Genetic profiling ofPlasmodium ovale wallikerirelapses with microsatellite markers and whole-genome sequencing

Abstract

Plasmodium ovale wallikeri and P. ovale curtisi were recently classified as two distinct species. Like P. vivax, both P. ovale curtisi and P. ovale wallikeri have the ability to cause relapse in humans. P. ovale spp. are still understudied and the development of genomic tools to study parasite genetic diversity parameters or medically-important traits such as relapses are needed. Here, we describe a protocol to type a set of eight putatively neutral P. ovale wallikeri microsatellite markers. Expected heterozygosity ranged from 0.764 to 0.940 in 69 P. ovale wallikeri samples from Sub-Saharan Africa and polyclonality was detected in 7 isolates. We genotyped 15 pairs of isolates from primary (D0) and relapsing infections (Drelapse) that occurred in metropolitan France from 2013 to 2021. For most pairs, the D0 and the Drelapse isolates were highly genetically related, an observation that was confirmed by whole-genome sequencing for the four pairs we further studied.

Population genomics ofPlasmodium ovalespecies in sub-Saharan Africa

“…Using such assays to better evaluate P. ovale parasite relatedness, transmission, and relapse patterns is critical for improving current malaria control strategies targeting P. falciparum that do not consider non-falciparum malaria species. 26,56,57…”

“…29,34 Ultimately, samples from 25 individuals were selected for whole-genome sequencing based on higher-density P. ovale infection, lack of or lower-density P. falciparum coinfection, and balance of ovale species and geographic diversity across the sample set. Characteristics of these 25 samples, and an additional four samples from a study of P. ovale wallikeri in French travelers that were whole genome sequenced by Joste et al, 26 are shown in Supplemental Table 1 .…”

“…25 Finally, genomic data from four P. ovale cases imported to France from west and central Africa were retrieved from the European Nucleotide Archive. 26 These isolates had undergone selective whole-genome amplification (sWGA) for parasite DNA enrichment prior to sequencing. Further data on all parasite isolates are found in Supplemental Table *Raw sequencing data for these 4 isolates were directly incorporated into the analysis pipeline after retrieval from the European Nucleotide Archive.…”