Population genetic structure of the malaria vector Anopheles funestus, in a recently re-colonized area of the Senegal River basin and human-induced environmental changes

Distribution and insecticide resistance profile of the major malaria vector Anopheles funestus group across the African continent

There has been significant progress in malaria control in the last 2 decades, with a decline in mortality and morbidity. However, these gains are jeopardised by insecticide resistance, which negatively impacts the core interventions, such as insecticide-treated nets (ITN) and indoor residual spraying (IRS). While most malaria control and research efforts are still focused on Anopheles gambiae complex mosquitoes, Anopheles funestus remains an important vector in many countries and, in some cases, contributes to most of the local transmission. As countries move towards malaria elimination, it is important to ensure that all dominant vector species, including An. funestus, an important vector in some countries, are targeted. The objective of this review is to compile and discuss information related to A. funestus populations' resistance to insecticides and the mechanisms involved across Africa, emphasising the sibling species and their resistance profiles in relation to malaria elimination goals. Data on insecticide resistance in An. funestus malaria vectors in Africa were extracted from published studies. Online bibliographic databases, including Google Scholar and PubMed, were used to search for relevant studies. Articles published between 2000 and May 2023 reporting resistance of An. funestus to insecticides and associated mechanisms were included. Those reporting only bionomics were excluded. Spatial variation in species distribution and resistance to insecticides was recorded from 174 articles that met the selection criteria. It was found that An. funestus was increasingly resistant to the four classes of insecticides recommended by the World Health Organisation for malaria vector control; however, this varied by country. Insecticide resistance appears to reduce the effectiveness of vector control methods, particularly IRS and ITN. Biochemical resistance due to detoxification enzymes (P450s and glutathione-S-transferases [GSTs]) in An. funestus was widely recorded. However, An. funestus in Africa remains susceptible to other insecticide classes, such as organophosphates and neonicotinoids. This review highlights the increasing insecticide resistance of An. funestus mosquitoes, which are important malaria vectors in Africa, posing a significant challenge to malaria control efforts. While An. funestus has shown resistance to the recommended insecticide classes, notably pyrethroids and, in some cases, organochlorides and carbamates, it remains susceptible to other classes of insecticides such as organophosphates and neonicotinoids, providing potential alternative options for vector control strategies. The study underscores the need for targeted interventions that consider the population structure and geographical distribution of An. funestus, including its sibling species and their insecticide resistance profiles, to effectively achieve malaria elimination goals.

Fine-scale spatial distribution of deltamethrin resistance and population structure of Anopheles funestus and Anopheles arabiensis populations in Southern Mozambique

BACKGROUND

Insecticide resistance in malaria vectors can be spatially highly heterogeneous, yet population structure analyses frequently find relatively high levels of gene flow among mosquito populations. Few studies have contemporaneously assessed phenotypic, genotypic and population structure analysis on mosquito populations and none at fine geographical scales. In this study, genetic diversity, population structure, and insecticide resistance profiles of Anopheles funestus and Anopheles arabiensis were examined across mosquito populations from and within neighbouring villages.

METHODS

Mosquitoes were collected from 11 towns in southern Mozambique, as well as from different neighbourhoods within the town of Palmeira, during the peak malaria transmission season in 2016. CDC bottle bioassay and PCR assays were performed with Anopheles mosquitoes at each site to determine phenotypic and molecular insecticide resistance profiles, respectively. Microsatellite analysis was conducted on a subsample of mosquitoes to estimate genetic diversity and population structure.

RESULTS

Phenotypic insecticide resistance to deltamethrin was observed in An. funestus sensu stricto (s.s.) throughout the area, though a high level of mortality variation was seen. However, 98% of An. funestus s.s. were CYP6P9a homozygous resistant. An. arabiensis was phenotypically susceptible to deltamethrin and 99% were kdr homozygous susceptible. Both Anopheles species exhibited high allelic richness and heterozygosity. Significant deviations from Hardy-Weinberg equilibrium were observed, and high linkage disequilibrium was seen for An. funestus s.s., supporting population subdivision. However, the FST values were low for both anophelines (- 0.00457 to 0.04213), Nm values were high (9.4-71.8 migrants per generation), AMOVA results showed almost 100% genetic variation among and within individuals, and Structure analysis showed no clustering of An. funestus s.s. and An. arabiensis populations. These results suggest high gene flow among mosquito populations.

