Pathogen genomic epidemiology has the potential to provide a deep
understanding of population dynamics, facilitating strategic planning of
interventions, monitoring their impact, and enabling timely responses,
and thereby supporting control and elimination efforts of parasitic
tropical diseases. Plasmodium vivax, responsible for most malaria cases
outside Africa, shows high genetic diversity at the population level,
driven by factors like sub-patent infections, a hidden reservoir of
hypnozoites, and early transmission to mosquitoes. While Latin America
has made significant progress in controlling Plasmodium falciparum, it
faces challenges with residual P. vivax. To characterize genetic
diversity and population structure and dynamics, we have analysed the
largest collection of P. vivax genomes to date, including 1474
high-quality genomes from 31 countries across Asia, Africa, Oceania, and
America. While P. vivax shows high genetic diversity globally, Latin
American isolates form a distinctive population, which is further
divided in sub-populations and occasional clonal pockets. Genetic
diversity within the continent was associated with the intensity of
transmission. Population differentiation exists between Central America
and the North Coast of South America, vs. the Amazon Basin, with
significant gene flow within the Amazon Basin, but limited connectivity
between the Northwest Coast and the Amazon Basin. Shared genomic regions
in these parasite populations indicate adaptive evolution, particularly
in genes related to DNA replication, RNA processing, invasion, and
motility -- crucial for the parasite's survival in diverse environments.
Understanding these population-level adaptations is crucial for
effective control efforts, offering insights into potential mechanisms
behind drug resistance, immune evasion, and transmission dynamics.