Spatial modelling for population replacement of mosquito vectors at continental scale

AbstractMalaria 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. To be deployed responsibly and successfully, proposed novel control strategies require detailed safety assessment. 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 as well as on some offshore islands. We explore transmission of the gene drive between the subspecies, 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. We find that given best current available knowledge on the subspecies’ life histories, 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 taking over within a decade. Our model demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. We thus show both the plausibility and importance of accounting for a wide range of mechanisms from regional to continental scales.

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Anopheles gambiae Genome Conservation as a Resource for Rational Gene Drive Target Site Selection

Insects ◽

10.3390/insects12020097 ◽

2021 ◽

Vol 12 (2) ◽

pp. 97

Author(s):

Nace Kranjc ◽

Andrea Crisanti ◽

Tony Nolan ◽

Federica Bernardini

Keyword(s):

Anopheles Gambiae ◽

Data Storage ◽

Genomic Variation ◽

Malaria Vectors ◽

Anopheles Coluzzii ◽

Structural Constraints ◽

Gene Drive ◽

Genetic Traits ◽

A Genome ◽

Insight Into

The increase in molecular tools for the genetic engineering of insect pests and disease vectors, such as Anopheles mosquitoes that transmit malaria, has led to an unprecedented investigation of the genomic landscape of these organisms. The understanding of genome variability in wild mosquito populations is of primary importance for vector control strategies. This is particularly the case for gene drive systems, which look to introduce genetic traits into a population by targeting specific genomic regions. Gene drive targets with functional or structural constraints are highly desirable as they are less likely to tolerate mutations that prevent targeting by the gene drive and consequent failure of the technology. In this study we describe a bioinformatic pipeline that allows the analysis of whole genome data for the identification of highly conserved regions that can point at potential functional or structural constraints. The analysis was conducted across the genomes of 22 insect species separated by more than hundred million years of evolution and includes the observed genomic variation within field caught samples of Anopheles gambiae and Anopheles coluzzii, the two most dominant malaria vectors. This study offers insight into the level of conservation at a genome-wide scale as well as at per base-pair resolution. The results of this analysis are gathered in a data storage system that allows for flexible extraction and bioinformatic manipulation. Furthermore, it represents a valuable resource that could provide insight into population structure and dynamics of the species in the complex and benefit the development and implementation of genetic strategies to tackle malaria.

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CLIPB10 is a Terminal Protease in the Regulatory Network That Controls Melanization in the African Malaria Mosquito Anopheles gambiae

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2020.585986 ◽

2021 ◽

Vol 10 ◽

Author(s):

Xin Zhang ◽

Miao Li ◽

Layla El Moussawi ◽

Sally Saab ◽

Shasha Zhang ◽

...

Keyword(s):

Anopheles Gambiae ◽

Serine Proteases ◽

Ex Vivo ◽

Protein A ◽

Tumor Formation ◽

Sub Saharan Africa ◽

Humoral Immune ◽

Wide Range ◽

Sub Saharan

Humoral immune responses in animals are often tightly controlled by regulated proteolysis. This proteolysis is exerted by extracellular protease cascades, whose activation culminates in the proteolytic cleavage of key immune proteins and enzymes. A model for such immune system regulation is the melanization reaction in insects, where the activation of prophenoxidase (proPO) leads to the rapid formation of eumelanin on the surface of foreign entities such as parasites, bacteria and fungi. ProPO activation is tightly regulated by a network of so-called clip domain serine proteases, their proteolytically inactive homologs, and their serpin inhibitors. In Anopheles gambiae, the major malaria vector in sub-Saharan Africa, manipulation of this protease network affects resistance to a wide range of microorganisms, as well as host survival. However, thus far, our understanding of the molecular make-up and regulation of the protease network in mosquitoes is limited. Here, we report the function of the clip domain serine protease CLIPB10 in this network, using a combination of genetic and biochemical assays. CLIPB10 knockdown partially reversed melanotic tumor formation induced by Serpin 2 silencing in the absence of infection. CLIPB10 was also partially required for the melanization of ookinete stages of the rodent malaria parasite Plasmodium berghei in a refractory mosquito genetic background. Recombinant serpin 2 protein, a key inhibitor of the proPO activation cascade in An. gambiae, formed a SDS-stable protein complex with activated recombinant CLIPB10, and efficiently inhibited CLIPB10 activity in vitro at a stoichiometry of 1.89:1. Recombinant activated CLIPB10 increased PO activity in Manduca sexta hemolymph ex vivo, and directly activated purified M. sexta proPO in vitro. Taken together, these data identify CLIPB10 as the second protease with prophenoloxidase-activating function in An. gambiae, in addition to the previously described CLIPB9, suggesting functional redundancy in the protease network that controls melanization. In addition, our data suggest that tissue melanization and humoral melanization of parasites are at least partially mediated by the same proteases.

