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

High-throughput screening reveals high diversity and widespread distribution of viruses in black soldier flies (Hermetia illucens)

Virus discovery in mass-reared insects is a growing topic of interest due to outbreak risks and for insect welfare concerns. In the case of black soldier flies (Hermetia illucens, BSF), pioneering bioinformatic studies have uncovered exogenous viruses from the orders Ghabrivirales and Bunyavirales, as well as endogenous viral elements from five virus families. This prompted further virome investigation of BSF metagenomes and metatranscriptomes, including from BSF individuals displaying signs and symptoms of disease. A high-throughput pipeline allowed the simultaneous investigation of 203 next generation sequencing datasets. This revealed the presence of seven viruses belonging to the families Dicistroviridae, Iflaviridae, Rhabdoviridae, Solinviviridae, Inseviridae, Lebotiviridae, and an unclassified Bunyavirales. Here we describe five viruses, which were detected in BSF from multiple origins, outlining the diversity of naturally occurring viruses associated with BSF colonies. As this viral community may also include BSF pathogens, we developed molecular detection tools which could be used for viral surveillance, both in mass-reared and wild populations of BSF.

Virome diversity and potential sharing of wild mammals in a biodiversity hotspot, Yunnan, China

BACKGROUND

Small mammals, including rodents, shrews and moonrats are widespread and serve as natural reservoirs for many viral pathogens. However, the composition and distribution of wild animal viromes remain poorly understood. At least 10,000 virus species have the ability to infect humans, but the vast majority are circulating silently in wild mammals. Understanding the virome profiles of these wild animals is crucial for outbreak preparedness, particularly in regions with high mammalian diversity.

METHODS

In this study, we enriched and extracted viral RNA from fecal samples of 459 wild mammals, representing 16 species, in the Xishuangbanna Dai Autonomous Prefecture of China, a recognized biodiversity hotspot in China. We then performed next-generation sequencing and comprehensive virome analyses across these different animal species.

RESULTS

We identified 5,346 nearly complete contigs annotated to 64 viral families, with 45 viral families identified in rodents and 46 viral families in shrews and moonrats, showing significant variation in viral diversity across different host species. Among these, 28 viral families were shared across species, including 11 identified viruses that were potential zoonotic pathogens. Additionally, numerous unidentified viral contigs containing the RdRp-gene showing close evolutionary relationships with viral families known to cause infections in animals. Importantly, several viruses detected in these animals, belonging to the family Hepeviridae, Flaviviridae, Astroviridae, Picornaviridae, and Picobirnaviridae, exhibited > 70% nucleotide sequence identity to viruses known to cause diseases in other wildlife species, domestic animals or even humans.

CONCLUSIONS

These findings significantly increase our knowledge of viral diversity and potential viral transmission within rodents and other sympatric small mammals in an emerging disease hotspot, shedding light on the need for continued surveillance of these small mammal populations.

Detection of multiple novel viruses in argasid and ixodid ticks in Mexico

We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.

Systematic Review of Phylogenetic Analysis Techniques for RNA Viruses Using Bioinformatics

The present paper addresses topics from various fields of biology. Its purpose is to enlarge the understanding of the usage of bioinformatics tools in the phylogenetic analysis of RNA viruses. The paper highlights the benefits of using information technology in virology, bringing the scientific community closer to unraveling the mysteries of RNA virus evolution and their adaptation to different niches and hosts and facilitating the understanding of their rapid mutation processes. Phylogenetic analysis of genetic sequences allows the exploration of the causes of these genetic changes in viruses and categorizes them into taxonomic groups. This paper is a systematic review of the most important scientific articles on the phylogenetic analysis of RNA viruses using bioinformatics. The studies included in the review were selected based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines and discuss methods for analyzing genetic and protein sequences (including codon sequences) and describe phylogenetic analyses and the bioinformatics tools used (such as VConTACT, RAxML, etc.). This review emphasizes the importance of further development in the fields of bioinformatics and virology, particularly with respect to RNA viruses, in order to mitigate the risk of a future pandemic. It also aims to provide a detailed understanding of the mutation and evolution mechanisms of these entities, which will help in efforts to limit viral virulence, for example. This article did not receive any funding for its creation and has not been registered in any database.

Uncovering the hidden RNA virus diversity in Lake Nam Co: Evolutionary insights from an extreme high-altitude environment

Alpine lakes, characterized by isolation, low temperatures, oligotrophic conditions, and intense ultraviolet radiation, remain a poorly explored ecosystem for RNA viruses. Here, we present the first comprehensive metatranscriptomic study of RNA viruses in Lake Nam Co, a high-altitude alkaline saline lake on the Tibetan Plateau. Using a combination of sequence- and structure-based homology searches, we identified 742 RNA virus species, including 383 novel genus-level groups and 84 novel family-level groups exclusively found in Lake Nam Co. These findings significantly expand the known diversity of the Orthornavirae, uncovering evolutionary adaptations such as permutated RNA-dependent RNA polymerase motifs and distinct RNA secondary structures. Notably, 14 additional RNA virus families potentially infecting prokaryotes were predicted, broadening the known host range of RNA viruses and questioning the traditional assumption that RNA viruses predominantly target eukaryotes. The presence of auxiliary metabolic genes in viral genomes suggested that RNA viruses (families f.0102 and Nam-Co_family_51) exploit host energy production mechanisms in energy-limited alpine lakes. Low nucleotide diversity, single nucleotide polymorphism frequencies, and pN/pS ratios indicate strong purifying selection in Nam Co viral populations. Our findings offer insights into RNA virus evolution and ecology, highlighting the importance of extreme environments in uncovering hidden viral diversity and further shed light into their potential ecological implications, particularly in the context of climate change.

