Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region

Abstract

The Asia-Pacific region faces formidable challenges in achieving malaria elimination by the proposed target in 2030. Molecular surveillance of Plasmodium parasites can provide important information on malaria transmission and adaptation, which can inform national malaria control programmes (NMCPs) in decision-making processes. In November 2019 a parasite genotyping workshop was held in Jakarta, Indonesia, to review molecular approaches for parasite surveillance and explore ways in which these tools can be integrated into public health systems and inform policy. The meeting was attended by 70 participants from 8 malaria-endemic countries and partners of the Asia Pacific Malaria Elimination Network. The participants acknowledged the utility of multiple use cases for parasite genotyping including: quantifying the prevalence of drug resistant parasites, predicting risks of treatment failure, identifying major routes and reservoirs of infection, monitoring imported malaria and its contribution to local transmission, characterizing the origins and dynamics of malaria outbreaks, and estimating the frequency of Plasmodium vivax relapses. However, the priority of each use case varies with different endemic settings. Although a one-size-fits-all approach to molecular surveillance is unlikely to be applicable across the Asia-Pacific region, consensus on the spectrum of added-value activities will help support data sharing across national boundaries. Knowledge exchange is needed to establish local expertise in different laboratory-based methodologies and bioinformatics processes. Collaborative research involving local and international teams will help maximize the impact of analytical outputs on the operational needs of NMCPs. Research is also needed to explore the cost-effectiveness of genetic epidemiology for different use cases to help to leverage funding for wide-scale implementation. Engagement between NMCPs and local researchers will be critical throughout this process.

Keywords: Genomics; Genotyping; Malaria; Molecular surveillance; Plasmodium falciparum; Plasmodium vivax; SNP barcode; Surveillance.

Fig. 1

Imported case proportions and total malaria case numbers in the Asia–Pacific region in 2018. a presents the percentage of imported cases (all species of malaria) in 2018 in order of highest to lowest percentage. b presents the total number of presumed and confirmed cases (for all species) in 2018 in the same order as (a). The numbers were derived from the World Malaria Report 2019 summary of reported malaria cases by method of confirmation 2010–2018 for countries in the WHO Southeast Asia and Western Pacific region. The percentage of imported cases was calculated as the number of imported cases divided by the total number of presumed and confirmed cases. The countries with the highest proportion of imported cases have amongst the lowest number of overall cases

Fig. 2

Example of a GenRe-Mekong drug resistance prevalence “traffic light” plot. Example of a map generated by the SpotMalaria GenRe-Mekong project, showing the predicted prevalence of artemisinin-resistant parasites at sites in 6 provinces of Vietnam before September 2018. District-level drug resistance-associated allele frequencies are coloured according to prevalence (ranging from 0–100% in a spectrum from green to red). Courtesy of the Institute of Malariology, Parasitology and Entomology, Quy Nhon and OUCRU, Vietnam