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Continental-scale modelling of the effects of climatic and non-climatic disturbances on woody plant encroachment in the grasslands of Africa

10.5194/egusphere-egu21-7425 ◽

2021 ◽

Author(s):

Francesco D'Adamo ◽

Rebecca Spake ◽

James Bullock ◽

Booker Ogutu ◽

Jadunandan Dash ◽

...

Keyword(s):

Soil Moisture ◽

Woody Plant ◽

Population Change ◽

Sub Saharan Africa ◽

Woody Vegetation ◽

Woody Plant Encroachment ◽

Continental Scale ◽

Wide Range ◽

Sub Saharan ◽

Climatic Disturbances

<p>Grasslands cover ca. 7% (2,100,000 km2) of the African continent. They provide a wide range of ecosystem services (e.g., forage, water, recreational spaces, carbon sequestration), and host large wildlife communities. Despite their importance, African grasslands are reported to be suffering from degradation and, perhaps more worryingly, have received little consideration within international policies (e.g., United Nations Sustainable Development Goals). A key issue at present is widespread woody plant encroachment (WPE), which it is shifting African grassland from a grassy- to a (less palatable) woody-dominated biome. However, the way climatic (e.g., precipitation, soil moisture) and non-climatic disturbances (e.g., fire, population density) affect WPE is still poorly understood, particularly at large spatiotemporal scales. Here we identified grasslands in sub-Saharan Africa according to the ESA Climate Change Initiative (CCI) land cover product and use vegetation optical depth (VOD) from passive microwave observations as a proxy for woody vegetation change between 1992 and 2011. We then use independent climatic (precipitation and soil moisture) and non-climatic (burn intensity, population change) data to assess how both spatiotemporal variations and interactions between climatic and non-climatic drivers controlled rates of VOD increase during 1992-2011. We consider not only annual precipitation, soil moisture, fire, and population data, but also integrated and lagged precipitation data (both up to five years ahead of VOD) in these models. Preliminary results reveal a large overall increase in woody vegetation in sub-Saharan Africa grasslands as well as considerable spatiotemporal variation in VOD change that is not due to climatic factors alone.</p>

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Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Wellcome Open Research ◽

10.12688/wellcomeopenres.14765.1 ◽

2018 ◽

Vol 3 ◽

pp. 113 ◽

Cited By ~ 3

Author(s):

Claire L. Jeffries ◽

Gena G. Lawrence ◽

George Golovko ◽

Mojca Kristan ◽

James Orsborne ◽

...

Keyword(s):

Control Strategies ◽

Mosquito Species ◽

Amplicon Sequencing ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Endosymbiotic Bacterium ◽

Prevalence Rates ◽

Republic Of The Congo ◽

Sub Saharan

Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing endosymbiotic bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis of samples was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species ‘A’, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species ‘A’. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species ‘A’, but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were also shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.

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Novel Wolbachia strains in Anopheles malaria vectors from Sub-Saharan Africa

Wellcome Open Research ◽

10.12688/wellcomeopenres.14765.2 ◽

2018 ◽

Vol 3 ◽

pp. 113 ◽

Cited By ~ 27

Author(s):

Claire L. Jeffries ◽

Gena G. Lawrence ◽

George Golovko ◽

Mojca Kristan ◽

James Orsborne ◽

...