CONCLUSION

Despite a relatively high level of phenotypic variation in the An. funestus population, molecular analysis shows the population is admixed. These data indicate that CYP6P9a resistance markers do not capture all phenotypic variation in the area, but also that resistance genes of high impact are likely to easily spread in the area. Conversely, other strategies, such as transgenic mosquito release programmes will likely not face challenges in this locality.

Genetic Diversity and Population Structure of Anopheles funestus in Western Kenya Based on Mitochondrial DNA Marker COII

The mitochondrial marker, COII, was employed to assess the genetic structure and diversity of Anopheles funestus, a very important malaria vector in Africa that adapt and colonize different ecological niches in western Kenya. Mosquitoes were collected using mechanical aspirators in four areas (Bungoma, Port Victoria, Kombewa, and Migori) in western Kenya. Following morphological identification, PCR was used to confirm the species. The COII gene was amplified, sequenced, and analyzed to determine genetic diversity and population structure. A total of 126 (Port Victoria-38, Migori-38, Bungoma-22, and Kombewa-28) sequences of COII were used for population genetic analysis. Anopheles funestus had a high haplotype diversity (Hd = 0.97 to 0.98) but low nucleotide diversity (Π = 0.004 to 0.005). The neutrality test revealed negative Tajima's D and Fs values indicating an excess of low-frequency variation. This could be attributed to either population expansion or negative selection pressure across all the populations. No genetic or structural differentiation (Fst = -0.01) and a high level of gene flow (Gamma St, Nm = 17.99 to 35.22) were observed among the populations. Population expansion suggests the high adaptability of this species to various ecological requirements, hence sustaining its vectorial capacity and malaria transmission.

Spatial statistical and environmental correlation analyses on vector density, vector infection index and Japanese encephalitis cases at the village and pigsty levels in Liyi County, Shanxi Province, China

Background

In the eco-epidemiological context of Japanese encephalitis (JE), geo-environmental features influence the spatial spread of the vector (Culex tritaeniorhynchus, Giles 1901) density, vector infection, and JE cases.

Methods

In Liyi County, Shanxi Province, China, the spatial autocorrelation of mosquito vector density, vector infection indices, and JE cases were investigated at the pigsty and village scales. The map and Enhanced Thematic Mapper (ETM) remote sensing databases on township JE cases and geo-environmental features were combined in a Geographic Information System (GIS), and the connections among these variables were analyzed with regression and spatial analyses.

Results

At the pigsty level, the vector density but not the infection index of the vector was spatially autocorrelated. For the pigsty vector density, the cotton field area was positively related, whereas the road length and the distance between pigsties and gullies were negatively related. In addition, the vector infection index was correlated with the pigsty vector density (PVD) and the number of pigs. At the village level, the vector density, vector infection index, and number of JE cases were not spatially autocorrelated. In the study area, the geo-environmental features, vector density, vector infection index, and JE case number comprised the Geo-Environment-Vector-JE (GEVJ) intercorrelation net system. In this system, pig abundance and cotton area were positive factors influencing the vector density first. Second, the infection index was primarily influenced by the vector density. Lastly, the JE case number was determined by the vector infection index and the wheat area.

Conclusions

This study provided quantitative associations among geo-environmental features, vectors, and the incidence of JE in study sties, one typical northern Chinese JE epidemiological area without rice cultivation. The results highlighted the importance of using a diverse range of environmental management methods to control mosquito disease vectors and provided useful information for improving the control of vector mosquitoes and reducing the incidence of JE in the northern Chinese agricultural context.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05305-8.

Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers

BACKGROUND

The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand.

METHODS

Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20 years ago.

RESULTS

The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection.

CONCLUSIONS

This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers.

A differential expression of pyrethroid resistance genes in the malaria vector Anopheles funestus across Uganda is associated with patterns of gene flow

BACKGROUND

Insecticide resistance is challenging the effectiveness of insecticide-based control interventions to reduce malaria burden in Africa. Understanding the molecular basis of insecticides resistance and patterns of gene flow in major malaria vectors such as Anopheles funestus are important steps for designing effective resistance management strategies. Here, we investigated the association between patterns of genetic structure and expression profiles of genes involved in the pyrethroid resistance in An. funestus across Uganda and neighboring Kenya.

METHODS

Blood-fed mosquitoes An. funestus were collected across the four localities in Uganda and neighboring Kenya. A Microarray-based genome-wide transcription analysis was performed to identify the set of genes associated with permethrin resistance. 17 microsatellites markers were genotyped and used to establish patterns of genetic differentiation.

