that do not rely on full allelic frequency spectra. Whole-genome sequencing and SNP chip data can be easily merged, extending the usefulness of both approaches.

Spatio-temporal characterization of phenotypic resistance in malaria vector species

BACKGROUND

Malaria, a deadly disease caused by Plasmodium protozoa parasite and transmitted through bites of infected female Anopheles mosquitoes, remains a significant public health challenge in sub-Saharan Africa. Efforts to eliminate malaria have increasingly focused on vector control using insecticides. However, the emergence of insecticide resistance (IR) in malaria vectors pose a formidable obstacle, and the current IR mapping models remain static, relying on fixed coefficients. This study introduces a dynamic spatio-temporal approach to characterize phenotypic resistance in Anopheles gambiae complex and Anopheles arabiensis. We developed a cellular automata (CA) model and applied it to data collected from Ethiopia, Nigeria, Cameroon, Chad, and Burkina Faso. The data encompasses georeferenced records detailing IR levels in mosquito vector populations across various classes of insecticides. In characterizing the dynamic patterns of confirmed resistance, we identified key driving factors through correlation analysis, chi-square tests, and extensive literature review.

RESULTS

The CA model demonstrated robustness in capturing the spatio-temporal dynamics of confirmed IR states in the vector populations. In our model, the key driving factors included insecticide usage, agricultural activities, human population density, Land Use and Land Cover (LULC) characteristics, and environmental variables.

CONCLUSIONS

The CA model developed offers a robust tool for countries that have limited data on confirmed IR in malaria vectors. The embrace of a dynamical modeling approach and accounting for evolving conditions and influences, contribute to deeper understanding of IR dynamics, and can inform effective strategies for malaria vector control, and prevention in regions facing this critical health challenge.

Insights and challenges of insecticide resistance modelling in malaria vectors: a review

BACKGROUND

Malaria is one of the most devastating tropical diseases, resulting in loss of lives each year, especially in children under the age of 5 years. Malaria burden, related deaths and stall in the progress against malaria transmission is evident, particularly in countries that have moderate or high malaria transmission. Hence, mitigating malaria spread requires information on the distribution of vectors and the drivers of insecticide resistance (IR). However, owing to the impracticality in establishing the critical need for real-world information at every location, modelling provides an informed best guess for such information. Therefore, this review examines the various methodologies used to model spatial, temporal and spatio-temporal patterns of IR within populations of malaria vectors, incorporating pest-biology parameters, adopted ecological principles, and the associated modelling challenges.

METHODS

The review focused on the period ending March 2023 without imposing restrictions on the initial year of publication, and included articles sourced from PubMed, Web of Science, and Scopus. It was also limited to publications that deal with modelling of IR distribution across spatial and temporal dimensions and excluded articles solely focusing on insecticide susceptibility tests or articles not published in English. After rigorous selection, 33 articles met the review's elibility criteria and were subjected to full-text screening.

RESULTS

Results show the popularity of Bayesian geostatistical approaches, and logistic and static models, with limited adoption of dynamic modelling approaches for spatial and temporal IR modelling. Furthermore, our review identifies the availability of surveillance data and scarcity of comprehensive information on the potential drivers of IR as major impediments to developing holistic models of IR evolution.

CONCLUSIONS

The review notes that incorporating pest-biology parameters, and ecological principles into IR models, in tandem with fundamental ecological concepts, potentially offers crucial insights into the evolution of IR. The results extend our knowledge of IR models that provide potentially accurate results, which can be translated into policy recommendations to combat the challenge of IR in malaria control.

A Globally Distributed Insecticide Resistance Allele Confers a Fitness Cost in the Absence of Insecticide in Aedes aegypti (Diptera: Culicidae), the Yellow Fever Mosquito

The cosmopolitan mosquito Aedes aegypti is a vector of harmful arboviruses. Pyrethroid insecticides are used to reduce adult populations and prevent the spread of disease. Pyrethroids target the insect voltage-gated sodium channel (VGSC). Collectively, mutations in Vgsc that confer resistance are referred to as knock-down resistance or kdr. There are numerous kdr mutations found in A. aegypti Vgsc, and there is co-occurrence of some mutations. Full-length cDNA sequences have identified nine known kdr (e.g., 1534C) alleles. The 1534C allele is among the most common kdr alleles, but allele frequencies between populations vary considerably. We used the 1534C:RK strain, which has the 1534C (kdr) allele in the genetic background of the insecticide susceptible Rockefeller (ROCK) strain, and conducted population cage experiments to assess the potential intrinsic fitness cost of the 1534C allele relative to the susceptible allele (F1534) in the ROCK strain. Individuals were genotyped across generations using allele specific PCR. A fitness cost of the 1534C allele was detected across seven generations of mosquitos reared in the absence of insecticide selection pressure. The decrease in allele frequency was not due to drift. Comparison of our results to previous studies suggests that the magnitude of the fitness cost of kdr alleles in the absence of insecticide is disconnected from the level of resistance they confer, and that the fitness costs of different kdr alleles can be variable.

