Malaria-causing P. vivax parasites can linger in the human liver for weeks to months and then reactivate to cause recurrent blood-stage infection. While recognized as an important point of intervention for malaria eradication, very little is known about the molecular composition of the actively-replicating and quiescent intracellular P. vivax parasite populations, nor the molecular features and dynamics that underlie host cell responses to infection in humans. Here, we leverage a bioengineered human microliver platform to culture Thai clinical isolates of P. vivax in primary human hepatocytes and to conduct transcriptional profiling of infected cultures. By coupling targeted enrichment strategies with bulk and single-cell analyses, we capture both parasite and host transcripts in individual infected hepatocytes throughout the course of infection. We define stage-specific transcriptional signatures and identify a novel population of actively replicating parasites, sharing features with sexual blood-stages. Within infected liver cells, we find that infection suppresses transcription of key hepatocyte function genes, and that P. vivax elicits an innate immune response that can be manipulated to control infection in curative therapy mode. Our work provides an extendible framework and a valuable resource for understanding host-parasite interactions and reveals new insights into the biology of relapsing human malaria.

Sample / time-points naming scheme: day of the sampling, replicate, type of libraries. "Seq" means direct sequencing of the corresponding SeqWell library, "Cap" means post-SeqWell library construction P. vivax hybrid capture.