RESULTS

Microarray-based genome-wide transcription profiling of pyrethroid resistance in four locations across Uganda (Arua, Bulambuli, Lira, and Tororo) and Kenya (Kisumu) revealed that resistance was mainly driven by metabolic resistance. The most commonly up-regulated genes in pyrethroid resistance mosquitoes include cytochrome P450s (CYP9K1, CYP6M7, CYP4H18, CYP4H17, CYP4C36). However, expression levels of key genes vary geographically such as the P450 CYP6M7 [Fold-change (FC) = 115.8 (Arua) vs 24.05 (Tororo) and 16.9 (Kisumu)]. In addition, several genes from other families were also over-expressed including Glutathione S-transferases (GSTs), carboxylesterases, trypsin, glycogenin, and nucleotide binding protein which probably contribute to insecticide resistance across Uganda and Kenya. Genotyping of 17 microsatellite loci in the five locations provided evidence that a geographical shift in the resistance mechanisms could be associated with patterns of population structure throughout East Africa. Genetic and population structure analyses indicated significant genetic differentiation between Arua and other localities (FST>0.03) and revealed a barrier to gene flow between Arua and other areas, possibly associated with Rift Valley.

CONCLUSION

The correlation between patterns of genetic structure and variation in gene expression could be used to inform future interventions especially as new insecticides are gradually introduced.

Genetic differentiation and population structure of Anopheles funestus from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe

Background

Anopheles funestus (s.s.) is a primary vector of the malaria parasite Plasmodium falciparum in Africa, a human pathogen that causes almost half a million deaths each year. The population structure of An. funestus was examined in samples from Uganda and the southern African countries of Malawi, Mozambique, Zambia and Zimbabwe.

Methods

Twelve microsatellites were used to estimate the genetic diversity and differentiation of An. funestus from 13 representative locations across five countries. These were comprised of four sites from Uganda, three from Malawi and two each from Mozambique, Zambia and Zimbabwe.

Results

All loci were highly polymorphic across the populations with high allelic richness and heterozygosity. A high genetic diversity was observed with 2–19 alleles per locus and an average number of seven alleles. Overall, expected heterozygosity (H_e) ranged from 0.65 to 0.79. When samples were pooled three of the 12 microsatellite loci showed Hardy–Weinberg equilibrium. Unsupervised Bayesian clustering analysis of microsatellite data revealed two clusters with An. funestus samples from Mozambique, Uganda and Zambia falling into one group and Malawi and Zimbabwe into another. The overall genetic differentiation between the populations was moderate (F_ST = 0.116). Pairwise differentiation between the pairs was low but significant. A weak but significant correlation was established between genetic and geographical distance for most populations.

Conclusions

High genetic diversity revealed by the loci with low to moderate differentiation, identified two clusters among the An. funestus populations. Further research on the population dynamics of An. funestus in east and southern Africa is essential to understand the implications of this structuring and what effect it may have on the efficient implementation of mosquito vector control strategies.

16S Metagenomic Comparison of Plasmodium falciparum-Infected and Noninfected Anopheles gambiae and Anopheles funestus Microbiota from Senegal

In the context of the pre-elimination of malaria, biological control may provide an alternative or additional tool to current malaria control strategies. During their various stages of development, mosquitoes undergo subsequent changes in their associated microbiota, depending on their environment and nutritional status. Although Anopheles gambiae s.l. and Anopheles funestus are the two major malaria vectors in Senegal, the composition of their microbiota is not yet well known. In this study, we explored the microbiota of mosquitoes naturally infected or not by Plasmodium falciparum (Pf) using the 16S ribosomal RNA gene-based bacterial metagenomic approach. In both vector species, the microbiota was more diverse in Pf-infected samples than in the noninfected ones, although the total number of reads appeared to be higher in noninfected mosquitoes. Overall, the microbiota was different between the two vector species. Noteworthy, the bacterial microbiota was significantly different between Pf-positive and Pf-negative groups whatever the species, but was similar between individuals of the same infection status within a species. Overall, the phylum of Proteobacteria was the most predominant in both species, with bacteria of the genus Burkholderia outweighing the others in noninfected vectors. The presence of some specific bacterial species such as Asaia bogorensis, Enterobacter cloacae, Burkholderia fungorum, and Burkholderia cepacia was also observed in Pf-free samples only. These preliminary observations pave the way for further characterization of the mosquito microbiota to select promising bacterial candidates for potential use in an innovative approach to controlling malaria and overcoming the challenges to achieving a malaria-free world.

