The effective population size of malaria mosquitoes: large impact of vector control

Genomic Data Characterize Reproductive Ecology Patterns in Michigan Invasive Red Swamp Crayfish (Procambarus clarkii)

The establishment and spread of invasive species are directly related to intersexual interactions as dispersal and reproductive success are related to distribution, effective population size, and population growth. Accordingly, populations established by r-selected species are particularly difficult to suppress or eradicate. One such species, the red swamp crayfish (Procambarus clarkii) is established globally at considerable ecological and financial costs to natural and human communities. Here, we develop a single nucleotide polymorphism (SNP) loci panel for P. clarkii using restriction-associated DNA-sequencing data. We use the SNP panel to successfully genotype 1800 individuals at 930 SNPs in southeastern Michigan, USA. Genotypic data were used to reconstruct pedigrees, which enabled the characterization of P. clarkii's mating system and statistical tests for associations among environmental, demographic, and phenotypic predictors and adult reproductive success estimates. We identified juvenile cohorts using genotype-based pedigrees, body size, and sampling timing, which elucidated the breeding phenology of multiple introduced populations. We report a high prevalence of multiple paternity in each surveyed waterbody, indicating polyandry in this species. We highlight the use of newly developed rapid genomic assessment tools for monitoring population reproductive responses, effective population sizes, and dispersal during ongoing control efforts.

Genetic differentiation and bottleneck effects in the malaria vectors Anopheles farauti and Anopheles punctulatus after an LLIN-based vector control program in Papua New Guinea

Implementation of long-lasting insecticide-treated net (LLIN) programs to control human malaria transmission leads to substantial reductions in the abundance of Anopheles mosquitoes, but the impact on the population genetic structure of the malaria vectors is poorly known, nor has it been investigated in Papua New Guinea, where malaria is highly endemic and where several species of Anopheles have vector roles. Here, we applied Wright's F-statistic, analysis of molecular variance, Bayesian structure analysis, and discriminant analysis of principle components to microsatellite genotype data to analyze the population genetic structure of Anopheles farauti between and within the northern and southern lowland plains and of Anopheles punctulatus within the northern plain of Papua New Guinea after such a program. Bottleneck effects in the two malaria vectors were analyzed using Luikart and Cornuet's tests of heterozygosity. A large, panmictic population of An. punctulatus pre-LLIN program diverged into two subregional populations corresponding to Madang and East Sepik provinces post-LLIN distribution and experienced a genetic bottleneck during this process. By contrast, the An. farauti population existed as two regional populations isolated by mountain ranges pre-LLIN, a genetic structure that persisted after the distribution of LLINs with no further geographic differentiation nor evidence of a genetic bottleneck. These findings show the differential response of populations of different vector species to interventions, which has implications for program sustainability and gene flow.

Effective population size of Culex quinquefasciatus under insecticide-based vector management and following Hurricane Harvey in Harris County, Texas

Introduction: Culex quinquefasciatus is a mosquito species of significant public health importance due to its ability to transmit multiple pathogens that can cause mosquito-borne diseases, such as West Nile fever and St. Louis encephalitis. In Harris County, Texas, Cx. quinquefasciatus is a common vector species and is subjected to insecticide-based management by the Harris County Public Health Department. However, insecticide resistance in mosquitoes has increased rapidly worldwide and raises concerns about maintaining the effectiveness of vector control approaches. This concern is highly relevant in Texas, with its humid subtropical climate along the Gulf Coast that provides suitable habitat for Cx. quinquefasciatus and other mosquito species that are known disease vectors. Therefore, there is an urgent and ongoing need to monitor the effectiveness of current vector control programs. Methods: In this study, we evaluated the impact of vector control approaches by estimating the effective population size of Cx. quinquefasciatus in Harris County. We applied Approximate Bayesian Computation to microsatellite data to estimate effective population size. We collected Cx. quinquefasciatus samples from two mosquito control operation areas; 415 and 802, during routine vector monitoring in 2016 and 2017. No county mosquito control operations were applied at area 415 in 2016 and 2017, whereas extensive adulticide spraying operations were in effect at area 802 during the summer of 2016. We collected data for eighteen microsatellite markers for 713 and 723 mosquitoes at eight timepoints from 2016 to 2017 in areas 415 and 802, respectively. We also investigated the impact of Hurricane Harvey's landfall in the Houston area in August of 2017 on Cx. quinquefasciatus population fluctuation. Results: We found that the bottleneck scenario was the most probable historical scenario describing the impact of the winter season at area 415 and area 802, with the highest posterior probability of 0.9167 and 0.4966, respectively. We also detected an expansion event following Hurricane Harvey at area 802, showing a 3.03-fold increase in 2017. Discussion: Although we did not detect significant effects of vector control interventions, we found considerable influences of the winter season and a major hurricane on the effective population size of Cx. quinquefasciatus. The fluctuations in effective population size in both areas showed a significant seasonal pattern. Additionally, the significant population expansion following Hurricane Harvey in 2017 supports the necessity for post-hurricane vector-control interventions.

