Search Results (177)

This study was conducted in Armenia and included 32 pregnant women with TV infection and 30 healthy controls. The vaginal virome includes viruses that infect human cells and unicellular eukaryotes such as Trichomonas vaginalis (TV). Among these are Trichomonas vaginalis viruses (TVVs), double-stranded RNA viruses from the Totiviridae family, and giant DNA viruses that replicate in protozoa. This study investigated the presence of TVVs and giant protozoan viruses in pregnant women with trichomoniasis in Armenia and explored their potential associations with adverse pregnancy outcomes. Vaginal and urethral samples were collected from 32 pregnant women with confirmed TV infection and 30 healthy pregnant controls. TVVs and giant viruses (Marseilleviridae, Mimiviridae, Phycodnaviridae) were detected using qRT-PCR. Viral RNA and DNA were extracted from clinical samples and TV cultures, followed by quantification and gene expression analysis. Selected TVVs were visualized via scanning electron microscopy. All TV-positive women carried at least one TVV strain, with 94% harboring multiple TVV types and TVV4 being the most common. TV infection was significantly associated with preterm birth and premature rupture of membranes (PPROM). Giant viruses were identified in all TV-positive cases but in only 40% of controls. Marseilleviridae gene expression was observed in TV cultures, suggesting possible interactions. These findings highlight a potential role for protozoan viruses in reproductive complications and warrant further investigation. Full article

A high-throughput sequencing-based grapevine metagenomic survey was conducted across all grape-growing Canadian provinces (British Columbia, Ontario, Nova Scotia, and Québec) with the objective of better understanding the grapevine virome composition. In total, 310 composite grapevine samples representing nine Vitis vinifera red; five V. vinifera white; seven American–French red; and five white hybrid cultivars were analyzed. dsRNA, enriched using two different methods, was used as the starting material and source of viral nucleic acids in HTS. The virome status on the distribution and incidence in different regions and grapevine cultivars is addressed. Results from this study revealed the presence of 20 viruses and 3 viroids in the samples tested. Twelve viruses, which are in the regulated viruses list under grapevine certification, were identified in this survey. The major viruses detected in this survey and their incidence rates are GRSPaV (26% to 100%), GLRaV-2 (1% to 18%), GLRaV-3 (15% to 63%), GRVFV (0% to 52%), GRGV (0% to 52%), GPGV (3.3% to 77%), GFkV (1.5% to 31.6%), and GRBV (0% to 19.4%). This survey is the first comprehensive virome study using viral dsRNA and a metagenomics approach on grapevine samples from the British Columbia, Ontario, Nova Scotia, and Quebec provinces in Canada. Results from this survey highlight the grapevine virome distribution across four major grapevine-growing regions and their cultivars. The outcome of this survey underlines the need for strengthening current management options to mitigate the impact of virus spread, and the implementation of a domestic grapevine clean plant program to improve the sanitary status of the grapevine ecosystem. Full article

Phlox are ornamentals of great decorative value, grown throughout the world for their attractive flowers. Phlox cultivar collections at the Tsitsin Main Botanical Garden and the Botanical Garden of Lomonosov Moscow State University (both Moscow, Russia) were surveyed for virus diseases. Tobacco streak ilarvirus (TSV), beet ringspot nepovirus (BRSV), and BRSV satellite RNA (satRNA) were first detected in phlox when viromes of symptomatic Phlox paniculata plants were studied using high-throughput sequencing. The nearly complete genomes of three TSV and BRSV isolates and two BRSV satRNAs were assembled and characterized. TSV isolates shared 96.9–99.7% nucleotide sequence identity and were 82.2–89.1% identical to their closest relatives from broad bean, dahlia, and echinacea. BRSV isolates were distantly related to each other (83.7–89.3% identity) and were closest to those from oxalis and potato. BRSV satRNAs shared 90.6% identity and were 87.8–94.1% identical to satRNAs associated with tomato black ring virus L and S serotypes. Thus, TSV, BRSV, and BRSV satRNA were for the first time detected in a new natural host P. paniculata in Russia, adding to the list of known phlox viruses and expanding information on the host range, geographic distribution, and genetic diversity of these viruses. Full article

