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BACKGROUND: Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. RESULTS: We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. CONCLUSIONS: Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.

Public health concerns about recent viral epidemics have motivated researchers to seek novel ways to understand pathogen infection in native, wildlife hosts. With its deep history of tools and perspectives for understanding the abundance and distribution of organisms, ecology can shed new light on viral infection dynamics. However, datasets allowing deep explorations of viral communities from an ecological perspective are lacking. We sampled 1086 bats from two, adjacent Puerto Rican caves and tested them for infection by herpesviruses, resulting in 3131 short, viral sequences. Using percent identity of nucleotides and a machine learning algorithm (affinity propagation), we categorized herpesviruses into 43 operational taxonomic units (OTUs) to be used in place of species in subsequent ecological analyses. Herpesvirus metacommunities demonstrated long-tailed rank frequency distributions at all analyzed levels of host organization (i.e., individual, population, and community). Although 13 herpesvirus OTUs were detected in more than one host species, OTUs generally exhibited host specificity by infecting a single core host species at a significantly higher prevalence than in all satellite species combined. We describe the natural history of herpesvirus metacommunities in Puerto Rican bats and suggest that viruses follow the general law that communities comprise few common and many rare species. To guide future efforts in the field of viral ecology, hypotheses are presented regarding mechanisms that contribute to these patterns.

Viruses are abundant and ubiquitous in soil, but their importance in modulating greenhouse gas (GHG) emissions in terrestrial ecosystems remains largely unknown. Here, various loads of viral communities are introduced into paddy soils with different fertilization histories via a reciprocal transplant approach to study the role of viruses in regulating greenhouse gas emissions and prokaryotic communities. The results showed that the addition of viruses has a strong impact on methane (CH4) and nitrous oxide (N2O) emissions and, to a minor extent, carbon dioxide (CO2) emissions, along with dissolved carbon and nitrogen pools, depending on soil fertilization history. The addition of a high viral load resulted in a decrease in microbial biomass carbon (MBC) by 31.4%, with changes in the relative abundance of 16.6% of dominant amplicon sequence variants (ASVs) in comparison to control treatments. More specifically, large effects of viral pressure are observed on some specific microbial communities with decreased relative abundance of prokaryotes that dissimilate sulfur compounds and increased relative abundance of Nanoarchaea. Structural equation modeling further highlighted the differential direct and indirect effects of viruses on CO2, N2O, and CH4 emissions. These findings underpin the understanding of the complex microbe‐virus interactions and advance current knowledge on soil virus ecology. [ABSTRACT FROM AUTHOR]

Simple Summary: Recently, during an outbreak of fatal enteritis involving European hedgehogs housed in a wildlife rescue center in Apulia Region (Southern Italy), a novel parvovirus closely related to chaphamaparvoviruses was identified. In this study, by using hedgehog chaphamaparvovirus (HhChPV)-specific primers and a probe, viral DNA was detected in duodenal and liver samples collected from necropsied European hedgehogs obtained from different areas of North-Western Italy, with an overall prevalence of 19.6% (38/194). When assessing the nearly complete genomes of four HhChPVs, the identified strains were genetically highly related (89.7–97.7% nucleotide identity) to the HhChPVs previously found in Amur and European hedgehogs. Upon phylogenetic analysis, all the Italian and Chinese HhChPV strains were tightly clustered as members of a proposed novel species in the genus Chaphamaparvovirus. Molecularly investigating the hedgehog virome is crucial for understanding the roles of these animals in the ecology of viral pathogens, which may pose threats to vulnerable hedgehog populations, and from a One Health perspective, given the synanthropic behavior of hedgehogs, for providing valuable insights into potential zoonotic risks. In 2022, a novel parvovirus was identified from an outbreak of fatal enteritis in weaned European hedgehogs (Erinaceus europaeus) at a wildlife rescue center in Southern Italy. During sequence analysis, the strain was found to be closely related (90.4% nucleotide identity) to a chaphamaparvovirus (ChPV) discovered in Amur hedgehogs (Erinaceus amurensis) during a large metaviromic investigation in game animals in China. In this study, we investigated the presence of this novel ChPV in necropsied European hedgehogs from different areas of North-Western Italy. Duodenal and liver samples collected from 194 necropsied hedgehogs were screened by using a specific quantitative PCR. A total of 38/194 animals (19.6%) tested positive, with ChPV DNA being detected in the duodenum (9.3%, 18/194), liver (7.2%, 14/194) or in both (3.1%, 6/194) tissue samples, with comparable rates and mean viral loads. The nearly full-length genome of four hedgehog ChPV strains was reconstructed. During phylogenetic analysis based on the NS1 and partial VP aa sequences, the four strains detected in this study tightly clustered with the prototype ChPVs previously identified in Amur and European hedgehogs within a potential novel candidate species of the genus Chaphamaparvovirus. [ABSTRACT FROM AUTHOR]

Sheep play an important role in China's agricultural development, but they are also potential hosts for many viruses, some of which have been identified as zoonotic pathogens, which may pose a serious threat to social public health and animal husbandry. Therefore, clarifying the characteristics of viruses in sheep will provide an important basis for the study of pathogenic ecology and viral evolution of viruses carried by sheep. We collected nasal and anal swabs from 688 sheep in 22 counties in Shaanxi, Gansu, and Ningxia, China, between January 2022 and July 2023, and utilized next-generation sequencing technology and bioinformatics approaches to identify the viruses in the samples. A total of 38 virus families carried by sheep were identified, including 12 ssRNA (+) virus families, 2 dsRNA virus families, 8 ssDNA (+) virus families, and 18 dsDNA virus families. Among them, Astroviridae, Coronaviridae, Picornaviridae, and Tobaniviridae in RNA virus families and Herpesviridae, Adenoviridae, and Circoviridae in DNA virus families are all viruses that are frequently detected in most ruminants. Alpha and beta diversity results showed that there was no difference in the overall richness and diversity of RNA and DNA viruses among the three provinces (p > 0.05). The evolutionary analysis demonstrated a tight link between the viral members carried by sheep and other ruminant viruses, implying that these viruses may spread across different species of ruminants. This study established a library of RNA and DNA viruses carried by sheep in the Shaanxi-Gansu-Ningxia region, providing an overview of the viruses present in this population. The findings offer valuable data for further research on virus evolution and monitoring in sheep. [ABSTRACT FROM AUTHOR]