Machine Learning and Its Applications for Protozoal Pathogens and Protozoal Infectious Diseases

In recent years, massive attention has been attracted to the development and application of machine learning (ML) in the field of infectious diseases, not only serving as a catalyst for academic studies but also as a key means of detecting pathogenic microorganisms, implementing public health surveillance, exploring host-pathogen interactions, discovering drug and vaccine candidates, and so forth. These applications also include the management of infectious diseases caused by protozoal pathogens, such as Plasmodium, Trypanosoma, Toxoplasma, Cryptosporidium, and Giardia, a class of fatal or life-threatening causative agents capable of infecting humans and a wide range of animals. With the reduction of computational cost, availability of effective ML algorithms, popularization of ML tools, and accumulation of high-throughput data, it is possible to implement the integration of ML applications into increasing scientific research related to protozoal infection. Here, we will present a brief overview of important concepts in ML serving as background knowledge, with a focus on basic workflows, popular algorithms (e.g., support vector machine, random forest, and neural networks), feature extraction and selection, and model evaluation metrics. We will then review current ML applications and major advances concerning protozoal pathogens and protozoal infectious diseases through combination with correlative biology expertise and provide forward-looking insights for perspectives and opportunities in future advances in ML techniques in this field.

Quantifying malaria acquired during travel and its role in malaria elimination on Bioko Island

BACKGROUND

Malaria elimination is the goal for Bioko Island, Equatorial Guinea. Intensive interventions implemented since 2004 have reduced prevalence, but progress has stalled in recent years. A challenge for elimination has been malaria infections in residents acquired during travel to mainland Equatorial Guinea. The present article quantifies how off-island contributes to remaining malaria prevalence on Bioko Island, and investigates the potential role of a pre-erythrocytic vaccine in making further progress towards elimination.

METHODS

Malaria transmission on Bioko Island was simulated using a model calibrated based on data from the Malaria Indicator Surveys (MIS) from 2015 to 2018, including detailed travel histories and malaria positivity by rapid-diagnostic tests (RDTs), as well as geospatial estimates of malaria prevalence. Mosquito population density was adjusted to fit local transmission, conditional on importation rates under current levels of control and within-island mobility. The simulations were then used to evaluate the impact of two pre-erythrocytic vaccine distribution strategies: mass treat and vaccinate, and prophylactic vaccination for off-island travellers. Lastly, a sensitivity analysis was performed through an ensemble of simulations fit to the Bayesian joint posterior probability distribution of the geospatial prevalence estimates.

RESULTS

The simulations suggest that in Malabo, an urban city containing 80% of the population, there are some pockets of residual transmission, but a large proportion of infections are acquired off-island by travellers to the mainland. Outside of Malabo, prevalence was mainly attributable to local transmission. The uncertainty in the local transmission vs. importation is lowest within Malabo and highest outside. Using a pre-erythrocytic vaccine to protect travellers would have larger benefits than using the vaccine to protect residents of Bioko Island from local transmission. In simulations, mass treatment and vaccination had short-lived benefits, as malaria prevalence returned to current levels as the vaccine's efficacy waned. Prophylactic vaccination of travellers resulted in longer-lasting reductions in prevalence. These projections were robust to underlying uncertainty in prevalence estimates.

CONCLUSIONS

The modelled outcomes suggest that the volume of malaria cases imported from the mainland is a partial driver of continued endemic malaria on Bioko Island, and that continued elimination efforts on must account for human travel activity.

Comparative population genetics of the invasive mosquito Aedes albopictus and the native mosquito Aedes flavopictus in the Korean peninsula

BACKGROUND

Aedes mosquitoes are important invasive species contributing to the spread of chikungunya, dengue fever, yellow fever, zika virus, and other dangerous vector-borne diseases. Aedes albopictus is native to southeast Asia, with rapid expansion due to human activity, showing a wide distribution in the Korean peninsula. Aedes flavopictus is considered to be native to East Asia, with a broad distribution in the region, including the Korean peninsula. A better understanding of the genetic diversity of these species is critical for establishing strategies for disease prevention and vector control.

METHODS

We obtained DNA from 148 specimens of Ae. albopictus and 166 specimens of Ae. flavopictus in Korea, and amplified two mitochondrial genes (COI and ND5) to compare the genetic diversity and structure of the two species.

RESULTS

We obtained a 658-bp sequence of COI and a 423-bp sequence of ND5 from both mosquito species. We found low diversity and a nonsignificant population genetic structure in Ae. albopictus, and high diversity and a nonsignificant structure in Ae. flavopictus for these two mitochondrial genes. Aedes albopictus had fewer haplotypes with respect to the number of individuals, and a slight mismatch distribution was confirmed. By contrast, Ae. flavopictus had a large number of haplotypes compared with the number of individuals, and a large unimodal-type mismatch distribution was confirmed. Although the genetic structure of both species was nonsignificant, Ae. flavopictus exhibited higher genetic diversity than Ae. albopictus.