Population structure and invasion history of Aedes aegypti (Diptera: Culicidae) in Southeast Asia and Australasia

The dengue mosquito, Aedes aegypti (Linnaeus, 1762), is a highly invasive and medically significant vector of dengue, yellow fever, chikungunya and Zika viruses, whose global spread can be attributed to increased globalization in the 15th through 20th century. Records of the invasion history of Ae. aegypti across Southeast Asia are sparse and there is little knowledge regarding the invasion routes that the species exploited to gain a foothold in the Indo-Pacific. Likewise, a broad and geographically thorough investigation of Ae. aegypti population genetics in the Indo-Pacific is lacking, despite this region being highly impacted by diseases transmitted by this species. We assess 11 nuclear microsatellites and mitochondrial COI sequences, coupled with widespread sampling through the Indo-Pacific region to characterise population structure at a broad geographic scale. We also perform a comprehensive literature search to collate documentation of the first known records of Ae. aegypti at various locations in the Indo-Pacific. We revealed additional spatial population genetic structure of Ae. aegypti in Southeast Asia, the Indo-Pacific and Australasia compared with previous studies and find differentiation between multiple Queensland and Torres Strait Islands populations. We also detected additional genetic breaks within Australia, Indonesia and Malaysia. Characterising the structure of previously unexplored populations through this region enhances the understanding of the population structure of Ae. aegypti in Australasia and Southeast Asia and may assist predictions of future mosquito movement, informing control strategies as well as assessing the risk of new invasion pathways.

A novel V263I mutation in the glutamate-gated chloride channel of Plutella xylostella (L.) confers a high level of resistance to abamectin

The frequent and extensive use of insecticides leads to the evolution of insecticide resistance, which has become one of the constraints on global agricultural production. Avermectins are microbial-derived insecticides that target a wide number of insect pests, including the diamondback moth Plutella xylostella, an important global pest of brassicaceous vegetables. However, field populations of P. xylostella have evolved serious resistance to avermectins, including abamectin, thereby threatening the efficiency of these insecticides. In this study, a novel valine to isoleucine mutation (V263I) was identified in the glutamate-gated chloride channel (GluCl) of field P. xylostella populations, which showed different levels of resistance to abamectin. Electrophysiological analysis revealed that the V263I mutation significantly reduced the sensitivity of PxGluCl to abamectin by 6.9-fold. Genome-modified Drosophila melanogaster carrying the V263I mutation exhibited 27.1-fold resistance to abamectin. Then, a knockin strain (V263I-KI) of P. xylostella expressing the homozygous V263I mutation was successfully constructed using the CRISPR/Cas9. The V263I-KI had high resistance to abamectin (106.3-fold), but significantly reduced fecundity. In this study, the function of V263I mutation in PxGluCl was verified for the first time. These findings provide a more comprehensive understanding of abamectin resistance mechanisms and lay the foundation for providing a new molecular detection method for abamectin resistance monitoring.

A comprehensive assessment of insecticide resistance mutations in source and immigrant populations of the diamondback moth Plutella xylostella (L.)

BACKGROUND

The diamondback moth (DBM) Plutella xylostella has developed resistance to almost all insecticides used to control it. Populations of DBM in temperate regions mainly migrate from annual breeding areas. However, the distribution pattern of insecticide resistance of DBM within the context of long-distance migration remains unclear.

RESULTS

In this study, we examined the frequency of 14 resistance mutations for 52 populations of DBM collected in 2010, 2011, 2017 and 2018 across China using a high-throughput KASP genotyping method. Mutations L1041F and T929I conferring pyrethroid resistance, and mutations G4946E and E1338D conferring chlorantraniliprole resistance were near fixation in most populations, whereas resistant alleles of F1020S, M918I, A309V and F1845Y were uncommon or absent in most populations. Resistance allele frequencies were relatively stable among different years, although the frequency of two mutations decreased. Principal component analysis based on resistant allele frequencies separated a southern population as an outlier, whereas the immigrants clustered with other populations, congruent with the migration pattern of northern immigrants coming from the Sichuan area of southwestern China. Most resistant mutations deviated from Hardy-Weinberg equilibrium due to a lower than expected frequency of heterozygotes. The deviation index of heterozygosity for resistant alleles was significantly higher than the index obtained from single nucleotide polymorphisms across the genome. These findings suggest heterogeneous selection pressures on resistant mutations.

CONCLUSION

Our results provide a picture of resistant mutation patterns in DBM shaped by insecticide usage and migration of this pest, and highlight the widespread distribution of resistance alleles in DBM. © 2022 Society of Chemical Industry.

Genomic profiling of climate adaptation in Aedes aegypti along an altitudinal gradient in Nepal indicates nongradual expansion of the disease vector

Driven by globalization, urbanization and climate change, the distribution range of invasive vector species has expanded to previously colder ecoregions. To reduce health-threatening impacts on humans, insect vectors are extensively studied. Population genomics can reveal the genomic basis of adaptation and help to identify emerging trends of vector expansion. By applying whole genome analyses and genotype-environment associations to populations of the main dengue vector Aedes aegypti, sampled along an altitudinal gradient in Nepal (200-1300 m), we identify putatively adaptive traits and describe the species' genomic footprint of climate adaptation to colder ecoregions. We found two differentiated clusters with significantly different allele frequencies in genes associated to climate adaptation between the highland population (1300 m) and all other lowland populations (≤800 m). We revealed nonsynonymous mutations in 13 of the candidate genes associated to either altitude, precipitation or cold tolerance and identified an isolation-by-environment differentiation pattern. Other than the expected gradual differentiation along the altitudinal gradient, our results reveal a distinct genomic differentiation of the highland population. Local high-altitude adaptation could be one explanation of the population's phenotypic cold tolerance. Carrying alleles relevant for survival under colder climate increases the likelihood of this highland population to a worldwide expansion into other colder ecoregions.

