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Fine S, Quiroz AA, Calle VS, Manrique P, Rodriguez H, Carrasco G, Benjamin-Chung J, Bennett A, Auburn S, Price R, Greenhouse B, Baird JK, Domingo G, Roh M, Rosas A, Llanos-Cuentas A, Hsiang M. FocaL mass drug Administration for Plasmodium vivax Malaria Elimination (FLAME): study protocol for an open-label cluster randomized controlled trial in Peru. RESEARCH SQUARE 2025:rs.3.rs-5594891. [PMID: 40321759 PMCID: PMC12047980 DOI: 10.21203/rs.3.rs-5594891/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/11/2025]
Abstract
Background Outside of sub-Saharan Africa, Plasmodium vivax has become the dominant species of malaria. Focal mass drug administration (fMDA) is a potential strategy to support elimination efforts, but controlled studies are lacking. Methods The FocaL mass drug Administration for Plasmodium vivax Malaria Elimination (FLAME) study is a 3-year cluster randomized controlled trial to determine the impact and safety of fMDA to reduce P. vivax transmission. The study will be conducted in Loreto, Peru, where standard interventions have reduced P. vivax cases, but transmission persists due to a high proportion of subclinical infections. Thirty low transmission communities (API < 250 cases/1000 population) will be randomized 1:1 to fMDA versus control using a restricted randomization. All communities will receive Peruvian national standard malaria control measures. In the intervention arm, high-risk individuals (living within 200 meters of a P. vivax case reported in the prior two years) without contraindication to study medications, including G6PD deficiency, will receive three cycles of fMDA over a two-year period. Each cycle will include two rounds of directly observed therapy delivered 2 months apart. The fMDA regimen will include 25mg/kg chloroquine (CQ) plus a single 300mg dose of tafenoquine (TQ) for individuals age ≥16 years, and 25mg/kg of CQ plus 7 days of 0.5mg/kg/day of primaquine (PQ) if younger. The primary outcome is the cumulative incidence of symptomatic P. vivax malaria. The sample size provides 80% power to detect at least a 68% relative reduction in cumulative P. vivax incidence, based on alpha of 0.05 and a coefficient of variation (k) of 0.87. Secondary outcomes include safety, cost-effectiveness, and infection prevalence and seroprevalence which will be assessed in annual cross-sectional surveys. Safety will be assessed in passive and active pharmacovigilance, including post-treatment screening for G6PD-associated hemolysis by assessing for anemia and hematuria in a sample. Discussion The trial will generate evidence regarding fMDA for P. vivax and inform malaria elimination efforts in Peru and similarly endemic settings. Findings will be in peer-reviewed publications and through stakeholder meetings in Peruvian and international policy and research forums. Trial registration Clinicaltrials.gov NCT05690841. This trial was registered on 09 January 2023.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sarah Auburn
- Menzies School of Health Research: Charles Darwin University
| | - Ric Price
- Menzies School of Health Research: Charles Darwin University
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Safarpour M, Cabrera-Sosa L, Gamboa D, Van geertruyden JP, Delgado-Ratto C. Detecting imported malaria infections in endemic settings using molecular surveillance: current state and challenges. FRONTIERS IN EPIDEMIOLOGY 2025; 5:1490141. [PMID: 40078574 PMCID: PMC11897264 DOI: 10.3389/fepid.2025.1490141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Accepted: 01/22/2025] [Indexed: 03/14/2025]
Abstract
The Global Technical Strategy for Malaria 2016-2030 targets eliminating malaria from at least 35 countries and reducing case incidence by 90% globally. The importation of parasites due to human mobilization poses a significant obstacle to achieve malaria elimination as it can undermine the effectiveness of local interventions. Gaining a comprehensive understanding of parasite importation is essential to support control efforts and advance progress toward elimination. Parasite genetic data is widely used to investigate the spatial and temporal dynamics of imported infections. In this context, this systematic review aimed to aggregate evidence on the application of parasite genetic data for mapping imported malaria and the analytical methods used to analyze it. We discuss the advantages and limitations of the genetic approaches employed and propose a suitable type of genetic data along with an analytical framework to discriminate imported malaria infections from local infections. The findings offer potential actionable insights for national control programs, enabling them select the most effective methods for detecting imported cases. This also may aid in the evaluation and refinement of elimination programs by identifying high-risk areas and enabling the targeted allocation of resources to these regions.