CONCLUSIONS

Aedes albopictus appears to be an introduced species, whereas Ae. flavopictus is endemic to the Korean peninsula, and the difference in genetic diversity between the two species is related to their adaptability and introduction history. Further studies on the genetic structure and diversity of these mosquitos will provide useful data for vector control.

A novel fluorescence and DNA combination for versatile, long-term marking of mosquitoes

Current mark-release-recapture methodologies are limited in their ability to address complex problems in vector biology, such as studying multiple groups overlapping in space and time. Additionally, limited mark retention, reduced post-marking survival and the large effort in marking, collection and recapture all complicate effective insect tracking.We have developed and evaluated a marking method using a fluorescent dye (SmartWater®) combined with synthetic DNA tags to informatively and efficiently mark adult mosquitoes using an airbrush pump and nebulizer. Using a handheld UV flashlight, the fluorescent marking enabled quick and simple initial detection of recaptures in a field-ready and non-destructive approach that when combined with an extraction-free PCR on individual mosquito legs provides potentially unlimited marking information.This marking, first tested in the laboratory with Anopheles gambiae s.l. mosquitoes, did not affect survival (median ages 24-28 days, p-adj > 0.25), oviposition (median eggs/female of 28.8, 32.5, 33.3 for water, green, red dyes, respectively, p-adj > 0.44) or Plasmodium competence (mean oocysts 5.56-10.6, p-adj > 0.95). DNA and fluorescence had 100% retention up to 3 weeks (longest time point tested) with high intensity, indicating marks would persist longer.We describe a novel, simple, no/low-impact and long-lasting marking method that allows separation of multiple insect subpopulations by combining unlimited length and sequence variation in the synthetic DNA tags. This method can be readily deployed in the field for marking multiple groups of mosquitoes or other insects.

Investigation of DDT resistance mechanisms in Anopheles funestus populations from northern and southern Benin reveals a key role of the GSTe2 gene

Background

Understanding the molecular basis of insecticide resistance in mosquito, such as Anopheles funestus, is an important step in developing strategies to mitigate the resistance problem. This study aims to assess the role of the GSTe2 gene in DDT resistance and determine the genetic diversity of this gene in An. funestus.

Methods

Gene expression analysis was performed using microarrays and PCR while the potential mutation associated with resistance was determined using sequencing.

Results

Low expression level of GSTe2 gene was recorded in Burkina-Faso samples with a fold change of 3.3 while high expression (FC 35.6) was recorded in southern Benin in Pahou (FC 35.6) and Kpome (FC 13.3). The sequencing of GSTe2 gene in six localities showed that L119F-GSTe2 mutation is almost getting fixed in highly DDT-resistant Benin (Pahou, Kpome, Doukonta) and Nigeria (Akaka Remo) mosquitoes with a low mutation rate observed in Tanongou (Benin) and Burkina-Faso mosquitoes.

Conclusion

This study shows the key role of the GSTe2 gene in DDT resistant An. funestus in Benin. Polymorphism analysis of this gene across Benin revealed possible barriers to gene flow, which could impact the design and implementation of resistance management strategies in the country.

The need for new vector control approaches targeting outdoor biting Anopheline malaria vector communities

Since the implementation of Roll Back Malaria, the widespread use of insecticide-treated nets (ITNs) and indoor residual spraying (IRS) is thought to have played a major part in the decrease in mortality and morbidity achieved in malaria-endemic regions. In the past decade, resistance to major classes of insecticides recommended for public health has spread across many malaria vector populations. Increasingly, malaria vectors are also showing changes in vector behaviour in response to current indoor chemical vector control interventions. Changes in the time of biting and proportion of indoor biting of major vectors, as well as changes in the species composition of mosquito communities threaten the progress made to control malaria transmission. Outdoor biting mosquito populations contribute to malaria transmission in many parts of sub-Saharan Africa and pose new challenges as they cannot be reliably monitored or controlled using conventional tools. Here, we review existing and novel approaches that may be used to target outdoor communities of malaria vectors. We conclude that scalable tools designed specifically for the control and monitoring of outdoor biting and resting malaria vectors with increasingly complex and dynamic responses to intensifying malaria control interventions are urgently needed. These are crucial for integrated vector management programmes designed to challenge current and future vector populations.

Robust Estimation of Recent Effective Population Size from Number of Independent Origins in Soft Sweeps

Estimating recent effective population size is of great importance in characterizing and predicting the evolution of natural populations. Methods based on nucleotide diversity may underestimate current day effective population sizes due to historical bottlenecks, whereas methods that reconstruct demographic history typically only detect long-term variations. However, soft selective sweeps, which leave a fingerprint of mutational history by recurrent mutations on independent haplotype backgrounds, holds promise of an estimate more representative of recent population history. Here, we present a simple and robust method of estimation based only on knowledge of the number of independent recurrent origins and the current frequency of the beneficial allele in a population sample, independent of the strength of selection and age of the mutation. Using a forward-time theoretical framework, we show the mean number of origins is a function of θ=2Nμ and current allele frequency, through a simple equation, and the distribution is approximately Poisson. This estimate is robust to whether mutants preexisted before selection arose and is equally accurate for diploid populations with incomplete dominance. For fast (e.g., seasonal) demographic changes compared with time scale for fixation of the mutant allele, and for moderate peak-to-trough ratios, we show our constant population size estimate can be used to bound the maximum and minimum population size. Applied to the Vgsc gene of Anopheles gambiae, we estimate an effective population size of roughly 6×107, and including seasonal demographic oscillations, a minimum effective population size >3×107, and a maximum <6×109, suggesting a mean ∼109.

Microevolution of medically important mosquitoes - A review

This review intends to discuss central issues regarding the microevolution of mosquito (Culicidae) vectors of several pathogens and how this process impacts vector biology, disease transmission, and vector control attempts. On the microevolutionary context, it comparatively discusses the current knowledge on the population genetics of representatives of the genera Aedes, Anopheles and Culex, and comments on insecticide resistance of culicids. It also discusses other biological aspects of culicids that are not usually addressed in microevolutionary studies, such as vectorial competence, endosymbiosis, and wing morphology. One conclusion is that mosquitoes are highly genetically variable, adaptable, fast evolving, and have versatile vectorial competence. Unveiling microevolutionary patterns is fundamental for the design and maintenance of all control programs. Sampling methods for assessing microevolution must be standardized and must follow meaningful guidelines, such as those of "landscape genetics". A good understanding of microevolution requires more than a collection of case studies on population genetics and resistance. Future research could deal not only with the microevolution sensu stricto, but also with evolutionarily meaningful issues, such as inheritable characters, epigenetics, physiological cost-free plasticity, vector immunity, symbiosis, pathogen-mosquito co-evolution and environmental variables. A genotyping panel for seeking adaptive phenotypes as part of the standardization of population genetics methods is proposed. The investigative paradigm should not only be retrospective but also prospective, despite the unpredictability of evolution. If we integrate all suggestions to tackle mosquito evolution, a global revolution to counter vector-borne diseases can be provoked.

Growth-disrupting Murraya koenigii leaf extracts on Anopheles gambiae larvae and identification of associated candidate bioactive constituents

Plant-based constituents have been proposed as eco-friendly alternatives to synthetic insecticides for control of mosquito vectors of malaria. In this study, we first screened the effects of methanolic leaf extracts of curry tree (Murraya koenigii) growing in tropical (Mombasa, Malindi) and semi-arid (Kibwezi, and Makindu) ecological zones of Kenya on third instar An. gambiae s.s. larvae. Extracts of the plant from the semi-arid region, and particularly from Kibwezi, led to high mortality of the larvae. Bioassay-guided fractionation of the methanolic extract of the leaves of the plants from Kibwezi was then undertaken and the most active fraction (20 fold more potent than the crude extract) was then analyzed by Liquid chromatography quadruple time of flight coupled with mass spectrometry (LC-QtoF-MS) and a number of constituents were identified, including a major alkaloid constituent, Neplanocin A (5). Exposure of the third instar larvae to a sub-lethal dose (4.43 ppm) of this fraction over 7-day periods induced gross morphogenetic abnormalities in the larvae, with reduced locomotion, and delayed pupation. Moreover, the few adults that emerged from some pupae failed to fly from the water surface, unlike in the untreated control group. These results demonstrate subtle growth-disrupting effects of the phytochemical blend from M. koenigii leaves on aquatic stages An. gambiae mosquito. The study lays down some useful groundwork for the downstream development of phytochemical blends that can be evaluated for integration into eco-friendly control of An. gambiae vector population targeting the often overlooked but important immature stages of the malaria vector.

Population genetics of Anopheles funestus, the African malaria vector, Kenya

Background

Anopheles funestus is among the major malaria vectors in Kenya and sub-Saharan Africa and has been recently implicated in persistent malaria transmission. However, its ecology and genetic diversity remain poorly understood in Kenya.

Methods

Using 16 microsatellite loci, we examined the genetic structure of An. funestus sampled from 11 locations (n = 426 individuals) across a wide geographical range in Kenya spanning coastal, western and Rift Valley areas.

Results

Kenyan An. funestus resolved as three genetically distinct clusters. The largest cluster (FUN1) broadly included samples from western and Rift Valley areas of Kenya with two clusters identified from coastal Kenya (FUN2 and FUN3), not previously reported. Geographical distance had no effect on population differentiation of An. funestus. We found a significant variation in the mean Plasmodium infectivity between the clusters (χ² = 12.1, df = 2, P = 0.002) and proportional to the malaria prevalence in the different risk zones of Kenya. Notably, there was variation in estimated effective population sizes between the clusters, suggesting possible differential impact of anti-vector interventions in represented areas.

