Using whole genome sequencing to reveal malaria parasite genetic diversity and drug resistance in Vietnam

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Malaria, a mosquito-borne disease caused by Plasmodium parasites, is an important public health problem causing an estimated 212 million cases and 429,000 deaths annually. In the WHO Western Pacific Region, 10 out of 37 countries, including Viet Nam, are endemic for malaria. In Viet Nam, there is heterogeneity in malaria prevalence, with the Southern and Central regions with the highest morbidity (7% of population with >1 case per 1000 people). After successfully reducing the malaria burden to pre-elimination levels over the past two decades, the National Malaria Control Programme (NMCP) has recently switched from control to elimination by 2030. Whilst the number of confirmed cases has more than halved between 2012 and 2016 to ~4,200 (P. falciparum 56%, P. vivax 42%), there is now evidence that P. falciparum malaria parasites resistant to frontline treatments have spread to five Vietnamese provinces. Very little data is available for P. vivax drug resistance. The imminent spread of drug-resistant parasites can undermine progress made towards elimination. Drug resistance is caused by mutations in the parasite genomes. Therefore to provide biological insights, we propose to characterise the genetic profiles of ~1,000 Pf and Pv samples sourced from endemic provinces in Viet Nam using cutting edge whole genome sequencing (WGS) technologies. We will investigate genetic differences between samples, within province, across time, and detect known and potentially novel drug resistance markers. Our findings will provide data to the NMCP on drug resistant parasites to assist policy development, and inform the development of diagnostics, vaccines and treatments for malaria. The work will lead to new insights into the genomes of Vietnamese malaria parasites, as well as establish a publically available genetic data resource to facilitate future malaria research. Further, the application of WGS technologies in Viet Nam will build capacity for future genomic investigations.