Biology subjects

Charon, J.

Publications and source records attributed to Charon, J..

10 recordsLinked to original sources

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↗

bioRxiv2026

RdRpCATCH: A unified resource for RNA virus discovery using viral RNA-dependent RNA polymerase profile Hidden Markov models

Recent advances in large-scale sequence mining have expanded our knowledge of RNA virus diversity. Most genome mining approaches for detecting RNA viruses that encode RNA-dependent RNA polymerase (RdRp) rely on identifying this conserved protein by employing profile Hidden Markov Models (pHMMs) to scan sequencing datasets. Recently, several new pHMM databases for RdRp detection have been released, each following distinct design principles. However, their relative performance is unclear and their accessibility to users without specialized computational expertise is limited. Here, we introduce the RdRp Collaborative Analysis Tool with Collections of pHMMs (RdRpCATCH: https://github.com/dimitris-karapliafis/RdRpCATCH), developed to consolidate publicly available RdRp pHMM resources into a single, accessible platform. RdRpCATCH enables the scanning of (meta)transcriptomic assemblies to discover RNA viruses and provides subsequent taxonomic annotation of detected contigs. A comparative analysis of RdRp pHMM databases reveals that most are highly effective at detecting known diversity of RNA viruses while minimizing false positives, supporting their joint use within RdRpCATCH. RdRpCATCH is distributed as both a conda package and a web server application (https://rdrpcatch.bioinformatics.nl), facilitating access for researchers with diverse expertise. By integrating multiple pHMM resources, this unified framework addresses fragmentation in the field and reduces technical barriers, enabling comprehensive viral discovery.

bioinformatics↗

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↗

bioRxiv2022

Diverse RNA viruses associated with diatom, eustigmatophyte, dinoflagellate and rhodophyte microalgae cultures

Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions on virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimised to detect highly divergent RNA viruses, we identified ten RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a great diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterisation and to investigate the effects of viral infections on microalgal physiology, biology and growth, considering their environmental and industrial roles. ImportanceIn comparison to animals or plants, our knowledge of the diversity of RNA viruses infecting microbial algae - the microalgae - is minimal. Yet describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economical levels because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte and euglena major clades of algae. This work identified ten new divergent RNA virus species, belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.

microbiology↗

bioRxiv2022

Analysis of the contribution of intrinsic disorder in shaping potyvirus genetic diversity

Intrinsically disordered regions (IDRs) are abundant in the proteome of RNA viruses. The multifunctional properties of these regions are widely documented and their structural flexibility is associated with low constraint in the amino acid positions. Therefore, from an evolutionary stand point, these regions could have a greater mutational permissiveness than highly structured regions (ORs for Ordered Regions). They could thus provide a potential adaptive reservoir. To address this hypothesis, we compared the mutational robustness of IDRs and ORs in the genome of potyviruses, a major genus of plant viruses. For this purpose, a simulation model (DOI: 10.5281/zenodo.6396239) was built and used to distinguish a possible selection phenomenon in the biological data sets from randomly generated mutations. We analyzed several short-term experimental evolution datasets. An analysis was also performed on the natural diversity of three different species of potyviruses reflecting the long-term evolution. We observed that the mutational robustness of IDRs is significantly higher than that of ORs. Moreover, the substitutions in the ORs are very constrained by the conservation of the physico-chemical properties of the amino acids. This feature is not found in the IDRs where the substitutions tend to be more random. This reflects the weak structural constraints in these regions, in which an amino acid polymorphism is naturally conserved in the course of evolution, potyvirus IDRs and ODRs follow different evolutive paths with respect to their mutational robustness. These results force to consider the hypothesis that during selection, adaptive solutions could emerge from the amino acid polymorphism carried by IDRs.

evolutionary biology↗

bioRxiv2022

RdRp-scan: A Bioinformatic Resource to Identify and Annotate Divergent RNA Viruses in Metagenomic Sequence Data

Despite a rapid expansion in the number of known RNA viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remains challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral "dusk matter": viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational and resource - RdRp-scan - that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific Hidden Markov models (HMM) and structural comparisons we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10% to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the known diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motif, as well as pre-built RdRp alignments. In parallel, our analysis of the sequence diversity detected by RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some sequences cluster into potential new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position, which might provide new insights into the structure, function and evolution of viral RdRps.