Conclusions

Heterogeneity among Kenyan populations of An. funestus will impact malaria vector control with practical implications for the development of gene-drive technologies. The difference in Plasmodium infectivity and effective population size between the clusters could suggest potential variation in phenotypic characteristics relating to competence or insecticide resistance. This is worth examining in future studies.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3252-3) contains supplementary material, which is available to authorized users.

Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda

BACKGROUND

Malaria is the leading cause of global paediatric mortality in children below 5 years of age. The number of fatalities has reduced significantly due to an expansion of control interventions but the development of new technologies remains necessary in order to achieve elimination. Recent attention has been focused on the release of genetically modified (GM) mosquitoes into natural vector populations as a mechanism of interrupting parasite transmission but despite successful in vivo laboratory studies, a detailed population genetic assessment, which must first precede any proposed field trial, has yet to be undertaken systematically. Here, the genetic structure of Anopheles gambiae populations in north-western Lake Victoria is explored to assess their suitability as candidates for a pilot field study release of GM mosquitoes.

METHODS

478 Anopheles gambiae mosquitoes were collected from six locations and a subset (N = 96) was selected for restriction site-associated DNA sequencing (RADseq). The resulting single nucleotide polymorphism (SNP) marker set was analysed for effective size (N_e), connectivity and population structure (PCA, F_ST).

RESULTS

5175 high-quality genome-wide SNPs were identified. A principal components analysis (PCA) of the collinear genomic regions illustrated that individuals clustered in concordance with geographic origin with some overlap between sites. Genetic differentiation between populations was varied with inter-island comparisons having the highest values (median F_ST 0.0480-0.0846). N_e estimates were generally small (124.2-1920.3).

CONCLUSIONS

A reduced-representation SNP marker set for genome-wide An. gambiae genetic analysis in the north-western Lake Victoria basin is reported. Island populations demonstrated low to moderate genetic differentiation and greater structure suggesting some limitation to migration. Smaller estimates of N_e indicate that an introduced effector transgene will be more susceptible to genetic drift but to ensure that it is driven to fixation a robust gene drive mechanism will likely be needed. These findings, together with their favourable location and suitability for frequent monitoring, indicate that the Ssese Islands contain several candidate field locations, which merit further evaluation as potential GM mosquito pilot release sites.

Human Interventions: Driving Forces of Mosquito Evolution

One of the most common strategies for controlling mosquito-borne diseases relies on the use of chemical pesticides to repel or kill the mosquito vector. Pesticide exposure interferes with several key biological functions in the mosquito and triggers a variety of adaptive responses whose underlying mechanisms are only partially elucidated. The availability of reference genome sequences opens up the possibility of tracking signatures of evolutionary changes, including the most recent, across the genomes of many vector species. In this review, we highlight the recent genomic changes, which contribute to the fascinating adaptation of malaria vectors of the sub-Saharan African region to intensive insecticide-based interventions. We emphasize the operational significance of detailed genomic knowledge for current monitoring and decision-making.

Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.

Tracing the origin of the early wet-season Anopheles coluzzii in the Sahel

In arid environments, the source of the malaria mosquito populations that re‐establish soon after first rains remains a puzzle and alternative explanations have been proposed. Using genetic data, we evaluated whether the early rainy season (RS) population of Anopheles coluzzii is descended from the preceding late RS generation at the same locality, consistent with dry season (DS) dormancy (aestivation), or from migrants from distant locations. Distinct predictions derived from these two hypotheses were assessed, based on variation in 738 SNPs in eleven A. coluzzii samples, including seven samples spanning 2 years in a Sahelian village. As predicted by the “local origin under aestivation hypothesis,” temporal samples from the late RS and those collected after the first rain of the following RS were clustered together, while larger genetic distances were found among samples spanning the RS. Likewise, multilocus genotype composition of samples from the end of the RS was similar across samples until the following RS, unlike samples that spanned the RS. Consistent with reproductive arrest during the DS, no genetic drift was detected between samples taken over that period, despite encompassing extreme population minima, whereas it was detected between samples spanning the RS. Accordingly, the variance in allele frequency increased with time over the RS, but not over the DS. However, not all the results agreed with aestivation. Large genetic distances separated samples taken a year apart, and during the first year, within‐sample genetic diversity declined and increased back during the late RS, suggesting a bottleneck followed by migration. The decline of genetic diversity followed by a mass distribution of insecticide‐treated nets was accompanied by a reduced mosquito density and a rise in the mutation conferring resistance to pyrethroids, indicating a bottleneck due to insecticidal selection. Overall, our results support aestivation in A. coluzzii during the DS that is accompanied by long‐distance migration in the late RS.

