PAMGEN: Genetic interactions between human populations and malaria parasites in different environmental settings across Africa

Project Leads

The Problem

Human populations in Africa possess extraordinary genetic diversity in the erythrocyte surface proteins known as glycophorins that are exploited as invasion receptors by the malaria parasite Plasmodium falciparum. The recent discovery of a large structural glycophorin variant that confers resistance to severe malaria in African children, together with the observation that parasite genes involved in erythrocyte invasion are also extremely diverse, suggests that an evolutionary arms race is going on. We seek to understand the genetic interactions between host and parasite invasion genes and how they are affected by the environment. With an African led team of scientists, this project is examining human, parasite and vector genomic data from 7 locations distributed across the continent, representing a wide range of ecological and epidemiological settings. We are focusing primarily on patterns of genetic diversity in parasite invasion genes, analysing how this varies according to (1) time (2) location (3) host genotype. This together with ecological and epidemiological information will allow for a deeper understanding of the heterogeneity of malaria across Africa. The project will engage communities and address ethical issues emerging from population genomic studies, and will help to build African research capacity in genomic data analysis.

Project Strategy

The research network hinges on the postulate that population-specific gene-environment interactions are key drivers of allelic variation in erythrocyte receptors – parasite ligands, their interactions and malaria outcomes. We are investigating this by leveraging advanced DNA sequencing technologies and computational/statistical analysis to achieve the following objectives:

1. Develop a comprehensive profile of human glycophorin receptor diversity across a gradient of malaria transmission in sub-Saharan Africa. This objective will allow us to determine the distribution of glycophorin polymorphisms and how they vary across 7 malaria endemic countries with high, moderate, and low malaria transmission. We are particularly focusing on infections of Plasmodium falciparum and Plasmodium vivax whose prevalence varies substantially in African populations. We will equally access archived data and genotype archived samples collected at the time malaria was highly prevalent.
2. Determine the correlation between human receptors and diversity of parasite ligands. Our current analysis of P. falciparum populations across sSA shows population substructure and differentiation at single nucleotide polymorphisms (SNPs) in invasion ligands and drug resistance genes. It is possible that parasite population stratification is driven by both human genetic variation at ligand receptors and environmental factors. Both DBL and RBL ligands families are present in all Plasmodium genomes already sequenced, indicating that they may not be absolute functional alternatives. Specific ligand receptor combinations may be selected in different endemic communities with environmental differences. Here, we will determine the association between alleles of parasite ligands and glycophorin receptors genotyped in objective 1. We will test if balancing selection on parasite ligands is driven by host-receptor variation. Parasite density, complexity and ligand diversity will be determined by NextGen amplicon sequencing assays at WTSI, MRCG and NHRC.
3. Collect background data on malaria vector diversity. While it is beyond the scope of the present study to examine parasite-vector or human-vector interactions in any detail, we wish to ensure that the data generated by this project are of maximal long-term value for malaria research, and therefore we consider it important to collect background data on malaria vector diversity at the same time as sampling the human and parasite populations. We will achieve this through integration with the Anopheles gambiae 1000 Genomes Project (Ag1000g) which is already sampling at multiple locations across Africa with plans to extend to other major African vector species within the timeframe of this study.
4. Training and technology transfer. We aim to increase the capacity for genomics data acquisition and analysis across PAMGEN.

Potential Impact

Explain what can be learned and the impact of (potential or current) findings from this project. Can also highlight

1. Characterise the diversity of erythrocyte invasion ligands in parasite population. We have projected to access ~200 parasite isolates from cross-sectional surveys and 300 clinical isolates over 3 years from each sites. We will determine ligand alleles and their frequencies in surveys and clinical isolates. The data will be combined with ligand sequences from genomes of 2200 isolates from 10 sSA countries collected between 2009 and 2014 in collaboration with the PDNA. These ligand sequence data will be analysed for balancing selection as previously described (Amambua-Ngwa et al, 2012). As the receptors for these samples will be genotyped, we will analyse the association between host-receptor and ligand alleles and the prevalence of combinations in clinical cases across sites. The outcome will be a comprehensive database of ligand-receptor combinations across sites. This may be explored to inform future erythrocytic vaccine design.
2. Compare temporal genomic variation in P. falciparum populations from high, moderate and low transmission regions. Our ongoing analysis of parasite genomes show that temporal variation and selection targets similar families of antigens, invasion ligands and drug resistance associated loci in the Gambia, Ghana and Mali. It is not known if such a temporal pattern is maintained across diverse endemic regions in sSA. Whole parasite genomes will be sequenced from 100 clinical cases per year for 3 years from each site, providing genomic data for 2,100 clinical isolates across all sites. They will be combined with 2,200 retrospective parasite genomes (2009-2014) to assay for temporal variance in parasite diversity in populations with differences in GYP receptor polymorphisms. The outcome will be signatures of local and temporal adaptation to different environments for 4300 parasite genomes. This may identify new immune and drug adaptation markers.
3. Determine the temporal evolution of Plasmodium vivax species. We will sequence 200 Plasmodium vivax isolates from Ethiopia and Madagascar collected over 3 years. This data will be combined with 200 available genomes from 2014 to assess temporal variation in ligand polymorphisms from these sites. We will also analyse for temporal trends in signatures of selection in parasites in these regions where there is co-transmission of falciparum and vivax malaria. The outcome will be 400 new P. Vivax genomes and markers of temporal evolution, which could be the result of adaption to interventions. The ligand-receptor combinations in vivax malaria will be determined for the first time.
4. Collect background data on malaria vector diversity. These data will provide an initial picture of the spatial and temporal diversity of vector populations across our study sites, and of major signals of recent selection. They will also provide a foundation for longer-term studies of whether there is clustering of parasite and vector sub-populations, and how variability across vector populations correlates with parasite genetic diversity and malaria transmission. This will be particularly interesting for study sites where both P. falciparum and P. vivax co-exist.
5. Training and technology transfer. Establishing NextGEN long read sequencing. We envisage rolling out minion sequencing across the network in subsequent projects.

Project Sites

A: Country
Gambia: Medical Research Council Unit The Gambia at LSHTM
Ghana: University of Ghana
Ethiopia: Addis Ababa University
Madagascar: Institut Pasteur de Madagascar
Mali: University of Science Technical and Technology of Bamako
Cameroon: University of Buea
Tanzania: National Institute for Medical Research (NIMR)

Non-African Collaborators:
United Kingdom: University of Oxford