Accumulating data suggest that some bat species host emerging viruses that are highly pathogenic in humans and agricultural animals. Laboratory-based studies have highlighted important adaptations in bat immune systems that allow them to better tolerate viral infections compared to humans. Simultaneously, ecological studies have discovered critical extrinsic factors, such as nutritional stress, that correlate with virus shedding in wild-caught bats. Despite some progress in independently understanding the role of bats as reservoirs of emerging viruses, there remains a significant gap in the molecular understanding of factors that drive virus spillover from bats. Driven by a collective goal of bridging the gap between the fields of bat virology, immunology, and disease ecology, we hosted a satellite symposium at the 2024 American Society for Virology meeting. Bringing together virologists, immunologists, and disease ecologists, we discussed the intrinsic and extrinsic factors such as virus receptor engagement, adaptive immunity, and virus ecology that influence spillover from bat hosts. This article summarizes the topics discussed during the symposium and emphasizes the need for interdisciplinary collaborations and resource sharing. [ABSTRACT FROM AUTHOR]

Bats are recognized as natural reservoirs for an array of diverse viruses, particularly coronaviruses, which have been linked to major human diseases like SARS-CoV and MERS-CoV. These viruses are believed to have originated in bats, highlighting their role in virus ecology and evolution. Our study focuses on the molecular characterization of bat-derived coronaviruses (CoVs) in Canada. Tissue samples from 500 bat specimens collected in Canada were analyzed using pan-coronavirus RT-PCR assays to detect the presence of CoVs from four genera: Alpha-CoVs, Beta-CoV, Gamma-CoV, and Delta-CoV. Phylogenetic analysis was performed targeting the RNA-dependent RNA polymerase (RdRP) gene. Our results showed an overall 1.4% CoV positivity rate in our bat sample size. Phylogenetic analysis based on the ~600 bp sequences led to the identification of an unclassified subgenus of Alpha-CoV, provisionally named Eptacovirus. The findings contribute to a better understanding of the diversity and evolution of CoVs found in the bat species of Canada. The current study underscores the significance of bats in the epidemiology of CoVs and enhances the knowledge of their genetic diversity and potential impact on global public health. [ABSTRACT FROM AUTHOR]

During the early days of the COVID-19 pandemic, popular narratives of a 'resurgent nature' and portrayals of the virus as a form of 'revenge' prompted geographical reflection on the promises and limitations of ecological perspectives on the SARS-CoV-2 virus. Revisiting these reflections in the light of what we have learned from the pandemic, this article asks what is to be gained by attempting to think critically with the virus about human space as multispecies composition. Thinking ecologically with the virus can become a method for critically reconsidering naturalised and dualistic orders of exclusion and inclusion, health and unhealth, or belonging and unbelonging. Specifically, we focus in this article on the overlap of immunological and trans-antagonistic discourses with viral imaginaries of the pandemic, exploring the paradox of vulnerability that arises at this point of intersection. COVID-19 simultaneously highlights humans' mutual vulnerability as a horizontalising force and amplifies differential social vulnerabilities. In examining this paradox of vulnerability as it relates to viral discursive constructions of transness, we explore tensions between different modes of engaging, identifying and thinking with the virus in recognition that the social and the ecological cannot properly be considered as separate domains. The aim is not simply to propose an extended epidemiology that takes into account the complex human–nonhuman entanglement, but to explore the social, cultural and political implications of pandemic vulnerabilities and of thinking ecologically with the virus. We trace the shared conceptual underpinnings of ecological and immunological thought, showing that these same conceptual lineages manifest in political responses to the COVID-19 pandemic and exploring how they are expressed in queer- and trans-antagonistic discourse and policy. Building on these analyses, we develop a proposal for 'transing' the virus and a model for 'thinking ecologically' that is simultaneously liberatory, messy and agnostic. [ABSTRACT FROM AUTHOR]

In this review, we investigated the genetic diversity and evolutionary dynamics of the Orthomarburgvirus marburgense species that includes both Marburg virus (MARV) and Ravn virus (RAVV). Using sequence data from natural reservoir hosts and human cases reported during outbreaks, we conducted comprehensive analyses to explore the genetic variability, constructing haplotype networks at both the genome and gene levels to elucidate the viral dynamics and evolutionary pathways. Our results revealed distinct evolutionary trajectories for MARV and RAVV, with MARV exhibiting higher adaptability across different ecological regions. MARV showed substantial genetic diversity and evidence of varied evolutionary pressures, suggesting an ability to adapt to diverse environments. In contrast, RAVV demonstrated limited genetic diversity, with no detected recombination events, suggesting evolutionary stability. These differences indicate that, while MARV continues to diversify and adapt across regions, RAVV may be constrained in its evolutionary potential, possibly reflecting differing roles within the viral ecology of the Orthomarburgvirus marburgense species. Our analysis explains the evolutionary mechanisms of these viruses, highlighting that MARV is going through evolutionary adaptation for human-to-human transmission, alarmingly underscoring the global concern about MARV causing the next pandemic. However, further transdisciplinary One Health research is warranted to answer some remaining questions including the host range and genetic susceptibility of domestic and wildlife species as well as the role of the biodiversity network in the disease's ecological dynamics. [ABSTRACT FROM AUTHOR]

Background: Predator‒prey interactions and their dynamic changes provide frequent opportunities for viruses to spread among organisms and thus affect their virus diversity. However, the connections between dietary diversity and virus diversity in predators have seldom been studied. The avivorous bats, Ia io, show a seasonal pattern of dietary diversity. Although most of them primarily prey on insects in summer, they mainly prey on nocturnally migrating birds in spring and autumn. Results: In this study, we characterized the RNA virome of three populations of I. io in Southwest China during summer and autumn using viral metatranscriptomic sequencing. We also investigated the relationships between dietary diversity and RNA virus diversity by integrating DNA metabarcoding and viral metatranscriptomic sequencing techniques at the population level of I. io. We found 55 known genera belonging to 35 known families of RNA viruses. Besides detecting mammal-related viruses, which are the usual concern, we also found a high abundance of insect-related viruses and some bird-related viruses. We found that insect-related viruses were more abundant in summer, while the bird-related viruses were predominantly detected in autumn, which might be caused by the seasonal differences in prey selection by I. io. Additionally, a significant positive correlation was identified between prey diversity and total virus diversity. The more similar the prey composition, the more similar the total virus composition and the higher the count of potential new viruses. We also found that the relative abundance of Picornaviridae increased with increasing prey diversity and body mass. Conclusions: In this study, significant links were found between RNA virus diversity and dietary diversity of I. io. The results implied that dynamic changes in predator–prey interactions may facilitate frequent opportunities for viruses to spread among organisms. -pQNSPFCJqqnkMh129yG7y Video Abstract [ABSTRACT FROM AUTHOR]