Insecticide resistance in malaria and arbovirus vectors in Papua New Guinea, 2017-2022

BACKGROUND

Insecticide resistance (IR) monitoring is essential for evidence-based control of mosquito-borne diseases. While widespread pyrethroid resistance in Anopheles and Aedes species has been described in many countries, data for Papua New Guinea (PNG) are limited. Available data indicate that the local Anopheles populations in PNG remain pyrethroid-susceptible, making regular IR monitoring even more important. In addition, Aedes aegypti pyrethroid resistance has been described in PNG. Here, Anopheles and Aedes IR monitoring data generated from across PNG between 2017 and 2022 are presented.

METHODS

Mosquito larvae were collected in larval habitat surveys and through ovitraps. Mosquitoes were reared to adults and tested using standard WHO susceptibility bioassays. DNA from a subset of Aedes mosquitoes was sequenced to analyse the voltage-sensitive sodium channel (Vssc) region for any resistance-related mutations.

RESULTS

Approximately 20,000 adult female mosquitoes from nine PNG provinces were tested. Anopheles punctulatus sensu lato mosquitoes were susceptible to pyrethroids but there were signs of reduced mortality in some areas. Some Anopheles populations were also resistant to DDT. Tests also showed that Aedes. aegypti in PNG are resistant to pyrethroids and DDT and that there was also likelihood of bendiocarb resistance. A range of Vssc resistance mutations were identified. Aedes albopictus were DDT resistant and were likely developing pyrethroid resistance, given a low frequency of Vssc mutations was observed.

CONCLUSIONS

Aedes aegypti is highly pyrethroid resistant and also shows signs of resistance against carbamates in PNG. Anopheles punctulatus s.l. and Ae. albopictus populations exhibit low levels of resistance against pyrethroids and DDT in some areas. Pyrethroid-only bed nets are currently the only programmatic vector control tool used in PNG. It is important to continue to monitor IR in PNG and develop proactive insecticide resistance management strategies in primary disease vectors to retain pyrethroid susceptibility especially in the malaria vectors for as long as possible.

Genome-wide SNPs of vegetable leafminer, Liriomyza sativae: Insights into the recent Australian invasion

Liriomyza sativae, the vegetable leafminer, is an important agricultural pest originally from the Americas, which has now colonized all continents except Antarctica. In 2015, L. sativae arrived on the Australian mainland and established on the Cape York Peninsula in the northeast of the country near the Torres Strait, which provides a possible pathway for pests to enter Australia and evade biosecurity efforts. Here, we assessed genetic variation in L. sativae based on genome-wide single nucleotide polymorphisms (SNPs) generated by double digest restriction-site-associated DNA sequencing (ddRAD-seq), aiming to uncover the potential origin(s) of this pest in Australia and contribute to reconstructing its global invasion history. Our fineRADstructure results and principal component analysis suggest Australian mainland populations were genetically close to populations from the Torres Strait, whereas populations from Asia, Africa, and Papua New Guinea (PNG) were more distantly related. Hawaiian populations were genetically distinct from all other populations of L. sativae included in our study. Admixture analyses further revealed that L. sativae from the Torres Strait may have genetic variation originating from multiple sources including Indonesia and PNG, and which has now spread to the Australian mainland. The L. sativae lineages from Asia and Africa appear closely related. Isolation-by-distance (IBD) was found at a broad global scale, but not within small regions, suggesting that human-mediated factors likely contribute to the local spread of this pest. Overall, our findings suggest that an exotic Liriomyza pest invaded Australia through the Indo-Papuan conduit, highlighting the importance of biosecurity programs aimed at restricting the movement of pests and diseases through this corridor.

Sex-specific distribution and classification of Wolbachia infections and mitochondrial DNA haplogroups in Aedes albopictus from the Indo-Pacific

The arbovirus vector Aedes albopictus (Asian tiger mosquito) is common throughout the Indo-Pacific region, where most global dengue transmission occurs. We analysed population genomic data and tested for cryptic species in 160 Ae. albopictus sampled from 16 locations across this region. We found no evidence of cryptic Ae. albopictus but found multiple intraspecific COI haplotypes partitioned into groups representing three Asian lineages: East Asia, Southeast Asia and Indonesia. Papua New Guinea (PNG), Vanuatu and Christmas Island shared recent coancestry, and Indonesia and Timor-Leste were likely invaded from East Asia. We used a machine learning trained on morphologically sexed samples to classify sexes using multiple genetic features and then characterized the wAlbA and wAlbB Wolbachia infections in 664 other samples. The wAlbA and wAlbB infections as detected by qPCR showed markedly different patterns in the sexes. For females, most populations had a very high double infection incidence, with 67% being the lowest value (from Timor-Leste). For males, the incidence of double infections ranged from 100% (PNG) to 0% (Vanuatu). Only 6 females were infected solely by the wAlbA infection, while rare uninfected mosquitoes were found in both sexes. The wAlbA and wAlbB densities varied significantly among populations. For mosquitoes from Torres Strait and Vietnam, the wAlbB density was similar in single-infected and superinfected (wAlbA and wAlbB) mosquitoes. There was a positive association between wAlbA and wAlbB infection densities in superinfected Ae. albopictus. Our findings provide no evidence of cryptic species of Ae. albopictus in the region and suggest site-specific factors influencing the incidence of Wolbachia infections and their densities. We also demonstrate the usefulness of ddRAD tag depths as sex-specific mosquito markers. The results provide baseline data for the exploitation of Wolbachia-induced cytoplasmic incompatibility (CI) in dengue control.