Cocoa (Theobroma cacao L.) is a major agricultural commodity, essential for the global chocolate industry and the livelihoods of millions of farmers. However, viral diseases pose a significant threat to cocoa production, with Badnavirus species causing severe losses in Africa. Despite its economic importance, the overall virome of T. cacao remains poorly characterized, limiting our understanding of viral diversity and potential disease interactions. This study aims to assess the cocoa-associated virome by analyzing 109 publicly available RNA-seq libraries from nine BioProjects, covering diverse conditions and geographic regions. We implemented a comprehensive bioinformatics pipeline integrating multiple viral sequence enrichment steps, a hybrid assembly strategy using different assemblers, and sequence similarity searches against NCBI non-redundant databases. Our approach identified ten putative novel viruses associated with the cocoa microbiome and a novel Badnavirus species. These findings provide new insights into the viral landscape of T. cacao, characterizing the diversity of cacao-associated viruses and their potential ecological roles. Expanding the catalog of viruses associated with cocoa plants not only enhances our understanding of plant–virus–microbiome interactions but also contributes to the development of more effective disease surveillance and management strategies, ultimately supporting sustainable cocoa production. Full article

The cabbage whitefly (A. proletella) (Hemiptera: Aleyrodidae) is a major agricultural pest that primarily targets cruciferous crops, such as cabbage, broccoli, and kale, causing extensive damage through feeding and honeydew. However, its associated virome has received limited research attention. In this study, we collected cabbage whiteflies in Xinjiang Agricultural University (43.80833 N, 87.56778 E, 882.3 m), systematically identified the RNA virome of the A. proletella and successfully identified three novel iflaviruses (Aleyrodes proletella iflavirus 1 (APIV1), Aleyrodes proletella iflavirus 2 (APIV2) and Aleyrodes proletella iflavirus 3 (APIV3)). APIV1–3 all have a 5′ structural protein region and a 3’ non-structural protein region. Phylogenetic and sequence identity analyses suggest that APIV1–3 are novel members of the family Iflaviridae. Structural modeling using AlphaFold3 revealed a conserved protein core region and a variable outer loop region. This study provides valuable insights into the virome diversity of A. proletella, establishing a foundation for future research on virus–host interactions and the potential for biocontrol applications in sustainable agriculture. Full article

Recent studies have identified Torquetenovirus (TTV) as a promising biomarker of immune competence, particularly in assessing the vaccine response of solid organ transplant (SOT) recipients. However, given the individual variability of viral load, it is not yet possible to define "normal levels”. Nevertheless, TTV is just one component of the broader Anelloviridae family, which also includes Torquetenominivirus (TTMV) and Torquetenomidivirus (TTMDV). This study explores whether the viremia of TTMV and TTMDV offers a stronger predictive marker for vaccine efficacy in SOT recipients. A cohort of 168 SOT patients (142 kidney and 26 lung transplant recipients) who received the BNT162B2 mRNA vaccine was examined, with viral loads quantified through virus-specific real-time PCR. While TTV remains a potentially useful biomarker for evaluating immune response, the combined analysis of all anelloviruses viremia provides deeper insights, particularly in cases where TTV is undetectable. Notably, only TTMV exhibited a pattern similar to TTV, suggesting its potential as an alternative biomarker when TTV is absent from the patient’s virome. Full article

