Search Results (611)

Cuba is in a unique situation in which it has a large (220,000 managed colonies) and isolated honey bee population due to a 60+ year ban on the importation of bees. Despite this, the ectoparasitic mite Varroa destructor arrived in 1996, and with it came deformed wing virus (DWV). In 2018, an island-wide survey detected varroa and DWV in 91% of colonies. In this study, we conducted a full-virome analysis on some of these samples, along with additional samples collected in 2021. For the first time, we detected two variants of Lake Sinai Virus and confirmed the absence of the normally widespread black queen cell virus in Cuba. We also detected both DWV-A and DWV-B master variants, with DWV-B being the dominant variant. Interestingly, the DWV-B/A recombinant was also detected, indicating that despite Cuba’s isolated nature, the pattern of DWV evolution mirrors that found in the USA and Europe. However, this pattern is not found in neighboring Latin America, China, or Japan, where the DWV-A master variant continues to be dominant. How and why two distinct evolutionary DWV pathways have arisen remain a mystery. Full article

Citrus yellow vein clearing virus (CYVCV) is the causative agent of the yellow vein clearing disease (YVCD), a worldwide and highly destructive disease in lemon (Citrus lemon) and sour orange trees (C. aurantium). The typical symptoms of vein clearing are believed to be associated with CYVCV infection in citrus, so virus-specific diagnostic systems are currently used to confirm infection. In the present study, virome analysis based on high-throughput sequencing (HTS) on a lemon plant showing YVCD revealed mixed infection of CYVCV, iris domestica betaflexyviridae 1 (IDBV), and hop stunt viroid (HSVd). This multiple infection was confirmed in other two lemon plants with similar symptoms using virus/viroid specific primers. This is the first report of IDBV in lemon. Through molecular characterization and the reconstruction of phylogenetic relationships, a possible origin of the viruses/viroid identified in lemon has been hypothesized. Such mixed infections raise new questions about their role in the expression of YVCD symptoms observed on lemon. Full article

Torque Teno Virus (TTV), a common and genetically diverse component of the human virome, is not linked to any known disease but reflects immune status. Its plasma viral load has shown clinical relevance in solid organ transplant recipients, correlating it with immunosuppression when present at high levels. However, the clinical significance of TTV viral load in hematopoietic stem cell transplantation (HSCT) recipients is less understood. This systematic review aims to evaluate whether plasma TTV DNA load directly correlates with the degree of T-cell immune reconstitution after HSCT, supporting its potential role as a biomarker for immune competence. The study protocol was registered in the PROSPERO International Prospective Register of Systematic Reviews (CRD420251116208) and followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Twenty-one studies were included. The results showed concordant data about TTV kinetics with peak levels reaching approximately between +90 to +120 days after transplantation. Contradictory results have instead been found for the association of TTV load with immune parameters (lymphocyte counts, viral opportunistic infection, and development of acute graft versus host diseases). Even if a low-risk bias assessment was classified in most studies (67%), it was possible to identify important clinical and methodological differences between them, which might account for the different findings observed. Therefore, future larger studies with standardized protocols are needed to assess whether TTV viral load can serve as a reliable tool for guiding clinical decisions in the context of HSCT. Full article

Human non-polio enteroviruses (NPEVs) cause a plethora of infections in humans, ranging from mild to severe neurological diseases including aseptic meningitis. NPEVs are the leading cause of aseptic meningitis in both children and adults worldwide. In Russia, reports of NPEV infections have surged, especially in the post-COVID era starting in 2022, with elevated infection rates into 2023. A comprehensive examination of the whole genome is crucial for understanding the evolution of NPEV genes and for predicting potential outbreaks. This study focused on identifying the circulating NPEV strains in the Ural Federal District and Western Siberia, using Sanger sequencing and next-generation sequencing (NGS) methodologies. Biological samples were collected from (n = 225) patients diagnosed with aseptic meningitis. Bioinformatics analysis targeted the nucleotide sequences of the major capsid protein (partial VP1) gene fragment, and the assembly of whole NPEV genomes. A total of 159 NPEVs were characterized, representing 70.7% of the collected samples. The main capsid variants forming the predominant genotypic profile included E30 (n = 39, 24.3%), E6 (n = 31, 19.3%), and CVA9 (n = 25, 15.6%). Using NGS, we successfully assembled 13 whole genomes for E6, E30, EV-B80, CVA9, CVB5, E11, and EV-A71 and 3 partial genomes for E6 and EV-B87. This molecular-genetic analysis provides contemporary insights into the genotypic composition, circulation patterns, and evolutionary dynamics of the dominant NPEV associated with aseptic meningitis in the Ural Federal District and Western Siberia. The laboratory-based monitoring and epidemiological surveillance for genetic changes and evolutionary studies are important for improving prevention and healthcare. Full article

