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Resistance to insecticides in Anopheles mosquitoes threatens the effectiveness of malaria control, but the genetics of resistance are only partially understood. We performed a large scale multi-country genome-wide association study of resistance to two widely used insecticides: deltamethrin and pirimiphos-methyl, using sequencing data from An. gambiae and An. coluzzii from ten locations in West Africa. Resistance was highly multi-genic, multi-allelic and variable between populations. While the strongest and most consistent association with deltamethrin resistance came from Cyp6aa1 , this was based on several independent copy number variants (CNVs) in An. coluzzii , and on a non-CNV haplotype in An. gambiae . For pirimiphos-methyl, signals included Ace1 , cytochrome P450s, glutathione S-transferases and the nAChR target site of neonicotinoid insecticides. The regions around Cyp9k1 and the Tep family of immune genes showed evidence of cross-resistance to both insecticides. These locally-varying, multi-allelic patterns highlight the challenges involved in genomic monitoring of resistance, and may form the basis for improved surveillance methods. Insecticide resistance in mosquitoes threatens the success of malaria control programmes. This study found that in different populations of a malaria mosquito species in West Africa, resistance is associated with different genes or different mutations in the same set of genes.

Vector population control using insecticides is a key element of current strategies to prevent malaria transmission in Africa. The introduction of effective insecticides, such as the organophosphate pirimiphos-methyl, is essential to overcome the recurrent emergence of resistance driven by the highly diverse Anopheles genomes. Here, we use a population genomic approach to investigate the basis of pirimiphos-methyl resistance in the major malaria vectors Anopheles gambiae and A . coluzzii . A combination of copy number variation and a single non-synonymous substitution in the acetylcholinesterase gene, Ace1 , provides the key resistance diagnostic in an A . coluzzii population from Côte d’Ivoire that we used for sequence-based association mapping, with replication in other West African populations. The Ace1 substitution and duplications occur on a unique resistance haplotype that evolved in A . gambiae and introgressed into A . coluzzii , and is now common in West Africa primarily due to selection imposed by other organophosphate or carbamate insecticides. Our findings highlight the predictive value of this complex resistance haplotype for phenotypic resistance and clarify its evolutionary history, providing tools to for molecular surveillance of the current and future effectiveness of pirimiphos-methyl based interventions.

Background Insecticides play a key role in rural farming; however, their over- or misuse has been linked with a negative impact on malaria vector control policies. This study was conducted amongst agricultural communities in Southern Côte d’Ivoire to identify which insecticides are used by local farmers and how it relates to the perception of farmers on malaria. Understanding the use of insecticides may help in designing awareness programme on mosquito control and pesticides management. Methods A questionnaire was administered to 1399 farming households across ten villages. Farmers were interviewed on their education, farming practices (e.g. crops cultivated, insecticides use), perception of malaria, and the different domestic strategies of mosquito control they use. Based on some pre-defined household assets, the socioeconomic status (SES) of each household was estimated. Statistical associations were calculated between different variables, showing significant risk factors. Results The educational level of farmers was significantly associated with their SES ( p  < 0.0001). Most of the householders (88.82%) identified mosquitoes as the principal cause of malaria, with good knowledge of malaria resulting as positively related to high educational level (OR = 2.04; 95%CI: 1.35, 3.10). The use of indoor chemical compounds was strongly associated to the SES of the households, their education level, their use of ITNs and insecticide in agricultural ( p  < 0.0001). Indoor application of pyrethroid insecticides was found to be widespread among farmers as well as the use of such insecticide for crops protection. Conclusion Our study shows that the education level remains the key factor influencing the use of insecticides by farmers and their awareness of malaria control. We suggest that better communication tailored to education level and including SES, controlled availability and access to chemical products, should be considered when designing campaigns on use of pesticides and vector borne disease control for local communities.

