Multi-locus genotyping reveals established endemicity of a geographically distinct Plasmodium vivax population in Mauritania, West Africa

Abstract

Background Plasmodium vivax has been recently discovered as a significant cause of malaria in Mauritania, although very rare elsewhere in West Africa. It has not been known if this is a recently introduced or locally remnant parasite population, nor whether the genetic structure reflects epidemic or endemic transmission. Methodology/Principal findings To investigate the P. vivax population genetic structure in Mauritania and compare with populations previously analysed elsewhere, multi-locus genotyping was undertaken on 100 clinical isolates, using a genome-wide panel of 38 single nucleotide polymorphisms (SNPs), plus seven SNPs in drug resistance genes. The Mauritanian P. vivax population is shown to be genetically diverse and divergent from populations elsewhere, indicated consistently by genetic distance matrix analysis, principal components analyses, and fixation indices. Only one isolate had a genotype clearly indicating recent importation, from a southeast Asian source. There was no linkage disequilibrium in the local parasite population, and only a small number of infections appeared to be closely genetically related, indicating that there is ongoing genetic recombination consistent with endemic transmission. The P. vivax diversity in a remote mining town was similar to that in the capital Nouakchott, with no indication of local substructure or of epidemic population structure. Drug resistance alleles were virtually absent in Mauritania, in contrast with P. vivax in other areas of the world. Conclusions/Significance The molecular epidemiology indicates that there is long-standing endemic transmission that will be very challenging to eliminate. The virtual absence of drug resistance alleles suggests that most infections have been untreated, and that this endemic infection has been more neglected in comparison to P. vivax elsewhere.

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria

“…The application and wider validation of the new GEO barcodes is underway, with Illumina amplicon-based sequencing assays already established by the Wellcome Sanger Institute malaria program for the 38-Broad barcode SNPs 13 and by collaborators at the Institute for Tropical Medicine, Antwerp, for GEO-33 18 . Further work will be needed to establish frameworks for implementation of parasite genotyping into the day-to-day activities of NMCPs: insights may be gained from the GenRe-Mekong framework, which has successfully implemented parasite genotyping into NMCP activities in several countries in the Greater Mekong Subregion for the purpose of tracking antimalarial drug resistance in P. falciparum 7 .…”

Molecular Epidemiology of G6PD Genotypes in Different Ethnic Groups Residing in Saharan and Sahelian Zones of Mauritania

“…At present, P. vivax infection in Duffy-negative individuals is generally thought to be more of an exception rather than the rule, and the underlying biochemical and molecular mechanisms are poorly understood [ 38 , 39 ]. Furthermore, many of the minority ethnic groups of black African ancestry reside in southern Mauritania, where the chances of being exposed to the risk of P. vivax malaria are slim [ 40 , 41 , 42 , 43 , 44 , 45 ]. Nonetheless, many Mauritanians living in the south often travel to the north, where P. vivax is endemic, and some migrate to the northern Saharan zone, often for economic reasons, especially to Nouakchott, which has become a melting pot of various ethnic groups.…”

Novel highly-multiplexed AmpliSeq targeted assay for Plasmodium vivax genetic surveillance use cases at multiple geographical scales

“…Microsatellites that are not under evolutionary pressure are popular markers for population genetic surveillance and can be used to study connectivity and transmission intensity ( Anderson TJ et al., 2000 ; Imwong et al., 2005 ; Koepfli et al., 2009 ; Escalante et al., 2015 ), but they are difficult to standardize and compare between datasets ( Havryliuk and Ferreira, 2009 ). A first P. vivax barcode targeting 42-SNPs in a high resolution melt assay ( Baniecki et al., 2015 ; Ba et al., 2020 ; Dewasurendra et al., 2020 ), designed for finger-printing P. vivax isolates and assigning the geographic origin, was based on genomic data from only 13 isolates from 7 countries and thus had limited efficacy ( Trimarsanto et al., 2019 ). More recently, SNP barcodes have been developed using higher numbers of genomes, which have better resolution for fine-scale population structure and combined with Identity-By-Descent (IBD) analysis, these are superior in connectivity analyses ( Friedrich et al., 2016 ; Henden et al., 2018 ; Schaffner et al., 2018 ; Taylor et al., 2019 ; Fola et al., 2020 ).…”