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ORIGINAL RESEARCH article

Front. Genet.
Sec. Evolutionary and Population Genetics
Volume 15 - 2024 | doi: 10.3389/fgene.2024.1488109
This article is part of the Research Topic Advanced Genetic and Genomic Methods and Applications for Malaria Surveillance View all 4 articles

Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon

Provisionally accepted
Luis Cabrera-Sosa Luis Cabrera-Sosa 1,2,3Mahdi Safarpour Mahdi Safarpour 3Johanna Helena Kattenberg Johanna Helena Kattenberg 4Roberson Ramirez Roberson Ramirez 5Joseph M Vinetz Joseph M Vinetz 2,5,6Anna Rosanas-Urgell Anna Rosanas-Urgell 4Dionicia Gamboa Dionicia Gamboa 1,2,5,7Christopher Delgado-Ratto Christopher Delgado-Ratto 3*
  • 1 Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
  • 2 Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia,, Lima, Peru
  • 3 Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
  • 4 Department of Biomedical Sciences, Institute of Tropical Medicine Antwerp, Antwerp, Antwerp, Belgium
  • 5 Laboratorio ICEMR-Amazonia y Enfermedades Emergentes, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
  • 6 Section of Infectious Diseases, Department of Internal Medicine, School of Medicine, Yale University, New Haven, Connecticut, United States
  • 7 Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru

The final, formatted version of the article will be published soon.

    Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control programs. We previously designed AmpliSeq assays for MMS, which include different traits of interest (resistance markers and pfhrp2/3 deletions), and SNP barcodes to provide population genetics estimates of Plasmodium vivax and Plasmodium falciparum parasites in the Peruvian Amazon. The present study compares the genetic resolution of the barcodes in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate population genetics of Amazonian malaria parasites.We analyzed 51 P. vivax and 80 P. falciparum samples from three distinct areas in the Loreto region of the Peruvian Amazon: Nueva Jerusalén (NJ), Mazan (MZ), and Santa Emilia (SE). Population genetics estimates and costs were compared using the SNP barcodes (P. vivax: 40 SNPs & P. facliparum 28 SNPs) and MS panels (P. vivax: 16 MS & P. falciparum: 7 MS). The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: HeMS=0.68-0.78 (p>0.05) and HeSNP=0.36-0.38 (p>0.05). P. vivax pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS=0.04-0.14 and FST-SNP=0.03-0.12 (pairwise p>0.05). In addition, P. falciparum genetic diversity trends (HeMS=0-0.48, p<0.05; HeSNP=0-0.09, p<0.05) and pairwise FST comparisons (FST-MS=0.14-0.65, FST-SNP=0.19-0.61, pairwise p >0.05) were concordant between both panels. For P. vivax, no geographic clustering was observed with any panel, whereas for P. falciparum, similar population structure clustering was observed with both markers, assigning most parasites from NJ to a distinct subpopulation from MZ and SE. We found significant differences in detecting polyclonal infections: for P. vivax, MS identified a higher proportion than SNP (69% vs 33%, p=3.3×10⁻⁵), while for P. falciparum, SNP and MS detected similar rates (46% vs 31%, p=0.21). The AmpliSeq assay had a higher estimated per-sample cost compared to MS

    Keywords: malaria molecular surveillance, microsatellites, SNP, NGS, Population Genetics, population structure, ampliseq

    Received: 29 Aug 2024; Accepted: 29 Nov 2024.

    Copyright: © 2024 Cabrera-Sosa, Safarpour, Kattenberg, Ramirez, Vinetz, Rosanas-Urgell, Gamboa and Delgado-Ratto. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Christopher Delgado-Ratto, Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium

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