Seasonal transcriptional profiling of malaria parasites using a new single-cell atlas of a Malian Plasmodium falciparum isolate

Asymptomatic persistence is crucial for the survival of malaria parasites in seasonal transmission settings, where transmission halts during dry months, while mosquitos are scarce and new infections rare. How Plasmodium falciparum avoids causing host symptoms or being cleared is not fully understood. Parasites that persist through the dry season circulate longer within the ∼48h replication cycle compared to parasites isolated from clinical cases, where only early stages circulate. The mechanisms promoting increased circulation and avirulent infections bridging two wet seasons remain unclear. We generated a single-cell RNA-seq reference atlas with P. falciparum erythrocytic stages of a recently adapted isolate, and with it defined the developmental stage of over 25000 parasites from six asymptomatic children at the dry-wet season transition, and nine children with clinical malaria in the wet season. Our data confirms that older parasites circulate in the dry season, and reveals transcriptional modulation of exported proteins that affect cytoadhesion of infected erythrocytes, which we validated by immuno-fluorescence microscopy.