Integration of malaria molecular surveillance in Rwanda

Malaria molecular surveillance (MMS) has a significant role in facilitating the national malaria control programs (NMCPs) to implement evidence-based control interventions towards its elimination however, molecular technology is limited to research. Many malaria endemic areas are still using epidemiological approaches like therapeutic efficacy studies (TES), which are time and resource consuming, to monitor antimalarial resistance. Therefore, there is a need for Malaria surveillance tools that are feasible and cost effective. Rwanda has done a lot of effort to reduce malaria morbidity and mortality, however challenges are hindering the sustainability of achievements already made. The 3 main challenges are: 1) emergence of artemisinin drug resistant markers associated with the delayed Plasmodium falciparum (P. Falciparum) clearance, 2) spread of P. Falciparum parasites carrying deletions of histidine rich protein genes 2 and 3 (pfhrp2 and pfhrp3), which affects HRP 2/3 Rapid Diagnostic Testing resulting in false negative results. 3) Heterogeneous transmission intensity. In Rwanda TES are used for surveillance which is not effective in promptly detecting emerging challenges due to the time-consuming process of patient recruitment therefore we intend to replace TES with implementing molecular surveillance.

This PhD project intends to integrate a molecular surveillance tool (Pf Ampliseq assay) that will generate information to guide and support the NMCP to better timely investigate and identify any of the above challenges. Pf AmpliSeq was designed at ITM in the malariology unit. It is a targeted NGS-assay that combines a specifically designed barcode for the target country, 14 full-length resistance associated genes, hrp2 and hrp3, and a ama1 microhaplotype region. Pf AmpliSeq applies a multiplex PCR to simultaneously amplify a high number of targets in a rapid procedure, and allows overlapping amplicons to cover large genes. The assay is multifunctional as it serves multiple ‘use cases’, and is adaptable to different settings at a lower cost compared to Whole Genome Sequencing (WGS). With Pf Ampliseq, this project will entail 4 studies: 1) to investigate the allele frequencies of the 192 SNP barcode for sufficient in-country resolution. 2) To identify the frequency of ART and partner drug resistance markers, monitor their emergence and predict the spread, moreover, assess their association with delayed parasite clearance rates to inform treatment policy. 3) Measure the frequency of pfhrp2/3 deletions in the pf populations in Rwanda to inform case management strategies. 4) Describe genetic diversity and parasite population structure in areas of low and high transmission in the country to measure gene flow and connectivity between areas to inform transmission dynamics and the control strategies. The objectives of this project are aligned well with the plans of the NMCP. Therefore, a close collaboration will be done between different institutions and ITM for the successful accomplishment of this project.