Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka
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Malaria Journal Open Access
RESEARCH
Use of a Plasmodium vivax genetic barcode for genomic surveillance and parasite tracking in Sri Lanka Rajika L. Dewasurendra1 , Mary Lynn Baniecki2, Stephen Schaffner2,3, Yamuna Siriwardena1, Jade Moon4, R. Doshi5, Sharmini Gunawardena1, Rachel F. Daniels3, Daniel Neafsey2,3, Sarah Volkman2,3, Naduviladath V. Chandrasekharan6, Dyann F. Wirth2,3 and Nadira D. Karunaweera1*
Abstract Background: Sri Lanka was certified as a malaria-free nation in 2016; however, imported malaria cases continue to be reported. Evidence-based information on the genetic structure/diversity of the parasite populations is useful to understand the population history, assess the trends in transmission patterns, as well as to predict threatening phenotypes that may be introduced and spread in parasite populations disrupting elimination programmes. This study used a previously developed Plasmodium vivax single nucleotide polymorphism (SNP) barcode to evaluate the population dynamics of P. vivax parasite isolates from Sri Lanka and to assess the ability of the SNP barcode for tracking the parasites to its origin. Methods: A total of 51 P. vivax samples collected during 2005–2011, mainly from three provinces of the country, were genotyped for 40 previously identified P. vivax SNPs using a high-resolution melting (HRM), single-nucleotide barcode method. Minor allele frequencies, linkage disequilibrium, pair-wise F ST values, and complexity of infection (COI) were evaluated to determine the genetic diversity. Structure analysis was carried out using STRUC TURE software (Version 2.3.4) and SNP barcode was used to identify the genetic diversity of the local parasite populations collected from different years. Principal component analysis (PCA) was used to determine the clustering according to global geographic regions. Results: The proportion of multi-clone infections was significantly higher in isolates collected during an infection outbreak in year 2007. The minor allele frequencies of the SNPs changed dramatically from year to year. Significant linkage was observed in sample sub-sets from years 2005 and 2007. The majority of the isolates from 2007 consisted of at least two genetically distinct parasite strains. The overall percentage of multi-clone infections for the entire parasite sample was 39.21%. Analysis using STRUC TURE software (Version 2.3.4) revealed the high genetic diversity of the sample sub-set from year 2007. In-silico analysis of these data with those available from other global geographical regions using PCA showed distinct clustering of parasite isolates according to geography, demonstrating the usefulness of the barcode in determining an isolate to be indigenous. Conclusions: Plasmodium vivax parasite isolates collected during a disease outbreak in year 2007 were more genetically diverse compared to those collected from other years. In-silico analysis using the 40 SNP barcode is a useful
*Correspondence: [email protected] 1 Department of Parasitology, Faculty of Medicine,
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