Wheat viruses are major yield-reducing factors, with mixed infections causing substantial economic losses. Determining field virus populations is crucial for effective management and developing virus-resistant cultivars. This study utilized the high-throughput Oxford Nanopore sequencing technique (ONT) to characterize wheat viral populations in major wheat-growing counties of Kansas from 2019 to 2021. Wheat leaves exhibiting virus-like symptoms were collected, total RNA was extracted, and cDNA libraries were prepared using a PCR-cDNA barcoding kit, then loaded onto ONT MinION flow cells. Sequencing reads aligned with cereal virus references identified eight wheat virus species. Tritimovirus tritici (wheat streak mosaic virus, WSMV), Poacevirus tritici (Triticum mosaic virus, TriMV), Bromovirus BMV (brome mosaic virus, BMV), as well as Emaravirus tritici, Luteovirus pavhordei, L. sgvhordei, Bymovirus tritici, and Furovirus tritici. Mixed infections involving two to five viruses in a single sample were common, with the most prevalent being WSMV + TriMV at 16.7% and WSMV + TriMV + BMV at 11.9%. Phylogenetic analysis revealed a wide distribution of WSMV isolates, including European and recombinant variants. A phylogenetic analysis of Emaravirus tritici based on RNA 3A and 3B segments and whole-genome characterization of Furovirus tritici were also conducted. These findings advance understanding of genetic variability, phylogenetics, and viral co-infections, supporting the development of sustainable management practices through host genetic resistance. Full article

The European grapevine moth (Lobesia botrana) poses a significant threat to vineyards worldwide, causing extensive economic losses. While its ecological interactions and control strategies have been well studied, its associated viral diversity remains unexplored. Here, we employ high-throughput sequencing data mining to comprehensively characterize the L. botrana virome, revealing novel and diverse RNA viruses. We characterized four new viral members belonging to distinct families, with evolutionary cues of cypoviruses (Reoviridae), sobemo-like viruses (Solemoviridae), phasmaviruses (Phasmaviridae), and carmotetraviruses (Carmotetraviridae). Phylogenetic analysis of the cypoviruses places them within the genus in affinity with other moth viruses. The bi-segmented and highly divergent sobemo-like virus showed a distinctive evolutionary trajectory of its encoding proteins at the periphery of recently reported invertebrate Sobelivirales. Notably, the presence of a novel phasmavirus, typically associated with mosquitoes, expands the known host range and diversity of this family to moths. Furthermore, the identification of a carmotetravirus branching in the same cluster as the Providence virus, a lepidopteran virus which replicates in plants, raises questions regarding the biological significance of this moth virus to the grapevine host. We further explored viral sequences in several publicly available transcriptomic datasets of the moth, indicating potential prevalence across distinct conditions. These results underscore the existence of a complex virome within L. botrana and lay the foundation for future studies investigating the ecological roles, evolutionary dynamics, and potential biocontrol applications of these viruses in the L. botrana–vineyard ecosystem. Full article

The green peach aphid (Myzus persicae) is a generalist pest damaging crops and transmitting viral pathogens. Using Illumina sequencing of small (s)RNAs and poly(A)-enriched long RNAs, we analyzed aphid virome components, viral gene expression and antiviral RNA interference (RNAi) responses. Myzus persicae densovirus (family Parvoviridae), a single-stranded (ss)DNA virus persisting in the aphid population, produced 22 nucleotide sRNAs from both strands of the entire genome, including 5′- and 3′-inverted terminal repeats. These sRNAs likely represent Dicer-dependent small interfering (si)RNAs, whose double-stranded RNA precursors are produced by readthrough transcription beyond poly(A) signals of the converging leftward and rightward transcription units, mapped here with Illumina reads. Additionally, the densovirus produced 26–28 nucleotide sRNAs, comprising those enriched in 5′-terminal uridine and mostly derived from readthrough transcripts and those enriched in adenosine at position 10 from their 5′-end and mostly derived from viral mRNAs. These sRNAs likely represent PIWI-interacting RNAs generated by a ping-pong mechanism. A novel ssRNA virus, reconstructed from sRNAs and classified into the family Flaviviridae, co-persisted with the densovirus and produced 22 nucleotide siRNAs from the entire genome. Aphids fed on plants versus artificial diets exhibited distinct RNAi responses affecting densovirus transcription and flavivirus subgenomic RNA production. In aphids vectoring turnip yellows virus (family Solemoviridae), a complete virus genome was reconstituted from 21, 22 and 24 nucleotide viral siRNAs likely acquired with plant phloem sap. Collectively, deep-sequencing analysis allowed for the identification and de novo reconstruction of M. persicae virome components and uncovered RNAi mechanisms regulating viral gene expression and replication. Full article

