Modelling the persistence of mosquito vectors of malaria in Burkina Faso

Variation in spatial population structure in the Anopheles gambiae species complex

Anopheles gambiae, Anopheles coluzzii , and Anopheles arabiensis are three of the most widespread vectors of malaria parasites, with geographical ranges stretching across wide swaths of Africa. Understanding the population structure of these closely related species, including the extent to which populations are connected by gene flow, is essential for understanding how vector control implemented in one location might indirectly affect vector populations in other locations. Here, we assessed the population structure of each species based on whole-genome sequences from the third phase of the Anopheles gambiae 1000 Genomes Project. The data set included single nucleotide polymorphisms from whole genomes of 2,242 individual mosquitoes sampled from 119 locations across 19 African countries. We found that A. gambiae sampled from several countries in West and Central Africa showed low genetic differentiation from each other according to principal components analysis (PCA) and ADMIXTURE modeling. Using Estimated Effective Migration Surfaces (EEMS), we showed that this low genetic differentiation indicates high effective migration rates for A. gambiae across this region. Outside of this region, we found six groups of sampling locations from Central, East, and Southern Africa for which A. gambiae showed higher genetic differentiation, and lower effective migration rates, between each other and the West/Central Africa group. These results indicate that the barriers to and corridors for migration between populations of A. gambiae differ across the geographical range of this malaria vector species. Using the same methods, we found higher genetic differentiation and lower migration rates between populations of A. coluzzii in West and Central Africa than for A. gambiae in the same region. On the other hand, we found lower genetic differentiation and higher migration rates between populations of A. arabiensis in Tanzania, compared to A. gambiae in the same region. These differences between A. gambiae, A. coluzzii , and A. arabiensis indicate that migration barriers and corridors may vary between species, even for very closely related species. Overall, our results demonstrate that migration rates vary both between and within species of Anopheles mosquitoes, presumably based on species-specific responses to the ecological or environmental conditions that may impede or facilitate migration, and the geographical patterns of these conditions across the landscape. Together with previous findings, this study provides robust evidence that migration rates between populations of malaria vectors depend on the ecological context, which should be considered when planning surveillance of vector populations, monitoring for insecticide resistance, and evaluating interventions.

Manipulating the Destiny of Wild Populations Using CRISPR

Genetic biocontrol aims to suppress or modify populations of species to protect public health, agriculture, and biodiversity. Advancements in genome engineering technologies have fueled a surge in research in this field, with one gene editing technology, CRISPR, leading the charge. This review focuses on the current state of CRISPR technologies for genetic biocontrol of pests and highlights the progress and ongoing challenges of using these approaches.

Potential persistence mechanisms of the major Anopheles gambiae species complex malaria vectors in sub-Saharan Africa: a narrative review

The source of malaria vector populations that re-establish at the beginning of the rainy season is still unclear yet knowledge of mosquito behaviour is required to effectively institute control measures. Alternative hypotheses like aestivation, local refugia, migration between neighbouring sites, and long-distance migration (LDM) are stipulated to support mosquito persistence. This work assessed the malaria vector persistence dynamics and examined various studies done on vector survival  via these hypotheses; aestivation, local refugia, local or long-distance migration across sub-Saharan Africa, explored a range of methods used, ecological parameters and highlighted the knowledge trends and gaps. The results about a particular persistence mechanism that supports the re-establishment of Anopheles gambiae, Anopheles coluzzii or Anopheles arabiensis in sub-Saharan Africa were not conclusive given that each method used had its limitations. For example, the Mark-Release-Recapture (MRR) method whose challenge is a low recapture rate that affects its accuracy, and the use of time series analysis through field collections whose challenge is the uncertainty about whether not finding mosquitoes during the dry season is a weakness of the conventional sampling methods used or because of hidden shelters. This, therefore, calls for further investigations emphasizing the use of ecological experiments under controlled conditions in the laboratory or semi-field, and genetic approaches, as they are known to complement each other. This review, therefore, unveils and assesses the uncertainties that influence the different malaria vector persistence mechanisms and provides recommendations for future studies.