A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics

Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.

Host Specificity and Geographic Dispersion Shape Virome Diversity in Rhinolophus Bats

Rhinolophus bats have been identified as natural reservoirs for viruses with global health implications, including severe acute respiratory syndrome-related coronaviruses (SARSr-CoV) and swine acute diarrhoea syndrome-related coronavirus (SADSr-CoV). In this study, we characterised the individual viromes of 603 bats to systematically investigate the diversity, abundance and geographic distribution of viral communities within R. affinis, R. sinicus and 11 other bat species. The massive metatranscriptomic data revealed substantial viral genome resources of 133 vertebrate-infecting viral clusters, which contain occasional cross-species transmission across mammalian orders and especially across bat families. Notably, those viruses included nine clusters closely related to human and/or livestock pathogens, such as SARS-CoVs and SADS-CoVs. The investigation also highlighted distinct features of viral diversity between and within bat colonies, which appear to be influenced by the distinct host population genetics of R. affinis and R. sinicus species. The comparison of SARSr-CoVs further showed varied impact of host specificity along genome-wide diversification and modular viral evolution among Rhinolophus species. Overall, the findings point to a complex interaction between host genetic diversity, and the way viruses spread and structure within natural populations, calling for continued surveillance efforts to understand factors driving viral transmission and emergence in human populations. These results present the underestimated spillover risk of bat viruses, highlighting the importance of enhancing preparedness and surveillance for emerging zoonotic viruses.

An orphan viral genome with unclear evolutionary status sheds light on a distinct lineage of flavi-like viruses infecting plants

Advancements in high-throughput sequencing and associated bioinformatics methods have significantly expanded the RNA virus repertoire, including novel viruses with highly divergent genomes encoding "orphan" proteins that apparently lack homologous sequences. This absence of homologs in routine sequence similarity search complicates their taxonomic classification and raises a fundamental question: Do these orphan viral genomes represent bona ide viruses? In 2022, an orphan viral genome encoding a large polyprotein was identified in alfalfa (Medicago sativa) and thrips (Frankliniella occidentalis), and named Snake River alfalfa virus (SRAV). SRAV was initially proposed as an uncommon flavi-like virus identified in a plant host distantly related to family Flaviviridae. Subsequently, another research group showed its common occurrence in alfalfa but challenged its taxonomic position, suggesting it belongs to the family Endornaviridae. In this study, a large-scale analysis of 77 publicly available small RNA datasets indicates that SRAV could be detected across various tissues and cultivars of alfalfa, and has a broad geographical distribution. Moreover, profiles of the SRAV-derived small interfering RNAs (vsiRNAs) exhibited typical characteristics of viruses in plant hosts. The evolutionary analysis suggests that SRAV represents a unique class of plant-hosted flavi-like viruses with an unusual genome organization and evolutionary status, distinct from previously identified flavi-like viruses documented to infect plants. The latter shows a close evolutionary relationship to flavi-like viruses primarily found in plant-feeding invertebrates and lacks evidence of triggering host RNA interference (RNAi) responses so far. Moreover, mining the transcriptome shotgun assembly (TSA) database identified two novel viral sequences with a similar genome organization and evolutionary status to SRAV. In summary, our study resolves the disagreement regarding the taxonomic status of SRAV and suggests the potential existence of two distinct clades of plant-hosted flavi-like viruses with independent evolutionary origins. Furthermore, our research provides the first evidence of plant-hosted flavi-like viruses triggering the host's RNAi antiviral response. The widespread occurrence of SRAV underscores its potential ecological significance in alfalfa, a crop of substantial economic importance.

Virome analysis unveils a rich array of newly identified viruses in the red swamp crayfish Procambarus clarkii

The red swamp crayfish (Procambarus clarkii) is the second most widely cultured crustacean globally. As a highly invasive species with a worldwide distribution, P. clarkii presents a substantial risk for the transmission of viral pathogens to native aquatic organisms. Recently, the emergence of growth retardation disease (GRD) in P. clarkii has led to significant production declines and economic losses. A comprehensive viromic analysis could offer valuable insights into the potential viral pathogens harbored by P. clarkii. Here we systematically examined the RNA viromes of healthy and GRD-affected P. clarkii collected from Qianjiang, China. Our investigation identified a total of 1729 viral species across 21 known viral taxa, with 1603 species being previously unreported. The orders Picornavirales, Tolivirales, and Nodamuvirales were predominant in both species count and relative abundance. Moreover, seven viruses exhibited higher abundance in GRD-affected P. clarkii compared to healthy individuals. Our work uncovers an unexpectedly diverse RNA viral community within P. clarkii and identifies potential viral pathogens associated with GRD in this species.

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

The Apicomplexa are a phylum of single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa affect the pathogen life cycle and disease outcomes. However, only one RNA 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 via metagenomic sequencing suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. From this, we identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group 'ormycoviruses'. By characterizing 15 additional ormycoviruses identified in the transcriptomes of arthropods, we show that this group of viruses exhibits a complex ecology as noninfecting passengers at the arthropod-mammal interface. With the addition of viral diversity discovered using the artificial intelligence-based analysis of metagenomic data, we also 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 advances in large-scale virus discovery, we characterize the diversity and confirm the putative genomic architecture of an unclassified viral taxon. This approach can 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.

