Global genetic diversity of var2csa in Plasmodium falciparum with implications for malaria in pregnancy and vaccine development

Abstract

Malaria infection during pregnancy, caused by the sequestering of Plasmodium falciparum parasites in the placenta, leads to high infant mortality and maternal morbidity. The parasite-placenta adherence mechanism is mediated by the VAR2CSA protein, a target for natural occurring immunity. Currently, vaccine development is based on its ID1-DBL2Xb domain however little is known about the global genetic diversity of the encoding var2csa gene, which could influence vaccine efficacy. In a comprehensive analysis of the var2csa gene in >2,000 P. falciparum field isolates across 23 countries, we found that var2csa is duplicated in high prevalence (>25%), African and Oceanian populations harbour a much higher diversity than other regions, and that insertions/deletions are abundant leading to an underestimation of the diversity of the locus. Further, ID1-DBL2Xb haplotypes associated with adverse birth outcomes are present globally, and African-specific haplotypes exist, which should be incorporated into vaccine design.

Figure 1

Plasmodium falciparum var2csa diversity across a 7 kb region covering the five DBL domains, and 1,249 field isolates. (A) Schematic structure of the var2csa gene including the N-terminal sequence (NTS, blue), 5 Duffy binding like-Domains (DBL, green), 3 Inter-Domains (ID, red) and the Cysteine-Rich Inter-Domain (CIDR, yellow); the lengths in amino acids of the 3D7 reference are presented in parentheses. (B) Accumulation of unique insertions and deletions (InDels) across the var2csa gene. (C) Distribution of nucleotide diversity (π) across the gene and by population. Regions of abnormal (“flat”) nucleotide diversity are highlighted in green (B and C).

Figure 2

Population structure using the ID1-DBL2Xb protein sequences (A) Four distinct clades are identified, with some overlap to the clades found in, where Clade 1 is 3D7-like and Clade 2 is FCR3-like. The PCA analysis (B and C) supports the separation of these clades and reveals the proximity of Clades 1 and 2. (D) The distribution of clades across the different regions and previous studies, with three of the clades present across all the populations (Clades 1, 2 and 4); 3D7-like clade associated with adverse outcome in pregnancy is in West Africa (41.2%), East Africa (27.5%), South East Asia (23.5%) and South America (20%); Clade 3 is present in African parasite populations and Clade 4 is predominantly in African populations.