The mosquito Aedes albopictus transmits dengue and other arboviruses. This study investigates the genetics of these mosquitoes and their endosymbiont Wolbachia in the Indo-Pacific region, where 70% of global dengue transmission occurs. The analysis of mitochondrial DNA sequences showed no evidence of cryptic Ae. albopictus but suggested three Asian lineages: East Asia, Southeast Asia and Indonesia. Papua New Guinea, Vanuatu and Christmas Island shared recent coancestry, and Indonesia and Timor-Leste were likely invaded from East Asia. We used bioinformatics to classify sexes and then characterized the wAlbA and wAlbB Wolbachia infections via both bioinformatics and quantitative PCR. We found markedly different patterns of wAlbA and wAlbB infections in the sexes. The wAlbA and wAlbB densities varied significantly among populations, suggesting site-specific factors influencing the incidence of Wolbachia infections and their densities. We also demonstrate the usefulness of next generation sequencing data in developing molecular markers that can be repeatedly reanalysed to investigate new issues as these arise. These results provide baseline data for the exploitation of Wolbachia-induced cytoplasmic incompatibility in dengue control.

Lab-scale characterization and semi-field trials of Wolbachia Strain wAlbB in a Taiwan Wolbachia introgressed Ae. aegypti strain

Dengue fever is one of the most severe viral diseases transmitted by Aedes mosquitoes, with traditional approaches of disease control proving insufficient to prevent significant disease burden. Release of Wolbachia-transinfected mosquitoes offers a promising alternative control methodologies; Wolbachia-transinfected female Aedes aegypti demonstrate reduced dengue virus transmission, whilst Wolbachia-transinfected males cause zygotic lethality when crossed with uninfected females, providing a method for suppressing mosquito populations. Although highly promising, the delicate nature of population control strategies and differences between local species populations means that controlled releases of Wolbachia-transinfected mosquitoes cannot be performed without extensive testing on specific local Ae. aegypti populations. In order to investigate the potential for using Wolbachia to suppress local Ae. aegypti populations in Taiwan, we performed lab-based and semi-field fitness trials. We first transinfected the Wolbachia strain wAlbB into a local Ae. aegypti population (wAlbB-Tw) and found no significant changes in lifespan, fecundity and fertility when compared to controls. In the laboratory, we found that as the proportion of released male mosquitoes carrying Wolbachia was increased, population suppression could reach up to 100%. Equivalent experiments in semi-field experiments found suppression rates of up to 70%. The release of different ratios of wAlbB-Tw males in the semi-field system provided an estimate of the optimal size of male releases. Our results indicate that wAlbB-Tw has significant potential for use in vector control strategies aimed at Ae. aegypti population suppression in Taiwan. Open field release trials are now necessary to confirm that wAlbB-Tw mediated suppression is feasible in natural environments.

A wAlbB Wolbachia transinfection displays stable phenotypic effects across divergent Aedes aegypti mosquito backgrounds

Aedes mosquitoes harboring intracellular Wolbachia bacteria are being released in arbovirus and mosquito control programs. With releases taking place around the world, understanding the contribution of host variation to Wolbachia phenotype is crucial. We generated a Wolbachia transinfection (wAlbB^Q) in Aedes aegypti and performed backcrossing to introduce the infection into Australian or Malaysian nuclear backgrounds. Whole Wolbachia genome sequencing shows that the wAlbB^Q transinfection is near-identical to the reference wAlbB genome, suggesting few changes since the infection was first introduced to Ae. aegypti over 15 years ago. However, these sequences were distinct from other available wAlbB genome sequences, highlighting the potential diversity of wAlbB in natural Ae. albopictus populations. Phenotypic comparisons demonstrate effects of wAlbB infection on egg hatch and nuclear background on fecundity and body size, but no interactions between wAlbB infection and nuclear background for any trait. The wAlbB infection was stable at high temperatures and showed perfect maternal transmission and cytoplasmic incompatibility regardless of host background. Our results demonstrate the stability of wAlbB across host backgrounds and point to its long-term effectiveness for controlling arbovirus transmission and mosquito populations. Importance Wolbachia bacteria are being used to control the transmission of dengue and other arboviruses by mosquitoes. For Wolbachia release programs to be effective globally, Wolbachia infections must be stable across mosquito populations from different locations. In this study, we transferred Wolbachia (strain wAlbB) to Aedes aegypti mosquitoes with an Australian genotype and introduced the infection to Malaysian mosquitoes through backcrossing. We found that the phenotypic effects of Wolbachia are stable across both mosquito backgrounds. We sequenced the genome of wAlbB and found very few genetic changes despite spending over 15 years in a novel mosquito host. Our results suggest that the effects of Wolbachia infections are likely to remain stable across time and host genotype.

Voltage-sensitive sodium channel (Vssc) mutations associated with pyrethroid insecticide resistance in Aedes aegypti (L.) from two districts of Jeddah, Kingdom of Saudi Arabia: baseline information for a Wolbachia release program

BACKGROUND

Dengue suppression often relies on control of the mosquito vector, Aedes aegypti, through applications of insecticides of which the pyrethroid group has played a dominant role. Insecticide resistance is prevalent in Ae. aegypti around the world, and the resulting reduction of insecticide efficacy is likely to exacerbate the impact of dengue. Dengue has been a public health problem in Saudi Arabia, particularly in Jeddah, since its discovery there in the 1990s, and insecticide use for vector control is widespread throughout the city. An alternative approach to insecticide use, based on blocking dengue transmission in mosquitoes by the endosymbiont Wolbachia, is being trialed in Jeddah following the success of this approach in Australia and Malaysia. Knowledge of insecticide resistance status of mosquito populations in Jeddah is a prerequisite for establishing a Wolbachia-based dengue control program as releases of Wolbachia mosquitoes succeed when resistance status of the release population is similar to that of the wild population.