New insights into RNA mycoviruses of fungal pathogens causing Fusarium head blight

Fusarium head blight (FHB) continues to be a major problem in wheat production and is considered a disease complex caused by several fungal pathogens including Fusarium culmorum, F. graminearum and F. equiseti. With the objective of investigating diversity of mycoviruses in FHB-associated pathogens, we isolated Fusarium spp. from six wheat (Triticum aestivum) cultivars. In total, 56 Fusarium isolates (29 F. culmorum, 24 F. graminearum, one F. equiseti) were screened for mycoviruses by extracting and sequencing double-stranded RNA. We found that a large proportion of Fusarium isolates (46 %) were infected with mycoviruses. F. culmorum, previously described to harbor only one mycovirus, tended to host more viruses than F. graminearum, with a few isolates harboring seven mycoviruses simultaneously. Based on the RNA-dependent RNA polymerase domain analysis, ten were positive-sense single-stranded RNA viruses (related to viruses from families Mitoviridae, Botourmiaviridae, Narnaviridae, Tymoviridae, Gammaflexiviridae, as well as proposed Ambiguiviridae and ormycovirus viral group), one was double-stranded RNA virus (Partitiviridae), and five were negative-sense single-stranded RNA viruses (related to members in the families of Yueviridae, Phenuiviridae, Mymonaviridae, as well as proposed Mycoaspiviridae). Five mycoviruses were shared between F. graminearum and F. culmorum. These results increase our general understanding of mycovirology. To our knowledge, this is the first in-depth report of the mycovirome in F. culmorum and the first report on the diversity of mycoviruses from Danish isolates of FHB-causing fungi in general.

Virology-The next fifty years

Virology has made enormous advances in the last 50 years but has never faced such scrutiny as it does today. Herein, we outline some of the major advances made in virology during this period, particularly in light of the COVID-19 pandemic, and suggest some areas that may be of research importance in the next 50 years. We focus on several linked themes: cataloging the genomic and phenotypic diversity of the virosphere; understanding disease emergence; future directions in viral disease therapies, vaccines, and interventions; host-virus interactions; the role of viruses in chronic diseases; and viruses as tools for cell biology. We highlight the challenges that virology will face moving forward-not just the scientific and technical but also the social and political. Although there are inherent limitations in trying to outline the virology of the future, we hope this article will help inspire the next generation of virologists.

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.

Predicting novel mosquito-associated viruses from metatranscriptomic dark matter

The exponential growth of metatranscriptomic studies dedicated to arboviral surveillance in mosquitoes has yielded an unprecedented volume of unclassified sequences referred to as the virome dark matter. Mosquito-associated viruses are classified based on their host range into Mosquito-specific viruses (MSV) or Arboviruses. While MSV replication is restricted to mosquito cells, Arboviruses infect both mosquito vectors and vertebrate hosts. We developed the MosViR pipeline designed to identify complex genomic discriminatory patterns for predicting novel MSV or Arboviruses from viral contigs as short as 500 bp. The pipeline combines the predicted probability score from multiple predictive models, ensuring a robust classification with Area Under ROC (AUC) values exceeding 0.99 for test datasets. To assess the practical utility of MosViR in actual cases, we conducted a comprehensive analysis of 24 published mosquito metatranscriptomic datasets. By mining this metatranscriptomic dark matter, we identified 605 novel mosquito-associated viruses, with eight putative novel Arboviruses exhibiting high probability scores. Our findings highlight the limitations of current homology-based identification methods and emphasize the potentially transformative impact of the MosViR pipeline in advancing the classification of mosquito-associated viruses. MosViR offers a powerful and highly accurate tool for arboviral surveillance and for elucidating the complexities of the mosquito RNA virome.

Genomic transfers help to decipher the ancient evolution of filoviruses and interactions with vertebrate hosts

Although several filoviruses are dangerous human pathogens, there is conflicting evidence regarding their origins and interactions with animal hosts. Here we attempt to improve this understanding using the paleoviral record over a geological time scale, protein structure predictions, tests for evolutionary maintenance, and phylogenetic methods that alleviate sources of bias and error. We found evidence for long branch attraction bias in the L gene tree for filoviruses, and that using codon-specific models and protein structural comparisons of paleoviruses ameliorated conflict and bias. We found evidence for four ancient filoviral groups, each with extant viruses and paleoviruses with open reading frames. Furthermore, we found evidence of repeated transfers of filovirus-like elements to mouse-like rodents. A filovirus-like nucleoprotein ortholog with an open reading frame was detected in three subfamilies of spalacid rodents (present since the Miocene). We provide evidence that purifying selection is acting to maintain amino acids, protein structure and open reading frames in these elements. Our finding of extant viruses nested within phylogenetic clades of paleoviruses informs virus discovery methods and reveals the existence of Lazarus taxa among RNA viruses. Our results resolve a deep conflict in the evolutionary framework for filoviruses and reveal that genomic transfers to vertebrate hosts with potentially functional co-options have been more widespread than previously appreciated.

