The utility of genomic data for<i>Plasmodium vivax</i>population surveillance

Daniels, Rachel F.; Rice, Benjamin L.; Daniels, Noah M.; Volkman, Sarah K.; Hartl, Daniel L.

doi:10.1179/2047773215y.0000000014

Cited by 10 publications

(15 citation statements)

References 61 publications

(72 reference statements)

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“…This increase in monoclonal infection may reflect a general decline in the Cambodian P . vivax population, which may be indicative of the success of elimination programs [ 57 ] (e.g., see [ 58 , 59 ] for a similar pattern in P . falciparum in Senegal).…”

Section: Discussionmentioning

confidence: 99%

Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax

et al. 2016

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BackgroundPlasmodium vivax is the most widely distributed human malaria parasite with 2.9 billion people living in endemic areas. Despite intensive malaria control efforts, the proportion of cases attributed to P. vivax is increasing in many countries. Genetic analyses of the parasite population and its dynamics could provide an assessment of the efficacy of control efforts, but, unfortunately, these studies are limited in P. vivax by the lack of informative markers and high-throughput genotyping methods.Methodology/Principal FindingsWe developed a sequencing-based assay to simultaneously genotype more than 100 SNPs and applied this approach to ~500 P. vivax-infected individuals recruited across nine locations in Cambodia between 2004 and 2013. Our analyses showed that the vast majority of infections are polyclonal (92%) and that P. vivax displays high genetic diversity in Cambodia without apparent geographic stratification. Interestingly, our analyses also revealed that the proportion of monoclonal infections significantly increased between 2004 and 2013, possibly suggesting that malaria control strategies in Cambodia may be successfully affecting the parasite population.Conclusions/SignificanceOur findings demonstrate that this high-throughput genotyping assay is efficient in characterizing P. vivax diversity and can provide valuable insights to assess the efficacy of malaria elimination programs or to monitor the spread of specific parasites.

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Section: Discussionmentioning

confidence: 99%

Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax

et al. 2016

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“…10 This topic is covered in more detail by a review included in this special issue. 34 Mitochondrial DNA…”

Section: Single Nucleotide Polymorphismsmentioning

confidence: 99%

“…Previous analyses suggested an Asian origin based on high mtDNA diversity in this region, but are likely to have been influenced by the lack of African parasites in the sample and by demographic processes such as population expansion, which increases diversity. 44 There have been some attempts to understand how P. vivax subsequently spread around the world using mtDNA [34][35][36]45 ; however, the population structure is complex and requires further deep sampling of strains from all major endemic regions. Nevertheless, some important insights have been gained into the evolutionary history of P. vivax in different geographic regions.…”

Section: Emergence Global Spread and Evolutionary Historymentioning

confidence: 99%

Uncovering the transmission dynamics ofPlasmodium vivaxusing population genetics

Barry

Waltmann

Koepfli

et al. 2015

Pathogens and Global Health

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Population genetic analysis of malaria parasites has the power to reveal key insights into malaria epidemiology and transmission dynamics with the potential to deliver tools to support control and elimination efforts. Analyses of parasite genetic diversity have suggested that Plasmodium vivax populations are more genetically diverse and less structured than those of Plasmodium falciparum indicating that P. vivax may be a more ancient parasite of humans and/or less susceptible to population bottlenecks, as well as more efficient at disseminating its genes. These population genetic insights into P. vivax transmission dynamics provide an explanation for its relative resilience to control efforts. Here, we describe current knowledge on P. vivax population genetic structure, its relevance to understanding transmission patterns and relapse and how this information can inform malaria control and elimination programmes.

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“…Moreover, recent intensive malaria control activities may lead to changes in MAF with a loss of rare variants [19,20] that could reduce the power of the existing SNP barcode to distinguish between different genotypes. The use of population genomic data to aid malaria control relies on having this insight at regional or sub-national resolution, and will vary for different endemic settings and stages in the elimination pipeline [23]. Therefore, validating available barcodes or developing a new barcode that accurately captures the diversity of a country's parasite population will facilitate characterization of the local malaria transmission scenario.…”

Section: Introductionmentioning

confidence: 99%

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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The utility of genomic data forPlasmodium vivaxpopulation surveillance

Cited by 10 publications

References 61 publications

Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax

Complexity of Infection and Genetic Diversity in Cambodian Plasmodium vivax

Uncovering the transmission dynamics ofPlasmodium vivaxusing population genetics

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

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