METHODS

WHO resistance bioassays of mosquitoes with deltamethrin, permethrin and DDT were used in conjunction with TaqMan® SNP Genotyping Assays to characterize mutation profiles of Ae. aegypti.

RESULTS

Screening of the voltage-sensitive sodium channel (Vssc), the pyrethroid target site, revealed mutations at codons 989, 1016 and 1534 in Ae. aegypti from two districts of Jeddah. The triple mutant homozygote (1016G/1534C/989P) was confirmed from Al Safa and Al Rawabi. Bioassays with pyrethroids (Type I and II) and DDT showed that mosquitoes were resistant to each of these compounds based on WHO definitions. An association between Vssc mutations and resistance was established for the Type II pyrethroid, deltamethrin, with one genotype (989P/1016G/1534F) conferring a survival advantage over two others (989S/1016V/1534C and the triple heterozygote). An indication of synergism of Type I pyrethroid activity with piperonyl butoxide suggests that detoxification by cytochrome P450s accounts for some of the pyrethroid resistance response in Ae. aegypti populations from Jeddah.

CONCLUSIONS

The results provide a baseline for monitoring and management of resistance as well as knowledge of Vssc genotype frequencies required in Wolbachia release populations to ensure homogeneity with the target field population. Vssc mutation haplotypes observed show some similarity with those from Ae. aegypti in southeast Asia and the Indo-Pacific, but the presence of the triple mutant haplotype in three genotypes indicates that the species in this region may have a unique population history.

Improving mosquito control strategies with population genomics

Mosquito control strategies increasingly apply knowledge from population genomics research. This review highlights recent applications to three research domains: mosquito invasions, insecticide resistance evolution, and rear and release programs. Current research trends follow developments in reference assemblies, either as improvements to existing assemblies (particularly Aedes) or assemblies for new taxa (particularly Anopheles). With improved assemblies, studies of invasive and rear and release target populations are better able to incorporate adaptive as well as demographic hypotheses. New reference assemblies are aiding comparisons of insecticide resistance across sister taxa while helping resolve taxon boundaries amidst frequent introgression. Anopheles gene drive deployments and improved Aedes genome assemblies should lead to a convergence in research aims for Anopheles and Aedes in the coming years.

Insights into invasive species from whole-genome resequencing

Studies of invasive species can simultaneously inform management strategies and quantify rapid evolution in the wild. The role of genomics in invasion science is increasingly recognised, and the growing availability of reference genomes for invasive species is paving the way for whole-genome resequencing studies in a wide range of systems. Here, we survey the literature to assess the application of whole-genome resequencing data in invasion biology. For some applications, such as the reconstruction of invasion routes in time and space, sequencing the whole genome of many individuals can increase the accuracy of existing methods. In other cases, population genomic approaches such as haplotype analysis can permit entirely new questions to be addressed and new technologies applied. To date whole-genome resequencing has only been used in a handful of invasive systems, but these studies have confirmed the importance of processes such as balancing selection and hybridization in allowing invasive species to reuse existing adaptations and rapidly overcome the challenges of a foreign ecosystem. The use of genomic data does not constitute a paradigm shift per se, but by leveraging new theory, tools, and technologies, population genomics can provide unprecedented insight into basic and applied aspects of invasion science.

Voltage-Gated Sodium Channel (Vgsc) Mutation-Based Pyrethroid Resistance in Aedes aegypti Populations of Three Endemic Dengue Risk Areas of Sri Lanka

Background

Pyrethroid insecticides are widely used in many countries for chemical-based control of Ae. aegypti. Regardless of their efficacy, the constant use of insecticides has induced insecticide resistance mechanisms, such as knockdown resistance (kdr) in mosquitoes. Sri Lankan Vector Controlling Entities (VCE) have been using a variety of pyrethroid insecticides as the primary approach for dengue control. However, development of any resistance among the Aedes mosquitoes has been limitedly studied in the country. Therefore, the current study was conducted to evaluate the prevalence of F1534C, V1016G, and S989P mutations among Ae. aegypti mosquito populations in three dengue endemic high-risk regions of Sri Lanka. Methodology. Immature (both pupae and larvae) stages of Ae. aegypti mosquitoes were collected from Colombo, Gampaha, and Kandy districts of Sri Lanka from February 2018 to December 2019. Polymerase Chain Reaction- (PCR-) based assay for molecular genotyping of mutations was performed to identify the prevalence of kdr mutations in collected Ae. aegypti populations, separately. The frequencies of the resistant and susceptible kdr alleles were determined by using the Hardy–Weinberg equilibrium.

Results

The Ae. aegypti populations from Colombo, Gampaha, and Kandy districts showed 46%, 42%, and 22% of F1534C mutation allele frequencies, along with 15%, 12%, and 6% of V1016G mutation allele frequencies, respectively. The mutation allele frequencies of S989 in Colombo, Gampaha, and Kandy districts were 9.5%, 8.5%, and 4.5%, respectively. The wild-type (PP) genotype remained predominant within all the three districts, whereas the homogenous (QQ) mutation genotype occurred only in minority. The abundance of Q allele frequency in Ae. aegypti mosquitoes was relatively higher for all the three mutations in Colombo.