Malaria control efforts and elimination in Africa are being challenged by the development of resistance of parasites to antimalarial drugs and vectors to insecticides. We investigated whether the combination of long-lasting insecticidal mosquito nets (LLINs) with indoor residual spraying (IRS) or carbamate-treated plastic sheeting (CTPS) conferred enhanced protection against malaria and better management of pyrethroid-resistance in vectors than did LLINs alone. We did a cluster randomised controlled trial in 28 villages in southern Benin, west Africa. Inclusion criteria of the villages were moderate level of pyrethroid resistance in malaria vectors and minimum distance between villages of 2 km. We assessed four malaria vector control interventions: LLIN targeted coverage to pregnant women and children younger than 6 years (TLLIN, reference group), LLIN universal coverage of all sleeping units (ULLIN), TLLIN plus full coverage of carbamate-IRS applied every 8 months (TLLIN+IRS), and ULLIN plus full coverage of CTPS lined up to the upper part of the household walls (ULLIN+CTPS). The interventions were allocated to villages by a block randomisation on the basis of preliminary surveys and children of each village were randomly selected to participate with computer-generated numbers. The primary endpoint was the incidence density rate of Plasmodium falciparum clinical malaria in children younger than 6 years as was analysed by Poisson regression taking into account the effect of age and the sampling design with a generalised estimating equation approach. Clinical and parasitological information were obtained by active case detection of malaria episodes during 12 periods of 6 consecutive days scheduled at six weekly intervals and by cross-sectional surveys of asymptomatic plasmodial infections. Children or study investigators were not masked to study group. This study is registered with Current Controlled Trials, number ISRCTN07404145. Of 58 villages assessed, 28 were randomly assigned to intervention groups. 413–429 children were followed up in each intervention group for 18 months. The clinical incidence density of malaria was not reduced in the children from the ULLIN group (incidence density rate 0·95, 95% CI 0·67–1·36, p=0·79), nor in those from the TLLIN+IRS group (1·32, 0·90–1·93, p=0·15) or from the ULLIN+CTPS group (1·05, 0·75–1·48, p=0·77) compared with the reference group (TLLIN). The same trend was observed with the prevalence and parasite density of asymptomatic infections (non significant regression coefficients). No significant benefit for reducing malaria morbidity, infection, and transmission was reported when combining LLIN+IRS or LLIN+CTPS compared with a background of LLIN coverage. These findings are important for national malaria control programmes and should help the design of more cost-effective strategies for malaria control and elimination. Ministère Français des Affaires Etrangères et Européennes (FSP project 2006-22), Institut de Recherche pour le Développement, President's Malaria Initiative (PMI) of US Governement.

To keep ahead of the evolution of resistance to insecticides in mosquitoes, national malaria control programmes must make use of a range of insecticides, both old and new, while monitoring resistance mechanisms. The outdoor-biting malaria vector Anopheles arabiensis is of increasing concern for malaria transmission because it is apparently less susceptible to many indoor control interventions, yet knowledge of its mechanisms of resistance remains limited. Furthermore, comparatively little is known in general about resistance to non-pyrethroid insecticides such as pirimiphos-methyl (PM), which are crucial for effective control in the context of globally high resistance to pyrethroids. We performed a genome-wide association study to determine the molecular mechanisms of resistance to the pyrethroid deltamethrin (commonly used in bednets) and PM (widespread use for indoor spraying), in An . arabiensis from 2 regions in Tanzania. Genomic regions of positive selection in these populations were largely driven by copy number variants (CNVs) in gene families involved in metabolic resistance. We found evidence of a new gene cluster involved in resistance to PM, identifying a strong selective sweep tied to a CNV in the carboxylesterase genes Coeae2g - Coeae6g . Using complementary data from another malaria vector, An . coluzzii , in Ghana, we show that copy number at this locus is significantly associated with PM resistance. Similarly, for deltamethrin, resistance was strongly associated with a novel CNV allele in the Cyp6aa / Cyp6p cluster ( Cyp6aap _Dup33). Against this background of metabolic resistance, resistance caused by mutations in the insecticide target sites was very rare or absent. Mutations in the pyrethroid target site Vgsc were at very low frequency in Tanzania, yet combining these samples with 3 An . arabiensis individuals from West Africa revealed a startling evolutionary diversity, with up to 5 independent origins of Vgsc -995 mutations found within just 8 haplotypes. Thus, despite having been first recorded over 10 years ago, Vgsc resistance mutations in Tanzanian An . arabiensis have remained at stable low frequencies. Overall, our results provide a new copy number marker for monitoring resistance to PM in malaria mosquitoes, and reveal the complex picture of resistance patterns in An . arabiensis .

A vertically transmitted microsporidian, Microsporidia MB , with the ability to disrupt Plasmodium development was reported in Anopheles arabiensis from Kenya, East Africa. To demonstrate its range of incidence, archived DNA samples from 7575 Anopheles mosquitoes collected from Ghana were screened. MB prevalence was observed at 1.8%. An. gambiae s.s constituted 87% of positive mosquitoes while the remaining were from An. coluzzii . Both sibling species had similar positivity rates (24% and 19%; p  = 0.42) despite the significantly higher number of An. gambiae s.s analysed ( An. gambiae s.s = 487; An. coluzzii  = 94; p  = 0.0005). The microsporidian was also more prevalent in emerged adults from field-collected larvae than field-caught adults ( p  < 0.0001) suggestive of an efficient vertical transmission and/or horizontal transfer among larvae. This is the first report of Microsporidia MB in Anopheles mosquitoes in West Africa. It indicates possible widespread among malaria vector species and warrants investigations into the symbiont’s diversity across sub-Saharan Africa.