Highly divergent and diverse viral community infecting sylvatic mosquitoes from Northeast Brazil

Mosquitoes can transmit several pathogenic viruses to humans, but their natural viral community is also composed of a myriad of other viruses such as insect-specific viruses (ISVs) and those that infect symbiotic microorganisms. Besides a growing number of studies investigating the mosquito virome, the majority are focused on few urban species, and relatively little is known about the virome of sylvatic mosquitoes, particularly in high biodiverse biomes such as the Brazilian biomes. Here, we characterized the RNA virome of 10 sylvatic mosquito species from Atlantic forest remains at a sylvatic-urban interface in Northeast Brazil employing a metatranscriptomic approach. A total of 16 viral families were detected. The phylogenetic reconstructions of 14 viral families revealed that the majority of the sequences are putative ISVs. The phylogenetic positioning and, in most cases, the association with a high RNA-dependent RNA polymerase amino acid divergence from other known viruses suggests that the viruses characterized here represent at least 34 new viral species. Therefore, the sylvatic mosquito viral community is predominantly composed of highly divergent viruses highlighting the limited knowledge we still have about the natural virome of mosquitoes in general. Moreover, we found that none of the viruses recovered were shared between the species investigated, and only one showed high identity to a virus detected in a mosquito sampled in Peru, South America. These findings add further in-depth understanding about the interactions and coevolution between mosquitoes and viruses in natural environments.

IMPORTANCE

Mosquitoes are medically important insects as they transmit pathogenic viruses to humans and animals during blood feeding. However, their natural microbiota is also composed of a diverse set of viruses that cause no harm to the insect and other hosts, such as insect-specific viruses. In this study, we characterized the RNA virome of sylvatic mosquitoes from Northeast Brazil using unbiased metatranscriptomic sequencing and in-depth bioinformatic approaches. Our analysis revealed that these mosquitoes species harbor a diverse set of highly divergent viruses, and the majority comprises new viral species. Our findings revealed many new virus lineages characterized for the first time broadening our understanding about the natural interaction between mosquitoes and viruses. Finally, it also provided several complete genomes that warrant further assessment for mosquito and vertebrate host pathogenicity and their potential interference with pathogenic arboviruses.

Sylvatic Mosquito Viromes in the Cerrado Biome of Minas Gerais, Brazil: Discovery of New Viruses and Implications for Arbovirus Transmission

Studies on animal virome have mainly concentrated on chordates and medically significant invertebrates, often overlooking sylvatic mosquitoes, constituting a major part of mosquito species diversity. Despite their potential role in arbovirus transmission, the viromes of sylvatic mosquitoes remain largely unexplored. These mosquitoes may also harbor insect-specific viruses (ISVs), affecting arboviral transmission dynamics. The Cerrado biome, known for rapid deforestation and its status as a biodiversity hotspot, offers an ideal setting for investigating mosquito viromes due to potential zoonotic spillover risks from land use changes. This study aimed to characterize the viromes of sylvatic mosquitoes collected from various locations within Minas Gerais state, Brazil. The total RNA was extracted from mosquito pools of Psorophora albipes, Sabethes albiprivus, Sa. chloropterus, Psorophora ferox, and Coquillettidia venezuelensis species, followed by high-throughput sequencing (HTS). Bioinformatic analysis included quality control, contig assembly, and viral detection. Sequencing data analysis revealed 11 near-complete viral genomes (new viruses are indicated with asterisks) across seven viral families and one unassigned genus. These included: Xinmoviridae (Ferox mosquito mononega-like virus* and Albipes mosquito Gordis-like virus*), Phasmaviridae (Sabethes albiprivus phasmavirus*), Lispiviridae (Pedras lispivirus variant MG), Iflaviridae (Sabethes albiprivus iflavivirus*), Virgaviridae (Buriti virga-like virus variant MG and Sabethes albiprivus virgavirus 1*), Flaviviridae (Psorophora ferox flavivirus*), Mesoniviridae (Alphamesonivirus cavallyense variant MG), and the genus Negevirus (Biggie virus variant MG virus and Coquillettidia venezuelensis negevirus*). Moreover, the presence of ISVs and potential novel arboviruses underscores the need for ongoing surveillance and control strategies to mitigate the risk of emerging infectious diseases.

SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes

Segmented RNA viruses are a complex group of RNA viruses with multisegment genomes. Reconstructing complete segmented viruses is crucial for advancing our understanding of viral diversity, evolution, and public health impact. Using metatranscriptomic data to identify known and novel segmented viruses has sped up the survey of segmented viruses in various ecosystems. However, the high genetic diversity and the difficulty in binning complete segmented genomes present significant challenges in segmented virus reconstruction. Current virus detection tools are primarily used to identify nonsegmented viral genomes. This study presents SegVir, a novel tool designed to identify segmented RNA viruses and reconstruct their complete genomes from complex metatranscriptomes. SegVir leverages both close and remote homology searches to accurately detect conserved and divergent viral segments. Additionally, we introduce a new method that can evaluate the genome completeness and conservation based on gene content. Our evaluations on simulated datasets demonstrate SegVir's superior sensitivity and precision compared to existing tools. Moreover, in experiments using real data, we identified some virus segments missing in the NCBI database, underscoring SegVir's potential to enhance viral metagenome analysis. The source code and supporting data of SegVir are available via https://github.com/HubertTang/SegVir.

