Biology subjects

Rosanas-Urgell, A.

Publications and source records attributed to Rosanas-Urgell, A..

10 recordsLinked to original sources

bioRxiv2026

A Plasmodium knowlesi A1-H.1 transcriptome time course focusing on the late asexual blood stages

BackgroundThe zoonotic parasite Plasmodium knowlesi is closely related to Plasmodium vivax, the second leading cause of human malaria. P. knowlesi line A1-H.1 can be maintained in human erythrocytes and is an experimental model for P. vivax biology. We present the first transcriptome time-course of the intraerythrocytic developmental cycle (IDC) of P. knowlesi A1-H.1 grown in human normocytes. ResultsBulk RNA-sequencing was performed at five IDC stages using tightly synchronised cultures, enabling identification of constitutively expressed genes and stage-specific biomarkers, and investigation of temporal expression patterns of multigene families. Comparative analysis with P. vivax orthologues revealed strong genome-wide conservation of temporal expression. Analysis of invasion-associated genes and ApiAP2 transcription factors identified genes with conserved expression patterns for which P. knowlesi is likely a good model to study the P. vivax gene. To support comparative analyses, we developed an open-access interactive webtool to explore and visualise P. knowlesi - P. vivax orthologue expression across the IDC. ConclusionsThis time-course dataset provides a reference transcriptome framework for P. knowlesi A1-H.1 and a resource for comparative Plasmodium biology. The interactive webtool facilitates rapid identification of candidate genes with conserved temporal expression, streamlining functional studies in which P. knowlesi A1-H.1 serves as a model for P. vivax.

genomics↗

bioRxiv2025

Elevated Plasmodium falciparum sexual conversion in HbAC and HbAS red blood cells without altered IgG/IgM levels to trophozoite and stage I gametocyte-specific antigens

Malaria transmission relies on the differentiation of asexual parasites into gametocytes, a process initiated by sexual conversion (SC). Mutations in the host hemoglobin beta (HBB) gene are known to influence parasite growth and disease outcome, yet their impact on SC remains unclear. We investigated the effect of HBB mutant genotypes on Plasmodium falciparum SC and humoral immunity in individuals from Nanoro, Burkina Faso. To measure SC rates in natural human malaria infections, we developed a new ex vivo SC assay (evSCA). We found that in human natural P. falciparum infections, SC rates were higher in individuals with HbAS or HbAC than in individuals with wild-type HBB (HbAA). Consistently, using an in vitro SC assay (ivSCA) based on the NF54-gexp02-Tom reporter line we found that cultures grown in HbAS red blood cells (RBCs) had higher SC rates than those grown in HbAA RBCs. Furthermore, IgG and IgM responses against trophozoite- and stage I gametocyte-infected RBC antigens, quantified by flow cytometry, did not differ between plasma from individuals with different HBB genotypes. These results demonstrate that exposure to RBCs with HBB mutations enhances SC, highlighting a host-genetic factor that may influence malaria transmission potential. AUTHOR SUMMARYTransmission of Plasmodium falciparum -a malaria causing parasite- depends on the parasites ability to produce gametocytes, the stage that infects mosquitoes. In many African regions where malaria is common, hemoglobin (Hb) variants such as hemoglobin S (the sickle-cell trait) and C are highly prevalent reflecting their role in protecting against severe disease. However, it remains unclear whether these variants also influence the parasites early shift toward gametocyte development (i.e., sexual conversion [SC]). In this study, we combined ex vivo and in vitro SC assays to measure SC in red blood cells with different hemoglobin genotypes. We found that SC was higher in parasites growing in red blood cells carrying hemoglobin AC and AS genotypes compared to normal AA hemoglobin. These findings provide experimental support for earlier epidemiological observations reporting that individuals with these hemoglobin variants often carry more gametocytes and are more infectious to mosquitoes. We also measured antibody levels in individuals with mutant RBCs and found no differences in immunity that could explain the variation in SC. Our results show that host genetic background can influence gametocyte development and may shape the infectious reservoir in high-burden settings. This knowledge is important for designing effective strategies for malaria elimination.

microbiology↗

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

Novel single-cell preservation and RNA sequencing technology unlocks field studies for Plasmodium natural infections