Comparison of Malaria Simulations Driven by Meteorological Observations and Reanalysis Products in Senegal

The analysis of the spatial and temporal variability of climate parameters is crucial to study the impact of climate-sensitive vector-borne diseases such as malaria. The use of malaria models is an alternative way of producing potential malaria historical data for Senegal due to the lack of reliable observations for malaria outbreaks over a long time period. Consequently, here we use the Liverpool Malaria Model (LMM), driven by different climatic datasets, in order to study and validate simulated malaria parameters over Senegal. The findings confirm that the risk of malaria transmission is mainly linked to climate variables such as rainfall and temperature as well as specific landscape characteristics. For the whole of Senegal, a lag of two months is generally observed between the peak of rainfall in August and the maximum number of reported malaria cases in October. The malaria transmission season usually takes place from September to November, corresponding to the second peak of temperature occurring in October. Observed malaria data from the Programme National de Lutte contre le Paludisme (PNLP, National Malaria control Programme in Senegal) and outputs from the meteorological data used in this study were compared. The malaria model outputs present some consistencies with observed malaria dynamics over Senegal, and further allow the exploration of simulations performed with reanalysis data sets over a longer time period. The simulated malaria risk significantly decreased during the 1970s and 1980s over Senegal. This result is consistent with the observed decrease of malaria vectors and malaria cases reported by field entomologists and clinicians in the literature. The main differences between model outputs and observations regard amplitude, but can be related not only to reanalysis deficiencies but also to other environmental and socio-economic factors that are not included in this mechanistic malaria model framework. The present study can be considered as a validation of the reliability of reanalysis to be used as inputs for the calculation of malaria parameters in the Sahel using dynamical malaria models.

The impact of long-lasting microbial larvicides in reducing malaria transmission and clinical malaria incidence: study protocol for a cluster randomized controlled trial

BACKGROUND

The massive scale-up of insecticide-treated nets (ITNs) and indoor residual spraying (IRS) has led to a substantial increase in malaria vector insecticide resistance as well as in increased outdoor transmission, both of which hamper the effectiveness and efficiency of ITN and IRS. Long-lasting microbial larvicide can be a cost-effective new supplemental intervention tool for malaria control.

METHODS/DESIGN

We will implement the long-lasting microbial larvicide intervention in 28 clusters in two counties in western Kenya. We will test FourStar controlled release larvicide (6 % by weight Bacillus thuringiensis israelensis and 1 % Bacillus sphaerius) by applying FourStar controlled release granule formulation, 90-day briquettes, and 180-day briquettes in different habitat types. The primary endpoint is clinical malaria incidence rate and the secondary endpoint is malaria vector abundance and transmission intensity. The intervention will be conducted as a two-step approach. First, we will conduct a four-cluster trial (two clusters per county, with one of the two clusters randomly assigned to the intervention arm) to optimize the larvicide application scheme. Second, we will conduct an open-label, cluster-randomized trial to evaluate the effectiveness and cost-effectiveness of the larvicide. Fourteen clusters in each county will be assigned to intervention (treatment) or no intervention (control) by a block randomization on the basis of clinical malaria incidence, vector density, and human population size per site. We will treat each treatment cluster with larvicide for three rounds at 4-month intervals, followed by no treatment for the following 8 months. Next, we will switch the control and treatment sites. The former control sites will receive three rounds of larvicide treatment at appropriate time intervals, and former treatment sites will receive no larvicide. We will monitor indoor and outdoor vector abundance using CO2-baited CDC light traps equipped with collection bottle rotators. Clinical malaria data will be aggregated from government-run malaria treatment centers.

DISCUSSION

Since current first-line vector intervention methods do not target outdoor transmission and will select for higher insecticide resistance, new methods beyond bed nets and IRS should be considered. Long-lasting microbial larviciding represents a promising new tool that can target both indoor and outdoor transmission and alleviate the problem of pyrethroid resistance. It also has the potential to diminish costs by reducing larvicide reapplications. If successful, it could revolutionize malaria vector control in Africa, just as long-lasting bed nets have done.

TRIAL REGISTRATION

U.S. National Institute of Health, study ID NCT02392832 . Registered on 3 February 2015.

Investigating molecular basis of lambda-cyhalothrin resistance in an Anopheles funestus population from Senegal

BACKGROUND

Anopheles funestus is one of the major malaria vectors in tropical Africa, notably in Senegal. The highly anthropophilic and endophilic behaviours of this mosquito make it a good target for vector control operations through the use of insecticide treated nets, long-lasting insecticide nets and indoor residual spraying. However, little is known about patterns of resistance to insecticides and the underlying resistance mechanisms in field populations of this vector in Senegal.

