Genomic surveillance of mosquito resistance to guide cost-effective insecticide policy in Rwanda

Introduction

Malaria remains a public health concern in Rwanda despite major reductions in incidence and mortality over the past decade. Vector control strategies, particularly bed nets used as physical protective barriers and pyrethroid and organophosphate products such as malathion and pirimiphos-methyl, an active ingredient in Actellic used for indoor residual spraying (IRS); it has performed well in controlling mosquito populations (1). Therefore, it can be used for IRS in areas with high pyrethroid resistance remain central to malaria prevention in high transmission zones (2). However, these interventions rely heavily on insecticides to kill mosquitoes. There is a crossover in the use of insecticides for both vector control and agricultural pest control. The resulting increasing insecticide resistance in Anopheles gambiae, the primary malaria vector in Rwanda, threatens the sustainability of current control gains and undermines progress toward malaria elimination. Evidence-based genomic surveillance integrated with essential climate variables is crucial to guide adaptive vector control policies. The link between research findings and policy implementation strategies remains weak. The effectiveness of malaria vector control in Rwanda is increasingly challenged by widespread pyrethroid resistance in An. gambiae populations. Where mosquitoes develop resistance, the insecticide in vector control interventions no longer causes mortality, leaving people at risk of infectious bites. Although bed nets and spray insecticides in households have significantly reduced malaria cases in Rwanda, ongoing dependence on pyrethroids or other insecticides without detailed resistance testing risks lowering their effectiveness (3). The study demonstrated substantial geographic variation in insecticide susceptibility across Rwanda, with resistance confirmed in multiple districts. Insecticide resistance in mosquitoes can be achieved through different genetic changes in the population. Depending on which mechanisms of resistance are present, different insecticidal products will have better health outcomes for the community. The PBO inhibits cytochrome P450 enzymes involved in insecticide detoxification; therefore, the improved mosquito mortality showed that P450-mediated metabolic resistance contributes to pyrethroid resistance. Phenotypic testing alone cannot identify the resistance mechanisms involved. The absence of routine genomic surveillance limits the ability to detect resistance-associated genetic markers across the country and anticipate resistance spread and on time. Without integrating genomic tools into national entomology surveillance routines, malaria control programs in Rwanda may continue to deploy suboptimal insecticides, leading to inefficient use of resources and the potential resurgence of malaria transmission. Addressing this is critical to sustain malaria control achievements and to inform climate- and resistance-adaptive vector management strategies. Figure 1 shows mosquito mortality rates from various sentinel sites in Rwanda, such as Bukora in the Kirehe district, Gahini in the Kayonza district, Gashora in the Bugesera district, Kajevuba in the Rulindo district, Mubuga in the Karongi district, Nyagasambu in the Rwamagana district, and Rwanza in the Musanze district, after being exposed to two widely used pyrethroid insecticides, permethrin (Perm_1X) and alphacypermethrin (Acyp_1X), between 2022 and 2023, both separately and in combination with the piperonyl butoxide (PBO) (4). The mortality rate from insecticides alone is consistently less than 80% at all sites, and in certain locations it ranges from 40 to 50%. This indicates significant pyrethroid resistance in An. gambiae populations. Because the resistance profile data align with the WHO recommendation to prioritize bed nets treated with PBO in high-resistance locations and not use it as a permanent solution. The findings have important implications for malaria control policy in Rwanda. Widespread pyrethroid resistance in An. gambiae populations pose a serious risk to the continued effectiveness of insecticide-treated mosquito nets, which remain the backbone of malaria prevention. Figure 2 indicates that insecticide resistance varies across different locations, emphasizing the need for village- or site-specific vector control interventions rather than using one insecticide for a nationwide malaria control approach. Evidence of metabolic resistance, as indicated after PBO exposure, supports the continued use of PBO-based bed nets in selected settings with high resistance. However, mosquitoes have an additional resistance mechanism that reduces the efficacy of bed nets treated with PBO. Relying on the WHO tube bioassay alone cannot support insecticide resistance management. The WHO tube assay can identify the presence of insecticide resistance at a specific site, but it cannot determine the resistance mechanism responsible for that resistance or predict how that resistance will be spread over time. In 2025, Munyakanage et al., showed that the pre-exposure of PBO to Anopheles gambiae renders partial restoration of susceptibility, suggesting cytochrome P450-mediated metabolic resistance, and mortality not reaching 100% indicated addition insecticide resistance mechanism that is not pyrethroid-targeted might be involved. To address these knowledge gaps, vector molecular surveillance should supplement the routine monitoring using the WHO tube assay. Tackling resistance markers and genes responsible for resistance would help in understanding how resistance spreads, identifying emerging resistance earlier, and supporting evidence for a site-specific intervention plan. Such information is needed because it can affect the efficacy of bed nets and insecticides in different ways. Therefore, vector molecular surveillance could strengthen decisions on insecticide rotation and selection of bed nets and prediction of emerging resistance.

This policy brief, aligned with H.E. President Paul Kagame, the African Union champion for domestic health financing during the 34th African Union Summit, emphasized that health investments should be assessed by their impact on service coverage and improved health outcomes rather than the amount spent. For instance, spraying insecticides inside households to kill mosquitoes may require an annual cost of approximately $2 million in a single district and up to $24 million when all target districts in Rwanda are included; the value of this investment should be measured by its effectiveness in reducing malaria transmission, reducing malaria cases and mortality, and protecting the population. Focusing on outcomes ensures that health resources are allocated to interventions that provide the greatest public health benefit and represent a cost-effective use of limited funds (5). Therefore, strengthening insecticide resistance monitoring and ensuring the targeted deployment of effective bed nets directly contribute to his vision by improving the efficiency of existing investments, reducing waste on ineffective interventions, and supporting evidence-based allocation of resources. Rwanda not only protects its population but also demonstrates leadership in advancing smarter health financing approaches in Africa.