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Affiliation(s)
- Mahdi Safarpour
- Malaria Research Group (MaRch), Family Medicine and Population Health Department, Faculty of Medicine and Health Sciences, Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Luis Cabrera-Sosa
- Malaria Research Group (MaRch), Family Medicine and Population Health Department, Faculty of Medicine and Health Sciences, Global Health Institute, University of Antwerp, Antwerp, Belgium
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Grupo Malaria: Epidemiología Molecular, Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Grupo Malaria: Epidemiología Molecular, Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jean-Pierre Van geertruyden
- Malaria Research Group (MaRch), Family Medicine and Population Health Department, Faculty of Medicine and Health Sciences, Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Christopher Delgado-Ratto
- Malaria Research Group (MaRch), Family Medicine and Population Health Department, Faculty of Medicine and Health Sciences, Global Health Institute, University of Antwerp, Antwerp, Belgium
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Czech E, Millar TR, Tyler W, White T, Elsworth B, Guez J, Hancox J, Jeffery B, Karczewski KJ, Miles A, Tallman S, Unneberg P, Wojdyla R, Zabad S, Hammerbacher J, Kelleher J. Analysis-ready VCF at Biobank scale using Zarr. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.11.598241. [PMID: 38915693 PMCID: PMC11195102 DOI: 10.1101/2024.06.11.598241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Background Variant Call Format (VCF) is the standard file format for interchanging genetic variation data and associated quality control metrics. The usual row-wise encoding of the VCF data model (either as text or packed binary) emphasises efficient retrieval of all data for a given variant, but accessing data on a field or sample basis is inefficient. Biobank scale datasets currently available consist of hundreds of thousands of whole genomes and hundreds of terabytes of compressed VCF. Row-wise data storage is fundamentally unsuitable and a more scalable approach is needed. Results Zarr is a format for storing multi-dimensional data that is widely used across the sciences, and is ideally suited to massively parallel processing. We present the VCF Zarr specification, an encoding of the VCF data model using Zarr, along with fundamental software infrastructure for efficient and reliable conversion at scale. We show how this format is far more efficient than standard VCF based approaches, and competitive with specialised methods for storing genotype data in terms of compression ratios and single-threaded calculation performance. We present case studies on subsets of three large human datasets (Genomics England: n=78,195; Our Future Health: n=651,050; All of Us: n=245,394) along with whole genome datasets for Norway Spruce (n=1,063) and SARS-CoV-2 (n=4,484,157). We demonstrate the potential for VCF Zarr to enable a new generation of high-performance and cost-effective applications via illustrative examples using cloud computing and GPUs. Conclusions Large row-encoded VCF files are a major bottleneck for current research, and storing and processing these files incurs a substantial cost. The VCF Zarr specification, building on widely-used, open-source technologies has the potential to greatly reduce these costs, and may enable a diverse ecosystem of next-generation tools for analysing genetic variation data directly from cloud-based object stores, while maintaining compatibility with existing file-oriented workflows.
