Monitoring<i>Plasmodium falciparum</i>and<i>Plasmodium vivax</i>using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Kattenberg, Johanna Helena; Razook, Zahra; Keo, Raksmei; Koepfli, Cristian; Jennison, Charlie; Lautu-Gumal, Dulcie; Fola, Abebe A.; Ome-Kaius, Maria; Barnadas, Céline; Siba, Peter; Felger, Ingrid; Kazura, James W.; Müeller, Ivo; Robinson, Leanne J.; Barry, Alyssa E.

doi:10.1111/mec.15654

Cited by 19 publications

(22 citation statements)

References 114 publications

(317 reference statements)

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“…Previous work with microsatellite markers in eight locations of PNG revealed geographic population structure between the mainland, islands and highland areas [9]. However, microsatellites were unable to differentiate populations at a finer spatial scale between the mainland north coast provinces of East Sepik and Madang [46,47,49]. Indeed, microsatellite performance has not previously been compared to SNPs in terms of their ability to differentiate between P. vivax populations.…”

Section: Discussionmentioning

confidence: 99%

“…1) [48]. These P. vivax isolates were selected due to the availability of published microsatellite data [49], which was used to compare with SNP barcode data.…”

Section: Geographic Areasmentioning

confidence: 99%

“…1) were then genotyped for all 178 SNPs using the parallel targeted amplicon sequencing assay. These samples had already been genotyped with ten microsatellite markers in a previous study [49]. A total of 28,934,460 reads were generated from the MiSeq Illumina run with a variable sequencing coverage across samples per locus (median = 563, range 56 -7586).…”

Section: Data Summary and Validation Of The Barcodementioning

confidence: 99%

“…There were no private SNPs (unique to any one population). Published genotyping data for MOI [72] and microsatellite data for these P. vivax isolates [49] was then used to compare the population genetic metrics with the new SNP barcode data.…”

Section: Data Summary and Validation Of The Barcodementioning

confidence: 99%

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SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

Fola

Kattenberg

Razook

et al. 2020

Malar J

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Background Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since ‘universal’ barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. Methods Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. Results From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56–7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. Conclusions High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.

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Section: Discussionmentioning

confidence: 99%

“…1) [48]. These P. vivax isolates were selected due to the availability of published microsatellite data [49], which was used to compare with SNP barcode data.…”

Section: Geographic Areasmentioning

confidence: 99%

Section: Data Summary and Validation Of The Barcodementioning

confidence: 99%

Section: Data Summary and Validation Of The Barcodementioning

confidence: 99%

See 2 more Smart Citations

SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

Fola

Kattenberg

Razook

et al. 2020

Malar J

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“…In humans, genome-wide SNPs have been used to infer population structure and admixture (Pickrell and Pritchard 2012;Lipson et al 2013;Hellenthal et al 2014;Bradburd et al 2016). Conversely, microsatellite markers, which have a larger number of alleles than SNPs, despite the smaller number of loci, are still usual tools in ecology and conservation biology (e.g., Sylvester et al 2018;D'Aloia et al 2020;Kattenberg et al 2020;Karamanlidis et al 2021). We use microsatellite data for illustrative purposes.…”

mentioning

confidence: 99%

Understanding population structure in an evolutionary context: population-specificF_STand pairwiseF_ST

Kitada

Nakamichi

Kishino

2020

Preprint

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Appropriate estimates of population structure are the basis of population genetics, with applications varying from evolutionary and conservation biology to association mapping and forensic identification. The common procedure is to first compute Wright’s FST over all samples (global FST) and then routinely estimate between-population FST values (pairwise FST). An alternative approach for estimating population differentiation is the use of population-specific FST measures. Here, we characterize population-specific FST and pairwise FST estimators by analyzing publicly available human, Atlantic cod and wild poplar data sets. The bias-corrected moment estimator of population-specific FST identified the source population and traced the migration and evolutionary history of its derived populations by way of genetic diversity, whereas the bias-corrected moment estimator of pairwise FST was found to represent current population structure. Generally, the first axis of multi-dimensional scaling for the pairwise FST distance matrix reflected population history, while subsequent axes indicated migration events, languages and the effect of environment. The relative contributions of these factors were dependent on the ecological characters of the species. Given shrinkage towards mean allele frequencies, maximum likelihood and Bayesian estimators of locus-specific global FST improved the power to detect genes under environmental selection. In contrast, bias-corrected moment estimators of global FST measured species divergence and enabled reliable interpretation of population structure. The genomic data highlight the usefulness of the bias-corrected moment estimators of FST. The R package FinePop2_ver.0.2 for computing these FST estimators is available at CRAN.

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Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Kattenberg,

Monsieurs,

De Meyer

et al. 2024

Ecology and Evolution

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Pathogen genomic epidemiology has the potential to provide a deep understanding of population dynamics, facilitating strategic planning of interventions, monitoring their impact, and enabling timely responses, and thereby supporting control and elimination efforts of parasitic tropical diseases. Plasmodium vivax, responsible for most malaria cases outside Africa, shows high genetic diversity at the population level, driven by factors like sub‐patent infections, a hidden reservoir of hypnozoites, and early transmission to mosquitoes. While Latin America has made significant progress in controlling Plasmodium falciparum, it faces challenges with residual P. vivax. To characterize genetic diversity and population structure and dynamics, we have analyzed the largest collection of P. vivax genomes to date, including 1474 high‐quality genomes from 31 countries across Asia, Africa, Oceania, and America. While P. vivax shows high genetic diversity globally, Latin American isolates form a distinctive population, which is further divided into sub‐populations and occasional clonal pockets. Genetic diversity within the continent was associated with the intensity of transmission. Population differentiation exists between Central America and the North Coast of South America, vs. the Amazon Basin, with significant gene flow within the Amazon Basin, but limited connectivity between the Northwest Coast and the Amazon Basin. Shared genomic regions in these parasite populations indicate adaptive evolution, particularly in genes related to DNA replication, RNA processing, invasion, and motility – crucial for the parasite's survival in diverse environments. Understanding these population‐level adaptations is crucial for effective control efforts, offering insights into potential mechanisms behind drug resistance, immune evasion, and transmission dynamics.

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MonitoringPlasmodium falciparumandPlasmodium vivaxusing microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Cited by 19 publications

References 114 publications

SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

Understanding population structure in an evolutionary context: population-specificF_STand pairwiseF_ST

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

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MonitoringPlasmodium falciparumandPlasmodium vivaxusing microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea

Cited by 19 publications

References 114 publications

SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics

Understanding population structure in an evolutionary context: population-specificFSTand pairwiseFST

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

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Product

Resources

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Understanding population structure in an evolutionary context: population-specificF_STand pairwiseF_ST