Filarial infections in lemurs: Evidence for a wide geographical distribution and low host specificity among lemur species

The relevance of emerging infectious diseases continues to grow worldwide as human activities increasingly extend into formerly remote natural areas. This is particularly noticeable on the island of Madagascar. As closest relatives to humans on the island, lemurs are of particular relevance as a potential origin of zoonotic pathogen spillover. Knowledge of pathogens circulating in lemur populations is, however, very poor. Particularly little is known about lemur hemoparasites. To infer host range, ecological and geographic spread of the recently described hemoparasitic nematode Lemurfilaria lemuris in northwestern Madagascar, a total of 942 individuals of two mouse lemur species (Microcebus murinus [n = 207] and Microcebus ravelobensis [n = 433]) and two rodent species (the endemic Eliurus myoxinus [n = 118] and the invasive Rattus rattus [n = 184]) were captured in two fragmented forest landscapes (Ankarafantsika National Park and Mariarano Classified Forest) in northwestern Madagascar for blood sample examination. No protozoan hemoparasites were detected by microscopic blood smear screening. Microfilaria were present in 1.0% (2/207) of M. murinus and 2.1% (9/433) of M. ravelobensis blood samples but not in rodent samples. Internal transcribed spacer 1 (ITS-1) sequences were identical to an unnamed Onchocercidae species previously described to infect a larger lemur species, Propithecus verreauxi, about 650 km further south. In contrast to expectations, L. lemuris was not detected. The finding of a pathogen in a distantly related host species, at a considerable geographic distance from the location of its original detection, instead of a microfilaria species previously described for one of the studied host species in the same region, illustrates our low level of knowledge of lemur hemoparasites, their host ranges, distribution, modes of transmission, and their zoonotic potential. Our findings shall stimulate new research that will be of relevance for both conservation medicine and human epidemiology.

Spatial modelling for population replacement of mosquito vectors at continental scale

Malaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. Novel control strategies require detailed safety assessment to ensure responsible and successful deployments. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors.

We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa by simulating introductions of genetically modified mosquitoes across the African mainland and its offshore islands. We explore transmission of the gene drive between the two subspecies that arise from different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. Given the best current available knowledge on the subspecies’ life histories, we find that an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance beginning to take over within a decade. Our model accounts for regional to continental scale mechanisms, and demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. As a result, it is well-placed to answer future questions relating to mosquito gene drives as important life history parameters become better understood.

Conventional control methods have dramatically reduced malaria, but it still kills over 300,000 children in Africa each year, and this number could increase as their effectiveness wanes. Novel control methods using gene drives rapidly reduce or modify malaria vector populations in laboratory settings, and hence are now being considered for field applications. We use modelling to assess how a gene drive might spread and persist in the malaria-carrying subspecies Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii. These two subspecies interbreed and compete, so we model how these interactions affect the spread of the drive at a continental scale. In scenarios that allow mosquitoes to travel on prevailing wind currents, we find that a gene drive can potentially spread across national borders—and jump from offshore islands to the African mainland—but spread is eventually arrested when the drive allele is ousted by a resistant allele. As we learn more about the population dynamics of both genetically modified and wild mosquitoes, and as gene drive systems are further developed to allow local containment and evade resistance, our model will be able to answer more detailed questions about how they can be applied in the field effectively and safely.

