Project: Genetic Profiling Of Drug Resistance And Population Structure Of Plasmodium Falciparum Using High-Throughput Next Generation Sequencing

Acronym	GRIPS-NGS (Reference Number: TMA2018CDF-2398)
Duration	01/01/2020 - 01/06/2022
Project Topic	Background: The emergence and spread of Plasmodium falciparum resistance presents major challenges for the control and elimination of malaria. Thus, molecular monitoring of drug resistance is assumed as an important undertaking in the detection and tracking of drug-resistant parasites. The recent advancement in next-generation sequencing (NGS) has facilitated the development of cost-effective high-throughput detection of resistance and the origin of parasite populations with different genetic backgrounds. This is relevant for monitoring antimalarial drug resistance and tracking geographic spread of parasite populations. The present study aims to leverage NGSbased sequencing approaches to determine molecular markers of resistance to both artemisinin and partner drugs, parasite genetic diversity and population structure in African settings. In addition, we will also generate evidence on the ex vivo susceptibility of antimalarial drugs. Methods: The samples will be collected from NMCP sentinel sites in Burkina Faso, DR Congo and Tanzania. The detection of molecular markers of drug resistance will be carried out using a high-throughput NGS platform (Illumina®-based technology) for targeted amplicon sequencing. Following multiplexing PCR amplification of the targeted sequences and indexing, pooled gene fragments will be sequenced using the Illumina Miseq® platform. To determine the geographical origin and spread of P. falciparum population to other regions, we will use SNPs barcode in the organellar genome. Photo-induced electron transfer real-time PCR (PET-PCR) assay will be used to detect plasmepsin 2-3 and pfmdr1 copy number of the P. falciparum. Ex vivo test will be performed using HRP-2 assay. Expected outcomes: The study will generate P. falciparum temporal genotyping data of molecular markers of resistance to artemisinin (Pfkelch 13), parasite background mutation (mdr2, fd, arps10, pfap2mu and pfubp1) and partner drugs (Pfmdr1, Pfcrt and Plasmepsin 2-3 copy numbers). The molecular evidence is critical to inform NMCPs, WHO and control strategies on the efficacy of ACTs as well as drugs used in chemoprevention strategies in the region. We will highlight the origin and spread of parasite population to track the geographical dispersal of the parasite populations. This is crucial to inform if there is dispersal of artemisinin-resistant strains to African settings. Furthermore, we will generate data on ex vivo sensitivity to antimalarial drugs. This is highly relevant in these settings as resistance against long-acting partner drugs is likely to accumulate due to post-treatment selection. Furthermore, the capacity building in NGS and bioinformatics will enhance local capacity and interactions among partner institutions in addressing relevant global health challenges.
Network	EDCTP2
Call	Career Development Fellowships 2018

Project partner

Number	Name	Role	Country
1	National Institute for Medical Research - Tanzania	Coordinator	Tanzania