Improving anti-malarial treatment of P. vivax by leveraging short and long read DNA sequencing technologies

Charnaud SC1,2, Munro JE1, Quah YW1, Bahlo M1,2 and Mueller I1,2,3

  1. Walter and Eliza Hall Institute, Parkville, Australia.
  2. University of Melbourne, Parkville, Australia.
  3. Institut Pasteur, Paris, France.

The Asia-Pacific region is aiming for malaria elimination by 2030, but despite falling malaria cases Plasmodium vivax persists. The reasons for the greater persistence of P. vivax relate to its unique biology, most importantly its ability to relapse from long-lasting, dormant liver stages (hypnozoites). There are no diagnostic tests for hypnozoites and the only currently available drug to clear hypnozoites is primaquine, which can cause severe haemolysis in people with glucose 6-phosphate dehydrogenase (G6PD) deficiency, and may not work in people with low cytochrome P450 2D6 activity. CYP2D6 is involved in some part in the metabolism of 20-25% of all drugs in clinical use, making it extremely interesting to determine what drugs are likely to work or be contra-indicated in a population. The advent of novel long-read sequencing now makes it possible to sequence complex genes with multiple mutations. We have developed long amplicon barcoded sequencing protocols using PacBio for G6PD and CYP2D6. We will link the genotypes with phenotypes of G6PD deficiency and CYP2D6 activity in populations in PNG and Solomon Islands. This will allow rapid assessment of pharmocogenomic characteristics of malaria endemic populations to tailor antihypnozoite therapy to achieve optimal safety and efficacy in each community. To determine the relatedness of multiple P. vivax infections over time within one person we are also developing a short amplicon based sequencing method. This will allow us to differentiate between (i) recrudescent parasites, indicating drug resistance, (ii) relapse infections from hypnozoite reactivation indicating liver stage treatment failure, and (iii) re-infections indicating high transmission. Together these sequencing methods will allow us to leverage genomics to improve current treatments and to potentially develop new treatments for P.vivax malaria.