Genomic approaches to asymptomatic chronic Malaria (A. Claessens)


How is the malaria parasite Plasmodium falciparum able to establish a chronic, asymptomatic infection in a human host? The GATAC-Malaria team is addressing this question using blood isolates collected in the field and Next Generation Sequencing technology.


Our ATIP-Avenir team is part of ParaFrap, a consortium of French molecular parasitologists, and MalariaGEN, a consortium for malaria genomics. We are currently funded by an ‘ANR-JCJC’ awarded to Antoine Claessens.


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. Our lab strives to understand how P. falciparum parasites can survive in human chronic infections over the 6-month long dry season, using a collection of blood samples from a cohort of asymptomatic volunteers in The Gambia. To explore how the parasite senses its environment and adapt to it, we measure the parasite multiplication rate and sequence its transcriptome. Our novel protocol can sequence a whole transcriptome from as few as 1000 parasites. We will identify genes associated with seasonality using dry and wet season samples from The Gambia. In parallel, we focus on parasite antigenic variation by analyzing the dynamicity of the var gene transcription pattern.  

In summary, we will advance our understanding of the parasite biology and discover key molecular drivers of asymptomatic infections, a critical step to enable the eradication of malaria.


We recently published our main aims in Trends in Parasitology, here is a 2min video summary.


RECRUTEMENT: Please get in touch if you are interested in joining our vibrant team as a Master / PhD /Post-doc.

Research projects



Basic facts about malaria:

  • Caused by Plasmodium parasites (unicellular eukaryote)
  • Transmitted by Anopheles mosquitoes
  • Plasmodium parasites spend most of their asexual life inside red blood cells, with a reinvasion cycle every 48 hours.
  • Over half a million deaths per year, mainly children in Sub-Saharan Africa infected with Plasmodium falciparum

Malaria in The Gambia, West Africa

Where malaria transmission is seasonal such as The Gambia in West Africa, this occurs during and immediately after the rains (June-December). During the dry season (January-May) there is no transmission, hardly any clinical case is diagnosed during these dry months, and there are fewer mosquitoes[1,2]. Most of these infections will clear naturally, inducing a parasite population bottleneck (Fig. 1). However some P. falciparum parasites survive by establishing chronic, asymptomatic infections across the whole dry season. These infections are the reservoir from which the seasonal peak will restart at the next transmission season.


Our current research focuses on P. falciparum asymptomatic infections for three main reasons: 

  1. Asymptomatic infections: out of sight, out of mind

On any given day, the vast majority of all P. falciparum infections are asymptomatic, yet they have been poorly investigated (Fig 2). Currently, our knowledge of the parasite biology is based on isolates derived from clinical cases, and usually from clonal culture-adapted parasites. How asymptomatic infections differ from clinical cases has hardly ever been investigated, with no genome, epigenome, transcriptome, proteome or phenotypic description of such parasites published to date, due to the technical challenges associated with very low amount of biological material. Today’s technology is at a turning point for addressing these issues.


  1. This reservoir, shown to produce gametocytes and transmit them[4], represents the biggest challenge for malaria eradication. However, clearing all infections would include treating carriers without clinical symptoms who are unlikely to seek treatment. A campaign that would only target clinical cases, the most virulent forms of the parasite, is at risk of inadvertently selecting for a population with an “asymptomatic profile” (i.e. low-parasitaemia, chronic infections), complicating the elimination effort.Asymptomatic infections, a challenge for malaria elimination
  1. Asymptomatic infections as a new model for host-pathogen interactions

Currently, pathogenesis studies typically collect a single blood sample from the patient on its arrival at hospital, giving us only a snapshot of the host-pathogen interaction. I believe we could “record the video” of the host-pathogen interaction with regular blood sampling of the same chronic asymptomatic carrier, to study the evolution of the same infection in real time (Fig 3).

    Figure 3

This is why in The Gambia we recruited a cohort of ~50 volunteers who were asymptomatic carriers at the start of the dry season (December 2016). These individuals were sampled monthly for up to 6 months. Epidemiology results will be described in a separate post.
Understanding how the parasite can survive in a human host for months will help us develop novel genetic surveillance & therapeutic tools.



To understand how the parasite is able to survive over the dry season, and start a new epidemic at the following wet season, we will characterize P. falciparum from chronic infections, at the genomic, transcriptomic and phenotypic levels, as well as the associated host immune response. More specifically:

Project 1: Identifying P. falciparum alleles under selection during the dry season

Sequencing of P. falciparum genomes collected during the wet and dry season will identify parasite alleles that are selected for by the parasite population bottleneck due to the lack of transmission in the dry season.

Project 2: Can P. falciparum sense its environment and adapt to it via transcriptional regulation?

2a: We will measure the in vitro parasite multiplication rate to determine whether isolates from asymptomatic infections grow slower than virulent infections.

2b: Using single-cell (sc) RNA-seq, we will compare the transcriptome of parasites collected in dry and wet seasons. Our hypothesis is that at the start of the dry season some subpopulations of parasites switch to a dormant-like state.

Project 3: Can antigenic variation explain chronic infections?

We will record var gene expression switching and its associated immune response monthly over the course of the same infections. This will reveal a long postulated but never formally tested hypothesis that variant surface antigen switching is sufficient for the parasite to evade the host immune system.




1        Ceesay, S.J. et al. (2008) Changes in malaria indices between 1999 and 2007 in The Gambia: a retrospective analysis. Lancet 372, 1545–54

2        Ceesay, S.J. et al. (2010) Continued decline of malaria in The Gambia with implications for elimination. PLoS One5, 4–13

3        Lindblade, K. a et al. (2013) The silent threat: asymptomatic parasitemia and malaria transmission. Expert Rev. Anti. Infect. Ther. 11, 623–39

4        Stone, W. et al. (2015) Assessing the infectious reservoir of falciparum malaria: Past and future. Trends Parasitol.31, 287–296

Team members

Head of the team

Research Associate (CR) INSERM

LPHI  Laboratory of Pathogens and Host Immunity
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