Pathogen dynamics and discovery of novel viruses and enzymes by deep nucleic acid sequencing of wastewater

Wastewater contains an extensive reservoir of genetic information, yet largely unexplored. Here, we analyzed by high-throughput sequencing total nucleic acids extracted from wastewater samples collected during a 17 month-period in Berlin, Germany. By integrating global wastewater datasets and applying a novel computational approach to accurately identify viral strains within sewage RNA-sequencing data, we demonstrated the emergence and global dissemination of a specific astrovirus strain. Astrovirus abundance and sequence variation mirrored temporal and spatial patterns of infection, potentially serving as footprints of specific timeframes and geographical locations. Additionally, we revealed more than 100,000 sequence contigs likely originating from novel viral species, exhibiting distinct profiles in total RNA and DNA datasets and including undescribed bunyaviruses and parvoviruses. Finally, we identified thousands of new CRISPR-associated protein sequences, including Transposase B (TnpB), a class of compact, RNA-guided DNA editing enzymes. Collectively, our findings underscore the potential of high-throughput sequencing of total nucleic acids derived from wastewater for a broad range of applications.

Analysis of the genetic diversity in RNA-directed RNA polymerase sequences: implications for an automated RNA virus classification system

RNA viruses are characterized by a broad host range and high levels of genetic diversity. Despite a recent expansion in the known virosphere following metagenomic sequencing, our knowledge of the species rank genetic diversity of RNA viruses, and how often they are misassigned and misclassified, is limited. We performed a clustering analysis of 7801 RNA-directed RNA polymerase (RdRp) sequences representing 1897 established RNA virus species. From this, we identified substantial genetic divergence within some virus species and inconsistency in RNA virus assignment between the GenBank database and The International Committee on Taxonomy of Viruses (ICTV). In particular, 27.57% virus species comprised multiple virus operational taxonomic units (vOTUs), including Alphainfluenzavirus influenzae, Mammarenavirus lassaense, Apple stem pitting virus, and Rotavirus A, with each having over 100 vOTUs. In addition, the distribution of average amino acid identity between vOTUs within single assigned species showed a relatively low threshold: <90% and sometimes <50%. However, when only exemplar sequences from virus species were analyzed, 1889 of the ICTV-designated RNA virus species (99.58%) were clustered into a single vOTU. Clustering of the RdRp sequences from different virus species also revealed that 17 vOTUs contained two distinct virus species. These potential misassignments were confirmed by phylogenetic analysis. A further analysis of average nucleotide identity (ANI) values ranging from 70% to 97.5% revealed that at an ANI of 82.5%, 1559 (82.18%) of the 1897 virus species could be correctly clustered into one single vOTU. However, at ANI values >82.5%, an increasing number of species were clustered into two or more vOTUs. In sum, we have identified some inconsistency and misassignment of the RNA virus species based on the analysis of RdRp sequences alone, which has important implications for the development of an automated RNA virus classification system.

A ~40-kb flavi-like virus does not encode a known error-correcting mechanism

It is commonly held that there is a fundamental relationship between genome size and error rate, manifest as a notional "error threshold" that sets an upper limit on genome sizes. The genome sizes of RNA viruses, which have intrinsically high mutation rates due to a lack of mechanisms for error correction, must therefore be small to avoid accumulating an excessive number of deleterious mutations that will ultimately lead to population extinction. The proposed exceptions to this evolutionary rule are RNA viruses from the order Nidovirales (such as coronaviruses) that encode error-correcting exonucleases, enabling them to reach genome lengths greater than 40 kb. The recent discovery of large-genome flavi-like viruses (Flaviviridae), which comprise genomes up to 27 kb in length yet seemingly do not encode exonuclease domains, has led to the proposal that a proofreading mechanism is required to facilitate the expansion of nonsegmented RNA virus genomes above 30 kb. Herein, we describe a ~40 kb flavi-like virus identified in a Haliclona sponge metatranscriptome that does not encode a known exonuclease. Structural analysis revealed that this virus may have instead captured cellular domains associated with nucleic acid metabolism that have not been previously found in RNA viruses. Phylogenetic inference placed this virus as a divergent pesti-like lineage, such that we have provisionally termed it "Maximus pesti-like virus." This virus represents an instance of a flavi-like virus achieving a genome size comparable to that of the Nidovirales and demonstrates that RNA viruses have evolved multiple solutions to overcome the error threshold.

Discovery of Novel Viruses in Culicoides Biting Midges in Chihuahua, Mexico

Biting midges (Culicoides) are vectors of many pathogens of medical and veterinary importance, but their viromes are poorly characterized compared to certain other hematophagous arthropods, e.g., mosquitoes and ticks. The goal of this study was to use metagenomics to identify viruses in Culicoides from Mexico. A total of 457 adult midges were collected in Chihuahua, northern Mexico, in 2020 and 2021, and all were identified as female Culicoides reevesi. The midges were sorted into five pools and homogenized. An aliquot of each homogenate was subjected to polyethylene glycol precipitation to enrich for virions, then total RNA was extracted and analyzed by unbiased high-throughput sequencing. We identified six novel viruses that are characteristic of viruses from five families (Nodaviridae, Partitiviridae, Solemoviridae, Tombusviridae, and Totiviridae) and one novel virus that is too divergent from all classified viruses to be assigned to an established family. The newly discovered viruses are phylogenetically distinct from their closest known relatives, and their minimal infection rates in female C. reevesi range from 0.22 to 1.09. No previously known viruses were detected, presumably because viral metagenomics had never before been used to study Culicoides from the Western Hemisphere. To conclude, we discovered multiple novel viruses in C. reevesi from Mexico, expanding our knowledge of arthropod viral diversity and evolution.