The coastal waters of Kerala, in the South Eastern Arabian Sea (SEAS), are unique during the Southwest monsoon season due to the concurrent occurrence of two physical processes, the upwelling and Mudbanks. However, little is known about the viral ecology and activity in a system where upwelling and Mudbanks coexist, though it is generally recognized that microbial assemblages play a vital role in the food web dynamics of marine systems, particularly in upwelling. Water samples were taken from monsoon and pre-monsoon period from three locations, (M1, M2, and M3) off Alappuzha, on the southwest coast of India to examine the viral activity and distribution. The dissolved oxygen levels showed the incursion of hypoxic waters in all the stations during the peak upwelling period. Upwelling signals were prominent in all the stations, but Mudbank and upwelling co-occurred at M2 alone during monsoon. The abundance of viruses ranged from 0.86 to 15.68 × 106 Viral-like Particles (VLPs mL−1) and prokaryotic abundance ranged from 2.73–16.26 × 105 cells mL−1. Viral and prokaryotic abundance was significantly higher in the monsoon compared to pre and late-monsoon. Based on Transmission electron microscopy (TEM) results, the non-tailed viruses constituted the major (43%) proportion of the total viruses in this study region. However, the viral production rates and viral-mediated bacterial mortality were high in the pre-monsoon compared to the monsoon and late-monsoon periods. There was no obvious effect of Mudbanks on viral dynamics and the observed variations in virological and hydrological features were governed mainly by coastal upwelling. [ABSTRACT FROM AUTHOR]

The avian influenza A (H7N9) virus, which circulates in wild birds and poultry, has been a major concern for public health since it was first discovered in China in 2013 due to its demonstrated ability to infect humans, causing severe respiratory illness with high mortality rates. According to the World Health Organization (WHO), a total of 1568 human infections with 616 fatal cases caused by novel H7N9 viruses have been reported in China from early 2013 to January 2024. This manuscript provides a comprehensive review of the virology, evolutionary patterns, and pandemic potential of H7N9. The H7N9 virus exhibits a complex reassortment history, receiving genes from H9N2 and other avian influenza viruses. The presence of certain molecular markers, such as mutations in the hemagglutinin and polymerase basic protein 2, enhances the virus's adaptability to human hosts. The virus activates innate immune responses through pattern recognition receptors, leading to cytokine production and inflammation. Clinical manifestations range from mild to severe, with complications including pneumonia, acute respiratory distress syndrome, and multiorgan failure. Diagnosis relies on molecular assays such as reverse transcription‐polymerase chain reaction. The increasing frequency of human infections, along with the virus's ability to bind to human receptors and cause severe disease, highlights its pandemic potential. Continued surveillance, vaccine development, and public health measures are crucial to limit the risk posed by H7N9. Understanding the virus's ecology, transmission dynamics, and pathogenesis is essential for developing effective prevention and control strategies. [ABSTRACT FROM AUTHOR]

Abstract Background Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. Results Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. Conclusions Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. Video Abstract

Abstract Background Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens. Results We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments. Conclusions Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract

Routes of virus transmission between hosts are key to understanding viral epidemiology. Different routes have large effects on viral ecology, and likelihood and rate of transmission; for example, respiratory and vector-borne viruses together encompass the majority of rapid outbreaks and high-consequence animal and plant epidemics. However, determining the specific transmission route(s) can take months to years, delaying mitigation efforts. Here, we identify the vial features and evolutionary signatures which are predictive of viral transmission routes and use them to predict potential routes for fully-sequenced viruses in silico and rapidly, for both viruses with no observed routes, as well as viruses with missing routes. This was achieved by compiling a dataset of 24,953 virus-host associations with 81 defined transmission routes, constructing a hierarchy of virus transmission encompassing those routes and 42 higher-order modes, and engineering 446 predictive features from three complementary perspectives. We integrated those data and features to train 98 independent ensembles of LightGBM classifiers. We found that all features contributed to the prediction for at least one of the routes and/or modes of transmission, demonstrating the utility of our broad multi-perspective approach. Our framework achieved ROC-AUC = 0.991, and F1-score = 0.855 across all included transmission routes and modes, and was able to achieve high levels of predictive performance for high-consequence respiratory (ROC-AUC = 0.990, and F1-score = 0.864) and vector-borne transmission (ROC-AUC = 0.997, and F1-score = 0.921). Our framework ranks the viral features in order of their contribution to prediction, per transmission route, and hence identifies the genomic evolutionary signatures associated with each route. Together with the more matured field of viral host-range prediction, our predictive framework could: provide early insights into the potential for, and pattern of viral spread; facilitate rapid response with appropriate measures; and significantly triage the time-consuming investigations to confirm the likely routes of transmission. Author summary: Routes of virus transmission–the mechanism(s) by which a virus physically gets from an infected to an uninfected host, are crucial to understanding how viral diseases spread among animals and plants. Here, we uncover the evolutionary signatures which can predict the transmission routes a virus uses to move from one host to another, enabling us to identify any unobserved routes for known viruses and even predict potential routes of newly emerged viruses. We first compile a comprehensive dataset of virus-host associations. Using this dataset, we employ a multi-perspective machine learning approach to achieve high predictive performance. Our framework ranks viral features by their significance in prediction, revealing genomic evolutionary signatures linked to each route. Our approach could provide early insights into viral spread patterns, facilitating prompt response efforts to new outbreaks and epidemics, and streamline laboratory investigations. Overall, our study represents a step forward in our ability to anticipate and mitigate the impact of emerging infectious diseases on human, animal, and plant health. [ABSTRACT FROM AUTHOR]

Knowledge of viral biodiversity within insects, particularly within ants, is extremely limited with only a few environmental viruses from invasive ant species identified to date. This study documents and explores the viral communities in ants. We comprehensively profile the metagenomes of a phylogenetically broad group of 35 ant species with varied ecological traits and report the discovery of 3710 novel and unique ant‐associated viral genomes. These previously unknown viruses discovered within this study constitute over 95% of all currently described ant viruses, significantly increasing our knowledge of the ant virosphere. The identified RNA and DNA viruses fill gaps in insect‐associated viral phylogenies and uncover evolutionary histories characterized by both frequent host switching and co‐divergence. Many ants also host diverse bacterial communities, and we discovered that approximately one‐third of these new ant‐associated viruses are bacteriophages. Two ecological categories, bacterial abundance in the host and habitat degradation are both correlated with ant viral diversity and help to structure viral communities within ants. These data demonstrate that the ant virosphere is remarkably diverse phylogenetically and genomically and provide a substantial foundation for studies in virus ecology and evolution within eukaryotes. We highlight the importance of studying insect‐associated viruses in natural ecosystems in order to more thoroughly and effectively understand host‐microbe evolutionary dynamics. [ABSTRACT FROM AUTHOR]

