Multi-locus genotyping reveals established endemicity of a geographically distinctPlasmodium vivaxpopulation in Mauritania, West Africa
Authors: Ba Hampate , Auburn Sarah , Jacob Christopher G. , Goncalves Sonia , Duffy Craig W. , Stewart Lindsay B. , Price Ric N. , Deh Yacine Boubou , Diallo Mamadou Yero , Tandia Abderahmane , Kwiatkowski Dominic P. , Conway David J. 
Published: September 2020

AbstractBackgroundPlasmodium vivaxhas 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 FindingsTo investigate theP. vivaxpopulation 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 MauritanianP. vivaxpopulation 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. TheP. vivaxdiversity 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 withP. vivaxin other areas of the world.Conclusions / SignificanceThe 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 toP. falciparumlocally or toP. vivaxelsewhere.Author SummaryPlasmodium vivaxis a widespread cause of malaria in Mauritania, in contrast to its rarity elsewhere throughout West Africa. To investigate whether the parasite may be recently introduced or epidemic, multi-locus genotyping was performed on 100 MauritanianP. vivaxmalaria cases. Analysis of a genome-wide panel of single nucleotide polymorphisms showed theP. vivaxpopulation to be genetically diverse and divergent from populations elsewhere, indicating that there has been long-standing endemic transmission. Almost all infections appear to be locally acquired, with the exception of one that was presumably imported with a genotype similar to infections seen in Southeast Asia. The MauritanianP. vivaxpopulation shows no linkage disequilibrium, and very few infections have closely related genotypes, indicating ongoing recombination. The parasite showed no indication of local substructure or epidemic population structure. Drug resistance alleles were virtually absent, suggesting that most infections have been untreated historically. The molecular epidemiology indicates that there has been long-standing endemic transmission of this neglected parasite that requires special attention for control.