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. ### Competing Interest Statement The authors have declared no competing interest. ### Clinical Trial NCT03496454 ### Funding Statement This work was funded by grants from the joint MRC/LSHTM fellowship, the French National Research Agency (18-CE15-0009-01), Mediteranee Infection (InfectioPole Sud), ATIP-Avenir, Fonds Medical de la Recherche (FRM). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study received approval from the Scientific Coordinating Committee of MRCG, The Gambia Government/MRCG Joint Ethics Committee, and the London School of Hygiene and Tropical Medicine Research and Ethics Committee and was conducted according to the International Conference on Harmonisation Good Clinical Practice guidelines and registered with ClinicalTrials.gov (identifier [NCT03496454][1]). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced are available online at Zenodo [1]: /lookup/external-ref?link_type=CLINTRIALGOV&access_num=NCT03496454&atom=%2Fmedrxiv%2Fearly%2F2024%2F01%2F02%2F2023.12.27.23300577.atom