Ngwana-Joseph, G.; Nguyen Thi Huong, B.; Nguyen Thi Hong, N.; Phelan, J. E.; Campino, S.; Nguyen Quang, T.; Clark, T. G.

Although malaria prevalence in Vietnam has markedly declined and the country presses closer to elimination, a highly focal reservoir of Plasmodium vivaxmalaria persists in its forested and border regions, threatening the countrys 2030 elimination targets. Genomic surveillance of malaria parasites can be a vital tool to produce fine-scale insights into the changing population dynamics of parasite populations, especially in population decline. Here, we analysed the genomic diversity of 18 newly sequenced P. vivaxisolates from the Central Highlands, South Central Coast, and Southeastern regions of Vietnam collected in 2019, analysing them alongside 115 publicly available sequences from Vietnam collected between 2009-2016. Over these 10 years, infections became increasingly monoclonal, transmission remained highly focal, and the overall population structure was weak. Geographic factors, and not temporal factors, were a major driver of genetic substructure. Identity-by-descent (IBD) analyses revealed pockets of inbreeding in transmission hotspots, and high relatedness in parasites from within the same or adjacent provinces. Whilst within-population haplotype-based testing revealed minimal selection pressures on the 2009-2016 and 2019 populations, we observed multiple signals of differential selection of genetic variants involved in life-cycle specific processes. Overall, our work provides the most recent assessment of the genomic diversity of P. vivaxin Vietnam, revealing relics of evolution in a parasite population in decline. Continued genomic surveillance, especially in outbreak contexts, and with more recent samples will be a crucial strategy to inform malaria elimination activities.