Biology subjects

Gamboa, D.

Publications and source records attributed to Gamboa, D..

8 recordsLinked to original sources

bioRxiv2026

Malaria control and the unexpected spread of diagnostic-resistant Plasmodium falciparum in Peru

Plasmodium falciparum parasites with deletions of the histidine-rich protein 2 and 3 (hrp2 and hrp3) genes evade detection by common rapid diagnostic tests (RDTs) and pose a growing threat to malaria control. While these deletions have emerged in multiple regions globally, the evolutionary forces driving their spread remain unclear. Here, we analyze 1,215 P. falciparum samples collected between 2003 and 2018 in Loreto, Peru. This region experienced a major decline in malaria transmission following the Project for Malaria Control in Andean Border Areas (PAMAFRO) and now harbors a high proportion of hrp2/3 deleted parasites despite limited RDT use. Using molecular inversion probe (MIP) sequencing across > 2,000 genome-wide loci, we observed a marked reduction in genetic diversity, increased clonality, and fixation of parasites with deletions of both hrp2 and hrp3 genes (hrp2-/3-) over time. Identity-by-descent (IBD) analysis revealed rapid expansion of a single hrp2-/3- dominant lineage in the post-PAMAFRO period, consistent with clonal replacement after intense malaria control. Targeted sequencing of the hrp2/3 regions showed conserved deletion breakpoints across three different lineages, indicative of recombination of a common haplotype into distinct genetic backgrounds. To investigate the evolutionary forces driving the fixation of hrp2-/3- in Loreto, we simulated allele frequency trajectories under different selection coefficients. We found that fixation of hrp2-/3- due solely to genetic drift (selection coefficient s = 0) is unlikely; a selection coefficient of s [≥] 0.03 was required for fixation to occur consistently. However, our simulations also indicate that a genetic bottleneck caused by PAMAFRO increased the likelihood of fixation through drift by 4.5- to 17-fold depending on the population. These findings suggest that hrp2-/3- fixation was likely driven by a combination of demographic changes resulting from PAMAFRO and selective advantage unrelated to RDT use. Our results demonstrate how intensive malaria control efforts can reshape parasite populations and underscore the value of expanded genomic surveillance as countries move toward malaria elimination.

genetics↗

bioRxiv2025

Population genomics of Anopheles darlingi, the principal South American malaria vector mosquito

Malaria in South America remains a serious public health problem. Anopheles (Nyssorhynchus) darlingi is the most important malaria vector across tropical Latin America. Vector-targeted disease control efforts require a thorough understanding of mosquito demographic and evolutionary patterns. We present and analyze whole genomes of 1094 A. darlingi (median depth 18x) from six South American countries. We observe deep geographic population structure, high genetic diversity including thirteen putative segregating inversions, and no evidence for cryptic sympatric taxa despite high interpopulation divergence. Strong signals of selection are plausibly driven by insecticides, especially on cytochrome P450 genes, one of which we validated experimentally. Our results will facilitate effective mosquito surveillance and control, while highlighting ongoing challenges that a diverse vector poses for malaria elimination in the western hemisphere.

evolutionary biology↗

bioRxiv2024

Comparing newly developed SNP barcode panels with microsatellites to explore population genetics of malaria parasites in the Peruvian Amazon