Background Malaria vector control methods involving the use of pyrethroids remain the strategies being used against malaria vectors in Ghana. These methods include the use of long-lasting insecticidal nets and indoor residual spraying in many areas in Ghana. However, there is evidence that pyrethroid resistance is widespread in many areas in Ghana. Synergists have been shown to be useful in inhibiting the enzymes that are responsible for the development of resistance and hence enhance the insecticide susceptibility of Anopheles gambiae sensu lato ( s.l. ) in many areas. The present study investigated the effect of piperonyl butoxide (PBO) on the susceptibility status of An. gambiae s.l. across some sentinel sites in Ghana. Methods Three to five day old An. gambiae s.l. reared from larvae were used in WHO susceptibility tube assays. Batches of 20–25 female adult An. gambiae s.l. were exposed simultaneously to the insecticide alone and to the PBO + insecticide. The knock down rate after 60 min and mortality at 24 h were recorded. Results Deltamethrin and permethrin resistance of An. gambiae s.l. was observed in all the sites in 2015 and 2016. The mortality after 24 h post exposure for deltamethrin ranged from 16.3% in Weija to 82.3% in Kade, whereas that for permethrin ranged from 3.8% in Gomoa Obuasi to 91.3% in Prestea. A significant increase in susceptibility to deltamethrin and less to permethrin was observed during both 2015 and 2016 years in most of the sites when An. gambiae s.l. mosquitoes were pre-exposed to PBO. Conclusion Findings from this study showed that the use of PBO significantly enhanced the susceptibility of An. gambiae s.l. mosquitoes in most of the sentinel sites. It is recommended that vector control strategies incorporating PBO as a synergist can be effective in killing mosquitoes in the presence of deltamethrin and permethrin resistance.

Urban malaria has become a challenge for most African countries due to urbanization, with increasing population sizes, overcrowding, and movement into cities from rural localities. The rapid expansion of cities with inappropriate water drainage systems, abundance of water storage habitats, coupled with recurrent flooding represents a concern for water-associated vector borne diseases, including malaria. This situation could threaten progress made towards malaria elimination in sub-Saharan countries, including Senegal, where urban malaria has presented as a threat to national elimination gains. To assess drivers of urban malaria in Senegal, a 5-month study was carried out from August to December 2019 in three major urban areas and hotspots for malaria incidence (Diourbel, Touba, and Kaolack) including the rainy season (August-October) and partly dry season (November–December). The aim was to characterize malaria vector larval habitats, vector dynamics across both seasons, and to identify the primary eco- environmental entomological factors contributing to observed urban malaria transmission. A total of 145 Anopheles larval habitats were found, mapped, and monitored monthly. This included 32 in Diourbel, 83 in Touba, and 30 in Kaolack. The number of larval habitats fluctuated seasonally, with a decrease during the dry season. In Diourbel, 22 of the 32 monitored larval habitats (68.75%) were dried out by December and considered temporary, while the remaining 10 (31.25%) were classified as permanent. In the city of Touba 28 (33.73%) were temporary habitats, and of those 57%, 71% and 100% dried up respectively by October, November, and December. However, 55 (66.27%) habitats were permanent water storage basins which persisted throughout the study. In Kaolack, 12 (40%) permanent and 18 (60%) temporary Anopheles larval habitats were found and monitored during the study. Three malaria vectors ( An . arabiensis , An . pharoensis and An . funestus s.l.) were found across the surveyed larval habitats, and An . arabiensis was found in all three cities and was the only species found in the city of Diourbel, while An . arabiensis , An . pharoensis , and An . funestus s.l. were detected in the cities of Touba and Kaolack. The spatiotemporal observations of immature malaria vectors in Senegal provide evidence of permanent productive malaria vector larval habitats year-round in three major urban centers in Senegal, which may be driving high urban malaria incidence. This study aimed to assess the presence and type of anopheline larvae habitats in urban areas. The preliminary data will better inform subsequent detailed additional studies and seasonally appropriate, cost-effective, and sustainable larval source management (LSM) strategies by the National Malaria Control Programme (NMCP).