Background: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied. Results: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes had greater species richness and total viral genome abundances than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment. Conclusions: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits. ADm-mTTAXM3aVZwCyoroCB Video Abstract [ABSTRACT FROM AUTHOR]

Usutu virus (USUV) is an emerging mosquito-transmitted flavivirus with increasing incidence of human infection and geographic expansion, thus posing a potential threat to public health. In this study, we established a comprehensive spatiotemporal database encompassing USUV infections in vectors, animals, and humans worldwide by an extensive literature search. Based on this database, we characterized the geographic distribution and epidemiological features of USUV infections. By employing boosted regression tree (BRT) models, we projected the distributions of three main vectors (Culex pipiens, Aedes albopictus, and Culiseta longiareolata) and three main hosts (Turdus merula, Passer domesticus, and Ardea cinerea) to obtain the mosquito index and bird index. These indices were further incorporated as predictors into the USUV infection models. Through an ensemble learning model, we achieved a decent model performance, with an area under the curve (AUC) of 0.992. The mosquito index contributed significantly, with relative contributions estimated at 25.51%. Our estimations revealed a potential exposure area for USUV spanning 1.80 million km2 globally with approximately 1.04 billion people at risk. This can guide future surveillance efforts for USUV infections, especially for countries located within high-risk areas and those that have not yet conducted surveillance activities. [ABSTRACT FROM AUTHOR]

Background: Madariaga virus (MADV), a member of the eastern equine encephalitis virus (EEEV) complex, circulates in Latin America and exhibits distinct evolutionary and ecological features compared to the North American EEEV. While published data have shed light on MADV ecology, several key aspects remain unknown. Methods: In this study, we compiled data on virus isolation, vector competence, and animal serology collected over six decades in Latin America to identify critical knowledge gaps on MADV transmission and ecology. Results: Specific vertebrate animals serving as amplifying hosts and the mosquito species acting as enzootic and epizootic vectors have not yet been identified. Other aspects that remain unclear are the virus current geographic distribution, the role of equines as hosts in epizootic cycles, and the full impact of MADV on human health in endemic regions. Conclusions: The numerous knowledge gaps surrounding MADV, its widespread distribution in Latin America, and its potential to cause severe disease in animals and humans emphasize the urgent need for increased research efforts, heightened awareness, and intensified surveillance towards this potential emerging threat. [ABSTRACT FROM AUTHOR]

Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets. Author summary: The ecology and evolution of microbial communities are deeply influenced by viruses. Metagenomics analysis, the non-targeted sequencing of community genomes, has led to the discovery of millions of novel viruses. Yet, through the sequencing process, only DNA sequences are recovered, begging the question: which microbial hosts do those novel viruses infect? To address this question, we developed a computational tool to allow researchers to predict virus-host interactions from such sequence data. The power of this tool is its use of a high-value, manually curated set of 8849 lab-verified virus-host pairs and their corresponding sequence data. For each pair, we computed signals of coevolution to use as the predictive features in a machine learning model designed to predict interactions between viruses and hosts. The resulting model, Virus-Host Interaction Predictor (VHIP), has an accuracy of 87.8% and can be applied to novel viral and host genomes reconstructed from metagenomic datasets. Because the model considers all possible virus-host pairs, it can resolve complete virus-host interaction networks and supports a new avenue to apply network thinking to viral ecology. [ABSTRACT FROM AUTHOR]

Influenza A virus (IAV) can cause high morbidity and mortality in domestic and wild avian species and it is able to infect mammals as well. IAV in cats is sporadic and self-limiting but the recent findings of high pathogenicity avian influenza virus (HPAIV) with genetic signatures ofmammalian adaptation, in domestic cats, has raised new concerns about the potential role of cats in the virus ecology. The present study aimed to investigate the circulation of IAV in companion animals' shelters in North-eastern Italy. All samples were collected from feral cats living in feline colonies that were hosted in the companion animals' shelters for the requisite period to administer the veterinary treatments. Between 2021 and 2022, 389 oropharyngeal swabs and 279 sera were collected. All swabs tested negative for IAV and the only one ELISA positive serum sample resulted H5 positive by HI test with a titer of 1:80. Despite the sporadic occurrence of influenza in cats, continuousmonitoring is crucial due to the evolving zoonotic nature of the virus. [ABSTRACT FROM AUTHOR]

The recent incursion of highly pathogenic influenza viruses into dairy cattle opens new insights for influenza virus ecology and its interspecies transmission and may have a significant impact on public health and agriculture. The aim of this study was to determine the stability of a bovine highly pathogenic avian influenza H5N1 virus isolate in the milk byproduct lactose and to evaluate two inactivation methods using industrial procedures. The bovine isolate of the highly pathogenic avian influenza H5N1 virus was stable for 14 days in a concentrated lactose solution under refrigerated conditions. Heat or citric acid treatments successfully inactivated the virus in lactose. This study highlights the persistence of HPAIV in lactose and its efficient inactivation under industrial standards. [ABSTRACT FROM AUTHOR]

DNA Stable Isotope Probing is emerging as a potent methodology for investigating host–virus interactions, based on the essential reliance of viruses on host organisms for the production of virions. Despite the anticipated link between host isotopic compositions and the generated virions, the application of stable isotope probing to viral DNA has never been evaluated on simple biological models. In this study, we assessed the efficacy of this method on the bacteriophage T4 and its host, Escherichia coli. Through the cultivation of E. coli cells on a 13C-enriched substrate and subsequent propagation of T4 bacteriophage, we examine the degree of isotopic enrichment in viral DNA. Our investigation reveals a strong correlation between the proportion of 13C6-d-glucose in the growth substrate and the buoyant density in CsCl gradient of T4 DNA, confirming the validity of DNA SIP in viral ecology. These findings underscore the potential of DNA SIP as a robust tool for characterizing the diversity of viruses infecting hosts with specific metabolic activities and provide then a foundation for further exploration in viral ecology research. [ABSTRACT FROM AUTHOR]

