Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis

Abstract

The most polymorphic gene family in P. falciparum is the ∼60 var genes distributed across parasite chromosomes, both in the subtelomeres and in internal regions. They encode hypervariable surface proteins known as P. falciparum erythrocyte membrane protein 1 (PfEMP1) that are critical for pathogenesis and immune evasion in Plasmodium falciparum. How var 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 var 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 var genes, with considerable variation in frequency between strains. Analysis of more than 100 recombination events involving var 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. Var exon 1, which encodes the immunologically exposed part of the protein, recombined in up to 0.2% of infected erythrocytes in vitro per life cycle. The high rate of var 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 var gene sequence polymorphism is mainly generated during the asexual part of the life cycle.

Indels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum

“…This is of particular concern with the recent spread of resistance to front-line therapies in Southeast Asia (Ashley et al 2014). High-throughput sequencing is a proven technology for the study of genome variation in P. falciparum and has yielded insights into parasite population structure (Manske et al 2012;Miotto et al 2013), transmission dynamics (Daniels et al 2015), multiplicity of infection (Nair et al 2014), the generation of antigenic diversity (Claessens et al 2014), and the genetic basis for artemisinin resistance (Ariey et al 2014). Despite these recent advances, our current understanding of P. falciparum genome variation remains incomplete due to multiple factors that are challenging both for sequencing technologies and for statistical methods used for variant discovery and genotyping.…”

Malaria Parasites in the Asymptomatic: Looking for the Hay in the Haystack

“…This differential expression suggests that once the initial var gene repertoire is exhausted by increasing immunity, var group C, or an alternative, unknown group of var gene variants that do not mediate cytoadherence in vital organs, might prevail in asymptomatic infections. Such chronic and asymptomatic malaria infections may survive their encounters with the host immune system by generating novel antigenic variants via mitotic recombination at a very high rate [27].…”

The immunological balance between host and parasite in malaria

“…It is interesting to note that a high rate of recombinations in the first exon of the var genes has been detected during mitosis of the erythrocytic stage of the parasite (Claessens et al 2014). These recombinations preserve the domain structure of the PfEMP-1 protein and may result in the formation of large numbers of new antigenic structures within a single patient, suggesting that the var gene sequence polymorphisms arise during the asexual parts of the life cycle of the parasite.…”