This study explores the virome of fifteen peanut cultivars in Korea. Through RNA sequencing, 305 viral contigs associated with cucumber mosaic virus (CMV), peanut mottle virus (PeMoV), bean common mosaic virus (BCMV), and brassica yellows virus (BrYV) were identified, with CMV notably prevalent across samples. Evaluation of viral abundance using viral reads and TPM values revealed CMV dominance in reads and PeMoV prominence in normalized values in select samples. Complete genomes of BCMV, PeMoV, BrYV, and CMV segments were assembled, enabling phylogenetic analysis that uncovered genetic relationships among viral isolates. RT-PCR confirmed BCMV, CMV, and PeMoV presence. Genetic diversity within BCMV was evident through single-nucleotide polymorphism (SNP) analysis, displaying diverse patterns and correlations with viral reads. This study discusses the implications for peanut cultivation, stressing the importance of ongoing research to manage viral diseases. It forms a foundational resource for future investigations into peanut virology, guiding strategies for disease management in peanut crops. Full article

Bacteriophages are a key ecological factor in the legume rhizosphere, controlling bacterial populations and affecting introduced inoculant strains. Despite their importance, rhizobiophage genomic diversity remains poorly characterized. We report the complete genome of a novel predicted temperate Sinorhizobium phage, AP-202, isolated from agricultural Chernozem. This siphovirus infects the symbiont Sinorhizobium meliloti. Its 121,599 bp dsDNA genome has a strikingly low GC content (27.1%), likely reflecting adaptive evolution and a strategy to evade host defenses. The linear genome is flanked by 240 bp direct terminal repeats (DTRs), and its DNA packaging follows a T7-like strategy. Annotation predicted 178 protein-coding genes and one tRNA. Functional analysis revealed a complete lysogeny module and a divergent, two-pronged codon-usage strategy for translational control. A significant part of the proteome (74.2%) comprises hypothetical proteins, with 50 CDSs having no database homologs, underscoring its genetic novelty. Complete-genome comparison shows minimal similarity to known rhizobiophages, defining AP-202 as a distinct lineage. Phenotypic analysis indicates AP-202 acts as a selective ecological filter, with host resistance being more prevalent in agricultural than in natural soils. The AP-202 genome provides a unique model for studying phage–host coevolution in the rhizosphere and is a valuable resource for comparative genomics and soil virome research. Full article

Inflammatory bowel diseases (IBD) are increasingly acknowledged not merely as confined gastrointestinal disorders but as systemic immunometabolic syndromes. Central to this paradigm is the gut microbiota including non-bacterial components such as the virome, whose functional disruption marked by reduced short-chain fatty acids (SCFAs), increasingly implicated in pathogenic processes extending beyond intestinal mucosa. This review outlines how these alternations compromise the epithelial barrier and immune regulation, increasing the risk of recurrent Clostridioides difficile infections to anemia, neuropsychiatric comorbidities, and extraintestinal manifestations. We critically evaluate emerging microbiota-targeted strategies, including fecal microbiota transplantation (FMT), live biotherapeutic products (LBPs), and precision postbiotics, positioning them as potential adjuncts to conventional immunosuppression. Finally, we discuss the current barriers to clinical translation, such as safety and heterogeneity, and propose a future framework for personalized, functionally integrated IBD care aimed at restoring long-term microbiota homeostasis. Full article

Canine parvovirus (CPV) is the primary cause of viral enteritis in dogs, while canine bocavirus (CBoV) and canine bufavirus (CBuV) have emerged as significant components of the canine enteric virome. Previous studies on CPV in Sichuan had limited geographic coverage and sample size, and lacked data on CBoV and CBuV. This study used PCR to investigate the genetic diversity of CPV, CBoV and CBuV and to examine their co-infection status in diarrheic dogs across five regions of Sichuan between 2020 and 2022. The results revealed that CPV-2 was the most prevalent virus (33.3%, 48/144), while CBoV (5.56%, 8/144) and CBuV (4.17%, 6/144) were detected for the first time in Sichuan province. Genetic analysis revealed CPV-2c to be the predominant genotype (95.8% (46/48)), replacing the previously circulating strains CPV-2a and CPV-new 2a. The study also identified several typical and novel mutations in the VP2 protein in the CPV-2c strains, including Ala5Gly, Trp214Cys and Thr440Ala. Additionally, four co-infection cases (2.78%) were observed, including a triple CPV/CBoV/CBuV infection in Xichang (XC05). Phylogenetic analysis revealed genetic diversity, with CBoV strains clustering into CBoV-1 and CBoV-2 subspecies, while CBuV strains formed two distinct clusters. Our findings emphasize the need for ongoing monitoring of the dynamic epidemiological situation of CPV, CBoV and CBuV in Sichuan Province. Full article