Gene Drive Dynamics in Natural Populations: The Importance of Density Dependence, Space, and Sex

The spread of synthetic gene drives is often discussed in the context of panmictic populations connected by gene flow and described with simple deterministic models. Under such assumptions, an entire species could be altered by releasing a single individual carrying an invasive gene drive, such as a standard homing drive. While this remains a theoretical possibility, gene drive spread in natural populations is more complex and merits a more realistic assessment. The fate of any gene drive released in a population would be inextricably linked to the population's ecology. Given the uncertainty often involved in ecological assessment of natural populations, understanding the sensitivity of gene drive spread to important ecological factors is critical. Here we review how different forms of density dependence, spatial heterogeneity, and mating behaviors can impact the spread of self-sustaining gene drives. We highlight specific aspects of gene drive dynamics and the target populations that need further research.

Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii

Mosquito control remains a central pillar of efforts to reduce malaria burden in sub-Saharan Africa. However, insecticide resistance is entrenched in malaria vector populations, and countries with a high malaria burden face a daunting challenge to sustain malaria control with a limited set of surveillance and intervention tools. Here we report on the second phase of a project to build an open resource of high-quality data on genome variation among natural populations of the major African malaria vector species Anopheles gambiae and Anopheles coluzzii We analyzed whole genomes of 1142 individual mosquitoes sampled from the wild in 13 African countries, as well as a further 234 individuals comprising parents and progeny of 11 laboratory crosses. The data resource includes high-confidence single-nucleotide polymorphism (SNP) calls at 57 million variable sites, genome-wide copy number variation (CNV) calls, and haplotypes phased at biallelic SNPs. We use these data to analyze genetic population structure and characterize genetic diversity within and between populations. We illustrate the utility of these data by investigating species differences in isolation by distance, genetic variation within proposed gene drive target sequences, and patterns of resistance to pyrethroid insecticides. This data resource provides a foundation for developing new operational systems for molecular surveillance and for accelerating research and development of new vector control tools. It also provides a unique resource for the study of population genomics and evolutionary biology in eukaryotic species with high levels of genetic diversity under strong anthropogenic evolutionary pressures.

Induction of long-lived potential aestivation states in laboratory An. gambiae mosquitoes

Background

How anopheline mosquitoes persist through the long dry season in Africa remains a gap in our understanding of these malaria vectors. To span this period in locations such as the Sahelian zone of Mali, mosquitoes must either migrate to areas of permanent water, recolonize areas as they again become favorable, or survive in harsh conditions including high temperatures, low humidity, and an absence of surface water (required for breeding). Adult mosquitoes surviving through this season must dramatically extend their typical lifespan (averaging 2–3 weeks) to 7 months. Previous work has found evidence that the malaria mosquito An. coluzzii, survives over 200 days in the wild between rainy seasons in a presumed state of aestivation (hibernation), but this state has so far not been replicated in laboratory conditions. The inability to recapitulate aestivation in the lab hinders addressing key questions such as how this state is induced, how it affects malaria vector competence, and its impact on disease transmission.

Methods

In effort to induce aestivation, we held laboratory mosquitoes in climate-controlled incubators with a range of conditions that adjusted humidity (40–85% RH), temperature (18–27 °C), and light conditions (8–12 h of light) and evaluated their survivorship. These conditions were chosen to mimic the late rainy and dry seasons as well as relevant extremes these mosquitoes may experience during aestivation.

Results

We found that by priming mosquitoes in conditions simulating the late wet season in Mali, and maintaining mosquitoes in reduced light/temperature, mean mosquito survival increased from 18.34 ± 0.65 to 48.02 ± 2.87 days, median survival increased from 19 (95% CI 17–21) to 50 days (95% CI 40–58), and the maximum longevity increased from 38 to 109 days (P-adj < 0.001). While this increase falls short of the 200 + day survival seen in field mosquitoes, this extension is substantially higher than previously found through environmental or dietary modulation and is hard to reconcile with states other than aestivation. This finding will provide a platform for future characterization of this state, and allow for comparison to field collected samples.

