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

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.

Malaria, caused by Plasmodium parasites, remains a barrier to social and economic development in resource poor areas of Viet Nam. Between 2012 and 2016, Viet Nam achieved a 52% reduction in malaria cases to ~4,200 (P. falciparum 56%, P. vivax 42%). The campaign against malaria by the Vietnamese Government is now being refocused from control to elimination by year 2030. However, this campaign is challenged by the threat of parasites, which are resistant to existing frontline artemisinin combination treatments and spreading in the Greater Mekong Sub-region (GMS); five Vietnamese provinces have been identified to harbour these drug-resistant parasites. Compared to P. falciparum, very little is known about drug resistance in Pv, but is driven by genetic mutations in the parasite genomes. New molecular tools to characterise circulating parasites are warranted. Here we propose to characterise the genetic diversity and the molecular basis of drug resistance of malaria parasites in Viet Nam using whole genome sequencing (WGS). By examining the genomic variation from both Pf and Pv sourced from 5 malaria endemic provinces, we will be able to detect crucial mutations in drug resistance genes (e.g. PfKelch, PfPlasmepsin2, Pfmdr1 and related genes in Pv), and potentially identify new loci by using population genetic approaches to uncover "selective sweeps". The genomic variation will allow an assessment of differences in population structure across time, between the geographical areas, and within the GMS context and beyond. We will also perform comparative Pf and Pv species analysis to highlight any differential effects of control practice.
As part of this application, it is also proposed to build capacity in Viet Nam in the area of malaria genomics and its applications through on-site training and workshops, as well as exchange of researchers between the UK and Viet Nam. These activities will assist Vietnamese scientists to undertake genomics research studies in the future.

The economy
Advances in sequencing technology now allow the genomic characterisation of malaria parasites on an unprecedented scale, and have the potential to greatly accelerate research aimed at understanding the biology of the parasite, its geographical spread, the underlying causes of its drug resistance and transmission, and the epidemiology of the disease. Genomic technologies have the ability to generate vast amounts of data, and there is a need to translate this information into knowledge useable by other research scientists and industry. The proposed work will provide tools useful for genomic data analysis and modelling. The knowledge generated in the project and application of the research could benefit the scientific community, including control programs looking at the spread of disease and drug resistance. Those in the pharmaceutical industry, particularly those developing malaria diagnostics, treatments and vaccines will also benefit from the research. The methods used in this project could have application beyond malaria, to support more widely in the control and prevention of infectious diseases with associated economic benefits.

The results will provide evidence to guide future research in academia and industry and policy decisions in government. It is envisaged that the findings can be used to inform malaria control activities and mitigate the spread of drug resistance strains, enabling Viet Nam to reach (and maintain) elimination status in 2030. Ultimately, the knowledge gained in this study could improve the health and wealth of the country, leading to a working population with lower burden of malarial disease. The NIMPE will facilitate the reach and potential uptake of research findings in Viet Nam through the National Malaria Control Programme (NMCP) and the MOH, as well as links at the national, regional and international levels.
Academic and industrial organisations
New high throughput genomic technologies have the ability to generate vast amounts of data, but there is a need to translate this information into knowledge useable by other research scientists and industry, especially in countries where malaria is endemic. Our work will provide tools useful for genomic data analysis and visualisation, which can be utilized across infectious diseases and in different settings. An understanding of genomic variation could lead to follow-up laboratory experiments, improved diagnostic tests for detecting pan-parasite species, and reveal new parasite gene targets for anti-malarial treatments and vaccines. Scientific developments arising would enhance the commercial private sector for the production of diagnostics, vaccines and other control measures, as well as academics involved in policy formulation. The LSHTM technology transfer office has processes to ensure pipelines to vaccine or other translation tool production and exploitation. Any technologies developed may have enormous implications for policy makers for future disease outbreaks and elimination of infectious diseases.

Training opportunities
The proposal will employ, train and develop a scientist with diverse experience and an 'omic mentality that can be applied in academia, the public sector and industry. The researchers working on the project will develop team working and project management skills, which they can apply in all employment sectors. The researchers employed will have unique opportunities for engagement with experts (e.g. in the LSHTM - Malaria Centre, The Applied Genomics Centre) in malaria biology, epidemiology, clinical care, genomic and public health. There will also be opportunities to train researchers and public health stakeholders in genomic data analysis, including the next generation of Vietnamese researchers. Thus, our proposal will impact on the creation of human resources that could subsequently be employed in challenging interdisciplinary projects in industry, academia and government, across countries.