A novel virus, temporarily named "Arctic wolf parvovirus" (AWPV), was discovered in a pharyngeal metagenomic library derived from an Arctic wolf (Canis lupus arctos) in China. The genome sequence was assigned GenBase accession number C_AA071902.1. AWPV has a genome comprised of 4,920 base pairs with a nucleotide composition of 36.4% A, 23.4% T, 18.2% G, and 22.0% C, with a GC content of 40.2%. Its structure resembles parvoviruses, containing two open reading frames: the nonstructural (NS) region encoding replication enzymes and the structural (VP) region encoding capsid protein. Pairwise sequence comparison and phylogenetic analysis suggest AWPV may represent a novel species within the genus Protoparvovirus. This discovery enhances our understanding of mammalian virus ecology and potential future infectious diseases. [ABSTRACT FROM AUTHOR]

Seagrasses are marine angiosperms that form highly productive and diverse ecosystems. These ecosystems, however, are declining worldwide. Plant-associated microbes affect critical functions like nutrient uptake and pathogen resistance, which has led to an interest in the seagrass microbiome. However, despite their significant role in plant ecology, viruses have only recently garnered attention in seagrass species. In this study, we produced original data and mined publicly available transcriptomes to advance our understanding of RNA viral diversity in Zostera marina, Zostera muelleri, Zostera japonica, and Cymodocea nodosa. In Z. marina, we present evidence for additional Zostera marina amalgavirus 1 and 2 genotypes, and a complete genome for an alphaendornavirus previously evidenced by an RNA-dependent RNA polymerase gene fragment. In Z. muelleri, we present evidence for a second complete alphaendornavirus and near complete furovirus. Both are novel, and, to the best of our knowledge, this marks the first report of a furovirus infection naturally occurring outside of cereal grasses. In Z. japonica, we discovered genome fragments that belong to a novel strain of cucumber mosaic virus, a prolific pathogen that depends largely on aphid vectoring for host-to-host transmission. Lastly, in C. nodosa, we discovered two contigs that belong to a novel virus in the family Betaflexiviridae. These findings expand our knowledge of viral diversity in seagrasses and provide insight into seagrass viral ecology. [ABSTRACT FROM AUTHOR]

Viruses as the prevailing biological entities are poorly understood in underground realms. Here, we establish the first metagenomic Groundwater Virome Catalogue (GWVC) comprising 280,420 viral species (≥ 5 kb) detected from 607 monitored wells in seven geo-environmental zones throughout China. In expanding ~10-fold the global portfolio of known groundwater viruses, we uncover over 99% novel viruses and about 95% novel viral clusters. By linking viruses to hosts from 119 prokaryotic phyla, we double the number of microbial phyla known to be virus-infected in groundwater. As keystone ultrasmall symbionts in aquifers, CPR bacteria and DPANN archaea are susceptible to virulent viruses. Certain complete CPR viruses even likely infect non-CPR bacteria, while partial CPR/DPANN viruses harbor cell-surface modification genes that assist symbiont cell adhesion to free-living microbes. This study reveals the unknown viral world and auxiliary metabolism associated with methane, nitrogen, sulfur, and phosphorus cycling in groundwater, and highlights the importance of subsurface virosphere in viral ecology. The authors present a metagenomic groundwater virome catalogue, unravelling unknown viral diversity, unique virus-host interaction, and diverse auxiliary metabolic genes in groundwater ecosystems. [ABSTRACT FROM AUTHOR]

Filoviruses are negative-sense single-stranded RNA viruses often associated with severe and highly lethal hemorrhagic fever in humans and nonhuman primates, with case fatality rates as high as 90%. Of the known filoviruses, Ebola virus (EBOV), the prototype of the genus Orthoebolavirus, has been a major public health concern as it frequently causes outbreaks and was associated with an unprecedented outbreak in several Western African countries in 2013–2016, affecting 28,610 people, 11,308 of whom died. Thereafter, filovirus research mostly focused on EBOV, paying less attention to other equally deadly orthoebolaviruses (Sudan, Bundibugyo, and Taï Forest viruses) and orthomarburgviruses (Marburg and Ravn viruses). Some of these filoviruses have emerged in nonendemic areas, as exemplified by four Marburg disease outbreaks recorded in Guinea, Ghana, Tanzania, and Equatorial Guinea between 2021 and 2023. Similarly, the Sudan virus has reemerged in Uganda 10 years after the last recorded outbreak. Moreover, several novel bat-derived filoviruses have been discovered in the last 15 years (Lloviu virus, Bombali virus, Měnglà virus, and Dehong virus), most of which are poorly characterized but may display a wide host range. These novel viruses have the potential to cause outbreaks in humans. Several gaps are yet to be addressed regarding known and emerging filoviruses. These gaps include the virus ecology and pathogenicity, mechanisms of zoonotic transmission, host range and susceptibility, and the development of specific medical countermeasures. In this review, we summarize the current knowledge on non-Ebola filoviruses (Bombali virus, Bundibugyo virus, Reston virus, Sudan virus, Tai Forest virus, Marburg virus, Ravn virus, Lloviu virus, Měnglà virus, and Dehong virus) and suggest some strategies to accelerate specific countermeasure development. [ABSTRACT FROM AUTHOR]

Effective visualization of infectious disease risks is crucial for the development of efficient prevention and control strategies. However, the efficacy of mainstream models is hindered by a scarcity of reliable data in target areas, a situation that is particularly acute when dealing with emerging or re‐emerging infectious diseases. Additionally, these models typically fail to integrate local disease‐related risk factors in line with the 'One Health' concept, resulting in inaccurate predictions. Consequently, accurately assessing infectious disease risks without reliable data is challenging.This study introduces SpatMCDA, an innovative R package designed to assess infectious disease risk areas through spatial multi‐criteria decision analysis (MCDA). SpatMCDA is structured around six core modelling steps: standardizing risk factors, determining factor weights, constructing risk maps, performing One‐at‐a‐Time sensitivity analysis, calculating the Mean of Absolute Change Rates and conducting an uncertainty analysis.By examining the case of West Nile virus (WNV) in China, this study illustrates how SpatMCDA can be useful in identifying disease transmission risks in the absence of reliable outbreak data. The assessment identified areas at risk for WNV in northwestern, eastern and southern China.By integrating spatial and epidemiological data, SpatMCDA enhances infectious diseases risk assessment in situations where data are limited. Its efficiency in using available data for accurate risk mapping and adaptability in weighting various risk factors enables tailored analyses. This tool enhances public health strategies, contributing to global health security. [ABSTRACT FROM AUTHOR]

The document "General Epidemiology of Animal Viruses" explores the impact of animal viruses on human health, agriculture, and wildlife conservation. It highlights the importance of understanding transmission mechanisms, globalization, and climate change in combating viral threats. The document features studies on various animal viruses, emphasizing the need for global collaboration and ongoing research to improve disease prevention and biosecurity measures. The comprehensive overview provided in this Special Issue aims to advance knowledge in virology, epidemiology, and disease control for the benefit of all species. [Extracted from the article]