Single-cell RNA sequencing (scRNA-seq) is a powerful technology used to investigate cellular heterogeneity. When applied to unicellular eukaryotes such as Plasmodium parasites, scRNA-seq provides a single-cell resolution particularly valuable to study complex infections which are often comprised of mixed life stages and clones. Until now, the application of scRNA-seq has been mainly limited to in vitro and animal malaria models, despite known transcriptional differences as compared to circulating parasite populations. This is primarily due to the challenges of working with Plasmodium natural infections in endemic settings. We validated sample preparation methods and a novel single-cell RNA sequencing technology for the first time in P. knowlesi parasites which can be effectively implemented to analyze natural infections in low-resource settings. We recovered 22,345 P. knowlesi single-cell transcriptomes containing all asexual blood stages from 6 in vitro culture samples, with conditions mimicking natural infections, and generated the most extensive P. knowlesi single-cell dataset to date. All 6 samples produced reproducible circular UMAP projections with consistent cluster localization and high gene expression correlation, regardless of the sample preparation methods used. Biomarker expression and life stage annotation using the Malaria Cell Atlas P. knowlesi reference dataset further confirmed these results. In conclusion, the combination of adaptable sample preparation methods with novel preservation and scRNA-seq technology has the potential to fundamentally transform the study of natural infections. This approach unlocks the use of scRNA-seq in field studies which will lead to new insights into Plasmodium parasite biology. ImportanceSequencing unicellular organisms, such as malaria parasites, at the single-cell level is important to understand the diversity present in cell populations. Until now, single-cell sequencing of malaria has been primarily limited to laboratory models. While these models are key to understanding biological processes, there are known differences between lab models and parasite populations circulating in natural human infections. This study presents sample preparation methods and a new single-cell RNA sequencing technology that enables sample collection from natural infections in low-resource settings. Using a mock natural infection, we validated this new single-cell RNA sequencing technology using marker genes with known expression patterns and a reference dataset from the Malaria Cell Atlas. We demonstrate that high-quality single-cell transcriptomes with consistent expression patterns can be recovered using various sample preparation methods, thereby unlocking single-cell sequencing for field studies and leading to additional insights into parasite biology in the future.

microbiology↗

bioRxiv2024

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

The population structure of the malaria parasite Plasmodium falciparum can reveal underlying demographic and adaptive evolutionary processes. Here, we analyse population structure in 4,376 P. falciparum genomes from 21 countries across Africa. We identified a strongly differentiated cluster of parasites, comprising [~]1.2% of samples analysed, geographically distributed over 13 countries across the continent. Members of this cluster, named AF1, carry a genetic background consisting of a large number of highly differentiated variants, rarely observed outside this cluster, at a multitude of genomic loci distributed across most chromosomes. At these loci, the AF1 haplotypes appear to have common ancestry, irrespective of the sampling location; outside the shared loci, however, AF1 members are genetically similar to their sympatric parasites. AF1 parasites sharing up to 23 genomic co-inherited regions were found in all major regions of Africa, at locations over 7,000 km apart. We coined the term cryptotype to describe a complex common background which is geographically widespread, but concealed by genomic regions of local origin. Most AF1 differentiated variants are functionally related, comprising structural variations and single nucleotide polymorphisms in components of the MSP1 complex and several other genes involved in interactions with red blood cells, including invasion and erythrocyte antigen export. We propose that AF1 parasites have adapted to some as yet unidentified evolutionary niche, by acquiring a complex compendium of interacting variants that rarely circulate separately in Africa. As the cryptotype spread across the continent, it appears to have been maintained mostly intact in spite of recombination events, suggesting a selective advantage. It is possible that other cryptotypes circulate in Africa, and new analysis methods may be needed to identify them.

genomics↗

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

Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by Nanopore adaptive sampling

BackgroundWhole-genome sequencing (WGS) is becoming an increasingly popular tool to study the population genetics and drug resistance of Plasmodium spp. However, the predominance of human DNA in a malaria patient blood sample requires time-consuming lab procedures to filter out human DNA or enrich Plasmodium DNA. Here, we investigated the potential of adaptive sampling to enrich for Plasmodium DNA while sequencing unenriched patient blood samples on a minION device. ResultsTo compare adaptive sampling versus regular sequencing, a dilution series consisting of 0% up to 100% P. falciparum DNA in human DNA was sequenced. Half of the flowcell channels were run in adaptive sampling mode, enriching for the P. falciparum reference genome, resulting in a 3.2 fold enrichment of P. falciparum bases on average. Samples with a lower concentration of parasite DNA had a higher enrichment potential. We confirmed these findings by sequencing two P. falciparum patient blood samples with common levels of parasitaemia (0.1% and 0.2%). The estimated enrichment was 3.9 and 5.8, which was sufficient to cover at least 97% of the P. falciparum reference genome at a median depth of 20 (highest parasitaemia) or 5 (lowest parasitaemia). A comparison of 38 drug resistance variants (WHO) obtained via adaptive sequencing or Sanger sequencing showed a high concordance between the two methods, suggesting that the obtained sequencing data is of sufficient quality to address common clinical research questions for patients with parasitaemias of 0.1% and higher. ConclusionsOur results demonstrate that adaptive Nanopore sequencing has the potential to replace more time-consuming Plasmodium-enrichment protocols and sequence directly from patient blood, given further improvements in cost-efficiency.