A parasite odyssey: An RNA virus concealed in Toxoplasma gondii

We are entering a 'Platinum Age of Virus Discovery', an era marked by exponential growth in the discovery of virus biodiversity, and driven by advances in metagenomics and computational analysis. In the ecosystem of a human (or any animal) there are more species of viruses than simply those directly infecting the animal cells. Viruses can infect all organisms constituting the microbiome, including bacteria, fungi, and unicellular parasites. Thus the complexity of possible interactions between host, microbe, and viruses is unfathomable. To understand this interaction network we must employ computationally assisted virology as a means of analyzing and interpreting the millions of available samples to make inferences about the ways in which viruses may intersect human health. From a computational viral screen of human neuronal datasets, we identified a novel narnavirus Apocryptovirus odysseus (Ao) which likely infects the neurotropic parasite Toxoplasma gondii. Previously, several parasitic protozoan viruses (PPVs) have been mechanistically established as triggers of host innate responses, and here we present in silico evidence that Ao is a plausible pro-inflammatory factor in human and mouse cells infected by T. gondii. T. gondii infects billions of people worldwide, yet the prognosis of toxoplasmosis disease is highly variable, and PPVs like Ao could function as a hitherto undescribed hypervirulence factor. In a broader screen of over 7.6 million samples, we explored phylogenetically proximal viruses to Ao and discovered nineteen Apocryptovirus species, all found in libraries annotated as vertebrate transcriptome or metatranscriptomes. While samples containing this genus of narnaviruses are derived from sheep, goat, bat, rabbit, chicken, and pigeon samples, the presence of virus is strongly predictive of parasitic Apicomplexa nucleic acid co-occurrence, supporting the fact that Apocryptovirus is a genus of parasite-infecting viruses. This is a computational proof-of-concept study in which we rapidly analyze millions of datasets from which we distilled a mechanistically, ecologically, and phylogenetically refined hypothesis. We predict that this highly diverged Ao RNA virus is biologically a T. gondii infection, and that Ao, and other viruses like it, will modulate this disease which afflicts billions worldwide.

Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation

BACKGROUND

Zoonotic viruses cause substantial public health and socioeconomic problems worldwide. Understanding how viruses evolve and spread within and among wildlife species is a critical step when aiming for proactive identification of viral threats to prevent future pandemics. Despite the many proposed factors influencing viral diversity, the genomic diversity and structure of viral communities in East Africa are largely unknown.

RESULTS

Using 38.3 Tb of metatranscriptomic data obtained via ultradeep sequencing, we screened vertebrate-associated viromes from 844 bats and 250 rodents from Kenya and Uganda collected from the wild. The 251 vertebrate-associated viral genomes of bats (212) and rodents (39) revealed the vast diversity, host-related variability, and high geographic specificity of viruses in East Africa. Among the surveyed viral families, Coronaviridae and Circoviridae showed low host specificity, high conservation of replication-associated proteins, high divergence among viral entry proteins, and frequent recombination. Despite major dispersal limitations, recurrent mutations, cocirculation, and occasional gene flow contribute to the high local diversity of viral genomes.

CONCLUSIONS

The present study not only shows the landscape of bat and rodent viromes in this zoonotic hotspot but also reveals genomic signatures driven by the evolution and dispersal of the viral community, laying solid groundwork for future proactive surveillance of emerging zoonotic pathogens in wildlife. Video Abstract.

A novel papillomavirus in a New Zealand fur seal (Arctocephalus forsteri) with oral lesions

Despite being the predominant seal species in the Australian-New Zealand region and serving as a key indicator of marine environmental health, little is known about infectious diseases in New Zealand fur seals (Long-nosed fur seal; Arctocephalus forsteri). Several papillomaviruses have been identified in earless seals and sea lions, with the latter linked to cutaneous plaques and invasive squamous cell carcinoma. To date, no papillomaviruses have been reported in fur seals. We used traditional veterinary diagnostic techniques and metatranscriptomic sequencing of tissue samples to investigate the virome of New Zealand fur seals. We identified a novel papillomavirus, provisionally termed A. forsteri papillomavirus 1 (AforPV1) in an animal with clinically and histologically identified oral papilloma-like lesions. RT-PCR confirmed the presence of AforPV1 only in oral papilloma samples from the affected individual. Phylogenetic analysis of the complete 7926 bp genome of AforPV1 revealed that it grouped with taupapillomaviruses found in related Carnivora species. These findings highlight the need for further research into the disease associations and impact of undiagnosed and novel viruses on New Zealand fur seals.

Greetings from virologists to mycologists: A review outlining viruses that live in fungi

Viruses are genetic elements that parasitize self-replicating cells. Therefore, organisms parasitized by viruses are not limited to animals and plants but also include microorganisms. Among these, viruses that parasitize fungi are known as mycoviruses. Mycoviruses with an RNA genome persistently replicate inside fungal cells and coevolve with their host cells, similar to a cellular organelle. Within host cells, mycoviruses can modulate various fungal characteristics and activities, including pathogenicity and the production of enzymes and secondary metabolites. In this review, we provide an overview of the mycovirus research field as introduction to fungal researchers. Recognition of all genetic elements in fungi aids towards better understanding and control of fungi, and makes fungi a significant model system for studying microorganisms containing multiple genetic elements.