Conclusions

The findings clearly indicate that long-term insecticide applications and multiple use of pyrethroids have led to the acquisition of kdr mutations, leading to the development of insecticide resistance among local Ae. aegypti populations, especially in the Colombo and Gampaha districts. Therefore, evaluation of the prevalence levels of these kdr mutations highlights the necessity for shifting towards novel vector control strategies.

Two Haplotypes of Aedes aegypti Detected by ND4 Mitochondrial Marker in Three Regions of Ecuador

Simple Summary

The yellow fever mosquito, Aedes aegypti, is a widespread species associated with the transmission of vector-borne diseases across tropical and subtropical areas of the world. The genetic variability of its populations has been assessed with the use of several molecular markers to understand aspects of the population dynamics and their implication in disease transmission. However, the genetic diversity of Ecuadorian populations of the vector have not been investigated. In this study, we evaluated the genetic diversity of Ecuadorian populations of Ae. aegypti from 17 sites (Galapagos Islands, Amazon basin, and Coastal regions). These analyses revealed the presence of only two haplotypes among the Ecuadorian population of the vector. Haplotype 1, appears to be related to previously reported haplotypes from America, Asia, and West Africa. While haplotype 2 is only related to samples from America. The genetic diversity of Ecuadorian populations seems to be low, according to different statistical analyses, which show only one main population across sampled localities and no effect of the main geographical barriers. Understanding the genetic diversity of local populations is a key element in vector control strategies.

Abstract

Aedes aegypti, also known as the yellow fever mosquito, is the main vector of several arboviruses. In Ecuador, dengue and chikungunya are the most prevalent mosquito-borne diseases. Hence, there is a need to understand the population dynamics and genetic structure of the vector in tropical areas for a better approach towards effective vector control programs. This study aimed to assess the genetic diversity of Ae. aegypti, through the analyses of the mitochondrial gene ND4, using a combination of phylogenetic and population genetic structure from 17 sites in Ecuador. Results showed two haplotypes in the Ecuadorian populations of Ae. aegypti. Haplotype 1 was closely related to Ae. aegypti reported from America, Asia, and West Africa. Haplotype 2 was only related to samples from America. The sampled vectors from the diverse localities showed low nucleotide diversity (π = 0–0.01685) and genetic differentiation (FST = 0.152). AMOVA analyses indicated that most of the variation (85–91%) occurred within populations, suggesting that geographical barriers have little effect on the genetic structure of Ecuadorian populations of Ae. aegypti. These results agree with the one main population (K = 1) detected by Structure. Vector genetic identity may be a key factor in the planning of vector control strategies.

Insecticide resistance and genetic structure of Aedes aegypti populations from Rio de Janeiro State, Brazil

Vector control largely relies on neurotoxic chemicals, and insecticide resistance (IR) directly threatens their effectiveness. In some cases, specific alleles cause IR, and knowledge of the genetic diversity and gene flow among mosquito populations is crucial to track their arrival, rise, and spread. Here we evaluated Aedes aegypti populations’ susceptibility status, collected in 2016 from six different municipalities of Rio de Janeiro state (RJ), to temephos, pyriproxyfen, malathion, and deltamethrin. We collected eggs of Ae. aegypti in Campos dos Goytacazes (Cgy), Itaperuna (Ipn), Iguaba Grande (Igg), Itaboraí (Ibr), Mangaratiba (Mgr), and Vassouras (Vsr). We followed the World Health Organization (WHO) guidelines and investigated the degree of susceptibility/resistance of mosquitoes to these insecticides. We used the Rockefeller strain as a susceptible positive control. We genotyped the V1016I and F1534C knockdown resistance (kdr) alleles using qPCR TaqMan SNP genotyping assay. Besides, with the use of Ae. aegypti SNP-chip, we performed genomic population analyses by genotyping more than 15,000 biallelic SNPs in mosquitoes from each population. We added previous data from populations from other countries to evaluate the ancestry of RJ populations.

All RJ Ae. aegypti populations were susceptible to pyriproxyfen and malathion and highly resistant to deltamethrin. The resistance ratios for temephos was below 3,0 in Cgy, Ibr, and Igg populations, representing the lowest rates since IR monitoring started in this Brazilian region. We found the kdr alleles in high frequencies in all populations, partially justifying the observed resistance to pyrethroid. Population genetics analysis showed that Ae. aegypti revealed potential higher migration among some RJ localities and low genetic structure for most of them. Future population genetic studies, together with IR data in Ae aegypti on a broader scale, can help us predict the gene flow within and among the Brazilian States, allowing us to track the dynamics of arrival and changes in the frequency of IR alleles, and providing critical information to improving vector control program.

Monitoring of insecticide resistance (IR) is mandatory for the effectiveness of vector control programs. We investigate six populations of Aedes aegypti regarding their IR status towards insecticides previously or currently in use, their frequency of IR alleles and resistance ratio, their genetic ancestry and structure, and the gene flow. We observed that Ae. aegypti populations from RJ are becoming susceptible to the larvicide organophosphate temephos. The resistance ratios of temephos are lower among populations where gene flow might be occurring. All RJ populations are highly resistant to deltamethrin, partially explained by the high frequency of kdr alleles. Besides, all populations are susceptible to pyriproxyfen’s insect growth regulator and the organophosphate malathion. Population genomic analyses using more than 15,000 SNPs identified three potential genetic clusters within RJ populations, with higher gene flow to and out of the touristic region called Região dos Lagos. IR data, together with knowledge of the genetic structure and gene flow among different mosquito populations, can help with vector control program decisions.

