Malaria Infectious Reservoir and Genomics: in search of elusive malaria parasites in the dry season – MIRaGe
MIRAGE - Malaria Infectious Reservoir and Genomics
I designed a longitudinal study in The Gambia that included a cohort of 42 volunteers with chronic malarial infections over the dry season. A total of 435 blood samples were collected, including time series of monthly samples from the same volunteers over a 6-month period. This dataset represents a unique opportunity to address novel questions about the parasite biology.
This proposal targets a big hurdle in this endeavour: Plasmodium falciparum asymptomatic infections, the hidden part of the malaria iceberg.
In Project 1, using parasite whole genome sequences collected all year round, we will test the hypothesis that the dry season induces a bottleneck on the parasite genetic diversity. <br /><br />In Project 2, we will address the question whether the parasite is able to sense its environment and adapt to it. <br />More specifically, in Project 2a, we will measure the Parasite Multiplication Rate (PMR) in isolates from the dry and wet seasons. <br />In Project 2b, we will characterise the transcriptome of these isolates with single-cell RNA-seq. I hypothesize that some parasites enter a dormancy-like state during the dry season, in other words reducing their PMR via transcriptomal modifications.<br /><br />In Project 3, we will test the hypothesis that P. falciparum establishes a chronic infection via regular switching of variant surface antigens (VSA), particularly the var gene family. It will involve qRT-PCR techniques as well as flow cytometry to determine the specificity of the immune response against VSAs.<br /><br />Overall, the MIRAGE project opens a new door in the malaria research field and has the potential to make key discoveries for guiding malaria eradication.
Project1: Genotyping and whole genome sequencing of Plasmodium falciparum
Project2: RNAseq of Plasmodium falciparum
Project 3: FACS and qRT-PCR
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Project 1 : Identifying P. falciparum alleles under selection during the dry season (PhD project of Marc-Antoine Guéry)
Prior to this ANR, we collected ~500 blood samples from a cohort in The Gambia. All Plasmodium falciparum positive blood samples were genotyped at the Sanger Institute.
The goal of Marc-Antoine’s PhD, using this dataset, is to characterise the P. falciparum genetic diversity in the dry and in the wet season. So far we have shown that the average Identity By Descent (IBD) is higher between samples collected from the wet season and the following dry season. However the genetic diversity is ‘reshuffled’ at the following wet season, due to an increase in transmission. Also, we measured the average duration of a P. falciparum infection, with the longest one being over 1.5 years.
Project 2: Can P. falciparum sense its environment and adapt to it via transcriptional regulation? (PhD project of Prince Nyarko)
The goal is to characterize the P. falciparum transcriptome from isolates derived from asymptomatic infections collected in the dry and wet season. The main challenge is the low parasitaemia in such samples. We developed a novel protocol using Streptolysin O and a cell sorter to enrich the parasitaemia. Using the SMARTseq_v4 kit (Takara) and Illumina HiSeq, we successfully sequenced 16 parasite transcriptomes in duplicate/triplicates. Data analysis is ongoing.
Project 3: Can antigenic variation explain chronic infections?
This project will start with a new PhD student in Sep 2021.
No major breakthrough yet, but stay tuned for more in formation.
One publication submitted
A major challenge for any malaria elimination campaign is Plasmodium falciparum asymptomatic infections, the hidden infectious reservoir. Nevertheless, these infections can provide useful information on the host-pathogen interactions over an extended period of time. Here, I want to understand how P. falciparum parasites can survive in chronic infections over the 6-month long dry season, using an already available collection of blood samples from a cohort of asymptomatic volunteers in The Gambia. With whole genome sequencing, we will identify parasite alleles under selection during the dry season population bottleneck. With single-cell RNA-seq, we will explore how the parasite senses its environment and adapt to it. With qPCR and flow cytometry, we will finally test the central dogma that antigenic variation is at the basis of a chronic infection. This proposal will greatly advance our understanding of the parasite, host and vector interactions, and could reveal key molecular drivers of asymptomatic infections, a critical step to enable the eradication of malaria.
Project coordination
Antoine Claessens (Dynamique des interactions membranaires normales et pathologiques)
The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.
Partner
DIMNP Dynamique des interactions membranaires normales et pathologiques
Help of the ANR 446,037 euros
Beginning and duration of the scientific project:
November 2018
- 48 Months