Emerging RNA virus infections are a growing concern among domestic poultry industries due to the severe impact they can have on flock health and economic livelihoods. Avian paramyxoviruses (APMV; avulaviruses, AaV) are pathogenic, negative-sense RNA viruses that cause serious infections in the respiratory and central nervous systems. APMV was detected in multiple avian species during the 2017 wild bird migration season in Ukraine and studied using PCR, virus isolation, and sequencing. Of 4090 wild bird samples collected, mostly from southern Ukraine, eleven isolates were grown in ovo and identified for APMV serotype by hemagglutinin inhibition test as: APMV-1, APMV-4, APMV-6, and APMV-7. To build One Healths capacity to characterize APMV virulence and analyze the potential risks of spillover to immunologically naïve populations, we sequenced virus genomes in veterinary research labs in Ukraine using a nanopore (MinION) platform. RNA was extracted and amplified using a multiplex tiling primer approach to specifically capture full-length APMV-1 (n = 5) and APMV-6 (n = 2) genomes at high read depth. All APMV-1 and APMV-6 fusion (F) proteins possessed a monobasic cleavage site, suggesting these APMVs were likely low virulence, annually circulating strains. Utilization of this low-cost method will identify gaps in viral evolution and circulation in this understudied but important critical region for Eurasia.

Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. We present an experimental method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A unique gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. We demonstrate this method's efficacy by spiking two known viral genomes, Simian virus 40 (SV40, 5,243 bp) and Human Adenovirus 5 (HAd5, 35,938 bp), into a sewage sample with a final abundance in the droplets of around 0.1% and 0.015%, respectively. We achieve 100% recovery of the complete sequence of the spiked-in SV40 genome with uniform coverage distribution. For the larger HAd5 genome, we cover approximately 99.4% of its sequence. Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables single-genome whole-genome amplification and targeting characterizations of rare viral species and will facilitate our ability to access the mutational profile in single-virus genomes and contribute to an improved understanding of viral ecology. [ABSTRACT FROM AUTHOR]

Soil microorganisms are pivotal in the global carbon cycle, but the viruses that affect them and their impact on ecosystems are less understood. In this study, we explored the diversity, dynamics, and ecology of soil viruses through 379 metagenomes collected annually from 2010 to 2017. These samples spanned the seasonally thawed active layer of a permafrost thaw gradient, which included palsa, bog, and fen habitats. We identified 5051 virus operational taxonomic units (vOTUs), doubling the known viruses for this site. These vOTUs were largely ephemeral within habitats, suggesting a turnover at the vOTU level from year to year. While the diversity varied by thaw stage and depth‐related patterns were specific to each habitat, the virus communities did not significantly change over time. The abundance ratios of virus to host at the phylum level did not show consistent trends across the thaw gradient, depth, or time. To assess potential ecosystem impacts, we predicted hosts in silico and found viruses linked to microbial lineages involved in the carbon cycle, such as methanotrophy and methanogenesis. This included the identification of viruses of Candidatus Methanoflorens, a significant global methane contributor. We also detected a variety of potential auxiliary metabolic genes, including 24 carbon‐degrading glycoside hydrolases, six of which are uniquely terrestrial. In conclusion, these long‐term observations enhance our understanding of soil viruses in the context of climate‐relevant processes and provide opportunities to explore their role in terrestrial carbon cycling. [ABSTRACT FROM AUTHOR]

Mycoviruses are viruses that infect fungi. In recent years, an increasing number of mycoviruses have been reported in a wide array of fungi. With the growing interest of scientists and society in reducing the use of agrochemicals, the debate about mycoviruses as an effective next-generation biocontrol has regained momentum. Mycoviruses can have profound effects on the host phenotype, although most viruses have neutral or no effect. We speculate that understanding multiple transmission modes of mycoviruses is central to unraveling the viral ecology and their function in regulating fungal populations. Unlike plant virus transmission via vegetative plant parts, seeds, pollen, or vectors, a widely held view is that mycoviruses are transmitted via vertical routes and only under special circumstances horizontally via hyphal contact depending on the vegetative compatibility groups (i.e., the ability of different fungal strains to undergo hyphal fusion). However, this view has been challenged over the past decades, as new possible transmission routes of mycoviruses are beginning to unravel. In this perspective, we discuss emerging studies with evidence suggesting that such novel routes of mycovirus transmission exist and are pertinent to understanding the full picture of mycovirus ecology and evolution. [ABSTRACT FROM AUTHOR]

The production of aquatic animals has more than doubled over the last 50 years and is anticipated to continually increase. While fish are recognized as a valuable and sustainable source of nutrition, particularly in the context of human population growth and climate change, the rapid expansion of aquaculture coincides with the emergence of highly pathogenic viruses that often spread globally through aquacultural practices. Here, we provide an overview of the fish virome and its relevance for disease emergence, with a focus on the insights gained through metagenomic sequencing, noting potential areas for future study. In particular, we describe the diversity and evolution of fish viruses, for which the majority have no known disease associations, and demonstrate how viruses emerge in fish populations, most notably at an expanding domestic-wild interface. We also show how wild fish are a powerful and tractable model system to study virus ecology and evolution more broadly and can be used to identify the major factors that shape vertebrate viromes. Central to this is a process of virus-host co-divergence that proceeds over many millions of years, combined with ongoing cross-species virus transmission. [ABSTRACT FROM AUTHOR]

Simple Summary: Viruses present a significant challenge to the sustainable growth of the aquaculture sector. Perinereis, a valuable live-feed source in aquaculture, carries the risk of harboring unknown viruses, potentially jeopardizing the biosecurity of aquatic organisms. Despite this risk, there is a notable absence of research investigating novel viruses in Perinereis using meta-transcriptomic sequencing techniques. Therefore, it becomes imperative to explore the viral diversity within Perinereis. In this report, 12 previously unidentified viruses was documented in two distinct Perinereis species through meta-transcriptomic sequencing. These newly identified viruses were classified into four major viral families, shedding light on the intricate viral landscape within Perinereis. By unveiling these novel viruses, this research contributes to a broader knowledge base of the viral ecology in Perinereis, offering valuable insights into the potential risks and impacts associated with Perinereis in aquaculture settings. Such findings also highlight the need for enhancing biosecurity measures and disease management strategies within the aquaculture industry. Perinereis species are essential benthonic animals in coastal ecosystems and have significant roles as live feed in aquaculture, owing to their high-protein and low-fat nutritional profile. Despite their ecological importance, the viral communities associated with these organisms need to be better understood. In this study, we generated 2.6 × 108 reads using meta-transcriptomic sequencing and de novo assembled 5.3 × 103 virus-associated contigs. We identified 12 novel RNA viruses from two species, Perinereis aibuhitensis and P. wilsoni, which were classified into four major viral groups: Picobirnaviridae, Marnaviridae, unclassified Picornavirales, and unclassified Bunyavirales. Our findings revealed the hidden diversity of viruses and genome structures in Perinereis, enriching the RNA virosphere and expanding the host range of Picobirnaviridae, Marnaviridae, and Bunyavirales. This study also highlighted the potential biosecurity risk of the novel viruses carried by Perinereis to aquaculture. [ABSTRACT FROM AUTHOR]