microbiology↗

bioRxiv2020

Exposure to artemisinin at the trophozoite stage increases sexual conversion rates in the malaria parasite Plasmodium falciparum

Malaria transmission is dependent on formation of gametocytes in the human blood. The sexual conversion rate, the proportion of asexual parasites that convert into gametocytes at each multiplication cycle, is variable and reflects the relative parasite investment between transmission and maintaining the infection. The impact of environmental factors such as drugs on sexual conversion rates is not well understood. We developed a robust assay using gametocyte-reporter parasite lines to accurately measure the impact of drugs on conversion rates, independently from their gametocytocidal activity. We found that exposure to subcurative doses of the frontline antimalarial drug dihydroartemisinin (DHA) at the trophozoite stage resulted in a ~4-fold increase in sexual conversion. In contrast, no increase was observed when ring stages were exposed or in cultures in which sexual conversion was stimulated by choline depletion. Our results reveal a complex relationship between antimalarial drugs and sexual conversion, with potential public health implications.

microbiology↗

bioRxiv2018

Access to and use of preventive intermittent treatment for Malaria during pregnancy: a qualitative study in Chokwe district, Southern Mozambique

BackgroundMalaria remains a significant health problem in Mozambique, particularly to pregnant women and children less than five years old. Intermittent preventive treatment is recommended for malaria prevention in pregnancy (IPTp). Despite the widespread use and cost-effectiveness of this intervention, the coverage remains low. In this study, we aimed to explore the factors limiting the access and use of IPTp-SP in Chokwe district.\n\nMethods and findingsWe used qualitative research methods through semi-structured interviews to collect data from 46 pregnant women and four health care staff from Chokwe, a rural area of southern Mozambique. Data were transcribed, manually coded and analysed using content and thematic method. Participants were not aware of pregnancy-related risks of malaria infection or the benefit of malaria prevention in pregnancy. Late and infrequently antenatal care (ANC) attendance, concerns about the long waiting time at ANC consultations,plus reluctance to disclose the pregnancy early, emerged as driving factors for inadequate IPTp delivery.\n\nConclusionsPregnant women experience substantial barriers to receive adequate IPTp-SP dosing for malaria prevention. Poor awareness, non-compliance with ANC attendance and poor attitude of health care staff were main barriers to IPTp-SP delivery. There is a need to strengthen actions that improve awareness about malaria and prevention among pregnant women, as well as quality services across the ANC services in order to increase IPTp-SP uptake.

epidemiology↗

bioRxiv2018

Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing

BackgroundLongitudinal tracking of individual Plasmodium falciparum strains in multi-clonal infections is essential for investigating infection dynamics of malaria. The traditional genotyping techniques did not permit tracking changes in individual clone density during persistent natural infections. Amplicon deep sequencing (Amp-Seq) offers a tool to address this knowledge gap.\n\nMethodsThe sensitivity of Amp-Seq for relative quantification of clones was investigated using three molecular markers, ama1-D2, ama1-D3, and cpmp. Amp-Seq and length-polymorphism based genotyping were compared for their performance in following minority clones in longitudinal samples from Papua New Guinea.\n\nResultsAmp-Seq markers were superior to length-polymorphic marker msp2 in detecting minority clones (sensitivity Amp-Seq: 95%, msp2: 85%). Multiplicity of infection (MOI) by Amp-Seq was 2.32 versus 1.73 for msp2. The higher sensitivity had no effect on estimates of force of infection because missed minority clones were detected in preceding or succeeding bleeds. Individual clone densities were tracked longitudinally by Amp-Seq despite MOI>1, thus providing an additional parameter for investigating malaria infection dynamics.\n\nConclusionAmp-Seq based genotyping of longitudinal samples improves detection of minority clones and estimates of MOI. Amp-Seq permits tracking of clone density over time to study clone competition or the dynamics of specific, i.e. resistance-associated genotypes.

microbiology↗