Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America

Ibrahim, Amy; Mańko, Emilia; Dombrowski, Jamille Gregório; Campos, Mónica; Benavente, Ernest Diez; Nolder, Debbie; Sutherland, Colin J.; Nosten, François; Fernández, Diana; Vélez-Tobón, Gabriel; Tobón-Castaño, Alberto; Aguiar, Anna Caroline Campos; Pereira, Dhélio Batista; Santos, Simone da Silva; Suárez-Mútis, Martha Cecília; Santi, Sílvia Maria Di; Baptista, Andréa Regina de Souza; Machado, Ricardo Luiz Dantas; Marinho, Cláudio R. F.; Clark, Taane G.; Campino, Susana

doi:10.1016/j.lana.2022.100420

Cited by 6 publications

(11 citation statements)

References 95 publications

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“…However, with the increased sample size in LAM, we do find an additional subpopulation in Latin America compared to earlier studies (Benavente et al, 2021;Cornejo et al, 2015). This increased resolution is confirmed in another very recent study with additional samples from Brazil (Ibrahim et al, 2023).…”

Section: Discussionsupporting

confidence: 85%

“…The global P. vivax population displays high genetic diversity compared to high diversity P. falciparum populations in high transmission regions (Ocholla et al, 2014;Volkman et al, 2007), and separates into three main continental populations, i.e., Eastern Asia and Oceania, Africa and West Asia, and Latin America, similar to other reports (Adam et al, 2022;Daron et al, 2021;Ibrahim et al, 2023).…”

Section: Discussionsupporting

confidence: 84%

“…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 with other studies of P. vivax populations from South America (Cornejo et al, 2015;Ibrahim et al, 2023), supporting the validity of our IBD-approach including polyclonal infections for selection analysis. Considering the similar approaches and findings from these studies using partly the same data, we did not further confirm se- (Hupalo et al, 2016;Pearson et al, 2016).…”

Section: Discussionsupporting

confidence: 62%

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Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Kattenberg,

Monsieurs,

De Meyer

et al. 2024

Ecology and Evolution

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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 analyzed 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 into 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.

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Section: Discussionsupporting

confidence: 85%

Section: Discussionsupporting

confidence: 84%

Section: Discussionsupporting

confidence: 62%

See 1 more Smart Citation

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Kattenberg,

Monsieurs,

De Meyer

et al. 2024

Ecology and Evolution

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“…Clinical malaria caused by simian Plasmodium species, e.g., Plasmodium knowlesi , have also increased in some geographic areas where human Plasmodium species have declined (Amir et al, 2018). We expect that the performance of IBD callers will be similar in other Plasmodium species, given their likely comparable high recombination rates (Bright et al, 2014; Ibrahim et al, 2023); however, generalization would need further exploration as part of future work, considering variations in evolutionary histories and parasite biology (Escalante et al, 2004; Lee et al, 2011; Loy et al, 2017). For other species that exhibit high recombination, but have markedly distinct evolutionary parameters from Plasmodium , the benchmarking framework established in this study can easily be tailored to prioritize and evaluate IBD detection methods in a context-specific manner.…”

Section: Discussionmentioning

confidence: 99%

Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent inPlasmodium falciparum

Guo,

Takala-Harrison,

O’Connor

2024

Preprint

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Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is being used inPlasmodiumpopulation genomics to estimate genetic relatedness, effective population size (Ne), population structure, and positive selection. However, a comprehensive evaluation of IBD segment detection tools is lacking for species with high rates of recombination. Here, we employ genetic simulations reflectingP. falciparum′s high recombination rate and decreasing Neto benchmark IBD callers, including probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD), using genealogy-based true IBD and downstream inference of population characteristics. Our findings reveal that low marker density per genetic unit, related to high recombination rates relative to mutation rates, significantly affects the quality of detected IBD segments. Most IBD callers suffer from high false negative rates, which can be improved with parameter optimization. Optimized parameters allow for more accurate capture of selection signals and population structure, but hmmIBD is unique in providing less biased estimates of Ne. Empirical data subsampled from the MalariaGENPf7 database, representing different transmission settings, confirmed these patterns. We conclude that the detection of IBD in high-recombining species requires context-specific evaluation and parameter optimization and recommend that hmmIBD be used for quality-sensitive analysis, such as estimation of Nein these species.

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“…6b). One previously described signal appeared to be under positive selection in Colombia and encompassed pvmsp1, encoding a merozoite surface protein, a promising vaccine candidate that is involved in merozoite formation, and red blood cell invasion and egress 39,40 . Comparisons of Colombia relative to Peru identi ed 10 signals, one of which was under positive selection in Colombia and contains a 1-acyl-sn-glycerol-3-phosphate acyltransferase gene, putatively involved in cell membrane formation (Fig.…”

Section: Genome-wide Scans To Identify New Adaptations In Colombiamentioning

confidence: 99%

Genomics of Plasmodium vivax in Colombia: evidence of local bottle-necking and inter-country connectivity in the Americas

Sutanto¹,

Pava

Echeverry

et al. 2023

Preprint

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Colombia aims to eliminate malaria by 2030 but remains one of the highest burden countries in the Americas. Plasmodium vivax contributes half of all malaria cases, with its control challenged by relapsing parasitaemia, drug resistance and cross-border spread. Using 64 Colombian P. vivax genomes collected between 2013 and 2017, we explored diversity and selection in two major foci of transmission: Chocó and Córdoba. Open-access data from other countries were used for comparative assessment of drug resistance candidates and to assess cross-border spread. Across Colombia, polyclonal infections were infrequent (12%), and infection connectivity was relatively high (median IBD = 5%), consistent with low endemicity. Chocó exhibited a higher frequency of polyclonal infections (23%) than Córdoba (7%), although the difference was not significant (P = 0.300). Most Colombian infections carried double pvdhfr (95%) and single pvdhps (71%) mutants, but other drug resistance mutations were less prevalent (< 10%). There was no evidence of selection at the pvaat1 gene, whose P. falciparum orthologue has recently been implicated in chloroquine resistance. Global population comparisons identified other putative adaptations. Within the Americas, low-level connectivity was observed between Colombia and Peru, highlighting potential for cross-border spread. Our findings demonstrate the potential of molecular data to inform on infection spread and adaptation.

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Population-based genomic study of Plasmodium vivax malaria in seven Brazilian states and across South America

Cited by 6 publications

References 95 publications

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Population genomic evidence of structured and connected Plasmodium vivax populations under host selection in Latin America

Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent inPlasmodium falciparum

Genomics of Plasmodium vivax in Colombia: evidence of local bottle-necking and inter-country connectivity in the Americas

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