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

Fola, Abebe A, Kattenberg, Eline, Razook, Zahra, Lautu-Gumal, Dulcie, Lee, Stuart, Mehra, Somya, Bahlo, Melanie, Kazura, James, Robinson, Leanne J, Laman, Moses, Mueller, Ivo and Barry, Alyssa E 2020, SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics, Malaria journal, vol. 19, no. 1, pp. 1-15, doi: 10.1186/s12936-020-03440-0.

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Title SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics
Author(s) Fola, Abebe A
Kattenberg, Eline
Razook, Zahra
Lautu-Gumal, Dulcie
Lee, Stuart
Mehra, Somya
Bahlo, Melanie
Kazura, James
Robinson, Leanne J
Laman, Moses
Mueller, Ivo
Barry, Alyssa EORCID iD for Barry, Alyssa E orcid.org/0000-0002-1189-2310
Journal name Malaria journal
Volume number 19
Issue number 1
Article ID 375
Start page 1
End page 15
Total pages 15
Publisher BioMed Central
Place of publication London, Eng.
Publication date 2020
ISSN 1475-2875
1475-2875
Keyword(s) Science & Technology
Life Sciences & Biomedicine
Infectious Diseases
Parasitology
Tropical Medicine
Malaria
Plasmodium vivax
Microsatellites
Single Nucleotide Polymorphisms (SNPs)
Diversity
Population structure
Papua New Guinea
Summary 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.
Language eng
DOI 10.1186/s12936-020-03440-0
Indigenous content off
Field of Research 0605 Microbiology
1108 Medical Microbiology
1117 Public Health and Health Services
HERDC Research category C1 Refereed article in a scholarly journal
Free to Read? Yes
Persistent URL http://hdl.handle.net/10536/DRO/DU:30144409

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.