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Affiliation(s)
- Eric Czech
- Open Athena AI Foundation, Lincoln, New Zealand
- Related Sciences, Lincoln, New Zealand
| | - Timothy R. Millar
- The New Zealand Institute for Plant & Food Research Ltd, Lincoln, New Zealand
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Tom White
- Tom White Consulting Ltd., Manchester, UK
| | | | - Jérémy Guez
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | | | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
| | - Konrad J. Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Alistair Miles
- Wellcome Sanger Institute, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sam Tallman
- Genomics England, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Shadi Zabad
- School of Computer Science, McGill University, Montreal, QC, Canada
| | - Jeff Hammerbacher
- Open Athena AI Foundation, Lincoln, New Zealand
- Related Sciences, Lincoln, New Zealand
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, UK
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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz JM, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. Front Genet 2024; 15:1488109. [PMID: 39748949 PMCID: PMC11693692 DOI: 10.3389/fgene.2024.1488109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2024] [Accepted: 11/29/2024] [Indexed: 01/04/2025] Open
Abstract
Introduction 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. Methods 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 and P. falciparum: 28 SNPs) and MS panels (P. vivax: 16 MS and P. falciparum: 7 MS). Results The P. vivax genetic diversity (expected heterozygosity, He) trends were similar for both markers: He MS = 0.68-0.78 (p > 0.05) and He SNP = 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 (He MS = 0-0.48, p < 0.05; He SNP = 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 of polyclonal infections 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 ($183 vs. $27-49). Discussion The SNP barcodes in the AmpliSeq assays offered comparable results to MS for investigating population genetics in P. vivax and P. falciparum populations, despite some discrepancies in determining polyclonality. Given both panels have their respective advantages and limitations, the choice between both should be guided by research objectives, costs, and resource availability.
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Affiliation(s)
- Luis Cabrera-Sosa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Mahdi Safarpour
- Malaria Research Group (MaRch), Global Health Institute (GHI), Family Medicine and Population Health Department (FAMPOP), Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | | | - Roberson Ramirez
- Laboratorio ICEMR-Amazonia y Enfermedades Emergentes, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joseph M. Vinetz
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia y Enfermedades Emergentes, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Section of Infectious Diseases, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Anna Rosanas-Urgell
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Dionicia Gamboa
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio ICEMR-Amazonia y Enfermedades Emergentes, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical “Alexander von Humboldt”, Universidad Peruana Cayetano Heredia, Lima, Peru
- 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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Pierre-Louis E, Kelley J, Patel D, Carlson C, Talundzic E, Jacobson D, Barratt JLN. Geo-classification of drug-resistant travel-associated Plasmodium falciparum using Pfs47 and Pfcpmp gene sequences (USA, 2018-2021). Antimicrob Agents Chemother 2024; 68:e0120324. [PMID: 39530682 PMCID: PMC11619247 DOI: 10.1128/aac.01203-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024] Open
Abstract
Travel-related malaria is regularly encountered in the United States, and the U.S. Centers for Disease Control and Prevention (CDC) characterizes Plasmodium falciparum drug-resistance genotypes routinely for travel-related cases. An important aspect of antimalarial drug resistance is understanding its geographic distribution. However, specimens submitted to CDC laboratories may have missing, incomplete, or inaccurate travel data. To complement genotyping for drug-resistance markers Pfcrt, Pfmdr1, Pfk13, Pfdhps, Pfdhfr, and PfcytB at CDC, amplicons of Pfs47 and Pfcpmp are also sequenced as markers of geographic origin. Here, a bi-allele likelihood (BALK) classifier was trained using Pfs47 and Pfcpmp sequences from published P. falciparum genomes of known geographic origin to classify clinical genotypes to a continent. Among P. falciparum-positive blood samples received at CDC for drug-resistance genotyping from 2018 to 2021 (n = 380), 240 included a travel history with the submission materials, though 6 were excluded due to low sequence quality. Classifications obtained for the remaining 234 were compared to their travel histories. Classification results were over 96% congruent with reported travel for clinical samples, and with collection sites for field isolates. Among travel-related samples, only two incongruent results occurred; a specimen submitted citing Costa Rican travel classified to Africa, and a specimen with travel referencing Sierra Leone classified to Asia. Subsequently, the classifier was applied to specimens with unreported travel histories (n = 140; 5 were excluded due to low sequence quality). For the remaining 135 samples, geographic classification data were paired with results generated using CDC's Malaria Resistance Surveillance (MaRS) protocol, which detects single-nucleotide polymorphisms in and generates haplotypes for Pfcrt, Pfmdr1, Pfk13, Pfdhps, Pfdhfr, and PfcytB. Given the importance of understanding the geographic distribution of antimalarial drug resistance, this work will complement domestic surveillance efforts by expanding knowledge on the geographic origin of drug-resistant P. falciparum entering the USA.