The human virome represents a fundamental yet understudied component of the microbiome, influencing immune regulation and disease. Given the profound immune dysregulation and microbial imbalance associated with HIV infection, understanding virome alterations during HIV and antiretroviral therapy is essential. This narrative review seeks to integrate and discuss the latest evidence regarding the structure and behavior of the human virome in healthy individuals, in the context of HIV infection, and under antiretroviral therapy. A comprehensive literature search was performed in MEDLINE and Google Scholar for peer-reviewed English-language articles published up to November 2025. Studies describing virome composition, diversity, and interactions in people living with HIV, as well as antiretroviral-induced changes, were included. Reference lists of relevant papers were screened to identify additional sources. Data were extracted and synthesized narratively, emphasizing human studies and supported by evidence from primate models where applicable. HIV infection induces profound alterations in the human virome, notably an expansion of eukaryotic viruses such as Anelloviridae, Adenoviridae, and Parvoviridae, accompanied by reduced bacteriophage diversity. Antiretroviral therapy partially restores virome balance but fails to fully re-establish pre-infection diversity, with persistent enrichment of Anelloviridae reflecting incomplete immune reconstitution. Virome perturbations correlate with immune activation, microbial translocation, and inflammation, contributing to comorbidities despite virological suppression. Emerging evidence suggests regimen-specific effects, with integrase inhibitor-based therapies showing more favorable viromic recovery. HIV and antiretroviral therapy profoundly remodel the human virome, with lasting implications for immune homeostasis and chronic inflammation. The ongoing disruption of the virome highlights its promise as both a biomarker and a potential therapeutic target in the management of HIV. Longitudinal, multi-omic studies are needed to clarify the causal role of virome alterations and guide future interventions. Full article

Protoparvovirus carnivoran 1 (PPVC-1), Canine adenovirus type 1 and 2 (CAdV-1 and CAdV-2), and Canine circovirus (CanineCV) are highly diffusive viruses that affect domestic and wild carnivores worldwide, yet limited data are available on their circulation in Eastern European countries. In this retrospective study, the presence of these DNA viruses was investigated using molecular assays on fecal samples from 89 companion animals (56 dogs and 33 cats) collected in Romania between 2019 and 2021. The pathogens identified were analyzed genetically. Overall, 36/56 (64.3%) dogs and 5/33 (15.2%) cats tested positive for PPVC-1, 1/56 (1.8%) dogs for CAdV-1 and CAdV-2, and 15/56 (26.8%) dogs for CanineCV. In total, 40/56 (71.4%) dogs were positive for at least one of the screened pathogens. Novel findings in dogs included the frequent detection of canine parvovirus type 2c of Asian origin (Asian-like CPV-2c) and the first genetic data on CAdV-1 and CanineCV circulating in Romania. This study provides new insights into the epidemiology of DNA viruses in dogs and cats from Romania and highlights the need for ongoing monitoring of circulating pathogens to safeguard animal health, prevent outbreaks and limit potential transboundary spread. Full article

The tea plant (Camellia sinensis (L.) O. Kuntze) is a globally important crop, yet its cultivation is continually challenged by a range of viral pathogens that can compromise plant health and product quality. In this study, eighteen symptomatic leaves were collected from the Hubei Province Tea Germplasm Resources Nursery, China, representing multiple cultivars and diverse genetic backgrounds. The samples were pooled into three groups and subjected to ribodepleted transcriptome sequencing. Analyses revealed a complex virome, with Tea plant necrotic ring blotch virus (TPNRBV) dominating Pools A and B, whereas Badnavirus betacolocalasiae was the most prevalent in Pool C. Functional enrichment of viral genes indicated involvement in multiple biological processes, including replication, host interaction, and metabolism. Notably, two previously uncharacterized viruses were identified: Tea plant-associated ourmia-like virus 1 (TeaOLV1) and Tea plant-associated rhabdo-like virus 1 (TeaRLV1). Phylogenetic reconstruction positioned TeaOLV1 within the Penoulivirus genus, while TeaRLV1 formed a distinct clade among plant-associated rhabdoviruses. Conserved motif analysis revealed typical viral domains, accompanied by lineage-specific variations in tea plants. Collectively, these findings enhance our understanding of the viral diversity in tea plants, provide refined taxonomic placement for newly identified viruses, and offer molecular insights into their evolutionary relationships and potential functional roles. Full article

