Poster Presentation First Malaria World Congress 2018

Development of a SNP barcode for high resolution monitoring of P. vivax transmission dynamics in Papua New Guinea (#433)

Abebe A Fola 1 2 , Stuart Lee 1 2 , Zahra Razook 2 , Dulcie Lautu 3 , Johanna H Kattenberg 3 , Lyndal Henden 1 2 , Somya Mehra 2 , Manuel Hetzel 4 , Melanie Bahlo 1 2 , Ivo Mueller 1 2 5 , Alyssa Barry 1 2
  1. Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
  2. Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
  3. Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
  4. Swiss TPS/University of Basel, Basel, Switzerland
  5. Department of Parasites and Insect Vectors, Institut Pasteur , Paris, France

Plasmodium vivax is the most widely distributed human malaria parasite outside sub-Saharan Africa and causes significant morbidity. Global efforts to control and eventually to eliminate malaria have had less impact on P. vivax relative to P. falciparum due to its unique biology especially relapse. Population genetics helps to design effective control strategies and to monitor the impact of malaria interventions. SNP barcodes are rapid, accurate and efficient genotyping tools however need to be tailored to specific malaria transmission settings, since the available SNP barcode lacks resolution at the local scale. Papua New Guinea (PNG) has scaled up its control program since 2008, resulting in a significant reduction in malaria transmission. To monitor P. vivax populations in PNG we developed a SNP barcode that captures the diversity of PNG parasites. Using 22 available P. vivax genome sequences from the country, 24283 SNPs with minor allele frequencies of more than 10% were identified in putatively neutral regions of the genome. A subset of 178 evenly spaced SNPs were selected and a high throughput assay was developed using multiplex PCR and Illumina amplicon sequencing. To validate the barcode, we genotyped 96 P. vivax isolates from four catchment areas on the north coast of PNG. Of 178 SNPs, 146 produced high quality genotypes in >85% of isolates. Compared to microsatellite markers the SNP barcode revealed more variable genetic diversity and population divergence and more population structure. The SNP barcode has low genotyping errors, and it is technically feasible to transfer the technology to field settings.