Generation of Antigenic Diversity in <i>Plasmodium falciparum</i> by Structured Rearrangement of <i>Var</i> Genes During Mitosis

<div><p>The most polymorphic gene family in <i>P. falciparum</i> is the ∼60 <i>var</i> genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as <i>P. falciparum</i> erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in <i>Plasmodium falciparum</i>. How <i>var</i> gene sequence diversity is generated is not currently completely understood. To address this, we constructed large clone trees and performed whole genome sequence analysis to study the generation of novel <i>var</i> gene sequences in asexually replicating parasites. While single nucleotide polymorphisms (SNPs) were scattered across the genome, structural variants (deletions, duplications, translocations) were focused in and around <i>var</i> genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving <i>var</i> exon 1 revealed that the average nucleotide sequence identity of two recombining exons was only 63% (range: 52.7–72.4%) yet the crossovers were error-free and occurred in such a way that the resulting sequence was in frame and domain architecture was preserved. <i>Var</i> exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes <i>in vitro</i> per life cycle. The high rate of <i>var</i> exon 1 recombination indicates that millions of new antigenic structures could potentially be generated each day in a single infected individual. We propose a model whereby <i>var</i> gene sequence polymorphism is mainly generated during the asexual part of the life cycle.</p></div>