Abstract Accurately targeting and measuring the impact of malaria control interventions is challenging. It is difficult and expensive to measure impact accurately with traditional surveillance metrics such as parasite prevalence. More complex assessments, such as the impact of importation on local transmission, can be even more difficult to estimate. Finally, additional information that may be relevant to guide policy is not routinely collected, such as whether the parasite population shows signs of immune evasion in the setting of widespread vaccine rollout or whether commonly used rapid diagnostic tests (RDTs) continue to be appropriate to diagnose malaria. These gaps may be mitigated effectively with the integration of molecular tools into routine surveillance. Malaria molecular surveillance can evaluate parasite DNA and/or human antibodies present in easily collected biological samples. However, these molecular data are underutilized because there is limited evidence systematically linking molecular metrics to disease burden. We will generate molecular data in conjunction with high-quality incidence data from 42 sites across Uganda and yearly prevalence data from cross-sectional surveys. We will use these data to identify a parsimonious set of metrics to estimate disease burden and characterize transmission. We will also generate data on the presence of HRP2/3 deletions in P. falciparum and prevalence of non-falciparum malaria species, which impact whether currently used HRP2- based diagnostics are appropriate. Leveraging samples and data generated in the other components of this ICEMR project, we will simultaneously generate molecular metrics for multiple aims using a multiplex amplicon panel to genotype parasite infections, and use a multiplexed serologic assay to evaluate IgG responses to multiple P. falciparum antigens. We will analyze these data to achieve the following aims in the setting of ongoing, varied malaria control interventions: 1) to characterize changes in the host antibody response and parasite genetics in response to varied malaria control interventions. We hypothesize that molecular metrics will provide more accurate estimates of changes in disease burden than changes in parasite prevalence and that the selective pressure of the RTS,S vaccine and other immunologic interventions will result in an increase in the proportion of P. falciparum with vaccine-unmatched CSP haplotypes; 2) to evaluate whether the current diagnostic strategy in Uganda is appropriate by surveilling for HRP2/3 deletion and non-falciparum malaria parasite infections. We hypothesize that the emergence of HRP2/3 deletions will increase over time and first occur in northern Uganda, due to spread of parasites from the Horn of Africa, and that the proportion of malaria infections that contain non-falciparum species will be higher in areas of low or declining transmission compared to areas of high or stable transmission; and 3) to evaluate the contribution of...