METHODS

Here, we assessed the susceptibility status of An. funestus populations from Gankette Balla, located in northern Senegal and investigated the potential resistance mechanisms.

RESULTS

WHO bioassays indicated that An. funestus is resistant to lambda-cyhalothrin 0.05 % (74.64 % mortality), DDT 4 % (83.36 % mortality) and deltamethrin 0.05 % (88.53 % mortality). Suspected resistance was observed to permethrin 0.75 % (91.19 % mortality), bendiocarb 0.1 % (94.13 % mortality) and dieldrin 4 % (96.41 % mortality). However, this population is fully susceptible to malathion 5 % (100 % mortality) and fenitrothion 1 % (100 % mortality). The microarray and qRT-PCR analysis indicated that the lambda-cyhalothrin resistance in Gankette Balla is conferred by metabolic resistance mechanisms under the probable control of cytochrome P450 genes among which CYP6M7 is the most overexpressed. The absence of overexpression of the P450 gene, CYP6P9a, indicates that the resistance mechanism in Senegal is different to that observed in southern Africa.

CONCLUSIONS

This study represents the first report of pyrethroid and DDT resistance in An. funestus from Senegal and shows that resistance to insecticides is not only confined to An. gambiae as previously thought. Therefore, urgent action should be taken to manage the resistance in this species to ensure the continued effectiveness of malaria control.

Microsatellite loci cross-species transferability in Aedes fluviatilis (Diptera:Culicidae): a cost-effective approach for population genetics studies

Background

Aedes fluviatilis is a neotropical mosquito species thought to be a potential vector of Yellow Fever viruses and can be infected with Plasmodium gallinaceum in laboratory. A better understanding of its genetic structure is very important to understand its epidemiologic potential and how it is responding to urbanization. The objective of this study was to survey the transferability of microsatellites loci developed for other Aedes to Ae. fluviatilis.

Findings

We tested in Ae. fluviatilis 40 pairs of primers known to flank microsatellite regions in Aedes aegypti, Aedes albopictus and Aedes caspius, and found eight loci that amplified consistently. The number of alleles per locus ranged from 2 to 15, and the expected heterozygosity ranged from 0.09 to 0.85.

Conclusions

We found that several microsatellite primers successfully transferred to Ae. fluviatilis. This finding opens avenues for cost-effective optimization of high-resolution population genetic tools.

Population genetic analysis and sub-structuring of Theileria parva in the northern and eastern parts of Zambia

BACKGROUND

Theileriosis, caused by Theileria parva, is an economically important disease in Africa. It is a major constraint to the development of the livestock industry in some parts of eastern, central and southern Africa. In Zambia, theileriosis causes losses of up to 10,000 cattle annually.

METHODS

Cattle blood samples were collected for genetic analysis of Theileria parva from Isoka and Petauke districts in Zambia. Microsatellite analysis was then performed on all Theileria parva positive samples for PCR using a panel of 9 microsatellite markers. Microsatellite data was analyzed using microsatellite toolkit, GenAlEx ver. 6, Fstat ver. 2.9.3.2, and LIAN computer softwares.

RESULTS

The combined percentage of positive samples in both districts determined by PCR using the p104 gene primers was 54.9% (95% CI: 46.7 - 63.1%, 78/142), while in each district, it was 44.8% (95% CI: 34.8 - 54.8%) and 76.1% (95% CI = 63.9 - 88.4%) for Isoka and Petauke districts, respectively. We analyzed the population genetic structure of Theileria parva from a total of 61 samples (33 from Isoka and 28 from Petauke) using a panel of 9 microsatellite markers encompassing the 4 chromosomes of Theileria parva. Wright's F index (FST = 0.178) showed significant differentiation between the Isoka and Petauke populations. Linkage disequilibrium was observed when populations from both districts were treated as a single population. When analyzed separately, linkage disequilibrium was observed in Kanyelele and Kalembe areas in Isoka district, Isoka district overall and in Petauke district. Petauke district had a higher multiplicity of infection than Isoka district.

CONCLUSION

Population genetic analyses of Theileria parva from Isoka and Petauke districts showed a low level of genotype exchange between the districts, but a high level of genetic diversity within each district population, implying genetic and geographic sub-structuring between the districts. The sub-structuring observed, along with the lack of panmixia in the populations, could have been due to low transmission levels at the time of sampling. However, the Isoka population was less diverse than the Petauke population.