Pollutants and Insecticides Drive Local Adaptation in African Malaria Mosquitoes

The Anopheles gambiae complex contains a number of highly anthropophilic mosquito species that have acquired exceptional ability to thrive in complex human habitats. Thus, examining the evolutionary history of this Afrotropical mosquito may yield vital information on the selective processes that occurred during the adaptation to human-dominated environments. We performed reduced representation sequencing on 941 mosquitoes of the Anopheles gambiae complex collected across four ecogeographic zones in Cameroon. We find evidence for genetic and geographic subdivision within An. coluzzii and An. gambiae sensu stricto-the two most significant malaria vectors in the region. Importantly, in both species, rural and urban populations are genetically differentiated. Genome scans reveal pervasive signatures of selection centered on genes involved in xenobiotic resistance. Notably, a selective sweep containing detoxification enzymes is prominent in urban mosquitoes that exploit polluted breeding sites. Overall, our study suggests that recent anthropogenic environmental modifications and widespread use of insecticides are driving population differentiation and local adaptation in vectors with potentially significant consequences for malaria epidemiology.

Geographical distributions of African malaria vector sibling species and evidence for insecticide resistance

Background

Many of the mosquito species responsible for malaria transmission belong to a sibling complex; a taxonomic group of morphologically identical, closely related species. Sibling species often differ in several important factors that have the potential to impact malaria control, including their geographical distribution, resistance to insecticides, biting and resting locations, and host preference. The aim of this study was to define the geographical distributions of dominant malaria vector sibling species in Africa so these distributions can be coupled with data on key factors such as insecticide resistance to aid more focussed, species-selective vector control.

Results

Within the Anopheles gambiae species complex and the Anopheles funestus subgroup, predicted geographical distributions for Anopheles coluzzii, An. gambiae (as now defined) and An. funestus (distinct from the subgroup) have been produced for the first time. Improved predicted geographical distributions for Anopheles arabiensis, Anopheles melas and Anopheles merus have been generated based on records that were confirmed using molecular identification methods and a model that addresses issues of sampling bias and past changes to the environment. The data available for insecticide resistance has been evaluated and differences between sibling species are apparent although further analysis is required to elucidate trends in resistance.

Conclusions

Sibling species display important variability in their geographical distributions and the most important malaria vector sibling species in Africa have been mapped here for the first time. This will allow geographical occurrence data to be coupled with species-specific data on important factors for vector control including insecticide resistance. Species-specific data on insecticide resistance is available for the most important malaria vectors in Africa, namely An. arabiensis, An. coluzzii, An. gambiae and An. funestus. Future work to combine these data with the geographical distributions mapped here will allow more focussed and resource-efficient vector control and provide information to greatly improve and inform existing malaria transmission models.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-017-1734-y) contains supplementary material, which is available to authorized users.

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas

Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

Increasing outdoor host-seeking in Anopheles gambiae over 6 years of vector control on Bioko Island

Background

Vector control through indoor residual spraying (IRS) has been employed on Bioko Island, Equatorial Guinea, under the Bioko Island Malaria Control Project (BIMCP) since 2004. This study analyses the change in mosquito abundance, species composition and outdoor host-seeking proportions from 2009 to 2014, after 11 years of vector control on Bioko Island.

Methods

All-night indoor and outdoor human landing catches were performed monthly in the Bioko Island villages of Mongola, Arena Blanca, Biabia and Balboa from 2009 to 2014. Collected mosquitoes were morphologically identified and a subset of Anopheles gambiae sensu lato (s.l.) were later identified molecularly to their sibling species. Mosquito collection rates, species composition and indoor/outdoor host-seeking sites were analysed using generalized linear mixed models to assess changes in mosquito abundance and behaviour.

Results

The overall mosquito collection rate declined in each of the four Bioko Island villages. Anopheles coluzzii and Anopheles melas comprised the An. gambiae s.l. mosquito vector population, with a range of species proportions across the four villages. The proportion of outdoor host-seeking An. gambiae s.l. mosquitoes increased significantly in all four villages with an average increase of 58.8 % [57.9, 59.64 %] in 2009 to 70.0 % [67.8, 72.0 %] in 2014. Outdoor host-seeking rates did not increase in the month after an IRS spray round compared to the month before, suggesting that insecticide repellency has little impact on host-seeking behaviour.

Conclusion

While vector control on Bioko Island has succeeded in substantial reduction in overall vector biting rates, populations of An. coluzzii and An. melas persist. Host-seeking behaviour has changed in these An. gambiae s.l. populations, with a shift towards outdoor host-seeking. During this study period, the proportion of host-seeking An. gambiae s.l. caught outdoors observed on Bioko Island increased to high levels, exceeding 80 % in some locations. It is possible that there may be a genetic basis underlying this large shift in host-seeking behaviour, in which case outdoor feeding could pose a serious threat to current vector control programmes. Currently, the BIMCP is preparing for this potential challenge by testing source reduction as a complementary control effort that also targets outdoor transmission.