Spatial population genomics of a recent mosquito invasion

Population genomic approaches can characterize dispersal across a single generation through to many generations in the past, bridging the gap between individual movement and intergenerational gene flow. These approaches are particularly useful when investigating dispersal in recently altered systems, where they provide a way of inferring long-distance dispersal between newly established populations and their interactions with existing populations. Human-mediated biological invasions represent such altered systems which can be investigated with appropriate study designs and analyses. Here we apply temporally restricted sampling and a range of population genomic approaches to investigate dispersal in a 2004 invasion of Aedes albopictus (the Asian tiger mosquito) in the Torres Strait Islands (TSI) of Australia. We sampled mosquitoes from 13 TSI villages simultaneously and genotyped 373 mosquitoes at genome-wide single nucleotide polymorphisms (SNPs): 331 from the TSI, 36 from Papua New Guinea (PNG) and four incursive mosquitoes detected in uninvaded regions. Within villages, spatial genetic structure varied substantially but overall displayed isolation by distance and a neighbourhood size of 232-577. Close kin dyads revealed recent movement between islands 31-203 km apart, and deep learning inferences showed incursive Ae. albopictus had travelled to uninvaded regions from both adjacent and nonadjacent islands. Private alleles and a co-ancestry matrix indicated direct gene flow from PNG into nearby islands. Outlier analyses also detected four linked alleles introgressed from PNG, with the alleles surrounding 12 resistance-associated cytochrome P450 genes. By treating dispersal as both an intergenerational process and a set of discrete events, we describe a highly interconnected invasive system.

Incursion pathways of the Asian tiger mosquito (Aedes albopictus) into Australia contrast sharply with those of the yellow fever mosquito (Aedes aegypti)

BACKGROUND

Understanding pest incursion pathways is critical for preventing new invasions and for stopping the transfer of alleles that reduce the efficacy of local control methods. The mosquitoes Aedes albopictus (Skuse) and Ae. aegypti (Linnaeus) are both highly invasive disease vectors, and through a series of ongoing international incursions are continuing to colonize new regions and spread insecticide resistance alleles among established populations. This study uses high-resolution molecular markers and a set of 241 reference genotypes to trace incursion pathways of Ae. albopictus into mainland Australia, where no successful invasions have yet been observed. We contrast these results with incursion pathways of Ae. aegypti, investigated previously.

RESULTS

Assignments successfully identified China, Japan, Singapore and Taiwan as source locations. Incursion pathways of Ae. albopictus were entirely different to those of Ae. aegypti, despite broad sympatry of these species throughout the Indo-Pacific region. Incursions of Ae. albopictus appeared to have come predominantly along marine routes from key trading locations, while Ae. aegypti was mostly linked to aerial routes from tourism hotspots.

CONCLUSION

These results demonstrate how genomics can help decipher otherwise cryptic incursion pathways. The inclusion of reference genotypes from the Americas may help resolve some unsuccessful assignments. While many congeneric taxa will share common incursion pathways, this study highlights that this is not always the case, and incursion pathways of important taxa should be specifically investigated. Species differences in aerial and marine incursion rates may reflect the efficacy of ongoing control programmes such as aircraft disinsection. © 2020 Society of Chemical Industry.

Variable resistance to spinetoram in populations of Thrips palmi across a small area unconnected to genetic similarity

The melon thrips, Thrips palmi, is an increasingly important pest of vegetables in northern China. Some populations have developed resistance in the field to the insecticide spinetoram. Understanding the origin and dispersal of insecticide-resistant populations can shed light on resistance management strategies. In this study, we tested susceptibility of seven greenhouse populations of T. palmi to spinetoram collected from a small area of about 300 km2 in Shandong Province and examined population genetic structure across the area based on a segment of mitochondrial cox1 gene and 22 microsatellite loci to infer the possible origin and dispersal of insecticide resistance. Levels of resistance to spinetoram differed among seven populations, which included one population with high resistance (LC50 = 759.34 mg/L), three populations with medium resistance (LC50 ranged from 28.69 to 34.79 mg/L), and three populations with low resistance (LC50 ranged from 7.61 to 8.97 mg/L). The populations were genetically differentiated into two groups unrelated to both levels of resistance and geographic distance. The molecular data indicated high levels of gene flow between populations with different levels of resistance to spinetoram and low gene flow among populations with the same level of resistance, pointing to a likely separate history of resistance evolution. Resistance levels of two tested populations to spinetoram decreased 23 and 4.6 times after five generations without any exposure to the pesticide. We therefore suspect that resistance of T. palmi most likely evolved in response to local applications of the insecticide. Our study suggests that the development of resistance could be avoided or resistance even reversed by reducing usage of spinetoram.

Characterization of Sodium Channel Mutations in the Dengue Vector Mosquitoes Aedes aegypti and Aedes albopictus within the Context of Ongoing Wolbachia Releases in Kuala Lumpur, Malaysia

Simple Summary

Mosquitoes, Aedes aegypti and Ae. albopictus are vectors of dengue and must be controlled to prevent and contain outbreaks of this disease. Control by insecticide application is common and pyrethroid insecticides provide rapid knockdown of mosquitoes combined with relatively low mammalian toxicity. However, resistance to pyrethroids and other chemicals is causing problems for mosquito control around the world. In Malaysia, an alternative method of dengue reduction is employed which comprises releases of Ae. aegypti mosquitoes infected with a bacterium, Wolbachia, found naturally in other insects. Wolbachia turns the mosquitoes into incompetent vectors so they do not transmit the disease. Wolbachia mosquitoes are reared in the laboratory before release and must be able to survive in the field where they will encounter insecticides. Our study demonstrates benefits of crossing laboratory mosquitoes to those from the field over generations, so that the mosquito lines acquire field resistance characteristics (mutations in the sodium channel gene). We demonstrate that resistance mutations provide a survival advantage to Wolbachia Ae. aegypti mosquitoes, which must be maintained in laboratory lines by regular backcrossing. We also describe appearance of a sodium channel mutation in Malaysian Ae. albopictus which may indicate that pyrethroid resistance is increasing in this species.