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Affiliation(s)
- Edwin Pierre-Louis
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA
| | - Julia Kelley
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dhruviben Patel
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Williams Consulting LLC, Atlanta, Georgia, USA
| | - Christina Carlson
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Eldin Talundzic
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - David Jacobson
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joel Leonard Nicholas Barratt
- Laboratory Science and Diagnostics Branch, Division of Parasitic Diseases and Malaria, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Popkin-Hall ZR, Niaré K, Crudale R, Simkin A, Fola AA, Sanchez JF, Pannebaker DL, Giesbrecht DJ, Kim IE, Aydemir Ö, Bailey JA, Valdivia HO, Juliano JJ. High-throughput genotyping of Plasmodium vivax in the Peruvian Amazon via molecular inversion probes. Nat Commun 2024; 15:10219. [PMID: 39587110 PMCID: PMC11589703 DOI: 10.1038/s41467-024-54731-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Accepted: 11/19/2024] [Indexed: 11/27/2024] Open
Abstract
Plasmodium vivax transmission occurs throughout the tropics and is an emerging threat in areas of Plasmodium falciparum decline, causing relapse infections that complicate treatment and control. Targeted sequencing for P. falciparum has been widely deployed to detect population structure and the geographic spread of antimalarial and diagnostic resistance. However, there are fewer such tools for P. vivax. Leveraging global variation data, we designed four molecular inversion probe (MIP) genotyping panels targeting geographically differentiating SNPs, neutral SNPs, putative antimalarial resistance genes, and vaccine candidate genes. We deployed these MIP panels on 866 infections from the Peruvian Amazon and identified transmission networks with clonality (IBD[identity by descent]>0.99), copy number variation in Pvdbp and multiple Pvrbps, mutations in antimalarial resistance orthologs, and balancing selection in 13 vaccine candidate genes. Our MIP panels are the broadest genotyping panel currently available and are poised for successful deployment in other regions of P. vivax transmission.
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Affiliation(s)
- Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Rebecca Crudale
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Alfred Simkin
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Abebe A Fola
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Juan F Sanchez
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Danielle L Pannebaker
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - David J Giesbrecht
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Isaac E Kim
- The Warren Alpert Medical School of Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Özkan Aydemir
- Program in Molecular Medicine, UMass Chan Medical School, Worcester, MA, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA
| | - Hugo O Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit SOUTH (NAMRU SOUTH), Lima, Peru
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
- Division of Infectious Diseases, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum of Genetics and Molecular Biology, University of North Carolina School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Dash M, Mallick PK. Microhaplotypes: the QR-code for Plasmodium vivax infection dynamics. Trends Parasitol 2024; 40:959-961. [PMID: 39428304 DOI: 10.1016/j.pt.2024.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 10/08/2024] [Indexed: 10/22/2024]
Abstract
An array of microhaplotypes - small segments of ≤200 nucleotides with heterozygous multiple-SNP exhibiting multiple allelic combinations - were identified in the Plasmodium vivax genome by Siegel et al. Interestingly, the microhaplotype has significant potential to distinguish relapse/reinfection and identify genetic relatedness across vivax-endemic areas. It is essential to validate the universal applicability of microhaplotypes.
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Affiliation(s)
- Manoswini Dash
- Centre for Aging, School of Medicine, Tulane University, New Orleans, LA, USA
| | - Prashant Kumar Mallick
- Department of Molecular Biology, ICMR-National Institute of Malaria Research, New Delhi, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India.