Highly pathogenic avian influenza (HPAI) has persisted as a One Health threat whose current circulation and impact are addressed in the companion Currents in One Health by Puryear and Runstadler, JAVMA, May 2024. Highly pathogenic avian influenza emerged as a by-product of agricultural practices and adapted to endemic circulation in wild bird species. Over more than 20 years, continued evolution in a complex ecology involving multiple hosts has produced a lineage that expanded globally over the last 2 years. Understanding the continued evolution and movement of HPAI relies on understanding how the virus is infecting different hosts in different contexts. This includes understanding the environmental factors and the natural ecology of viral transmission that impact host exposure and ultimately evolutionary trajectories. Particularly with the rapid host expansion, increased spillover to mammalian hosts, and novel clinical phenotypes in infected hosts, despite progress in understanding the impact of specific mutations to HPAI viruses that are associated with spillover potential, the threat to public health is poorly understood. Active research is focusing on new approaches to understanding the relationship of viral genotype to phenotype and the implementation of research and surveillance pipelines to make sense of the enormous potential for diverse HPAI viruses to emerge from wild reservoirs amid global circulation. [ABSTRACT FROM AUTHOR]

Ecophysiological stress and the grazing of diatoms are known to elicit the production of chemical defense compounds called oxylipins, which are toxic to a wide range of marine organisms. Here we show that (1) the viral infection and lysis of diatoms resulted in oxylipin production; (2) the suite of compounds produced depended on the diatom host and the infecting virus; and (3) the virus-mediated oxylipidome was distinct, in both magnitude and diversity, from oxylipins produced due to stress associated with the growth phase. We used high-resolution accurate-mass mass spectrometry to observe changes in the dissolved lipidome of diatom cells infected with viruses over 3 to 4 days, compared to diatom cells in exponential, stationary, and decline phases of growth. Three host virus pairs were used as model systems: Chaetoceros tenuissimus infected with CtenDNAV; C. tenuissimus infected with CtenRNAV; and Chaetoceros socialis infected with CsfrRNAV. Several of the compounds that were significantly overproduced during viral infection are known to decrease the reproductive success of copepods and interfere with microzooplankton grazing. Specifically, oxylipins associated with allelopathy towards zooplankton from the 6-, 9-, 11-, and 15-lipogenase (LOX) pathways were significantly more abundant during viral lysis. 9-hydroperoxy hexadecatetraenoic acid was identified as the strongest biomarker for the infection of Chaetoceros diatoms. C. tenuissimus produced longer, more oxidized oxylipins when lysed by CtenRNAV compared to CtenDNAV. However, CtenDNAV caused a more statistically significant response in the lipidome, producing more oxylipins from known diatom LOX pathways than CtenRNAV. A smaller set of compounds was significantly more abundant in stationary and declining C. tenuissimus and C. socialis controls. Two allelopathic oxylipins in the 15-LOX pathway and essential fatty acids, arachidonic acid (ARA), eicosapentaenoic acid (EPA), and docosahexaenoic acid (DHA) were more abundant in the stationary phase than during the lysis of C. socialis. The host–virus pair comparisons underscore the species-level differences in oxylipin production and the value of screening more host–virus systems. We propose that the viral infection of diatoms elicits chemical defense via oxylipins which deters grazing with downstream trophic and biogeochemical effects. [ABSTRACT FROM AUTHOR]

Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.

High-throughput RNA sequencing offers broad opportunities to explore the Earth RNA virome. Mining 5,150 diverse metatranscriptomes uncovered >2.5 million RNA virus contigs. Analysis of >330,000 RNA-dependent RNA polymerases (RdRPs) shows that this expansion corresponds to a 5-fold increase of the known RNA virus diversity. Gene content analysis revealed multiple protein domains previously not found in RNA viruses and implicated in virus-host interactions. Extended RdRP phylogeny supports the monophyly of the five established phyla and reveals two putative additional bacteriophage phyla and numerous putative additional classes and orders. The dramatically expanded phylum Lenarviricota, consisting of bacterial and related eukaryotic viruses, now accounts for a third of the RNA virome. Identification of CRISPR spacer matches and bacteriolytic proteins suggests that subsets of picobirnaviruses and partitiviruses, previously associated with eukaryotes, infect prokaryotic hosts.

Background: Ruminants are important livestock animals that have a unique digestive system comprising multiple stomach compartments. Despite significant progress in the study of microbiome in the gastrointestinal tract (GIT) sites of ruminants, we still lack an understanding of the viral community of ruminants. Here, we surveyed its viral ecology using 2333 samples from 10 sites along the GIT of 8 ruminant species. Results: We present the Unified Ruminant Phage Catalogue (URPC), a comprehensive survey of phages in the GITs of ruminants including 64,922 non-redundant phage genomes. We characterized the distributions of the phage genomes in different ruminants and GIT sites and found that most phages were organism-specific. We revealed that ~ 60% of the ruminant phages were lytic, which was the highest as compared with those in all other environments and certainly will facilitate their applications in microbial interventions. To further facilitate the future applications of the phages, we also constructed a comprehensive virus-bacteria/archaea interaction network and identified dozens of phages that may have lytic effects on methanogenic archaea. Conclusions: The URPC dataset represents a useful resource for future microbial interventions to improve ruminant production and ecological environmental qualities. Phages have great potential for controlling pathogenic bacterial/archaeal species and reducing methane emissions. Our findings provide insights into the virome ecology research of the ruminant GIT and offer a starting point for future research on phage therapy in ruminants. CJAF8kS71Z3NBgTNJ_uZFe Video Abstract [ABSTRACT FROM AUTHOR]