Modelling the suppression of a malaria vector using a CRISPR-Cas9 gene drive to reduce female fertility

BACKGROUND

Gene drives based on CRISPR-Cas9 technology are increasingly being considered as tools for reducing the capacity of mosquito populations to transmit malaria, and one of the most promising options is driving endonuclease genes that reduce the fertility of female mosquitoes. In particular, there is much interest in constructs that target the conserved mosquito doublesex (dsx) gene such that the emergence of functional drive-resistant alleles is unlikely. Proof of principle that these constructs can lead to substantial population suppression has been obtained in population cages, and they are being evaluated for use in sub-Saharan Africa. Here, we use simulation modelling to understand the factors affecting the spread of this type of gene drive over a one million-square kilometre area of West Africa containing substantial environmental and social heterogeneity.

RESULTS

We found that a driving endonuclease gene targeting female fertility could lead to substantial reductions in malaria vector populations on a regional scale. The exact level of suppression is influenced by additional fitness costs of the transgene such as the somatic expression of Cas9, and its deposition in sperm or eggs leading to damage to the zygote. In the absence of these costs, or of emergent drive-resistant alleles that restore female fertility, population suppression across the study area is predicted to stabilise at ~ 95% 4 years after releases commence. Small additional fitness costs do not greatly affect levels of suppression, though if the fertility of females whose offspring transmit the construct drops by more than ~ 40%, then population suppression is much less efficient. We show the suppression potential of a drive allele with high fitness costs can be enhanced by engineering it also to express male bias in the progeny of transgenic males. Irrespective of the strength of the drive allele, the spatial model predicts somewhat less suppression than equivalent non-spatial models, in particular in highly seasonal regions where dry season stochasticity reduces drive efficiency. We explored the robustness of these results to uncertainties in mosquito ecology, in particular their method of surviving the dry season and their dispersal rates.

CONCLUSIONS

The modelling presented here indicates that considerable suppression of vector populations can be achieved within a few years of using a female sterility gene drive, though the impact is likely to be heterogeneous in space and time.

Modelling the potential of genetic control of malaria mosquitoes at national scale

BACKGROUND

The persistence of malaria in large parts of sub-Saharan Africa has motivated the development of novel tools to complement existing control programmes, including gene-drive technologies to modify mosquito vector populations. Here, we use a stochastic simulation model to explore the potential of using a driving-Y chromosome to suppress vector populations in a 10⁶ km² area of West Africa including all of Burkina Faso.

RESULTS

The consequence of driving-Y introductions is predicted to vary across the landscape, causing elimination of the target species in some regions and suppression in others. We explore how this variation is determined by environmental conditions, mosquito behaviour, and the properties of the gene-drive. Seasonality is particularly important, and we find population elimination is more likely in regions with mild dry seasons whereas suppression is more likely in regions with strong seasonality.

CONCLUSIONS

Despite the spatial heterogeneity, we suggest that repeated introductions of modified mosquitoes over a few years into a small fraction of human settlements may be sufficient to substantially reduce the overall number of mosquitoes across the entire geographic area.

Large-cage assessment of a transgenic sex-ratio distortion strain on populations of an African malaria vector

Background

Novel transgenic mosquito control methods require progressively more realistic evaluation. The goal of this study was to determine the effect of a transgene that causes a male-bias sex ratio on Anopheles gambiae target populations in large insectary cages.

Methods

Life history characteristics of Anopheles gambiae wild type and Ag(PMB)1 (aka ^gfp124L-2) transgenic mosquitoes, whose progeny are 95% male, were measured in order to parameterize predictive population models. Ag(PMB)1 males were then introduced at two ratios into large insectary cages containing target wild type populations with stable age distributions and densities. The predicted proportion of females and those observed in the large cages were compared. A related model was then used to predict effects of male releases on wild mosquitoes in a west African village.