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Cabrera-Sosa L, Safarpour M, Kattenberg JH, Ramirez R, Vinetz J, Rosanas-Urgell A, Gamboa D, Delgado-Ratto C. Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.09.611954. [PMID: 39314390 PMCID: PMC11418992 DOI: 10.1101/2024.09.09.611954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He ) was similar across the subpopulations for both makers: He MS = 0.68 - 0.78 (p = 0.23) and He SNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, F ST ) was also comparable: F ST-MS = 0.04 - 0.14 and F ST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends ( He MS = 0 - 0.48 p = 0.03 - 1; He SNP = 0 - 0.09, p = 0.03 - 1) and pairwise F ST comparisons (F ST-MS = 0.14 - 0.65, F ST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.
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9
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Siegel SV, Trimarsanto H, Amato R, Murie K, Taylor AR, Sutanto E, Kleinecke M, Whitton G, Watson JA, Imwong M, Assefa A, Rahim AG, Nguyen HC, Tran TH, Green JA, Koh GCKW, White NJ, Day N, Kwiatkowski DP, Rayner JC, Price RN, Auburn S. Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites. Nat Commun 2024; 15:6757. [PMID: 39117628 PMCID: PMC11310204 DOI: 10.1038/s41467-024-51015-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Challenges in classifying recurrent Plasmodium vivax infections constrain surveillance of antimalarial efficacy and transmission. Recurrent infections may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or reinfection. Molecular inference of familial relatedness (identity-by-descent or IBD) can help resolve the probable origin of recurrences. As whole genome sequencing of P. vivax remains challenging, targeted genotyping methods are needed for scalability. We describe a P. vivax marker discovery framework to identify and select panels of microhaplotypes (multi-allelic markers within small, amplifiable segments of the genome) that can accurately capture IBD. We evaluate panels of 50-250 microhaplotypes discovered in a global set of 615 P. vivax genomes. A candidate global 100-microhaplotype panel exhibits high marker diversity in the Asia-Pacific, Latin America and horn of Africa (median HE = 0.70-0.81) and identifies 89% of the polyclonal infections detected with genome-wide datasets. Data simulations reveal lower error in estimating pairwise IBD using microhaplotypes relative to traditional biallelic SNP barcodes. The candidate global panel also exhibits high accuracy in predicting geographic origin and captures local infection outbreak and bottlenecking events. Our framework is open-source enabling customised microhaplotype discovery and selection, with potential for porting to other species or data resources.
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Affiliation(s)
- Sasha V Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
| | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Jakarta, 10430, Indonesia
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Kathryn Murie
- Wellcome Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
| | - Aimee R Taylor
- Institut Pasteur, University de Paris, Infectious Disease Epidemiology and Analytics Unit, Paris, France
| | - Edwin Sutanto
- Exeins Health Initiative, Jakarta Selatan, 12870, Indonesia
| | - Mariana Kleinecke
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
| | | | - James A Watson
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Institute for Global Health and Infectious Diseases, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Awab Ghulam Rahim
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Afghan International Islamic University, Kabul, Afghanistan
| | - Hoang Chau Nguyen
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Tinh Hien Tran
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | | | - Gavin C K W Koh
- Department of Infectious Diseases, Northwick Park Hospital, Harrow, UK
| | - Nicholas J White
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Nicholas Day
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | | | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Ric N Price
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, 0811, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7LJ, UK.