Active prokaryotic and eukaryotic viral ecology across spatial scale in a deep-sea brine pool

Deep-sea brine pools represent rare, extreme environments, providing unique insight into the limits of life on Earth, and by analogy, the plausibility of life beyond it. A distinguishing feature of many brine pools is presence of thick microbial mats that develop at the brine-seawater interface. While these bacterial and archaeal communities have received moderate attention, viruses and their host interactions in these environments remain underexplored. To bridge this knowledge gap, we leveraged metagenomic and metatranscriptomic data from three distinct zones within the NEOM brine pool system (Gulf of Aqaba) to reveal the active viral ecology around the pools. We report a remarkable diversity and activity of viruses infecting microbial hosts in this environment, including giant viruses, RNA viruses, jumbo phages, and Polinton-like viruses. Many of these form distinct clades-suggesting presence of untapped viral diversity in this ecosystem. Brine pool viral communities exhibit zone-specific differences in infection strategy-with lysogeny dominating the bacterial mat further away from the pool's center. We linked viruses to metabolically important prokaryotes-including association between a jumbo phage and a key manganese-oxidizing and arsenic-metabolizing bacterium. These foundational results illuminate the role of viruses in modulating brine pool microbial communities and biogeochemistry through revealing novel viral diversity, host associations, and spatial heterogeneity in viral dynamics.

Characterisation of putative novel tick viruses and zoonotic risk prediction

Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.

Metatranscriptomics Reveals the RNA Virome of Ixodes Persulcatus in the China-North Korea Border, 2017

In recent years, numerous viruses have been identified from ticks, and some have been linked to clinical cases of emerging tick-borne diseases. Chinese northeast frontier is tick infested. However, there is a notable lack of systematic monitoring efforts to assess the viral composition in the area, leaving the ecological landscape of viruses carried by ticks not clear enough. Between April and June 2017, 7101 ticks were collected to perform virus surveillance on the China-North Korea border, specifically in Tonghua, Baishan, and Yanbian. A total of 2127 Ixodes persulcatus were identified. Further investigation revealed the diversity of tick-borne viruses by transcriptome sequencing of Ixodes persulcatus. All ticks tested negative for tick-borne encephalitis virus. Transcriptome sequencing expanded 121 genomic sequence data of 12 different virus species from Ixodes persulcatus. Notably, a new segmented flavivirus, named Baishan Forest Tick Virus, were identified, closely related to Alongshan virus and Harz mountain virus. Therefore, this new virus may pose a potential threat to humans. Furthermore, the study revealed the existence of seven emerging tick-borne viruses dating back to 2017. These previously identified viruses included Mudanjiang phlebovirus, Onega tick phlebovirus, Sara tick phlebovirus, Yichun mivirus, and three unnamed viruses (one belonging to the Peribunyaviridae family and the other two belonging to the Phenuiviridae family). The existence of these emerging tick-borne viruses in tick samples collected in 2017 suggests that their history may extend further than previously recognized. This study provides invaluable insights into the virome of Ixodes persulcatus in the China-North Korea border region, enhancing our ongoing efforts to manage the risks associated with tick-borne viruses.

Virus replication in the honey bee parasite, Varroa destructor

IMPORTANCE

The parasitic mite Varroa destructor is a significant driver of worldwide colony losses of our most important commercial pollinator, the Western honey bee Apis mellifera. Declines in honey bee health are frequently attributed to the viruses that mites vector to honey bees, yet whether mites passively transmit viruses as a mechanical vector or actively participate in viral amplification and facilitate replication of honey bee viruses is debated. Our work investigating the antiviral RNA interference response in V. destructor demonstrates that key viruses associated with honey bee declines actively replicate in mites, indicating that they are biological vectors, and the host range of bee-associated viruses extends to their parasites, which could impact virus evolution, pathogenicity, and spread.

Known phyla dominate the Tara Oceans RNA virome

A recent study proposed five new RNA virus phyla, two of which, 'Taraviricota' and 'Arctiviricota', were stated to be 'dominant in the oceans'. However, the study's assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study's classifications, and that contigs originally assigned to 'Arctiviricota' accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum 'Pomiviricota' were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum 'Taraviricota' were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.

Evidence for an ancient aquatic origin of the RNA viral order Articulavirales

The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.

Divergent hepaciviruses, delta-like viruses, and a chu-like virus in Australian marsupial carnivores (dasyurids)

Although Australian marsupials are characterised by unique biology and geographic isolation, little is known about the viruses present in these iconic wildlife species. The Dasyuromorphia are an order of marsupial carnivores found only in Australia that include both the extinct Tasmanian tiger (thylacine) and the highly threatened Tasmanian devil. Several other members of the order are similarly under threat of extinction due to habitat loss, hunting, disease, and competition and predation by introduced species such as feral cats. We utilised publicly available RNA-seq data from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database to document the viral diversity within four Dasyuromorph species. Accordingly, we identified fifteen novel virus sequences from five DNA virus families (Adenoviridae, Anelloviridae, Gammaherpesvirinae, Papillomaviridae, and Polyomaviridae) and three RNA virus taxa: the order Jingchuvirales, the genus Hepacivirus, and the delta-like virus group. Of particular note was the identification of a marsupial-specific clade of delta-like viruses that may indicate an association of deltaviruses with marsupial species. In addition, we identified a highly divergent hepacivirus in a numbat liver transcriptome that falls outside of the larger mammalian clade. We also detect what may be the first Jingchuvirales virus in a mammalian host-a chu-like virus in Tasmanian devils-thereby expanding the host range beyond invertebrates and ectothermic vertebrates. As many of these Dasyuromorphia species are currently being used in translocation efforts to reseed populations across Australia, understanding their virome is of key importance to prevent the spread of viruses to naive populations.

