High genetic diversity, clonal activation of hypnozoites and relapse of Plasmodium vivax isolates in low-transmission setting of Ethiopia

Recurrent infection is more common in Plasmodium vivax malaria. The recurrence of P. vivax can be due to recrudescence, reinfection, or relapse. To characterize the genetic signature of P. vivax genetic diversity and multiplicity of infection (MOI) were assessed using merozoite surface protein 1 gene ( pvmsp1 ). A total of 370 blood samples were collected from 215 individuals visiting health facilities within Arjo-Didessa sugarcane plantations and it’s surrounding of Oromia, southwestern Ethiopia. All samples were subjected to amplicon deep sequencing of the pvmsp1 gene. High population genetic diversity was observed—generating 67 unique haplotypes, haplotype diversity (Hd = 0.799), nucleotide diversity (ℼ = 0.044), and expected heterozygosity (HE) = 0.826. However, low MOI = 1.4 and 34.6% polyclonal infections. Of the 215 participant, 82 patients experienced one to five recurrent infections. In paired analysis of primary and recurrent episodes, high genetic homology (81.3%) was observed, with 55.6% of the homologous pairs sharing identical alleles. The high genetic diversity at population and low diversity at individual level likely driven by migrant workers introducing diverse parasite genotypes into a low-transmission setting. Most of the recurrent infections were relapses, as evidenced by shared alleles. The finding highlights the need for strengthening malaria surveillance and tailored intervention particularly for mobile population.