Bats have been identified as reservoir hosts for an exceptional diversity of viruses, including multiple taxa of high zoonotic concern. Over a hundred bat species inhabit Vietnam, which, combined with significant biodiversity, carry high risk of zoonotic spillover due to dense human–animal interfaces, extensive wildlife trade, and proximity to recent outbreak epicenters. This review systematically synthesizes data on the bat virome in Vietnam and neighboring Southeast Asian countries, assessing viral diversity, host species involvement, and zoonotic potential. By prioritizing virus groups with established zoonotic capacity and pandemic potential, the systematic search identified studies reporting viruses from 32 families across 13 bat families. Based on the WHO 2024 risk classification, seven of these viral families were categorized as high-risk, three as medium-risk, and twelve as low-risk. The comparatively higher viral diversity reported in neighboring countries suggests that the current study likely represents an underestimation of the true virome present in Vietnamese bat populations. We emphasize the urgent need for expanded virological studies integrating metagenomic sequencing, serological surveys, and ecological modeling to improve early detection of emerging threats, as the comparatively higher viral diversity reported in neighboring countries suggests existing research likely represents an underestimation of the true virome present in Vietnamese bat populations. Strengthening regional collaboration is critical for establishing proactive pandemic prevention strategies in this high-risk zoonotic hotspot. Full article

Wildlife can act as both a reservoir and a sentinel for emerging pathogens, but surveillance is often constrained by difficulties in obtaining samples without disturbing animals. This study explored the viral diversity of wild mammals inhabiting the Foreste Casentinesi National Park (Central Italy) using non-invasive fecal sampling. From 2021 to 2022, 99 fecal samples from several species were collected and analyzed by PCR and metagenomic next-generation sequencing. Of 26 pools examined, 10 (38.5%) tested positive for at least one viral target. Astroviruses were the most frequently detected, found in deer, foxes, wolves, small mustelids, and porcupines. Several sequences showed low similarity to known strains, suggesting divergent or novel viral lineages. Metagenomic analysis also identified members of Circoviridae, Anelloviridae, and Picobirnaviridae. While none of these virus families are currently recognized as major zoonotic agents, their widespread occurrence in wildlife and domestic animals underscores the importance of continued surveillance to better assess their ecological roles, host range, and potential implications for both animal and human health. These results provide new insights into the virome of European wildlife, including the first reports of some viruses in certain species. Overall, our study demonstrates that non-invasive surveillance is a valuable tool for monitoring ecosystem health and supports a One Health approach to early detection of viral threats. Full article

Over the past five years, research has progressively revealed a rich diversity of RNA viruses in Botrytis cinerea. In this study, we identified nine RNA viruses from the viromes of three B. cinerea strains, including five mitoviruses, one umbra-like virus, and three partitiviruses. Among these, Sclerotinia sclerotiorum partitivirus 1 (SsPV1) was artificially introduced in a previous study. Excluding SsPV1, we cloned the other two partitiviruses and confirmed that both belong to Gammapartitivirus and contain three genomic segments, with dsRNA3 as an RNA satellite. In addition to RNA viruses, we discovered 12 retroplasmids in the three B. cinerea strains. These retroplasmids utilize the mitochondrial genetic codes and only encode a single open reading frame, which is predicted to produce a reverse transcriptase. It is also well known that mitoviruses use the mitochondrial genetic codes to encode their RNA-dependent RNA polymerase. Given the similarities between mitoviruses and retroplasmids in several aspects, we suggest that the mycovirus community could consider whether retroplasmids should be included within the conceptual scope of viruses. Furthermore, this study calls on researchers to pay attention to mobile genetic elements beyond typical RNA viruses, such as the retroplasmids reported here. Additionally, it underscores the importance of using single-spore or single-protoplast isolation methods in mycoviral studies to maintain a consistent genetic and viral background when investigating viral effects on the fungal host. Full article

Florida’s bat virome remains poorly characterized despite the state’s high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments. Full article