Biology subjects

Piera, K. A.

Publications and source records attributed to Piera, K. A..

9 recordsLinked to original sources

bioRxiv2026

Pfcrt copy number amplification detected in a Plasmodium falciparum outbreak

Antimalarial resistance is one of the greatest threats to malaria elimination. Following an outbreak of Plasmodium falciparum infection in Sabah Malaysia in 2019, 98 samples were sequenced to search for adaptations driving the outbreak. The genomic data revealed evidence of clonal expansion of a strain carrying multiple copies of the chloroquine resistance transporter gene (pfcrt) in 86 cases. A TaqMan qPCR assay was developed to quantify pfcrt copy number, confirming the in silico evidence of duplication. Whilst point mutations in pfcrt have been associated with resistance to chloroquine and other drugs, copy number amplification has not been widely explored as a resistance mechanism. We investigated the genetic architecture of the duplication, revealing a wildtype haplotype (3D7 reference-type with 76K variant) and a novel mutant (with 76T mutation). Application of the TaqMan assay in 43 P. falciparum cases from neighbouring Palawan Island, the Philippines, identified a further two cases with pfcrt duplication. Assessment of the global genomic data in the MalariaGEN Pf8 repository identified a further 86 cases, including 73 (85%) from West Africa with evidence of pfcrt duplication. Amongst 47 monoclonal MalariaGEN cases, majority (95%) comprised wild type and mutant variants at codon 76. Our study reveals a potential previously unconsidered antimalarial resistance mechanism for P. falciparum and provides an assay for surveillance in other populations.

genomics↗

bioRxiv2026

Splenic tropism of Plasmodium vivax in acute infection and spleen-attenuated systemic inflammation

BackgroundIn chronic asymptomatic Plasmodium vivax infections, the spleen accounts for more than 98% of total-body parasite biomass. Whether this splenic tropism also exists in acute infection and how the spleen influences pathogenesis have not been systematically explored. Materials and MethodsIn Papua, Indonesia, we compared plasma levels of P. vivax lactate dehydrogenase [PvLDH]) and circulating parasitemia in 24 spleen-intact and 25 previously splenectomized patients with acute uncomplicated vivax malaria. Clinical and hematology data were collected and plasma markers of intravascular hemolysis (cell-free hemoglobin [CFHb]), endothelial activation (angiopoietin-2), inflammation (interleukin [IL]-1 beta, IL-6, IL-18, IL-10, tumor necrosis factor-alpha) and neutrophil activation (elastase) were measured by ELISA. Giemsa-based histology in one spleen from an untreated patient splenectomized for trauma during an episode of acute vivax malaria enabled direct assessment of splenic and circulating parasitemia and biomass microscopically. ResultsCirculating parasitemia was 4-times higher in splenectomized compared to spleen-intact patients (median 21,100 vs 4,820 parasites/{micro}L, p=0.0002) but total-body P. vivax biomass (PvLDH) was 3-times lower in patients without a spleen (median 721 vs 2,140 ng/mL, p=0.026). Parasite staging and greater organ-specific symptoms suggest redistribution of parasites in the absence of a spleen. Linear regression modeling, adjusting for circulating parasitemia, patient age, sex and duration of fever, demonstrated an 8.1-fold higher PvLDH concentration in spleen-intact patients (95% confidence interval [CI]: 3.4-19.5-fold, p<0.0001), indicating a splenic biomass accounting for 89% (95%CI: 77.3-95.1%) of total-body parasites. Histopathology revealed a spleen-to-blood biomass ratio of 10.7, in-line with the PvLDH-based estimate. In spleen-intact patients, splenic P. vivax biomass correlated strongly with markers of disease intensity, endothelial activation and systemic inflammation, whereas circulating parasitemia correlated weakly or not at all. Compared to spleen-intact patients, CFHb, endothelial activation and systemic inflammation were higher in splenectomized patients while inflammasome-dependent responses were lower. ConclusionsP. vivax is predominantly an infection of the spleen, even in acute clinical vivax malaria. We conservatively estimate that 89% of total-body parasite biomass in acute infection is splenic. While the size of this hidden population correlates with disease intensity, the spleen likely regulates inflammatory pathways and heme-associated pathology.

