Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites

Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes (textquotedbllefttime-to-eventtextquotedblright analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within lt;200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median HE = 0.70-0.81) and it captured 89273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew’s correlation coefficient gt;0.9 in 90 and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe study was supported by the National Health and Medical Research Council of Australia (APP2001083 supporting SA and SVS), the Wellcome Trust (200909 and ICRG GR071614MA Senior Fellowships in Clinical Science to RNP, 206194/Z17/Z supporting JCR and SVS) the National Institutes of Health (R01AI137154 to JCR) and the Bill amp; Melinda Gates Foundation (INV-043618 supporting SA and RNP).The whole genome sequencing component of the study was supported by the Medical Research Council and UK Department for International Development (award number M006212 to DK) and the Wellcome Trust (award numbers 206194 and 204911 to DK). The IMPROV clinical trial was supported by the Bill amp; Melinda Gates Foundation (OPP1054404 awarded to RNP).Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The study used ONLY openly available genomic data on Plasmodium vivax parasites that were originally located at: https://wellcomeopenresearch.org/articles/7-136. As detailed in the corresponding data note for the Pv4.0 data set, all isolates were collected in the framework of studies with ethical approval from the local research ethics boards, and with written, informed consent provided by patients or guardians for individuals of age 18 or youngerI confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable.YesAll data produced in the present study are available upon reasonable request to the authors