Results

The frequency of transgenic mosquitoes in target populations reached an average of 0.44 ± 0.02 and 0.56 ± 0.02 after 6 weeks in the 1:1 and in the 3:1 release ratio treatments (transgenic male:wild male) respectively. Transgenic males caused sex-ratio distortion of 73% and 80% males in the 1:1 and 3:1 treatments, respectively. The number of eggs laid in the transgenic treatments declined as the experiment progressed, with a steeper decline in the 3:1 than in the 1:1 releases. The results of the experiment are partially consistent with predictions of the model; effect size and variability did not conform to the model in two out of three trials, effect size was over-estimated by the model and variability was greater than anticipated, possibly because of sampling effects in restocking. The model estimating the effects of hypothetical releases on the mosquito population of a West African village demonstrated that releases could significantly reduce the number of females in the wild population. The interval of releases is not expected to have a strong effect.

Conclusions

The biological data produced to parameterize the model, the model itself, and the results of the experiments are components of a system to evaluate and predict the performance of transgenic mosquitoes. Together these suggest that the Ag(PMB)1 strain has the potential to be useful for reversible population suppression while this novel field develops.

Insects With Survival Kits for Desiccation Tolerance Under Extreme Water Deficits

The year 2002 marked the tercentenary of Antonie van Leeuwenhoek's discovery of desiccation tolerance in animals. This remarkable phenomenon to sustain 'life' in the absence of water can be revived upon return of hydrating conditions. Today, coping with climate change-related factors, especially temperature-humidity imbalance, is a global challenge. Under such adverse circumstances, desiccation tolerance remains a prime mechanism of several plants and a few animals to escape the hostile consequences of fluctuating hydroperiodicity patterns in their habitats. Among small animals, insects have demonstrated impressive resilience to dehydration and thrive under physiological water deficits without compromising on revival and survival upon rehydration. The focus of this review is to compile research insights on insect desiccation tolerance, gathered over the past several decades from numerous laboratories worldwide working on different insect groups. We provide a comparative overview of species-specific behavioral changes, adjustments in physiological biochemistry and cellular and molecular mechanisms as few of the noteworthy desiccation-responsive survival kits in insects. Finally, we highlight the role of insects as potential mechanistic models in tracking global warming which will form the basis for translational research to mitigate periods of climatic uncertainty predicted for the future.

A trade-off between dry season survival longevity and wet season high net reproduction can explain the persistence of Anopheles mosquitoes

Background

Plasmodium falciparum malaria remains a leading cause of death in tropical regions of the world. Despite efforts to reduce transmission, rebounds associated with the persistence of malaria vectors have remained a major impediment to local elimination. One area that remains poorly understood is how Anopheles populations survive long dry seasons to re-emerge following the onset of the rains.

Methods

We developed a suite of mathematical models to explore the impact of different dry-season mosquito survival strategies on the dynamics of vector populations. We fitted these models to an Anopheles population data set from Mali to estimate the model parameters and evaluate whether incorporating aestivation improved the fit of the model to the observed seasonal dynamics. We used the fitted models to explore the impact of intervention strategies that target aestivating mosquitoes in addition to targeting active mosquitoes and larvae.

Results

Including aestivation in the model significantly improved our ability to reproduce the observed seasonal dynamics of vector populations as judged by the deviance information criterion (DIC). Furthermore, such a model resulted in more biologically plausible active mosquito survival times (for A. coluzzii median wet season survival time of 10.9 days, 95% credible interval (CrI): 10.0–14.5 days in a model with aestivation versus 38.1 days, 95% CrI: 35.8–42.5 days in a model without aestivation; similar patterns were observed for A. arabiensis). Aestivation also generated enhanced persistence of the vector population over a wider range of both survival times and fecundity levels. Adding vector control interventions that target the aestivating mosquito population is shown to have the potential to enhance the impact of existing vector control.

Conclusions

Dry season survival attributes appear to drive vector population persistence and therefore have implications for vector control. Further research is therefore needed to better understand these mechanisms and to evaluate the additional benefit of vector control strategies that specifically target dormant mosquitoes.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3158-0) contains supplementary material, which is available to authorized users.