Electronic supplementary material

The online version of this article (doi:10.1186/s12936-016-1286-6) contains supplementary material, which is available to authorized users.

Implications for changes in Anopheles darlingi biting behaviour in three communities in the peri-Iquitos region of Amazonian Peru

BACKGROUND

Malaria transmission in the peri-Iquitos region of Amazonian Peru has been designated as seasonal and hypo-endemic with recently described hyper-endemic hotspots. Despite relatively recent distribution of long-lasting insecticidal bed nets (LLINs), malaria in Amazonian Peru persists and increased substantially in 2014 compared to previous years. Anopheles darlingi, identified as the main malaria vector, is known for its variable behaviour depending on locality and environment.

METHODS

To evaluate vector biology metrics in relation to seasonality and malaria transmission, mosquito collections were carried out in three localities in the peri-Iquitos region, Loreto, Peru in 2011-2012. Human landing catch (HLC) collection method, Shannon (SHA) and CDC trap types were compared for effectiveness in a neotropical setting. Abundance, human biting rate and entomological inoculation rate (EIR) were measured to provide an updated view of transmission patterns post-LLIN distribution.

RESULTS

HLC collected significantly more anopheline mosquitoes than SHA and CDC light traps. Anopheles darlingi was the most prevalent species in all three villages (84% overall). Biting patterns varied depending on trap type, season and village. EIR varied temporally (monthly) and spatially and the highest (2.52) occurred during the 2012 malaria outbreak in Cahuide. Unexpectedly there was a high infection rate (1.47 and 1.75) outside the normal malaria transmission season, coincident with a second local outbreak in Cahuide. The first identification of Anopheles dunhami and Anopheles oswaldoi C in Peru, using molecular markers, is also reported in this study.

CONCLUSION

These data underscore the importance of HLC as the most meaningful collection method for measuring vector biology indices in this region. The highest monthly EIR provides additional evidence of seasonal transmission in riverine localities correlated with high river levels, and An. darlingi as the only contributor to transmission. The trend of an increase in outdoor-biting together with early-evening infected mosquitoes may undermine the effectiveness of LLINs as a primary malaria intervention.

Temporal Genetic Dynamics of an Invasive Species, Frankliniella occidentalis (Pergande), in an Early Phase of Establishment

Many species can successfully colonize new areas despite their propagules having low genetic variation. We assessed whether the decreased genetic diversity could result in temporal fluctuations of genetic parameters of the new populations of an invasive species, western flower thrips, Frankliniella occidentalis, using mitochondrial and microsatellite markers. This study was conducted in eight localities from four climate regions in China, where F. occidentalis was introduced in the year 2000 and had lower genetic diversity than its native populations. We also tested the level of genetic differentiation in these introduced populations. The genetic diversity of the samples at different years in the same locality was not significantly different from each other in most localities. F_ST and STRUCTURE analysis also showed that most temporal population comparisons from the same sites were not significantly differentiated. Our results showed that the invasive populations of F. occidentalis in China can maintain temporal stability in genetic composition at an early phase of establishment despite having lower genetic diversity than in their native range.

Large fluctuations in the effective population size of the malaria mosquito Anopheles gambiae s.s. during vector control cycle

On Bioko Island, Equatorial Guinea, indoor residual spraying (IRS) has been part of the Bioko Island Malaria Control Project since early 2004. Despite success in reducing childhood infections, areas of high transmission remain on the island. We therefore examined fluctuations in the effective population size (N e ) of the malaria vector Anopheles gambiae in an area of persistent high transmission over two spray rounds. We analyzed data for 13 microsatellite loci from 791 An. gambiae specimens collected at six time points in 2009 and 2010 and reconstructed the demographic history of the population during this period using approximate Bayesian computation (ABC). Our analysis shows that IRS rounds have a large impact on N e , reducing it by 65%-92% from prespray round N e . More importantly, our analysis shows that after 3-5 months, the An. gambiae population rebounded by 2818% compared shortly following the spray round. Our study underscores the importance of adequate spray round frequency to provide continuous suppression of mosquito populations and that increased spray round frequency should substantially improve the efficacy of IRS campaigns. It also demonstrates the ability of ABC to reconstruct a detailed demographic history across only a few tens of generations in a large population.

Five years of malaria control in the continental region, Equatorial Guinea

Background

A successful malaria control programme began in 2004 on Bioko Island, Equatorial Guinea. From 2007, the same multiple malaria interventions, though reduced in scope for funding reasons, were introduced to the four mainland provinces of Equatorial Guinea (the continental region) aiming to recreate Bioko’s success. Two provinces received long-lasting insecticidal nets (LLINs) and two provinces received biannual indoor residual spraying (IRS). Enhanced case management and communications were introduced throughout.

Methods

Estimates of intervention coverage and indicators of malaria transmission for 2007 to 2011 were derived from annual malaria indicator surveys (MIS). Results were complemented by health information system (HIS) and entomological data. The personal protection offered by LLINs and IRS against Plasmodium falciparum infection was estimated with logistic regression.

