Discussion
Here we report the genomic analysis of the largest collection (n=1474)
of high-quality P. vivax genomes to date, originating from 31
countries across Asia, Africa, Oceania and Americas. The global P.
vivax population displays high genetic diversity and separates into
three main continental populations, i.e. Eastern Asia and
Oceania, Africa and West Asia, and Latin America, similar to other
reports . The geographical clustering largely matches the previously
defined zoogeographical zones with similar ecological and
epidemiological characteristics and P. vivax relapse rates . Most
of the clusters identified in the admixture analysis are relatively
isolated within one region, with little admixture between regions, with
the exception of Africa and West Asia, as reported previously . In
contrast, a high degree of admixture is observed within regions,
especially in South-East Asia and in LAM. In this study we increased the
number of genomes compared to previous reports, in particular from West
Africa, Vietnam, Brazil and Peru, with the largest genomic analysis of
Latin American isolates (n= 399) to date. With additional samples from
South-East Asia compared to earlier studies , we do not find additional
subpopulations in admixture analysis in this region. However, with the
increased sample size in LAM, we do find an additional subpopulation in
Latin America compared to earlier studies . This increased resolution is
confirmed in another very recent study with additional samples from
Brazil .
P. vivax isolates from Latin America form a distinct group within
the global P. vivax population, characterized by structured
subpopulations, sporadic clonal clusters at specific sites, and lower
genetic diversity compared to other regions in the world. This analysis
confirms the pattern of low-local but relatively high-regional genetic
diversity in LAM measured previously using microsatellites .
The lower genetic diversity of P. vivax in LAM might be explained
by a founder effect of relatively recent colonization events of this
parasite species in this region, potentially through multiple waves of
human migrations . In addition, a lower transmission intensity in LAM
compared to other regions in the world can contribute to the lower
diversity . In turn, Brazil, which is the country with the highest
incidence of malaria -among those included in the LAM region in this
study- exhibited the greatest level of genetic diversity. Furthermore,
in comparison to genetic diversity of P. falciparum populations
in high transmission African regions P. vivax diversity in LAM is
high . This is typically the effect of random genetic drift in small
populations that remain relatively isolated from each other; rare
alleles disappear (decreased diversity) and increased divergence between
sites. Gene flow and admixture were detected across populations from
Mexico, Panama, and the North Coast of Colombia, and across countries in
the Amazon region, however connectivity between these two separate
regions is highly limited. This marked population differentiation
between these two regions might be attributed to factors such as
differentiated ecological environments, distinct vector populations,
different human occupation and mobility patterns, and history of
antimalarial interventions . These differentiation patterns are very
similar to those observed in P. falciparum populations in South
America . While the Amazon region and coastline regions of South and
Central America are suitable habitats for various malaria vectors, there
are ecological and human barriers between the Central and Northern South
American coastlines and the Amazon region. These regions are separated
by mountain ranges and have clear differences in climate and vegetation
where the north coast region has a tropical climate with a dry season,
while the Amazon rainforest has a tropical rainforest climate with
year-round rainfall. The observed limited connectivity of parasite
populations also suggests limited human mobility and thereby limited
transmission between these regions.
Indeed, the Amazon basin is a vast territory of tropical rainforest
encompassing several countries and including large regions of indigenous
territories intersected by numerous rivers and scattered cities and
villages that offer natural barriers contributing to the observed
subpopulation structure . On the other hand, connectivity and admixtures
within this region in all likelihood is due to patterns of human
mobility, which are closely related to occupational patterns like
logging and illegal gold mining . In addition, transmission of malaria
(and gene flow) across large geographic distances is facilitated by the
large human reservoir of asymptomatic and low-density P. vivaxinfections characteristic for this region as well as the dormant
reservoir of hypnozoites characteristic for P. vivax in general .
Conversely, further North, in Colombia, Panama and Mexico we observe
less admixture than in the Amazon region and distinct populations by
country. We identified a specific subpopulation that is predominant in
Colombia, but also observed (in a lower proportion) in Panama and even
into Mexico likely reflecting human migration facilitating spread of
this population from the North coast of Colombia into countries further
to the North. According to a recent study, the majority of P.
vivax genomes in Panama are part of a highly clonal population that has
been present in the country for at least ten years . In addition, the
same study reported likely imported parasites, which we identified to
belong to Colombian population.
