Focal inbreeding and clonal transmission of Plasmodium vivax in pre-elimination Vietnam

Abstract Although malaria prevalence in Vietnam has markedly declined and the country presses closer to elimination, a highly focal reservoir of Plasmodium vivax malaria persists in its forested and border regions, threatening the country’s 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. vivax isolates 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. vivax in 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. Author Summary Plasmodium vivax is the most geographically widespread malaria parasite and the predominant species in the Greater Mekong Subregion. In Vietnam, P. vivax malaria continues to persist in remote forested settings and along its international borders. Using genomic approaches, we analysed 133 P. vivax genomes from the Central Highlands, South Central Coast, and Southeastern regions of Vietnam, including 18 newly sequenced isolates collected in 2019 and 115 publicly available genomes sampled between 2009 and 2016. Our work describes the evolutionary and genetic consequences of intensive control efforts that have led to decreasing transmission and population decline. We found decreasing infection complexity and increasing clonal inbreeding, which suggests localised transmission of clonal lineages in transmission hotspots. Over the 10-year sampling period, we observed consistent allele frequencies in putative drug resistance loci, suggesting an absence of drug-driven directional selection. Our findings highlight the importance of genomic surveillance in monitoring parasite persistence, which will be critical for guiding public health decisions to sustain progress towards malaria elimination. Competing Interest Statement The authors have declared no competing interest. Footnotes Gabrielle.Ngwana-Joseph{at}lshtm.ac.uk, nguyenhuongbinh74{at}gmail.com, ngocnimpe{at}gmail.com, Jody.Phelan{at}lshtm.ac.uk, Data Availability All raw Illumina sequence data used in this work is publicly available on the European Nucleotide Archive. Newly sequenced isolates from Vietnam are publicly available under Project PRJEB111293. Accession numbers and sample provenance for all samples are available in Table S2.