pathology↗

bioRxiv2026

Integrative genomics of Plasmodium knowlesi reveals parasite-intrinsic regulators of severe human malaria

To dissect parasite determinants of clinical disease severity in Plasmodium knowlesi, we performed the first integrative genome-wide association (GWAS), transcriptomic, and expression quantitative trait locus (eQTL) analysis from clinical malaria isolates. We identify distinct parasite programs associated with WHO-defined severe disease, characterized by transcriptional activation of stress-response and host-interaction pathways. In contrast, invasion-linked programs were more strongly associated with parasite burden, while immune-evasion pathways showed overlapping but distinct associations with both burden and severity. GWAS and eQTL analyses revealed genetic regulation of transcriptional states, including immune-evasion variant antigen families (SICAvar and kir) and chromatin-associated regulators. Mature gametocyte transcripts were detectable across infections, including those with low parasitaemia, indicating that transmission-stage expression occurs independently of both clinical severity and parasite density. Together, these findings show that severe P. knowlesi malaria is associated with genetically regulated parasite transcriptional programs that are not fully explained by parasite burden.

genomics↗

bioRxiv2026

Mapping the global distribution and spread of the Plasmodium vivax-associated virus MaRNAV-1

Matryoshka RNA virus 1 is a bi-segmented and single-stranded RNA virus associated with Plasmodium vivax, a cause of human malaria. Little has been uncovered about the epidemiology and ecology of this virus since its discovery in 2019. To address this, we used a combination of primary and publicly available metatranscriptomic data to map the geographic distribution and host associations of MaRNAV-1. We detected this virus throughout Southeast Asia, in parts of South America, and, for the first time, in Oceania. Despite its broad distribution, MaRNAV-1 was found exclusively in metatranscriptomes containing P. vivax, suggesting that there is a specific virus-host relationship that has shaped the evolutionary history of this virus. We were unable to estimate the emergence date of the MaRNAV-1 lineage; however, phylogeographic mapping analysis suggested that MaRNAV-1 may have radiated from Southeast Asia. Our findings have both evolutionary and public health implications and can serve as the basis for future investigations in these fields.

evolutionary biology↗

bioRxiv2024

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon

Apicomplexa are single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Increasing rates of drug resistance in human-only Plasmodium species are reducing the efficacy of control efforts and antimalarial treatments. There are also rising cases of P. knowlesi, the only zoonotic Plasmodium species that causes severe disease and death in humans. Thus, there is a need to develop additional innovative strategies to combat malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa have been shown to affect pathogen life cycle and disease outcomes. However, only one virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere using structure- and artificial intelligence-based methods suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged these newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. We identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group ormycoviruses. By characterising fifteen additional ormycoviruses identified in the transcriptomes of arthropods we show that this group of viruses exhibits a complex ecology at the arthropod-mammal interface. Through the application of artificial intelligence methods, we then demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to large-scale virus discovery advances, we characterise the diversity and genomic architecture of an unclassified viral taxon. This approach should be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.

evolutionary biology↗

bioRxiv2024

Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.

Sabah, Malaysia, has amongst the highest burden of human Plasmodium knowlesi infection in the country, associated with increasing encroachment on the parasites macaque host habitat. However, the genomic make-up of P. knowlesi in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of P. knowlesi human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using IBD-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from P. knowlesi infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in P. knowlesi populations. Future expanded analyses of evolving P. knowlesi genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies. Author SummaryThe zoonotic P. knowlesi parasite is an emerging, yet understudied, cause of malaria in Southeast Asia. Sabah, Malaysia, has amongst the highest burden of human P. knowlesi infection in the country, however, the region is currently understudied. Thus, we produced a collection of high-quality P. knowlesi genomes from Sabah, and in combination with publicly available data, performed an extensive population genetics analysis. Our work contributes novel insights for Plasmodium knowlesi population genetics and genetic epidemiology.