Keyword(s):

Control Strategies ◽

Mosquito Species ◽

Amplicon Sequencing ◽

Pathogen Transmission ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Prevalence Rates ◽

Population Replacement ◽

Republic Of The Congo ◽

Sub Saharan

Background: Wolbachia, a common insect endosymbiotic bacterium that can influence pathogen transmission and manipulate host reproduction, has historically been considered absent from the Anopheles (An.) genera, but has recently been found in An. gambiae s.l. populations in West Africa. As there are numerous Anopheles species that have the capacity to transmit malaria, we analysed a range of species across five malaria endemic countries to determine Wolbachia prevalence rates, characterise novel Wolbachia strains and determine any correlation between the presence of Plasmodium, Wolbachia and the competing bacterium Asaia. Methods: Anopheles adult mosquitoes were collected from five malaria-endemic countries: Guinea, Democratic Republic of the Congo (DRC), Ghana, Uganda and Madagascar, between 2013 and 2017. Molecular analysis was undertaken using quantitative PCR, Sanger sequencing, Wolbachia multilocus sequence typing (MLST) and high-throughput amplicon sequencing of the bacterial 16S rRNA gene. Results: Novel Wolbachia strains were discovered in five species: An. coluzzii, An. gambiae s.s., An. arabiensis, An. moucheti and An. species A, increasing the number of Anopheles species known to be naturally infected. Variable prevalence rates in different locations were observed and novel strains were phylogenetically diverse, clustering with Wolbachia supergroup B strains. We also provide evidence for resident strain variants within An. species A. Wolbachia is the dominant member of the microbiome in An. moucheti and An. species A but present at lower densities in An. coluzzii. Interestingly, no evidence of Wolbachia/Asaia co-infections was seen and Asaia infection densities were shown to be variable and location dependent. Conclusions: The important discovery of novel Wolbachia strains in Anopheles provides greater insight into the prevalence of resident Wolbachia strains in diverse malaria vectors. Novel Wolbachia strains (particularly high-density strains) are ideal candidate strains for transinfection to create stable infections in other Anopheles mosquito species, which could be used for population replacement or suppression control strategies.

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Determination of the discriminating concentration of chlorfenapyr (pyrrole) and Anopheles gambiae sensu lato susceptibility testing in preparation for distribution of Interceptor® G2 insecticide-treated nets

Malaria Journal ◽

10.1186/s12936-021-03847-3 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Richard M. Oxborough ◽

Aklilu Seyoum ◽

Yemane Yihdego ◽

Joseph Chabi ◽

Francis Wat’senga ◽

...

Keyword(s):

Anopheles Gambiae ◽

Large Scale ◽

Resistance Mechanisms ◽

Probit Analysis ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Insecticide Treated Nets ◽

Distributed Testing ◽

The Difference ◽

Sub Saharan

Abstract Background Following agricultural use and large-scale distribution of insecticide-treated nets (ITNs), malaria vector resistance to pyrethroids is widespread in sub-Saharan Africa. Interceptor® G2 is a new dual active ingredient (AI) ITN treated with alpha-cypermethrin and chlorfenapyr for the control of pyrethroid-resistant malaria vectors. In anticipation of these new nets being more widely distributed, testing was conducted to develop a chlorfenapyr susceptibility bioassay protocol and gather susceptibility information. Methods Bottle bioassay tests were conducted using five concentrations of chlorfenapyr at 12.5, 25, 50, 100, and 200 µg AI/bottle in 10 countries in sub-Saharan Africa using 13,639 wild-collected Anopheles gambiae sensu lato (s.l.) (56 vector populations per dose) and 4,494 pyrethroid-susceptible insectary mosquitoes from 8 colonized strains. In parallel, susceptibility tests were conducted using a provisional discriminating concentration of 100 µg AI/bottle in 16 countries using 23,422 wild-collected, pyrethroid-resistant An. gambiae s.l. (259 vector populations). Exposure time was 60 min, with mortality recorded at 24, 48 and 72 h after exposure. Results Median mortality rates (up to 72 h after exposure) of insectary colony mosquitoes was 100% at all five concentrations tested, but the lowest dose to kill all mosquitoes tested was 50 µg AI/bottle. The median 72-h mortality of wild An. gambiae s.l. in 10 countries was 71.5, 90.5, 96.5, 100, and 100% at concentrations of 12.5, 25, 50, 100, and 200 µg AI/bottle, respectively. Log-probit analysis of the five concentrations tested determined that the LC95 of wild An. gambiae s.l. was 67.9 µg AI/bottle (95% CI: 48.8–119.5). The discriminating concentration of 203.8 µg AI/bottle (95% CI: 146–359) was calculated by multiplying the LC95 by three. However, the difference in mortality between 100 and 200 µg AI/bottle was minimal and large-scale testing using 100 µg AI/bottle with wild An. gambiae s.l. in 16 countries showed that this concentration was generally suitable, with a median mortality rate of 100% at 72 h. Conclusions This study determined that 100 or 200 µg AI/bottle chlorfenapyr in bottle bioassays are suitable discriminating concentrations for monitoring susceptibility of wild An. gambiae s.l., using mortality recorded up to 72 h. Testing in 16 countries in sub-Saharan Africa demonstrated vector susceptibility to chlorfenapyr, including mosquitoes with multiple resistance mechanisms to pyrethroids.