Abstract

Specific sodium channel gene mutations confer target site resistance to pyrethroid insecticides in mosquitoes and other insects. In Aedes mosquito species, multiple mutations that contribute to resistance vary in their importance around the world. Here, we characterize voltage sensitive sodium channel (Vssc) mutations in populations of Aedesaegypti from Kuala Lumpur, Malaysia, and look at their persistence in populations affected by ongoing Wolbachia releases (a dengue control measure). We also describe a Vssc mutation in Aedesalbopictus (F1534L) found for the first time in Malaysia. We show that there are three predominant Vssc haplotypes in Aedesaegypti in this region, which all persist with regular backcrossing, thereby maintaining the original genetic composition of the populations. We identify changes in genotype frequency in closed populations of Ae. aegypti maintained for multiple generations in laboratory culture, suggesting different fitness costs associated with the genotypes, some of which may be associated with the sex of the mosquito. Following population replacement of Ae. aegypti by Wolbachia in the target area, however, we find that the Vssc mutations have persisted at pre-release levels. Mosquitoes in two genotype classes demonstrate a type I pyrethroid resistance advantage over wildtype mosquitoes when exposed to 0.25% permethrin. This resistance advantage is even more pronounced with a type II pyrethroid, deltamethrin (0.03%). The results point to the importance of these mutations in pyrethroid resistance in mosquito populations and the need for regular backcrossing with male mosquitoes from the field to maintain similarity of genetic background and population integrity during Wolbachia releases.

Genetic structure of the mosquito Aedes aegypti in local forest and domestic habitats in Gabon and Kenya

Background

The mosquito Aedes aegypti is a devastating disease vector transmitting several important human arboviral diseases. In its native range in Africa, the mosquito can be found in both the ancestral forest habitat and anthropogenic habitats such as villages. How do the different habitats impact the population genetic structure of the local mosquito populations?

Methods

To address this question, we simultaneously sampled Ae. aegypti from the forest and local villages in La Lopé, Gabon and Rabai, Kenya. The mosquitoes were genotyped at 12 microsatellite loci and a panel of ~25,000 single nucleotide polymorphisms (SNPs), which allowed us to estimate their genetic ancestries and the population genetic structure related to habitats and sampling sites.

Results

In the context of the global population genetic structure of Ae. aegypti, clustering analysis showed that mosquitoes from the same locality (La Lopé or Rabai) have similar genetic ancestry, regardless of their habitats. Further analysis at the local scale also found no strong genetic differentiation between the forest and village mosquitoes in both La Lopé and Rabai. Interestingly, these results from our 2017 samples from Rabai, Kenya contrast to the documentation of genetic differentiation between village and forest mosquito collections from 1975–1976 and 2009. Between-habitat measures of genetic difference (F_st) vary across the genome, with a peak of high divergence observed at the third chromosome only in the La Lopé populations.

Conclusion

Collectively, these results demonstrated that there is little genetic isolation between forest and village habitats, which suggests possible extensive gene flow between them. From an epidemiological perspective, the forest habitat could act as a refuge for mosquitoes against vector control programmes in the domestic settings. Moreover, sylvatic populations could play a role in zoonotic pathogen transferred to humans. Therefore, future studies on disease transmission and vector control planning in the study area should take natural populations into consideration.

Population genomics of two invasive mosquitoes (Aedes aegypti and Aedes albopictus) from the Indo-Pacific

The arbovirus vectors Aedes aegypti (yellow fever mosquito) and Ae. albopictus (Asian tiger mosquito) are both common throughout the Indo-Pacific region, where 70% of global dengue transmission occurs. For Ae. aegypti all Indo-Pacific populations are invasive, having spread from an initial native range of Africa, while for Ae. albopictus the Indo-Pacific includes invasive populations and those from the native range: putatively, India to Japan to Southeast Asia. This study analyses the population genomics of 480 of these mosquitoes sampled from 27 locations in the Indo-Pacific. We investigated patterns of genome-wide genetic differentiation to compare pathways of invasion and ongoing gene flow in both species, and to compare invasive and native-range populations of Ae. albopictus. We also tested landscape genomic hypotheses that genetic differentiation would increase with geographical distance and be lower between locations with high connectivity to human transportation routes, the primary means of dispersal at these scales. We found that genetic distances were generally higher in Ae. aegypti, with Pacific populations the most highly differentiated. The most differentiated Ae. albopictus populations were in Vanuatu, Indonesia and Sri Lanka, the latter two representing potential native-range populations and potential cryptic subspeciation respectively. Genetic distances in Ae. aegypti increased with geographical distance, while in Ae. albopictus they decreased with higher connectivity to human transportation routes. Contrary to the situation in Ae. aegypti, we found evidence of long-distance Ae. albopictus colonisation events, including colonisation of Mauritius from East Asia and of Fiji from Southeast Asia. These direct genomic comparisons indicate likely differences in dispersal ecology in these species, despite their broadly sympatric distributions and similar use of human transport to disperse. Our findings will assist biosecurity operations to trace the source of invasive material and for biocontrol operations that benefit from matching genetic backgrounds of released and local populations.