Malaria molecular surveillance (MMS) can provide insights into transmission dynamics, guiding national control/elimination programs. Considering the genetic differences among parasites from different areas in the Peruvian Amazon, we previously designed SNP barcode panels for Plasmodium vivax (Pv) and P. falciparum (Pf), integrated into AmpliSeq assays, to provide population genetics estimates of malaria parasites. These AmpliSeq assays are ideal for MMS: multiplexing different traits of interest, applicable to many use cases, and high throughput for large numbers of samples. The present study compares the genetic resolution of the SNP barcode panels in the AmpliSeq assays with widely used microsatellite (MS) panels to investigate Amazonian malaria parasites. Malaria samples collected in remote areas of the Peruvian Amazon (51 Pv & 80 Pf samples) were characterized using the Ampliseq assays and MS. Population genetics estimates (complexity of infection, genetic diversity and differentiation, and population structure) were compared using the SNP barcodes (Pv: 40 SNPs & Pf: 28 SNPs) and MS panels (Pv: 16 MS & Pf: 7 MS). The genetic diversity of Pv (expected heterozygosity, He) was similar across the subpopulations for both makers: HeMS = 0.68 - 0.78 (p = 0.23) and HeSNP = 0.36 - 0.38 (p = 0.80). Pairwise genetic differentiation (fixation index, FST) was also comparable: FST-MS = 0.04 - 0.14 and FST-SNP = 0.03 - 0.12 (p = 0.34 - 0.85). No geographic clustering was observed with any panel. In addition, Pf genetic diversity trends (HeMS = 0 - 0.48 p = 0.03 - 1; HeSNP = 0 - 0.09, p = 0.03 - 1) and pairwise FST comparisons (FST-MS= 0.14 - 0.65, FST-SNP = 0.19 - 0.61, p = 0.24 - 0.83) were concordant between the panels. Similar population structure clustering was observed with both SNP and MS, highlighting one Pf subpopulation in an indigenous community. The SNP barcodes in the Pv AmpliSeq v2 Peru and Pf AmpliSeq v1 Peru assays offer comparable results to MS panels when investigating population genetics in Pv and Pv populations. Therefore, the AmpliSeq assays can efficiently characterize malaria transmission dynamics and population structure and support malaria elimination efforts in Peru.

genomics↗

bioRxiv2024

Human mobility and malaria risk in peri-urban and rural communities in the Peruvian Amazon

BackgroundWhile the global burden of malaria cases has decreased over the last two decades, the disease remains a major international threat, even on the rise in many regions. More than 85% of Peruvian malaria cases are in the Amazonian region of Loreto. Internal mobility primarily related to occupation is thought to be primarily responsible for maintaining endemicity and introducing and reintroducing malaria parasites into areas of anophelism, a challenge for malaria eradication. MethodsThe assessment of connectivity produced by human mobility was evaluated in three districts of Loreto, through 10 cross-sectional population screening from 2018 to 2020. We use social network analysis (SNA) to obtain weighted and unweighted degrees of connectivity and explore its variability by socio-demographic characteristics. In addition, we integrated travel history and malaria incidence data to estimate parasite connectivity due to internal human mobility between locations. Finally, we used logistic multivariate regressions to explore the factors associated with Plasmodium spp. infection in mobile individuals. ResultsWe found that internal human mobility results in high connectivity between communities from the Mazan, Iquitos, and San Juan Bautista districts. We identified nearby destinations that may act as sinks or sources for malaria transmission, including densely populated towns and rural campsites. In addition, we found that being a male, traveling to rural campsites, and working outdoors are associated with Plasmodium spp. infection in travelers from the Mazan district. ConclusionsWe provide compelling evidence about how human mobility connects rural communities in the Peruvian Amazon. Using SNA, we uncovered district-specific patterns and destinations, providing further evidence of human mobility heterogeneity in the region. To address the challenge of human mobility and malaria in this setting, geographic heterogeneity of malaria transmission must be considered. Author summaryMalaria transmission is complex, involving interactions of parasite, vector biology and ecology, human immune response, and human host behavior. We used social network analysis to understand how the daily lives including occupation-related mobility leads to the maintenance of malaria endemicity and transmission. Rural communities (within the districts of Mazan) and peri-urban communities around the city of Iquitos have different socio-demographic characteristics that determine malaria transmission rates. Networks of fixed rural communities and occupation-related distant camp sites play a key role as reservoirs and sources of parasite movement. Factors including male sex, outdoor occupational activity outdoors, and having rural camp sites as travel destination increase the risk of Plasmodium infection. Factors associated with occupation-related mobility are correlated with incidence and prevalence of malarial disease and parasite infection rates, respectively. This work provides a detailed understanding of the importance of work-related travel to target in malaria elimination programs, key to maintaining malaria transmission both in the Amazon region and more generally.

microbiology↗

bioRxiv2023

A new Plasmodium vivax reference genome for South American isolates

BackgroundPlasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering. ResultsThis study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM. The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions. ConclusionsOur findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.

genetics↗

bioRxiv2022

Plasmodium exoerythrocytic parasites redirect trafficking of human proteins to the parasitophorous vacuole