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Evolution of the Pyrethroids Target-Site Resistance Mechanisms in Senegal: Early Stage of the Vgsc-1014F and Vgsc-1014S Allelic Frequencies Shift

Genes ◽

10.3390/genes12121948 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1948

Author(s):

Moussa Diallo ◽

Majidah Hamid-Adiamoh ◽

Ousmane Sy ◽

Pape Cheikh Sarr ◽

Jarra Manneh ◽

...

Keyword(s):

Insecticide Resistance ◽

Anopheles Gambiae ◽

Pyrethroid Resistance ◽

Early Stage ◽

Resistance Mechanisms ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Malaria Control Programme ◽

Anopheles Coluzzii ◽

Resistance Mutations

The evolution and spread of insecticide resistance mechanisms amongst malaria vectors across the sub-Saharan Africa threaten the effectiveness and sustainability of current insecticide-based vector control interventions. However, a successful insecticide resistance management plan relies strongly on evidence of historical and contemporary mechanisms circulating. This study aims to retrospectively determine the evolution and spread of pyrethroid resistance mechanisms among natural Anopheles gambiae s.l. populations in Senegal. Samples were randomly drawn from an existing mosquito sample, collected in 2013, 2017, and 2018 from 10 sentinel sites monitored by the Senegalese National Malaria Control Programme (NMCP). Molecular species of An. gambiae s.l. and the resistance mutations at the Voltage-gated Sodium Channel 1014 (Vgsc-1014) locus were characterised using PCR-based assays. The genetic diversity of the Vgsc gene was further analyzed by sequencing. The overall species composition revealed the predominance of Anopheles arabiensis (73.08%) followed by An. gambiae s.s. (14.48%), Anopheles coluzzii (10.94%) and Anopheles gambiae–coluzii hybrids (1.48%). Both Vgsc-1014F and Vgsc-1014S mutations were found in all studied populations with a spatial variation of allele frequencies from 3% to 90%; and 7% to 41%, respectively. The two mutations have been detected since 2013 across all the selected health districts, with Vgsc-L1014S frequency increasing over the years while Vgsc-1014F decreasing. At species level, the Vgsc-1014F and Vgsc-1014S alleles were more frequent amongst An. gambiae s.s. (70%) and An. arabiensis (20%). The Vgsc gene was found to be highly diversified with eight different haplotypes shared between Vgsc-1014F and Vgsc-1014S. The observed co-occurrence of Vgsc-1014F and Vgsc-1014S mutations suggest that pyrethroid resistance is becoming a widespread phenomenon amongst malaria vector populations, and the NMCP needs to address this issue to sustain the gain made in controlling malaria.

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Potential Roles of Environmental and Socio-Economic Factors in the Distribution of Insecticide Resistance in Anopheles gambiae sensu lato (Culicidae: Diptera) Across Togo, West Africa

Journal of Medical Entomology ◽

10.1093/jme/tjaa023 ◽

2020 ◽

Vol 57 (4) ◽

pp. 1168-1175

Author(s):

Koffi Mensah Ahadji-Dabla ◽

Daniel Romero-Alvarez ◽

Innocent Djègbè ◽

Adjovi Djifa Amoudji ◽

Georges Yawo Apétogbo ◽

...