Policy options and implications

• Pyrethroid resistance is widespread in Anopheles gambiae. WHO guidelines indicate that insecticides used in mosquito nets are becoming less effective in Rwanda (6), requiring urgent vector molecular surveillance and insecticide resistance management.
• Resistance levels vary significantly by district and ecological zone, and WHO guidelines recommend that surveillance must be stratified and context-specific, reflecting ecological differences.
• Combining PBO with common insecticides indicates that resistance is largely driven by metabolic mechanisms (Figure 1). WHO guidelines recommend investing in mosquito nets treated with PBO and using rotation of alternative non-pyrethroid insecticides.
• Non-metabolic resistance mechanisms such as kdr mutations (L1014F and L1014S), Ace-1 G119S mutation, N1575Y mutation, cuticular resistance including increased cuticle thickness or changes in cuticular hydrocarbon composition, behavioral resistance such as decreased or increased outdoor biting, changes in biting time, and avoidance of sprayed surfaces are probably present in some areas, and WHO guidelines recommend that resistance mechanisms be identified using a vector molecular surveillance approach.
• Lack of molecular confirmation limits precise resistance characterization, and for informed decision-making, the WHO guidelines recommend advanced molecular analyses.

Actionable recommendations: SMART approach-based

• Integrate molecular and genomic tools into routine national entomological surveillance. By 2027, integrating genomic tools, including polygenic risk scores (7) and amplicon sequencing panels like AgVampIR (8), might provide multiple resistance markers in mosquito populations to support early warning and proactive vector-control decision-making. The WHO supports routine entomological and insecticide-resistance surveillance using molecular and biochemical assays, emphasizing that accurate species identification and detection of resistance mechanisms require advanced molecular analysis (9). The Division of Malaria and Other Parasitic Diseases, under the Rwanda Biomedical Centre (RBC), should lead the integration and implementation of genomics tools.
• Vector-control interventions should be guided by local insecticide resistance profiles and mosquito ecology, whether mosquitoes bite indoors at night or outdoors at night. For the next malaria control intervention, use resistance profile data at the village level to select and rotate insecticides rather than implementing a single intervention everywhere. The WHO emphasizes that intervention should be based on village resistance profiles, including intensity and molecular mechanisms. The RBC should coordinate at the district, sector, and village levels for malaria control interventions.
• Expand insecticide resistance surveillance twice annually at sentinel sites. Conduct surveillance every six months at all sentinel sites to detect seasonal and emerging changes in resistance. The WHO recommends regular insecticide resistance monitoring, using the same methods each time and in different parts of the country, to inform effective vector control decisions. The RBC should coordinate surveillance across all sites.
• Prioritize bed nets with PBO or dual active-ingredient bed nets, which are costly and alternative insecticide in locations with high insecticide resistance. Scale up deployment of bed nets with PBO in the village where metabolic resistance is confirmed, and rotate non-pyrethroid insecticides where susceptibility allows, within two years, as recommended by the WHO. The Ministry of Health, through RBC, should prioritize the procurement and distribution of PBO-treated nets and establish an insecticide rotation schedule in collaboration with partners.
• Rwanda has two major malaria transmission seasons during long rains from March to May and during short rains from September to December, which influence mosquito breeding and malaria transmission. Biannual vector molecular surveillance would also facilitate the early detection of emerging resistance markers and provide timely evidence to guide insecticide selection, deployment of vector control interventions, and resistance management plans. Therefore, collecting mosquitoes before and after the main rainy seasons would allow the RBC to capture seasonal variations in mosquito abundance, insecticide exposure, and resistance levels. This approach aligns with WHO recommendations published in 2022 for routine and longitudinal insecticide resistance surveillance at sentinel sites to support evidence-based decision-making.
• Co-design pesticide regulations with the community, coordinated by the health and agriculture sectors. By 2027, establish a joint task force of community and institutional partners to monitor pesticide use. The WHO highlights the importance of cross-sectoral coordination, especially health-agriculture collaboration, to mitigate insecticide resistance in mosquito populations. Ministry of Health, under the RBC, should establish coordination with the Rwanda Agriculture and Animal Resources Development Board (RAB), RICA (Rwanda Inspectorate, Competition and Consumer Protection Authority), MINAGRI (Ministry of Agriculture and Animal Resources), the Rwanda Environment Management Authority (REMA), Rwanda FDA (Rwanda Food and Drugs Authority), Rwanda Revenue Authority (RRA), Rwanda Standards Board (RSB), and the University of Rwanda (UR).

Conclusion

Given the threat of increasing insecticide resistance, traditional vector control tools alone are insufficient to achieve malaria elimination. Insecticide selection and rotation should be informed by regular genomic surveillance of mosquitoes. To enhance pesticide stewardship, utilization, and safety. We need collaboration among public health, agricultural, regulatory, and community stakeholders.

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Footnotes

Edited by: José A. De Fuentes Vicente, University of Science and Arts of Chiapas, Mexico

Reviewed by: Arum Siwiendrayanti, Universitas Negeri Semarang, Indonesia