Changes in host cell morphology and transcription after apicomplexan parasite infection have long been noted, but there have been few studies of the functional consequences of host cell remodeling. Here we show, using time-dependent immunofluorescence microscopy of multiple human cell lines (HepG2, HC-04, Huh7.5.1 and primary human hepatocytes), infected with multiple Plasmodium species (Plasmodium berghei, P. falciparum and P. vivax (hypnozoites and schizonts)), and antibodies to multiple human proteins (HsNR4A3, HsMUC13, HsGOLGA8A, HsCGA, HsBiP, HsCXCL2), that human protein trafficking is extensively modified in Plasmodium infected cells. Using conventional as well as ultrastructure expansion microscopy we show that newly-synthesized human proteins are trafficked to the parasitophorous vacuole instead of the infected-cell plasma membrane, nucleus or extracellular space. Universal redirection of human signaling proteins cells the parasitophorous vacuole may provide a mechanistic explanation for how apicomplexan parasites can block host cells response to infection.

cell biology↗

bioRxiv2021

Population dynamics of the primary malaria vector Nyssorhynchus darlingi in a high transmission setting dominated by fish farming in western Amazonian Brazil

Vale do Rio Jurua in western Acre, Brazil, has reported highest malaria numbers since 2005, and is considered persistent transmission hotspot. Fish farming development was encouraged to improve standard of living, resulting in productive breeding sites for Amazonian malaria vector species, including Nyssorhynchus darlingi that, combined with the high human density and mobility, adds to the local malaria burden. This study reports entomological profile of immature and adult Ny. darlingi at three sites in Mancio Lima, Acre, during the rainy and dry season (February to September, 2017). From 63 fishponds, 10,859 larvae were collected, including 5,512 first-instar Anophelinae larvae and 4,927 second, third and fourth-instars, of which 8.5% (n = 420) were Ny. darlingi. This species was most abundant in not-abandoned fishponds and in the presence of emerging aquatic vegetation. Seasonal analysis of immatures in urban landscapes found no significant difference in the numbers of Ny. darlingi, corresponding to equivalent population density during the rainy to dry transition period. However, in the rural landscape, significantly higher numbers of Ny. darlingi larvae were collected in August (IRR = 5.80, p = 0.037) and September (IRR = 6.62, p = 0.023) (dry season), compared to February (rainy season), suggesting important role of fishponds for vector population maintenance during the seasonal transition in this landscape type. Adult sampling detected mainly Ny. darlingi (~93%), with similar outdoor feeding behavior, but different abundance according to landscape profile: urban site 1 showed higher peaks of human biting rate in May (46 bites/person/hour), than February (4) and September (15), while rural site 3 shows similar HBR during the same sampling period (22, 24 and 21, respectively). This study contributes to a better understanding of the larvae biology of the main malaria vector in the Vale do Rio Jurua region and, ultimately will support vector control efforts.

ecology↗

bioRxiv2019

Quantification of malaria antigens PfHRP2 and pLDH by quantitative suspension array technology in whole blood, dried blood spot and plasma

BackgroundMalaria diagnostics by rapid diagnostic tests (RDTs) relies primarily on the qualitative detection of Plasmodium falciparum histidine-rich protein 2 (PfHRP2) and Plasmodium sp lactate dehydrogenase (pLDH). As novel RDTs with increased sensitivity are being developed and implemented as point of care diagnostics, highly sensitive laboratory based assays are needed for evaluating RDTs performance. Here, a quantitative suspension array technology (qSAT) was developed, validated and applied for the simultaneous detection of PfHRP2 and pLDH in a variety of clinical samples (whole blood, plasma and dried blood spots) from different endemic countries.\n\nResultsThe qSAT was specific for the target antigens, with analytical ranges of 6.8 to 762.8 pg/ml for PfHRP2 and 78.1 to 17076.6 pg/ml for P. falciparum (Pf-LDH). The assay detected P. vivax LDH (Pv-LDH) at a lower sensitivity than Pf-LDH (analytical range of 1093.20 to 187288.5 pg/ml). Both PfHRP2 and pLDH levels determined using the qSAT showed to positively correlate with parasite densities determined by quantitative PCR (Spearman r=0.59 and 0.75, respectively) as well as microscopy (Spearman r=0.40 and 0.75, respectively), suggesting the assay to be a good predictor of parasite density.\n\nConclusionThis immunoassay can be used as a reference test for the detection and quantification of PfHRP2 and pLDH, and could serve for external validation of RDTs performance, to determine antigen persistence after parasite clearance, as well as a complementary tool to assess malaria burden in endemic settings.

microbiology↗