Insecticide resistance in malaria vectors poses a significant threat to effective control of malaria vectors across sub-Saharan Africa. In Côte d'Ivoire, Anopheles gambiae s.l. exhibits considerable variability in species distribution and insecticide resistance levels across distinct ecological areas. This study reports on insecticide resistance profiles within An. gambiae complex as well as species composition dynamics in various ecological settings in Côte d'Ivoire. From July to October 2020, larval and adult mosquitoes were collected across three ecological settings (savannah, pre-forest and forest) in Côte d'Ivoire. Larvae were reared to adult stage for susceptibility bioassays. Diagnostic concentrations (DCs) applied against An. gambiae s.l. were deltamethrin 0.05%, permethrin 0.75% and pirimiphos methyl 0.25% using WHO susceptibility test kits. When increased survival to diagnostic concentrations (DCs) was observed, intensity bioassays were conducted using 5x and 10x DCs. In addition, synergist assays were performed at the DC level with pre-exposure to 4% piperonyl butoxide (PBO). Together with adults directly collected from the field, female samples from the bioassays outcome were speciated and resistance target site mechanisms (Kdr L1014F and Ace-1R G119S) were determined using PCR. Species distribution and insecticide resistance were analyzed across ecological areas. Significant variations in insecticide resistance phenotypes and mechanisms in An. gambiae s.l. were found across the three ecological areas in Côte d'Ivoire. Mortality rates, following pyrethroid exposure, were significantly higher in An. gambiae s.l. collected in the savannah zone compared to those collected from the forest zone (p < 0.05). An. gambiae was more predominant in the savannah area (98.8%, 95% confidence of interval (CI) [93.5-100.0]), whereas An. coluzzii dominated in the pre-forest (92.9%, 95% CI [88.9-95.8]) and forest zones (61.3%, 95% CI [53.4-68.9]). Such predominance of An. coluzzii was associated with high intensity of pyrethroid resistance in these areas. Overall, the allelic frequencies of the resistance mutations in An. gambiae were higher than those in An. coluzzii regardless of the area. Kdr L1014F frequency in the forest zone was 78.1% (95% CI [68.0-88.2]) in An. gambiae larvae, 51.8% (95% CI [33.3-70.4]) in adults, and 63.1% (95% CI [52.4-73.8]) in An. coluzzii larvae. Variations in species distribution and insecticide resistance in ecological areas in Côte d'Ivoire should be carefully considered when developing and implementing vector control strategies.

Background Insecticide resistance of Anopheles gambiae ( s.l. ) against public health insecticides is increasingly reported in Ghana and need to be closely monitored. This study investigated the intensity of insecticide resistance of An. gambiae ( s.l. ) found in a vegetable growing area in Accra, Ghana, where insecticides, herbicides and fertilizers are massively used for plant protection. The bioefficacy of long-lasting insecticidal nets (LLINs) currently distributed in the country was also assessed to delimitate the impact of the insecticide resistance intensity on the effectiveness of those nets. Methods Three- to five-day-old adult mosquitoes that emerged from collected larvae from Opeibea, Accra (Ghana), were assayed using CDC bottle and WHO tube intensity assays against different insecticides. The Vgsc-L1014F and ace-1 mutations within the population were also characterized using PCR methods. Furthermore, cone bioassays against different types of LLINs were conducted to evaluate the extent and impact of the resistance of An. gambiae ( s.l. ) from Opeibea. Results Anopheles gambiae ( s.l. ) from Opeibea were resistant to all the insecticides tested with very low mortality observed against organochlorine, carbamates and pyrethroid insecticides using WHO susceptibility tests at diagnostic doses during three consecutive years of monitoring. The average frequencies of Vgsc-1014F and ace-1 in the An. gambiae ( s.l. ) population tested were 0.99 and 0.76, respectively. The intensity assays using both CDC bottle and WHO tubes showed high resistance intensity to pyrethroids and carbamates with survivals at 10× the diagnostic doses of the insecticides tested. Only pirimiphos methyl recorded a low resistance intensity with 100% mortality at 5× the diagnostic dose. The bioefficacy of pyrethroid LLINs ranged from 2.2 to 16.2% mortality while the PBO LLIN, PermaNet ® 3.0, was 73%. Conclusions WHO susceptibility tests using the diagnostic doses described the susceptibility status of the mosquito colony while CDC bottle and WHO tube intensity assays showed varying degrees of resistance intensity. Although both methods are not directly comparable, the indication of the resistance intensity showed the alarming insecticide resistance intensity in Opeibea and its surroundings, which could have an operational impact on the efficacy of vector control tools and particularly on pyrethroid LLINs.