We identified genomic regions shared across Latin American parasite
populations that exhibit signatures of positive selection. Genes in
these shared regions are predominantly involved in DNA replication
binding and repair, RNA transcription and processing, parasite invasion,
as well as microtubule-related motility, suggesting that genes involved
in these biological processes are key for P. vivax evolution and
survival. Positive selection on DNA replication, binding, and repair
genes suggests adaptive evolution to environmental challenges such us
host immune responses, while positive selection on genes associated with
RNA transcription and processing hints at the potential role of
post-transcriptional gene regulation in parasite adaptation and survival
to varying conditions , such as parasite transition between hosts or
life cycle stages (such as the male and female development through MD1
and FD1). Moreover, microtubules are essential components of the
cytoskeleton and play a critical role in cell division, motility, and
intracellular transport.
The selection signals in LAM are dissimilar to P. vivaxpopulations in other regions, as previous investigations with globalP. vivax isolate collections detected selective sweeps at drug
resistance-associated loci (e.g., dhfr, dhps , andmdr1 ), . However, these studies also found evidence of local
adaptation within distinct P. vivax populations and differential
selection on surface antigens such as msp genes. Results from
this study are in agreement with previous studies of P. vivaxpopulations from South America , supporting the validity of our
IBD-approach including polyclonal infections for selection analysis. In
contrast to previous studies, we included sub-telomeric regions in the
selection analysis. We identified genes under selection putatively
involved in antigenicity and host–parasite interactions, including
parasite invasion, which is poorly understood in P. vivax .
Positive selection in invasion genes has the potential to identify new
candidate genes with a role in reticulocyte invasion and hence, can
inform vaccine development, for example against antigens such aslsa3 and msp3 found under selection here. In P.
falciparum , lsa3 is a candidate vaccine target and has been used
to elicit sterile immunity in animal models .
Sub-telomeric regions are often excluded in genome analysis due to
challenges in aligning their highly variable and polymorphic short
reads, particularly with the incomplete PvSalI reference genome, but
newer genomes like PvP01 now provide improved assembly for these regions
. Our results of positive selection in these sub-telomeric regions match
well with a proposed model of P. vivax adaptation from a genomic
study of P. vivax strains compared to P. cynomolgi andP. knowlesi . That study proposed that positive and negative
selection might be less effective in low recombination areas
(i.e. in the core genome). They suggested that in P.
vivax, genome structure might be an adaptive mechanism to deal with
changing environments, like the host’s immune system, in addition to
adaptations through genetic variation. In contrast, in P.
falciparum populations, which need to survive in the host for a longer
period before they can be transmitted, strong selection signals and high
IBD are found in the core genome, for example surrounding drug
resistance associated genes .
This study used a convenience sampling approach, limiting the ability to
generalize findings. The majority of genomes included were from Brazil,
Peru, and the Colombian coastal region, while genomes from other highP. vivax burden areas such as Venezuela, Nicaragua, and the
Amazon region of Colombia are lacking. To complete the picture of
genetic diversity in Latin America genomes from these regions, often
remote or challenging to access, need to be generated.
This regional analysis of P. vivax populations in Latin America
highlights the significant genetic diversity within the continent, and
regional adaptation of the parasites to their hosts and different
environmental challenges, which may contribute to the resilience ofP. vivax to current malaria control strategies. Connectivity
patterns between parasite populations are highly relevant for control
and elimination programs in the region where human mobility is a major
driver of malaria transmission. IBD-analysis confirmed connectivity
between different ancestral clusters within and between countries,
whilst showing a lack of connectivity between parasites in northern
regions of Central and South America and the Amazon parasite population.
While temporal differences in relatedness can serve as evidence for
changes in transmission over time , the populations identified were very
stable over time, indicating ongoing and stable transmission.
Genomic surveillance of parasitic pathogens, coupled with
epidemiological data, offers valuable insights for control and
elimination programs. This study highlights the use of genetic
information to uncover patterns to address key epidemiological questions
related to P. vivax in Latin America, and demonstrates how
parasite genetic information can reveal transmission patterns and
connections among populations. Furthermore, understanding
population-level diversity is important for controlling malaria
effectively, as it can provide insights into drug resistance
development, immune evasion strategies, and transmission dynamics. For
example, measuring genetic diversity and within-host infection
complexity can indicate the intensity of P. vivax transmission in
Latin America, similar to approaches used for P. falciparumpopulations . In contrast, these indicators have been less accurate forP. vivax in areas with higher genetic diversity like Southeast
Asia and Oceania .
Finally, as malaria risk is increasing in spatial and temporal
variability worldwide, the diversity of available malaria control tools
continues to grow, and funding constraints on control programs increase,
there is an increasing need for malaria-endemic countries to adopt
intervention policies that move away from a one-size-fits-all approach
to one that is specifically tailored to their subnational context.
However, the high level of connectivity between regions and countries
observed in this study rather shows that a wider view and regional
approach remains very important in this continent and should remain
incorporated in regional malaria control and elimination strategies.