Search Results (187)

Preserving Peruvian cacao germplasm requires preventing the spread of pathogens such as viruses, yet cacao viral diseases in Peru remain poorly studied. In this study, we characterized the viral sequences associated with native cacao trees from the department of Amazonas, northwestern Peru. Leaf samples from two symptomatic plants (mosaic, yellowing, leaf deformation) and one asymptomatic plant were collected from the cacao germplasm bank of the Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas. RNA high-throughput sequencing identified four RNA segments consistent with the genus Emaravirus: RNA1 (7142 nt; replicase P1), RNA2 (2225 nt; glycoprotein P2), RNA3 (1269 nt; nucleocapsid P3), and RNA4 (1286 nt; movement protein P4), sharing 32.6–45.9% amino acid identity with European mountain ash ringspot-associated emaravirus (EMARaV). Phylogenetic analysis of P1–P4 proteins placed this virus in a distinct lineage, confirming it as a novel species, Theobroma cacao emaravirus A (ThCEV-A). Specific RT-PCR detected ThCEV-A in 11 additional accessions, with symptoms including yellow mosaic and mottling. This study documents for the first time the presence of a novel Emaravirus in cacao, highlighting the need to assess its epidemiology, vector(s), and potential impact on cacao production in its center of origin. Full article

During the 2023 surveillance of mosquito-borne viruses in Ningxia Hui Autonomous Region, a strain of Umatilla virus (UMAV) was isolated from a pool of Culex pipiens pallens (NX23166) collected in Xiji County and cultured in C6/36 cells. Electron microscopy revealed that NX23166-infected mosquito cells showed approximately 70-nm virus particles, typical of the genus Orbivirus. Through next-generation sequencing, 10 double-stranded RNA (dsRNA) segments of the virus were obtained. Phylogenetic and homology analyses based on these sequences revealed that this strain was most closely related to the first Chinese isolate from Yunnan in 2013 (DH13M98) and an Australian isolate from 2015 (M4941_15). However, the VP3 protein of this strain showed the closest evolutionary relationship to a German isolate from 2019 (ED-I-205-19), with an amino acid sequence identity of 94.00%. In contrast, the identity of the VP3 protein to that of other strains ranged only from 47.38% to 51.49%, suggesting that these two strains may belong to the same serotype. Nevertheless, this hypothesis needs to be further verified by a serum neutralization test. Furthermore, transcriptome sequencing analysis showed that infection with the Ningxia isolate of UMAV induced significant temporal transcriptomic reprogramming in C6/36 cells. This reprogramming was characterized by early activation of innate immune responses such as the Toll signaling pathway and autophagy, followed by significant suppression of metabolic pathways, including oxidative phosphorylation in the mid to late stages of infection, demonstrating a molecular phenotype of coordinated immune activation and metabolic suppression. These results provide new insights into the genetic diversity and geographic distribution of the species UMAV. 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

Hantaviridae (order Bunyavirales) is a family of negative-sense, single-stranded RNA viruses. To date, several genetically distinct hantaviruses have been found in the same species of shrews and moles. In this report, we describe Biya River virus (BIRV), a novel hantavirus detected in the Eurasian water shrew (Neomys fodiens), the principal host of Boginia virus (BOGV). Genetic analysis of the complete L- and M-genomic segments and partial S-genomic segments showed that BIRV shared a common evolutionary origin with shrew-borne Altai (ALTV) and Lena (LENV) viruses, belonging to the Mobatvirus genus, and that BIRV was distantly related to BOGV and other shrew- and mole-borne orthohantaviruses. Ancient cross-species transmission of hantaviruses, with subsequent diversification within the Soricinae subfamily in Eurasia, might have shaped the evolutionary history of BIRV, ALTV, and LENV. Full article

The emergence of H5N1 highly pathogenic avian influenza virus (HPAIV) clade 2.3.4.4b in dairy cattle across multiple U.S. states in early 2024 marks a major shift in the virus’s host range and epidemiological profile. Traditionally limited to bird species, the ongoing detection of H5N1 in cattle, a mammalian host not previously considered vulnerable, raises urgent animal and human health concerns about zoonoses and mammalian adaptation. We assessed the feasibility of using commercially available pasteurized milk as a sentinel matrix for the molecular detection and genetic characterization of H5N1 HPAIV. Our aim was to determine whether retail milk could serve as a practical tool for virological monitoring and to evaluate the use of full-length genome segment amplification for extracting genomic sequence information from this highly processed matrix. Our results link HPAIV sequences in store-bought milk to the cattle outbreak and highlight both the potential and the limitations of retail milk as a surveillance window. Together, these findings provide evidence that influenza A virus RNA can be repeatedly detected in retail milk in patterns linked to specific supply chains, with genomic data confirming close relationships with the viruses circulating in cattle. Full article