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10
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Kattenberg JH, Cabrera-Sosa L, Figueroa-Ildefonso E, Mutsaers M, Monsieurs P, Guetens P, Infante B, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Plasmodium vivax genomic surveillance in the Peruvian Amazon with Pv AmpliSeq assay. PLoS Negl Trop Dis 2024; 18:e0011879. [PMID: 38991038 PMCID: PMC11265702 DOI: 10.1371/journal.pntd.0011879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 07/23/2024] [Accepted: 06/12/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Plasmodium vivax is the most predominant malaria species in Latin America, constituting 71.5% of malaria cases in 2021. With several countries aiming for malaria elimination, it is crucial to prioritize effectiveness of national control programs by optimizing the utilization of available resources and strategically implementing necessary changes. To support this, there is a need for innovative approaches such as genomic surveillance tools that can investigate changes in transmission intensity, imported cases and sources of reintroduction, and can detect molecular markers associated with drug resistance. METHODOLOGY/PRINCIPAL FINDINGS Here, we apply a modified highly-multiplexed deep sequencing assay: Pv AmpliSeq v2 Peru. The tool targets a newly developed 41-SNP Peru barcode for parasite population analysis within Peru, the 33-SNP vivaxGEN-geo panel for country-level classification, and 11 putative drug resistance genes. It was applied to 230 samples from the Peruvian Amazon (2007-2020), generating baseline surveillance data. We observed a heterogenous P. vivax population with high diversity and gene flow in peri-urban areas of Maynas province (Loreto region) with a temporal drift using all SNPs detected by the assay (nSNP = 2909). In comparison, in an indigenous isolated area, the parasite population was genetically differentiated (FST = 0.07-0.09) with moderate diversity and high relatedness between isolates in the community. In a remote border community, a clonal P. vivax cluster was identified, with distinct haplotypes in drug resistant genes and ama1, more similar to Brazilian isolates, likely representing an introduction of P. vivax from Brazil at that time. To test its applicability for Latin America, we evaluated the SNP Peru barcode in P. vivax genomes from the region and demonstrated the capacity to capture local population clustering at within-country level. CONCLUSIONS/SIGNIFICANCE Together this data shows that P. vivax transmission is heterogeneous in different settings within the Peruvian Amazon. Genetic analysis is a key component for regional malaria control, offering valuable insights that should be incorporated into routine surveillance.
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Affiliation(s)
| | - Luis Cabrera-Sosa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Erick Figueroa-Ildefonso
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mathijs Mutsaers
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Monsieurs
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Pieter Guetens
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
| | - Berónica Infante
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Christopher Delgado-Ratto
- Malaria Research Group (MaRCH), Global Health Institute, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Malaria: Parásitos y Vectores, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Malariology Unit, Biomedical Sciences Department, Institute of Tropical Medicine, Antwerp, Belgium
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11
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Wang T, Zhang Z, Feng Y, Xiao L. Analytic Approaches in Genomic Epidemiological Studies of Parasitic Protozoa. Transbound Emerg Dis 2024; 2024:7679727. [PMID: 40303014 PMCID: PMC12017464 DOI: 10.1155/2024/7679727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/21/2024] [Accepted: 05/28/2024] [Indexed: 05/02/2025]
Abstract
Whole genome sequencing (WGS) plays an important role in the advanced characterization of pathogen transmission and is widely used in studies of major bacterial and viral diseases. Although protozoan parasites cause serious diseases in humans and animals, WGS data on them are relatively scarce due to the large genomes and lack of cultivation techniques for some. In this review, we have illustrated bioinformatic analyses of WGS data and their applications in studies of the genomic epidemiology of apicomplexan parasites. WGS has been used in outbreak detection and investigation, studies of pathogen transmission and evolution, and drug resistance surveillance and tracking. However, comparative analysis of parasite WGS data is still in its infancy, and available WGS data are mainly from a few genera of major public health importance, such as Plasmodium, Toxoplasma, and Cryptosporidium. In addition, the utility of third-generation sequencing technology for complete genome assembly at the chromosome level, studies of the biological significance of structural genomic variation, and molecular surveillance of pathogens has not been fully exploited. These issues require large-scale WGS of various protozoan parasites of public health and veterinary importance using both second- and third-generation sequencing technologies.
