Plasmodium vivax genome evolution for erythrocyte invasion in Duffy-negative infections from East Africa

Compared to other regions around the world, Plasmodium vivax ( Pv ) malaria is historically less common in Africa due to the lack of Duffy antigen receptor for chemokines (DARC) expression on host erythrocytes that Pv Duffy Binding Protein (DBP1) interacts and utilizes for erythrocyte invasion. However, increased reports of Pv across Africa lead to the hypothesis that the parasites have evolved alternate invasion mechanisms that are DARC-independent but rely on other ligand-receptor interactions. In this study, we analyzed single nucleotide polymorphisms (SNPs) based on whole genome sequence data of 110 Pv samples isolated from 38 Duffy-negative and 72 Duffy-positive individuals in Ethiopia. SNPs detected in Pv from Duffy positives (477,561 SNPs) were more than two-fold higher than Duffy negatives (197,461 SNPs).

Chromosomes 9, 10, and 12 were shown to be most variable in both Duffy groups. Among 43 erythrocyte binding gene candidates, tryptophan rich antigen 3 and 34 (TRAg3 and TRAg34) and members of the merozoite surface protein (MSP) 3 family had the highest variation. In Duffy positive Pv , significant signal of positive selection was observed in genes related to drug resistance (chloroquine resistance associated protein CG1 and the 26S proteasome regulatory subunit RPN2) and erythrocyte binding (membrane associated erythrocyte binding-like protein MAEBL); whereas in Duffy negative Pv , positive selection was observed in the plastid replication repair enzyme and the AP-5 complex subunit beta 1 genes associated with parasite mobility, transport and DNA repair. Several amino acid substitutions were found in PvDBP 1, PvEBP/DBP 2, and PvRBP 2b of Duffy positive but not Duffy negative samples, with almost half of the mutations located in the binding regions. No genetic differentiation was detected between Duffy positive and Duffy negative Pv from Ethiopia. These isolates were genetically similar to other East Africa Pv , but markedly different from those from Southeast Asia and South America. The highly conserved Pv genomes in Duffy negatives suggest stringent selective pressures and restricted binding interactions of Pv with Duffy negative erythrocytes. These findings shed light on alternate parasite invasion mechanisms in Duffy negative Africans.