Results

The estimated proportion of children aged 1–4 using either an LLIN the previous night or living in a house sprayed in the last six months was 23% in 2007 and 42% in 2011. The estimated prevalence of P. falciparum in children aged 1–4 was 68% (N=1,770; 95% confidence interval [CI]: 58-76%) in 2007 and 52% (N=1,602; 95% CI: 44-61%) in 2011. Children 1–4 years had lower prevalence if they used an LLIN the previous night (N=1,124, 56%; adjusted odds ratio [aOR] 0.64, 95% CI: 0.55-0.74) or if they lived in a sprayed house (N=1,150, 57%; aOR 0.80, 95% CI: 0.62-1.03) compared to children with neither intervention (N=4,131, 66%, reference group). The minority of children who both used an LLIN and lived in a sprayed house had the lowest prevalence of infection (N=171, 45%; aOR 0.52, 95% CI: 0.35-0.78). High site-level intervention coverage did not always correlate with lower site-level P. falciparum prevalence. The malaria season peaked in either June or July, not necessarily coinciding with MIS data collection.

Conclusions

Though moderate impact was achieved after five years of vector control, case management, and communications, prevalence remained high due to an inability to sufficiently scale-up coverage with either IRS or LLINs. Both LLINs and IRS provided individual protection, but greater protection was afforded to children who benefitted from both.

Insecticide resistance allele frequencies in Anopheles gambiae before and after anti-vector interventions in continental Equatorial Guinea

Anti-malaria interventions that rely on insecticides can be compromised by insecticide-resistance alleles among malaria vectors. We examined frequency changes of resistance alleles at two loci, knockdown resistance (kdr) and acetylcholinesterase-1 (ace-1), which confer resistance to pyrethroids and DDT, and carbamates, respectively. A total of 7,059 Anopheles gambiae sensu stricto mosquitoes were analyzed from multiple sites across continental Equatorial Guinea. A subset of sites included samples collected pre-intervention (2007) and post-intervention (2009-2011). Both L1014S and L1014F resistance alleles were observed in almost all pre-intervention collections. In particular, L1014F was already at substantial frequencies in M form populations (17.6-74.6%), and at high frequencies (> 50%) in all but two S form populations. Comparison before and throughout anti-vector interventions showed drastic increases in L1014F, presumably caused by intensified selection pressure imposed by pyrethroids used in vector control efforts. In light of these findings, inclusion of other insecticide classes in any anti-vector intervention can be considered prudent.

Malaria transmission after five years of vector control on Bioko Island, Equatorial Guinea

Background

Malaria is endemic with year-round transmission on Bioko Island. The Bioko Island Malaria Control Project (BIMCP) started in 2004 with the aim to reduce malaria transmission and to ultimately eliminate malaria. While the project has been successful in reducing overall malaria morbidity and mortality, foci of high malaria transmission still persist on the island. Results from the 2009 entomological collections are reported here.

Methods

Human landing collections (HLC) and light trap collections (LTC) were carried out on Bioko Island, Equatorial Guinea in 2009. The HLCs were performed in three locations every second month and LTCs were carried out in 10 locations every second week. Molecular analyses were performed to identify species, detect sporozoites, and identify potential insecticide resistance alleles.

Results

The entomological inoculation rates (EIR) on Bioko Island ranged from 163 to 840, with the outdoor EIRs reaching > 900 infective mosquito bites per year. All three human landing collection sites on Bioko Island had an annual EIR exceeding the calculated African average of 121 infective bites per year. The highest recorded EIRs were in Punta Europa in northwestern Bioko Island with human biting rates of 92 and 66 mosquito landings per person per night, outdoors and indoors, respectively. Overall, the propensity for mosquito biting on the island was significantly higher outdoors than indoors (p < 0.001). Both Anopheles gambiae s.s. and An. melas were responsible for malaria transmission on the island, but with different geographical distribution patterns. Sporozoite rates were the highest in An. gambiae s.s. populations ranging from 3.1% in Punta Europa and 5.7% in Riaba in the southeast. Only the L1014F (kdr-west) insecticide resistance mutation was detected on the island with frequencies ranging from 22-88% in An. gambiae s.s. No insecticide resistance alleles were detected in the An. melas populations.

Conclusions

In spite of five years of extensive malaria control and a generalized reduction in the force of transmission, parasite prevalence and child mortality, foci of very high transmission persist on Bioko Island, particularly in the northwestern Punta Europa area. This area is favorable for anopheline mosquito breeding; human biting rates are high, and the EIRs are among the highest ever recorded. Both vector species collected in the study have a propensity to bite outdoors more frequently than indoors. Despite current vector control efforts mosquito densities remain high in such foci of high malaria transmission. To further reduce transmission, indoor residual spraying (IRS) needs to be supplemented with additional vector control interventions.