Title: Plasmodium Falciparum anti-malaria drug resistance in The Gambia: Identification of potential genetic markers by retrospective whole genome approaches
Funder: Medical Research Council

Abstract: The project aims at characterizing genetic mechanisms of antimalarial drug resistance in a West African population by adopting an innovative retrospective genomic approach to produce data on genome-wide signatures of selection from drugs and their association with parasite response to current artemisinin-based antimalarials. The major scientific goal will be achieved by combining epidemiology, innovative parasite genomic and phenotyping technologies to identify novel genetic markers that can be developed into tools for surveillance and containment of antimalarial drug resistance, via the following specific research objectives; 1. To characterize patterns of genomic variation prior to and since the introduction of artemisinin-based combination therapies (ACTs). The selection of genetic loci enabling adaptation to drug resistance would increase their frequency over time as they are under directional selection. Genome wide microsatellite analysis and sequencing for nucleotide polymorphisms in archived samples collected between 2003 and 2013 will employ Bioinformatic and statistical methods to determine the evolution of infection complexity and selective sweeps following the implementation of ACTs. Candidate markers identified will be further studied in current natural infections. 2. To identify possible 'hotspots' of drug resistance and transmission. Hypothetically, the prevalence of drug resistant parasite genotypes will vary between communities with intensity of transmission and access to drugs. Communities in The Gambia with varying prevalence of candidate markers of resistance identified from retrospective surveys will be identified by analyzing samples collected within the ongoing program grant entitled 'Dynamics of malaria transmission and determinants of heterogeneity'. Infected samples will be genotyped for candidate drug resistance markers identified by retrospective analysis (objective 1). Two communities, one with high and the other with low prevalence of resistant genotypes will be compared for ex vivo and in vivo parasite drug sensitivity. 3. To determine the association between predicted genetic markers, ex vivo drug sensitivities and gametocyte conversion rates. It is expected that parasites from communities with higher prevalence of candidate drug resistance markers will have reduced ex vivo sensitivity to drugs. Parasite isolates from study villages identified in objective 2, will be tested against artemisinin and partner antimalarials following recent protocols that can distinguish the effect of these drugs on early developmental blood stages. Each isolate will also be analysed for gametocyte production to determine the fitness cost to resistant genotypes. Recurrent infections within 42 days of treatment will also be analysed for phenotypic and genotypic adaptation to drugs. Characterized phenotypes (susceptible/resistant) will undergo genome sequencing and association analysis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION