Abstract
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.