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Affiliation(s)
- Tianpeng Wang
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern RegionShaoguan UniversityShaoguan512005China
| | - Ziding Zhang
- State Key Laboratory of Animal Biotech BreedingCollege of Biological SciencesChina Agricultural UniversityBeijing100193China
| | - Yaoyu Feng
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
| | - Lihua Xiao
- State Key Laboratory for Animal Disease Control and PreventionSouth China Agricultural UniversityGuangzhou510642China
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhou510642China
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12
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Sohail A, Barry A, Auburn S, Cheng Q, Lau CL, Lee R, Price RN, Furuya-Kanamori L, Bareng P, McGuinness SL, Leder K. Imported malaria into Australia: surveillance insights and opportunities. J Travel Med 2024; 31:taad164. [PMID: 38127641 PMCID: PMC10998534 DOI: 10.1093/jtm/taad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND Malaria continues to pose a significant burden in endemic countries, many of which lack access to molecular surveillance. Insights from malaria cases in travellers returning to non-endemic areas can provide valuable data to inform endemic country programmes. To evaluate the potential for novel global insights into malaria, we examined epidemiological and molecular data from imported malaria cases to Australia. METHODS We analysed malaria cases reported in Australia from 2012 to 2022 using National Notifiable Disease Surveillance System data. Molecular data on imported malaria cases were obtained from literature searches. RESULTS Between 2012 and 2022, 3204 malaria cases were reported in Australia. Most cases (69%) were male and 44% occurred in young adults aged 20-39 years. Incidence rates initially declined between 2012 and 2015, then increased until 2019. During 2012-2019, the incidence in travellers ranged from 1.34 to 7.71 per 100 000 trips. Cases were primarily acquired in Sub-Saharan Africa (n = 1433; 45%), Oceania (n = 569; 18%) and Southern and Central Asia (n = 367; 12%). The most common countries of acquisition were Papua New Guinea (n = 474) and India (n = 277). Plasmodium falciparum accounted for 58% (1871/3204) of cases and was predominantly acquired in Sub-Saharan Africa, and Plasmodium vivax accounted for 32% (1016/3204), predominantly from Oceania and Asia. Molecular studies of imported malaria cases to Australia identified genetic mutations and deletions associated with drug resistance and false-negative rapid diagnostic test results, and led to the establishment of reference genomes for P. vivax and Plasmodium malariae. CONCLUSIONS Our analysis highlights the continuing burden of imported malaria into Australia. Molecular studies have offered valuable insights into drug resistance and diagnostic limitations, and established reference genomes. Integrating molecular data into national surveillance systems could provide important infectious disease intelligence to optimize treatment guidelines for returning travellers and support endemic country surveillance programmes.
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Affiliation(s)
- Asma Sohail
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Department of Infectious Diseases, Grampians Health, Ballarat 3350, Australia
| | - Alyssa Barry
- Institute for Physical and Mental Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong 3220, Australia
- Disease Elimination Program, Burnet Institute, Melbourne 3004, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0800, Australia
| | - Qin Cheng
- Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane 4051, Australia
| | - Colleen L Lau
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston 4006, Australia
| | - Rogan Lee
- Parasitology Unit, Institute of Clinical Pathology and Medical Research, Sydney 2145, Australia
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin 0800, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, UK
| | - Luis Furuya-Kanamori
- School of Public Health, Faculty of Medicine, The University of Queensland, Herston 4006, Australia
| | - Paolo Bareng
- Institute for Physical and Mental Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong 3220, Australia
| | - Sarah L McGuinness
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Department of Infectious Diseases, Alfred Health, Melbourne 3004, Australia
| | - Karin Leder
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
- Victorian Infectious Diseases Service, Melbourne Health, Melbourne 3052, Australia
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13
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Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S, Barry AE. Molecular markers for malaria genetic epidemiology: progress and pitfalls. Trends Parasitol 2024; 40:147-163. [PMID: 38129280 DOI: 10.1016/j.pt.2023.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kirsty McCann
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jessy Vibin
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia.