Viral community composition of hypersaline lakes

Despite their widespread distribution and remarkable antiquity no RNA viruses definitively associated with the domain Archaea have been identified. In contrast, 17 families of DNA viruses are known to infect archaea. In an attempt to uncover more of the elusive archaeal virosphere, we investigated the metatranscriptomes of hypersaline lakes that are a rich source of archaea. We sequenced RNA extracted from water filter samples of Lake Tyrrell (Victoria, Australia) and cultures seeded from four lakes in Antarctica. To identify highly divergent viruses in these data, we employed a variety of search tools, including Hidden Markov models (HMMs) and position-specific scoring matrices (PSSMs). From this, we identified 12 highly divergent, RNA virus-like candidate sequences from the virus phyla Artverviricota, Duplornaviricota, Kitrinoviricota, Negarnaviricota, and Pisuviricota, including those with similarity to the RNA-dependent RNA polymerase (RdRp). An additional analysis with an artificial intelligence (AI)-based approach that utilises both sequence and structural information identified seven putative and highly divergent RdRp sequences of uncertain phylogenetic position. A sequence matching the Pisuviricota from Deep Lake in Antarctica had the strongest RNA virus signal. Analyses of the dinucleotide representation of the virus-like candidates in comparison to that of potential host species were in some cases compatible with an association to archaeal or bacterial hosts. Notably, however, the use of archaeal CRISPR spacers as a BLAST database failed to detect any RNA viruses. We also described DNA viruses from the families Pleolipoviridae, Sphaerolipoviridae, Halspiviridae, and the class Caudoviricetes. Although we were unable to provide definitive evidence the existence of an RNA virus of archaea in these hypersaline lakes, this study lays the foundations for further investigations of highly divergent RNA viruses in natural environments.

Virome Analysis Provides an Insight into the Viral Community of Chinese Mitten Crab Eriocheir sinensis

Recent advances in viromics have led to the discovery of a great diversity of RNA viruses and the identification of a large number of viral pathogens. A systematic exploration of viruses in Chinese mitten crab (Eriocheir sinensis), one of the most important aquatic commercial species, is still lacking. Here, we characterized the RNA viromes of asymptomatic, milky disease (MD)-affected, and hepatopancreatic necrosis syndrome (HPNS)-affected Chinese mitten crabs collected from 3 regions in China. In total, we identified 31 RNA viruses belonging to 11 orders, 22 of which were first reported here. By comparing viral composition between samples, we observed high variation in viral communities across regions, with most of the viral species being region-specific. We proposed to establish several novel viral families or genera based on the phylogenetic relationships and genome structures of viruses discovered in this study, expanding our knowledge of viral diversity in brachyuran crustaceans. IMPORTANCE High-throughput sequencing and meta-transcriptomic analysis provide us with an efficient tool to discover unknown viruses and explore the composition of viral communities in specific species. In this study, we investigated viromes in asymptomatic and diseased Chinese mitten crabs collected from three distant locations. We observed high regional variation in the composition of viral species, highlighting the importance of multi-location sampling. In addition, we classified several novel and ICTV-unclassified viruses based on their genome structures and phylogenetic relationships, providing a new perspective on current viral taxa.

Identification of RNA Virus-Derived RdRp Sequences in Publicly Available Transcriptomic Data Sets

RNA viruses are abundant and highly diverse and infect all or most eukaryotic organisms. However, only a tiny fraction of the number and diversity of RNA virus species have been catalogued. To cost-effectively expand the diversity of known RNA virus sequences, we mined publicly available transcriptomic data sets. We developed 77 family-level Hidden Markov Model profiles for the viral RNA-dependent RNA polymerase (RdRp)-the only universal "hallmark" gene of RNA viruses. By using these to search the National Center for Biotechnology Information Transcriptome Shotgun Assembly database, we identified 5,867 contigs encoding RNA virus RdRps or fragments thereof and analyzed their diversity, taxonomic classification, phylogeny, and host associations. Our study expands the known diversity of RNA viruses, and the 77 curated RdRp Profile Hidden Markov Models provide a useful resource for the virus discovery community.

Novel polyomaviruses identified in fecal samples from four carnivore species

Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).

Meta-transcriptomics reveals potential virus transfer between Aedes communis mosquitoes and their parasitic water mites

Arthropods harbor a largely undocumented diversity of RNA viruses. Some arthropods, like mosquitoes, can transmit viruses to vertebrates but are themselves parasitized by other arthropod species, such as mites. Very little is known about the viruses of these ectoparasites and how they move through the host-parasite relationship. To address this, we determined the virome of both mosquitoes and the mites that feed on them. The mosquito Aedes communis is an abundant and widely distributed species in Sweden, in northern Europe. These dipterans are commonly parasitized by water mite larvae (Trombidiformes: Mideopsidae) that are hypothesized to impose negative selection pressures on the mosquito by reducing fitness. In turn, viruses are dual-host agents in the mosquito-mite interaction. We determined the RNA virus diversity of mite-free and mite-detached mosquitoes, as well as their parasitic mites, using meta-transcriptomic sequencing. Our results revealed an extensive RNA virus diversity in both mites and mosquitoes, including thirty-seven putative novel RNA viruses that cover a wide taxonomic range. Notably, a high proportion of viruses (20/37) were shared between mites and mosquitoes, while a limited number of viruses were present in a single host. Comparisons of virus composition and abundance suggest potential virus transfer between mosquitoes and mites during their symbiotic interaction. These findings shed light on virome diversity and ecology in the context of arthropod host-parasite-virus relationships.