microbiology↗

bioRxiv2022

Human land-use impacts viral diversity and abundance in a New Zealand river

Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land-use on viral diversity and evolution in water systems such as rivers. We used metagenomic next-generation sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land use impact, ranging from pristine to urban. From this we identified 504 putative virus species, of which 97% were novel. Many of the novel viruses were highly divergent, and likely included a new subfamily within the Parvoviridae. We identified at least 63 virus species that may infect vertebrates - most likely fish and water birds - from the Astroviridae, Birnaviridae, Parvoviridae and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land-use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n=150) and pristine sites (n=119), and more viruses were shared between the urban and farming sites (n=76) than between the pristine and farming or urban sites (n=24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Overall, our study shows that human land-use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanization on water systems.

microbiology↗

bioRxiv2021

Revealing RNA virus diversity and evolution in unicellular algae transcriptomes

Remarkably little is known about the diversity and evolution of RNA viruses in unicellular eukaryotes. We screened a total of 570 transcriptomes from the Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP) project that encompasses a wide diversity of microbial eukaryotes, including most major photosynthetic lineages (i.e. the microalgae). From this, we identified 30 new and divergent RNA virus species, occupying a range of phylogenetic positions within the overall diversity of RNA viruses. Approximately one-third of the newly described viruses comprised single-stranded positive-sense RNA viruses from the order Lenarviricota associated with fungi, plants and protists, while another third were related to the order Ghabrivirales, including members of the protist and fungi-associated Totiviridae. Other viral species showed sequence similarity to positive-sense RNA viruses from the algae-associated Marnaviridae, the double-stranded RNA Partitiviridae, as well as a single negative-sense RNA virus related to the Qinviridae. Importantly, we were able to identify divergent RNA viruses from distant host taxa, revealing the ancestry of these viral families and greatly extending our knowledge of the RNA viromes of microalgal cultures. Both the limited number of viruses detected per sample and the low sequence identity to known RNA viruses imply that additional microalgal viruses exist that could not be detected at the current sequencing depth or were too divergent to be identified using sequence similarity. Together, these results highlight the need for further investigation of algal-associated RNA viruses as well as the development of new tools to identify RNA viruses that exhibit very high levels of sequence divergence.

microbiology↗

bioRxiv2020

Meta-transcriptomic detection of diverse and divergent RNA viruses in green and chlorarachniophyte algae

Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae in few RNA viruses have been documented to date. By combining meta-transcriptomic approaches with sequence and structural-based homology detection, followed by PCR confirmation, we identified 18 novel RNA viruses in two major groups of microbial algae - the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to those from the families Tombusviridae and Amalgaviridae that have previously been associated with plants, suggesting that these viruses have an evolutionary history that extends to when their host groups shared a common ancestor. In contrast, seven ulvophyte associated viruses exhibited clear similarity with the mitoviruses that are most commonly found in fungi. This is compatible with horizontal virus transfer between algae and fungi, although mitoviruses have recently been documented in plants. We also document, for the first time, RNA viruses in the chlorarachniophytes, including the first observation of a negative-sense (bunya-like) RNA virus in microalgae. The other virus-like sequence detected in chlorarachniophytes is distantly related to those from the plant virus family Virgaviridae, suggesting that they may have been inherited from the secondary chloroplast endosymbiosis event that marked the origin of the chlorarachniophytes. More broadly, this work suggests that the scarcity of RNA viruses in algae most likely results from limited investigation rather than their absence. Greater effort is needed to characterize the RNA viromes of unicellular eukaryotes, including through structure-based methods that are able to detect distant homologies, and with the inclusion of a wider range of eukaryotic microorganisms. Author summaryRNA viruses are expected to infect all living organisms on Earth. Despite recent developments in and the deployment of large-scale sequencing technologies, our understanding of the RNA virosphere remains anthropocentric and largely restricted to human, livestock, cultivated plants and vectors for viral disease. However, a broader investigation of the diversity of RNA viruses, especially in protists, is expected to answer fundamental questions about their origin and long-term evolution. This study first investigates the RNA virus diversity in unicellular algae taxa from the phylogenetically distinct ulvophytes and chlorarachniophytes taxa. Despite very high levels of sequence divergence, we were able to identify 18 new RNA viruses, largely related to plant and fungi viruses, and likely illustrating a past history of horizontal transfer events that have occurred during RNA virus evolution. We also hypothesise that the sequence similarity between a chlorarachniophyte-associated virga-like virus and members of Virgaviridae associated with plants may represent inheritance from a secondary endosymbiosis event. A promising approach to detect the signals of distant virus homologies through the analysis of protein structures was also utilised, enabling us to identify potential highly divergent algal RNA viruses.

microbiology↗

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↗