Viromics studies are allowing us to understand not only the enormous diversity of the virosphere, but also the potential threat posed by the emerging viruses. Regarding the latter, the main concern lies in monitoring the presence of RNA viruses, but the zoonotic potential of some DNA viruses, on which we have focused in the present study, should also be highlighted. For this purpose, we analyzed 160 fecal samples from 14 species of small terrestrial mammals, 9 of them belonging to the order Rodentia. This allowed us to identify a total of 25 complete or near-complete genomes belonging to the families Papillomaviridae, Polyomaviridae, Adenoviridae, Circoviridae, and Genomoviridae, 18 of which could be considered new species or types. Our results provide a significant increase in the number of complete genomes of DNA viruses of European origin with zoonotic potential in databases, which are at present under-represented compared to RNA viruses. In addition, the characterization of whole genomes is of relevance for the further study of the evolutionary forces governing virus adaptation, such as recombination, which may play an important role in cross-species transmission. Full article

The biting midges Culicoides Latreille, 1809 (Diptera: Ceratopogonidae) is highly relevant to epidemiology and public health, as it includes species that are potential vectors of human and animal arboviruses. The aim of this study was to investigate the presence of RNA viruses in species of the genus Culicoides collected in the Carajás mining complex in the state of Pará. The biting midges were collected in the municipalities of Canaã dos Carajás, Curionópolis and Marabá and morphologically identified. A total of 1139 specimens of seven Culicoides species were grouped into eight pools and subjected to metagenomic analysis. Eight new insect-specific viruses (ISVs) were characterized and assigned to the order Tolivirales, the families Chuviridae, Nodaviridae, Iflaviridae, Mesoniviridae, and Flaviviridae, and the taxon Negevirus. All viruses identified were assigned to clades, families and taxa never reported in Culicoides in Brazil. This study demonstrated that biting midges harbor a significant diversity of RNA viruses, many of which are still unknown, highlighting the importance of studies aiming at virome of these insects. Full article

Background: Mycosis fungoides (MF) represents the most prevalent entity of cutaneous T cell lymphoma (CTCL). The MF aetiopathogenesis is incompletely understood, due to significant transcriptomic heterogeneity and conflicting views on whether oncologic transformation originates in early thymocytes or mature effector memory T cells. Recently, using clinical specimens, our group showed that the skin microbiome aggravates disease course, mainly driven by an outgrowing, pathogenic S. aureus strain carrying the virulence factor spa, which was shown by others to activate the T cell signalling pathway NF-κB. Methods: To explore the role of the skin microbiome in MF aetiopathogenesis, we here performed RNA sequencing, multi-omic data integration of the skin microbiome and skin transcriptome using Multi-Omic Factor Analysis (MOFA), virome profiling, and T cell receptor (TCR) sequencing in 10 MF patients from our previous study group. Results: We observed that inter-patient transcriptional heterogeneity may be largely attributed to differential activation of T cell signalling pathways. Notably, the MOFA model resolved the heterogenous activation pattern of T cell signalling after denoising the transcriptome from microbial influence. The MOFA model suggested that the outgrowing S. aureus strain evoked signalling by non-canonical NF-κB and IL-1B, which in turn may have fuelled the aggravated disease course. Further, the MOFA model indicated aberrant pathways of early thymopoiesis alongside enrichment of antiviral innate immunity. In line with this, viral prevalence, particularly of Epstein–Barr virus (EBV), trended higher in both lesional skin and the blood compared to nonlesional skin. Additionally, TCRs in both MF skin lesions and the blood were significantly more likely to recognize EBV peptides involved in latent infection. Conclusions: First, our findings suggest that S. aureus with its virulence factor spa fuels MF progression through non-canonical NF-κB and IL-1B signalling. Second, our data provide insights into the potential role of viruses in MF aetiology. Last, we propose a model of microbiome-driven MF aetiopathogenesis: Thymocytes undergo initial oncologic transformation, potentially caused by viruses. After maturation and skin infiltration, an outgrowing, pathogenic S. aureus strain evokes activation and maturation into effector memory T cells, resulting in aggressive disease. Further studies are warranted to verify and extend our data, which are based on computational analyses. Full article