genomics↗

bioRxiv2023

Characterisation of Plasmodium vivax lactate dehydrogenase dynamics in P. vivax infections

Plasmodium vivax lactate dehydrogenase (PvLDH) is an essential enzyme in the glycolytic pathway of Plasmodium vivax. It can also be used as a diagnostic biomarker. Quantitation of plasma PvLDH has been used as a measure of P. vivax biomass in clinical studies of uncomplicated and severe vivax malaria. With the increasing importance of PvLDH in studying P. vivax diagnosis and infection, improved characterisation of the dynamics of this biomarker is important. In this study, we developed mathematical models that capture parasite and matrix PvLDH dynamics in ex vivo culture and the human host. We estimated the biological parameters using ex vivo and in vivo longitudinal data of parasitemia and PvLDH concentration collected from P. vivax-infected humans using Bayesian hierarchical inference. We found that the ex vivo and in vivo estimates of PvLDH in a parasitized red blood cell differed significantly across the asexual life cycle, with in vivo estimates at least ten-fold higher than ex vivo estimates (for example, the median estimate of intraerythrocytic PvLDH mass at the end of the life cycle was 9.4x10-3 ng in vivo vs. 5.1x10-4 ng ex vivo). We also estimated the ex vivo PvLDH half-life to be 65.3 h (95% credible interval: 60.8--70.7 h), which is approximately three times longer than the median estimate of the in vivo PvLDH half-life, 21.9 h (16.7--29.9 h). Our findings provide an important foundation to further improve quantitative understanding of P. vivax biology and facilitate the development of PvLDH-based diagnostic tools.

biophysics↗

bioRxiv2022

Malaria drives unique regulatory responses across multiple immune cell subsets

Plasmodium falciparum malaria results in immunoregulatory responses across multiple cell subsets, which protects the individual from inflammatory mediated immunopathogenesis. However, these anti-inflammatory responses also hamper the development of effective anti-parasitic immunity. Understanding malaria induced tolerogenic responses in specific cell subsets may inform the development of strategies to boost protective immunity during drug treatment and vaccination. Here, we analysed the immune landscape with single cell RNA sequencing of peripheral blood mononuclear cells during falciparum malaria and at convalescence in children and adults from a low malaria transmission area in Malaysia. To understand malaria driven changes specific to each immune cell subset, we interrogated transcriptional changes in sub-clustered major immune cell types during infection. We found that malaria drove development of immunosuppressive monocytes, alongside NK and {gamma}{delta} T cells which regulated inflammatory function but maintained cytolytic capacity. IL10-producing CD4 T cells and IL10-producing regulatory B cells were also induced. Type I interferon responses were identified across all cell types, linking Type I interferon signalling with the induction of immunoregulatory networks during malaria. Together, these findings provide insights into cell-specific and shared immunoregulatory changes induced during malaria, and provides a data set resource for additional analysis of anti-parasitic immunity and disease pathogenesis.

immunology↗

bioRxiv2019

Matryoshka RNA virus 1: a novel RNA virus associated with Plasmodium parasites in human malaria

Parasites of the genus Plasmodium cause human malaria. Yet nothing is known about the viruses that infect these divergent eukaryotes. We investigated the Plasmodium virome by performing a meta-transcriptomic analysis of blood samples from malaria patients infected with P. vivax, P. falciparum or P. knowlesi. This revealed a novel bi-segmented narna-like RNA virus restricted to P. vivax and named Matryoshka RNA virus 1 (MaRNAV-1) to reflect its \"Russian doll\" nature: a virus, infecting a parasite, infecting an animal. MaRNAV-1 was abundant in geographically diverse P. vivax from humans and mosquitoes. Notably, a related virus (MaRNAV-2) was identified in Australian birds infected with a Leucocytozoon - eukaryotic parasites that group with Plasmodium in the Apicomplexa subclass hematozoa. This is the first report of a Plasmodium virus. As well as broadening our understanding of the eukaryotic virosphere, the restriction to P. vivax may help understand P. vivax-specific biology in humans and mosquitoes.

evolutionary biology↗