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14
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Hoon KS, Holt DC, Auburn S, Shaw P, Giffard PM. minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data. PeerJ 2023; 11:e15339. [PMID: 37250706 PMCID: PMC10224671 DOI: 10.7717/peerj.15339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Here, we present the R package, minSNPs. This is a re-development of a previously described Java application named Minimum SNPs. MinSNPs assembles resolution-optimised sets of single nucleotide polymorphisms (SNPs) from sequence alignments such as genome-wide orthologous SNP matrices. MinSNPs can derive sets of SNPs optimised for discriminating any user-defined combination of sequences from all others. Alternatively, SNP sets may be optimised to determine all sequences from all other sequences, i.e., to maximise diversity. MinSNPs encompasses functions that facilitate rapid and flexible SNP mining, and clear and comprehensive presentation of the results. The minSNPs' running time scales in a linear fashion with input data volume and the numbers of SNPs and SNPs sets specified in the output. MinSNPs was tested using a previously reported orthologous SNP matrix of Staphylococcus aureus and an orthologous SNP matrix of 3,279 genomes with 164,335 SNPs assembled from four S. aureus short read genomic data sets. MinSNPs was shown to be effective for deriving discriminatory SNP sets for potential surveillance targets and in identifying SNP sets optimised to discriminate isolates from different clonal complexes. MinSNPs was also tested with a large Plasmodium vivax orthologous SNP matrix. A set of five SNPs was derived that reliably indicated the country of origin within three south-east Asian countries. In summary, we report the capacity to assemble comprehensive SNP matrices that effectively capture microbial genomic diversity, and to rapidly and flexibly mine these entities for optimised marker sets.
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Affiliation(s)
- Kian Soon Hoon
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Deborah C. Holt
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- CDU Menzies School of Medicine, Faculty of Health, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Sarah Auburn
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Peter Shaw
- Oujian Laboratory, Wenzhou, Zhejiang, China
| | - Philip M. Giffard
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
- CDU Menzies School of Medicine, Faculty of Health, Charles Darwin University, Darwin, Northern Territory, Australia
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15
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Siegel SV, Amato R, Trimarsanto H, Sutanto E, Kleinecke M, Murie K, Whitton G, Taylor AR, Watson JA, Imwong M, Assefa A, Rahim AG, Chau NH, Hien TT, Green JA, Koh G, White NJ, Day N, Kwiatkowski DP, Rayner JC, Price RN, Auburn S. Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.13.23287179. [PMID: 36993192 PMCID: PMC10055443 DOI: 10.1101/2023.03.13.23287179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
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 ("time-to-event" 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 <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 89% (273/307) 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 >0.9 in 90% countries tested) 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.
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Affiliation(s)
- Sasha V. Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Roberto Amato
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Eijkman Institute for Molecular Biology, National Research and Innovation Agency, Jakarta 10430, Indonesia
| | - Edwin Sutanto
- Exeins Health Initiative, Jakarta Selatan 12870, Indonesia
| | - Mariana Kleinecke
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
| | - Kathryn Murie
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | | | - Aimee R. Taylor
- Institut Pasteur, University de Paris, Infectious Disease Epidemiology and Analytics Unit, Paris, France
| | - James A. Watson
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Mallika Imwong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Awab Ghulam Rahim
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Nangarhar Medical Faculty, Nangarhar University, Ministry of Higher Education, Afghanistan
| | - Nguyen Hoang Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 764 Vo Van Kiet, W.1, Dist.5, Ho Chi Minh City, Vietnam
| | | | | | - Nicholas J. White
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Nicholas Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Dominic P. Kwiatkowski
- Wellcome Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Julian C. Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 0XY, UK
| | - Ric N. Price
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, OX3 7LJ, UK
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory 0811, Australia
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
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