Different viruses are abundant in aquatic ecosystems. There has been limited research on the viral communities in the upper reaches of the Yangtze River. Yellow catfish (Pelteobagrus fulvidraco), an important economic fish that is widely distributed in the upper reaches of the Yangtze River, was selected as the research object. Using RNA sequencing, we identified 11 viruses belonging to the Adintoviridae, Tombusviridae, Caudovirales, Microviridae, Picornavirales, and other bacteriophage families. The predominant viral families/order in Luzhou (LZ), Fuling (FL), and Wanzhou (WZ) were Caudovirales, Adinoviridae, and Microviridae, respectively. The virome from WZ had a unique community composition, with a high abundance of Picornavirales compared with LZ and FL. In LZ, the predominant double-stranded RNA virus family was Siphoviridae. Phylogenetic analyses showed that viruses presented high genetic diversity. Phylogenetically, Wenling pleuronectiformes picornavirus was close to the family Caliciviridae, which includes yellow catfish calicivirus (YcCV), responsible for the massive mortality of yellow catfish in 2020. This study provides insights into the viral community composition in yellow catfish in the upper reaches of the Yangtze River, revealing a diverse and unique river water virome and providing clues for future research on the origin of viral pathogens. Full article

In an attempt to explore the RNA viromes of two German rivers, we searched the virus particle contents of one 50 L water sample each from the Teltow Canal and the Havel River for viruses assumed to infect invertebrates. More than 330 complete and partial virus genomes up to a length of 37 kb were identified, with noda-like and reo-like viruses being most abundant, followed by bunya-like and birna-like viruses. Viruses related to the Permutotetraviridae, Nidovirales, Flaviviridae, Rhabdoviridae and Chuviridae as well as the unclassified Jῑngmén virus and Negev virus groups were also present. The results indicate a broad extent of recombinant virus genomes, supporting the concept of the modularity of eukaryotic viruses. For example, novel combinations of genes encoding replicase and structural proteins with a jellyroll fold have been observed. Less than 35 viruses could be assigned to existing virus genera. These are (i) an avian deltacoronavirus which was represented by only one short contig, albeit with 98% similarity, (ii) a seadornavirus and a rotavirus, and (iii) some 30 nodaviruses. All remaining viruses are novel and too diverse for accommodation in existing genera. Many of the virus genomes exhibit ORFans encoding hypothetical proteins of up to 2000 amino acids without conserved protein domains. Full article

Kobuviruses (KoVs) are a group of small, non-enveloped RNA viruses classified in the genus Kobuvirus within the Picornaviridae family, comprising Aichivirus species A to F. KoVs have been identified in humans and several mammals, including domestic ungulates. This study investigated the presence of KoVs in a collection of bovine stool samples (n = 38) obtained from animals with enteritis or without clinical signs. By RT-PCR screening, KoV RNA was detected in 10/38 animals (26.3%). Six of the ten positive animals had enteric signs. On sequence analysis of the amplicons, eight strains were related to species Aichivirus B, commonly identified in cattle. In contrast, two strains (ITA/2019/572-1 and ITA/2020/bovine/30-2), displayed the highest nt identity (up to 97.1%) to cattle, yak, and goat Aichivirus D strains. On whole genome analysis, strains ITA/2019/572-1 and ITA/2020/30-2 showed 88.9% nt identity to each other and 87.8–90.3% nt to the bovine kobuvirus strain CHN/2021/ON730709 identified in China. Interestingly these three Aichivirus D strains showed a recombinant makeup, clustering with D1 genotype in the capsid region and with D2 genotype in the non-structural genes. These findings suggest that Aichivirus D KoVs are common components of livestock virome. Understanding the genetic diversity of KoVs in animals will be useful to improve the diagnostics and gather epidemiological data. Full article