Avian influenza viruses of the H6 subtype are prevalent in wild ducks and likely play an important role in the ecology of influenza viruses through reassortment with other avian influenza viruses. Yet, only 152 Vietnamese H6 virus sequences were available in GISAID (Global Initiative on Sharing All Influenza Data) prior to this study with the most recent sequences being from 2018. Through surveillance in Vietnamese live bird markets from 2018 to 2021, we identified 287 samples containing one or several H6 viruses and other influenza A virus subtypes, demonstrating a high rate of co-infections among birds in Vietnamese live bird markets. For the 132 H6 samples with unique influenza virus sequences, we conducted phylogenetic and genetic analyses. Most of the H6 viruses were similar to each other and closely related to other H6 viruses; however, signs of reassortment with other avian influenza viruses were evident. At the genetic level, the Vietnamese H6 viruses characterized in our study encode a single basic amino acid at the HA cleavage site, consistent with low pathogenicity in poultry. The Vietnamese H6 viruses analyzed here possess an amino acid motif in HA that confers binding to both avian- and human-type receptors on host cells, consistent with their ability to infect mammals. The frequent detection of H6 viruses in Vietnamese live bird markets, the high rate of co-infections of birds with different influenza viruses, and the dual receptor-binding specificity of these viruses warrant their close monitoring for potential infection and spread among mammals. [ABSTRACT FROM AUTHOR]

Cross‐protection was first described a century ago. In practical terms, cross‐protection consists of the pre‐inoculation of plants with mild or attenuated viral isolates that protect the plants from subsequent infections with aggressive isolates. Experimentally, cross‐protection has been shown to apply to numerous virus and viroid species infecting numerous plant hosts, but the number of cases in which it has been successfully used for the control of the damage caused by viruses in crops is rather limited. Significant examples include citrus tristeza virus and zucchini yellow mosaic virus, and more recently, pepino mosaic virus (PepMV). PepMV is a pandemic virus affecting tomato crops worldwide. During the first decade of the current century, a number of mild PepMV isolates useful in cross‐protection were identified and characterized. Soon after, cross‐protection programs against PepMV were implemented in the Netherlands, Belgium, Morocco, and Spain. These programs were easily adopted by farmers, as no other efficient control methods were available and the losses caused by PepMV were unbearable for tomato producers. PepMV cross‐protection has been working exceedingly well during this time, although the potential interaction of the PepMV mild isolates with the recently emerging tomato brown rugose fruit virus (ToBRFV) may be threatening its viability. In this review, we describe our experience in deploying cross‐protection against PepMV in Spain. In our view, this is an underexploited technology that holds promise, but when it is used and how it is used requires careful thinking and preparation, as not all situations are as favourable for the use of cross‐protection as the PepMV pandemic has been. [ABSTRACT FROM AUTHOR]

When viruses have segmented genomes, the set of frequencies describing the abundance of segments is called the genome formula. The genome formula is often unbalanced and highly variable for both segmented and multipartite viruses. A growing number of studies are quantifying the genome formula to measure its effects on infection and to consider its ecological and evolutionary implications. Different approaches have been reported for analyzing genome formula data, including qualitative description, applying standard statistical tests such as ANOVA, and customized analyses. However, these approaches have different shortcomings, and test assumptions are often unmet, potentially leading to erroneous conclusions. Here, we address these challenges, leading to a threefold contribution. First, we propose a simple metric for analyzing genome formula variation: the genome formula distance. We describe the properties of this metric and provide a framework for understanding metric values. Second, we explain how this metric can be applied for different purposes, including testing for genome-formula differences and comparing observations to a reference genome formula value. Third, we re-analyze published data to illustrate the applications and weigh the evidence for previous conclusions. Our re-analysis of published datasets confirms many previous results but also provides evidence that the genome formula can be carried over from the inoculum to the virus population in a host. The simple procedures we propose contribute to the robust and accessible analysis of genome-formula data. [ABSTRACT FROM AUTHOR]

Viruses, with an estimated abundance of 1031 on Earth, are an important component of soil ecosystems. As obligate parasites that entirely depend on hosts for reproduction and survival, viruses have been linked to microbial community diversity and metabolic activities in soil. Emerging evidence indicates that soil viruses influence a broad-spectrum of processes that sustain soil biodiversity, biogeochemical cycling, fertility, and plant health. Research on soil viruses is in its early stages. Even observational assessments of viral ecology such as abundance, diversity, distribution, life strategies, ecological relevance, and functions, are only just beginning to be revealed. In this review, we summarize the state of knowledge concerning the potential function(s) of soil viruses and how they likely influence microbial community composition, nutrient cycles, and carbon dynamics for example. As major drivers of microbial mortality and functioning across a wide range of spatial and temporal scales, soil viruses appear to be key regulators of cellular metabolism and microbial community properties and as well as biogeochemical processes critical to ecosystem function. We conclude that soil viruses are an indispensable component of soil ecology demanding further investigation. Defining abiotic interactions of viruses within the soil environment, revealing the virus-host interaction networks, and elucidating the roles of soil viruses in carbon and nutrient cycling are but a few of the many aspects of soil viral ecology worthy of future investigation. A more complete view of viral participation in soil food webs in the face of a changing climate will lead to improved management of soil ecosystem services and environmental sustainability. [ABSTRACT FROM AUTHOR]

The Ebolavirus genus contains several of the deadliest zoonotic viruses known. One of these, Bundibugyo virus (BDBV), has been the causative agent of two outbreaks of human disease that have resulted in 211 known cases with a case fatality rate of 33.6%. Although bats are routinely implicated as the possible reservoir species for the ebolaviruses, the source of infection for index cases in almost all outbreaks is unknown with only limited epidemiological evidence directly linking human cases to bats. This lack of evidence leaves open the possibility that maintenance of one or more of these viruses could involve multiple host species or more complex spillover dynamics. Domestic pigs have been found naturally infected with Reston virus (RESTV) and are experimentally susceptible to infection with Ebola virus (EBOV), two other members of the Ebolavirus genus. Infection of pigs resulted in shedding of infectious virus with subsequent transmission to naïve animals being documented, including transmission to humans for RESTV and to nonhuman primates for EBOV. The susceptibility and subsequent viral shedding and pathogenesis of domestic pigs to other ebolaviruses and the potential role this species may play in virus ecology, spillover dynamics, and human public health risk is unknown. For these reasons, we conducted a series of studies aimed at determining the susceptibility of domestic pigs to BDBV thereby demonstrating that pigs are not only susceptible to experimental infection but that the development of productive infection, tissue dissemination, and shedding of infectious virus can also occur while animals remain clinically normal. The role of pigs as a possible interim or amplifying host for ebolaviruses is a concern for both human public health and food security. [ABSTRACT FROM AUTHOR]

Background: Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses. Results: Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages. Conclusion: This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species. [ABSTRACT FROM AUTHOR]