Diverse and weakly immunogenic var gene expression facilitates malaria infection

Plasmodium falciparum is believed to escape immunity via antigenic variation, mediated in part by 60 var genes. These genes undergo mutually exclusive expression and encode the PfEMP1 surface antigen. The frequency of var switching and the immunogenicity of each expressed PfEMP1 remain unclear. To this end, we carried out a Controlled Human Malaria Infection (CHMI) study with 19 adult African volunteers in The Gambia to gain insight into the effect of naturally acquired immunity on the expressed var gene repertoire during early phase of an infection. Our findings demonstrated a strong correlation between the diversity of var expression, quantified through entropy, and infection outcome. Low-immunity individuals were characterised by high var entropy profiles, higher parasitaemia, and lower sero-recognised PfEMP1 domains compared to high-immunity individuals. For the first time we recorded the probability of var gene switching in vitro and of turnover in vivo, enabling us to estimate both intrinsic switching and negative-selection effects. These processes are rapid, resulting in estimated turnover/switching probabilities of 69% - 97% and 7% - 57% per generation, in vivo and in vitro, respectively. Var (PfEMP1) expression triggered time-dependent humoral immune responses in low immunity individuals, with many PfEMP1 domains remaining weakly immunogenic. We conclude that the role of intrinsic var switching is to reset and maintain a diverse var repertoire. The high var switching rates and weak PfEMP1 immunogenicity benefit parasite survival during the CHMI.