Keyword(s):

Anopheles Gambiae ◽

Resistance Genes ◽

Control Strategies ◽

Pearson Correlation ◽

Correlation Coefficients ◽

World Health ◽

Tree Cover ◽

Malaria Vectors ◽

Anopheles Coluzzii ◽

Landscape Characteristics

Abstract Vector control strategies recommended by the World Health Organization are threatened by resistance of Anopheles mosquitoes to insecticides. Information on the distribution of resistant genotypes of malaria vectors is increasingly needed to address the problem. Ten years of published and unpublished data on malaria vector susceptibility/resistance and resistance genes have been collected across Togo. Relationships between the spatial distribution of resistance status and environmental, socio-economic, and landscape features were tested using randomization tests, and calculating Spearman rank and Pearson correlation coefficients between mosquito mortality and different gridded values. Anopheles gambiae sensu lato was resistant to DDT, pyrethroids, and the majority of carbamates and organophosphates. Three sibling species were found (i.e., An. gambiae, Anopheles coluzzii, and Anopheles arabiensis) with four resistance genes, including kdr (L1014F, L1014S, and N1575Y) and ace1 (G119S). The most frequent resistance gene was L1014F. Overall, no association was found between the susceptibility/resistance status and environmental features, suggesting that evolution of resistance may be most closely related to extreme selection from local insecticide use. Nevertheless, further research is necessary for firm conclusions about this lack of association, and the potential role of landscape characteristics such as presence of crops and percentage of tree cover.

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Ecological drivers of genetic connectivity for African malaria vectors Anopheles gambiae and An. arabiensis

Scientific Reports ◽

10.1038/s41598-020-76248-2 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Elizabeth Hemming-Schroeder ◽

Daibin Zhong ◽

Maxwell Machani ◽

Hoan Nguyen ◽

Sarah Thong ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Anopheles Gambiae ◽

Population Genetic ◽

Sub Saharan Africa ◽

Tree Cover ◽

Genetic Connectivity ◽

Malaria Vectors ◽

Western Kenya ◽

Sub Saharan

AbstractAnopheles gambiae and An. arabiensis are major malaria vectors in sub-Saharan Africa. Knowledge of how geographical factors drive the dispersal and gene flow of malaria vectors can help in combatting insecticide resistance spread and planning new vector control interventions. Here, we used a landscape genetics approach to investigate population relatedness and genetic connectivity of An. gambiae and An. arabiensis across Kenya and determined the changes in mosquito population genetic diversity after 20 years of intensive malaria control efforts. We found a significant reduction in genetic diversity in An. gambiae, but not in An. arabiensis as compared to prior to the 20-year period in western Kenya. Significant population structure among populations was found for both species. The most important ecological driver for dispersal and gene flow of An. gambiae and An. arabiensis was tree cover and cropland, respectively. These findings highlight that human induced environmental modifications may enhance genetic connectivity of malaria vectors.

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Chromosome-level genome assemblies of the malaria vectors Anopheles coluzzii and Anopheles arabiensis

GigaScience ◽

10.1093/gigascience/giab017 ◽

2021 ◽

Vol 10 (3) ◽

Cited By ~ 1

Author(s):

Anton Zamyatin ◽

Pavel Avdeyev ◽

Jiangtao Liang ◽

Atashi Sharma ◽

Chujia Chen ◽

...

Keyword(s):

Anopheles Arabiensis ◽

De Novo ◽

Mosquito Species ◽

Sub Saharan Africa ◽

Malaria Vectors ◽

Anopheles Coluzzii ◽

Reference Quality ◽

Sub Saharan ◽

Genome Assemblies ◽

Chromosome Level

Abstract Background Anopheles coluzzii and Anopheles arabiensis belong to the Anopheles gambiae complex and are among the major malaria vectors in sub-Saharan Africa. However, chromosome-level reference genome assemblies are still lacking for these medically important mosquito species. Findings In this study, we produced de novo chromosome-level genome assemblies for A. coluzzii and A. arabiensis using the long-read Oxford Nanopore sequencing technology and the Hi-C scaffolding approach. We obtained 273.4 and 256.8 Mb of the total assemblies for A. coluzzii and A. arabiensis, respectively. Each assembly consists of 3 chromosome-scale scaffolds (X, 2, 3), complete mitochondrion, and unordered contigs identified as autosomal pericentromeric DNA, X pericentromeric DNA, and Y sequences. Comparison of these assemblies with the existing assemblies for these species demonstrated that we obtained improved reference-quality genomes. The new assemblies allowed us to identify genomic coordinates for the breakpoint regions of fixed and polymorphic chromosomal inversions in A. coluzzii and A. arabiensis. Conclusion The new chromosome-level assemblies will facilitate functional and population genomic studies in A. coluzzii and A. arabiensis. The presented assembly pipeline will accelerate progress toward creating high-quality genome references for other disease vectors.

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