Sphenophorus levis, commonly known as the sugarcane weevil, is one of the most important pests affecting Brazilian sugarcane crops. It has spread to all sugarcane-producing regions of Brazil, mainly through contaminated stalks. Effective control of this pest is difficult due to the protection conferred by the host plant during the larval stage. As a result, despite current control measures, S. levis populations continue to grow, and reports of new infestations remain frequent. Biotechnological control measures, such as the use of viruses, stands as a promising tool for pest control in agriculture. The aim of this study was to explore the RNA virome associated with S. levis using a viral metagenomic approach. Through the Read Annotation Tool (RAT) pipeline, we characterized, for the first time, the gut-associated viral community in adult weevils, identifying several novel viral genomes. Sphenophorus levis-associated virus (SLAV) had 12,414 nucleotides (nt); Sphenophorus levis tombus-like virus (SLTV) had 4085 nt; and the four genomic segments of Sphenophorus levis reo-like virus (SLRV) ranged from 2021 to 4386 nt. These genomes were assembled from 65,759 reads (SLAV), 114,441 reads (SLTV), and 270,384 reads (SLRV). Among the detected viral families, Partitiviridae was the most abundant. The identification of possible viral pathogens lays the foundation for future research into their potential use as biological control agents against S. levis. Full article

A new negative-strand RNA virus was identified in grapevines from a 38-year-old ‘Chardonnay’ block in Idaho through high-throughput sequencing (HTS) of total RNA. This virus was tentatively named grapevine-associated cogu-like Idaho virus (GaCLIdV). GaCLIdV has three negative-sense, single-stranded RNA genome segments of ca. 7 kb, 1.9 kb, and 1.3 kb, encoding L protein (RNA-dependent RNA polymerase, RdRP), a movement protein (MP), and a nucleocapsid protein (NC), respectively, identified based on pair-wise comparisons with other cogu- and cogu-like viruses. In phylogenetic analysis based on the RdRP, GaCLIdV grouped within the family Phenuiviridae and was placed in a lineage of plant-infecting phenuiviruses as a sister clade of the genus Laulavirus, clustering most closely with switchgrass phenui-like virus 1 (SgPLV-1) and more distantly related to grapevine-associated cogu-like viruses from the Laulavirus and Coguvirus clades. Both GaCLIdV and SgPhLV-1 are proposed to form a new genus, Switvirus, within the family Phenuiviridae. The presence of GaCLIdV in the original ‘Chardonnay’ samples was confirmed by RT-PCR amplification and Sanger sequencing. This new virus was found in five wine grape cultivars and in six vineyards sampled in Idaho and in Oregon during the 2020–2024 seasons. GaCLIdV may have contributed to the decline observed in the old ‘Chardonnay’ block, although the role of the virus in symptom development awaits further investigation. Full article

Surveillance of swine influenza A virus (swIAV) traditionally focuses on respiratory matrices, yet emerging evidence suggests that fecal shedding and secondary environmental contamination may also contribute to viral dissemination. In this study, we collected and analyzed nasal, rectal, environmental, milk, and colostrum samples from naturally infected pigs in a commercial farm in Minas Gerais, Brazil. IAV RNA was detected in 25% of samples, including 42% from asymptomatic animals, with nasal swabs showing higher detection rates (30%) than rectal swabs (20%), though rectal Ct values were consistently higher, indicative of lower viral loads. We successfully isolated viable viruses from feces and effluent samples. Whole-genome sequencing revealed co-circulation of enzootic pH1N1 clade #2 (HA) and pN1 clade #4 (NA), alongside human-origin H3N2 sequences clustering within clade 3C.2a1b.2a.2a.1, and N2 segments related to pre-3C human lineages from 2001 to 2002. Phylogenetic and p-distance analyses support both recent reverse zoonosis and historical transmission events. Detection of complete HA/NA sequences from rectal swabs and treated effluent further emphasizes the surveillance value of non-respiratory matrices. The integration of respiratory and fecal/environmental sampling appears important to achieve more comprehensive IAV monitoring in swine herds and may have significant implications for One Health strategies in Brazil and beyond. Full article

Objectives: Most antiviral vaccines are created by inactivating the virus using chemical methods. The inactivation and production of viral vaccine preparations after the irradiation of viruses with accelerated electrons has a number of significant advantages. Determining the integrity of the genome of the resulting viral particles is necessary to assess the quality and degree of inactivation after irradiation. Methods: This work was performed on the Sabin 2 model polio virus. To determine the most sensitive and most radiation-resistant part, the polio virus genome was divided into 20 segments. After irradiation at temperatures of 25 °C, 2–8 °C, −20 °C, or −70 °C, the amplification intensity of these segments was measured in real time. Results: The best correlation between the amplification cycle and the irradiation dose at all temperatures was observed for segment 3D, left. Consequently, this section of the poliovirus genome is the least resistant to the action of accelerated electrons and is the most representative for determining genome integrity. The worst dependence was observed for the VP1 right section, which, therefore, cannot be used to determine genome integrity during inactivation. The electrochemical approach was also employed for a comparative assessment of viral RNA integrity before and after irradiation. An increase in the irradiation dose was accompanied by an increase in signals indicating the electrooxidation of RNA heterocyclic bases. The increase in peak current intensity of viral RNA electrochemical signals confirmed the breaking of viral RNA strands during irradiation. The shorter the RNA fragments, the greater the peak current intensities. In turn, this made the heterocyclic bases more accessible to electrooxidation on the electrode. Conclusions: These results are necessary for characterizing the integrity of the viral genome for the purpose of creating of antiviral vaccines. Full article

Orthohantaviruses are tri-segmented negative-sense RNA viruses that can cause severe pathologies in humans. Currently, limited information exists on the molecular interactions driving orthohantavirus assembly in infected cells. Specifically, it is not clear how its glycoproteins (i.e., Gn and Gc) interact with other viral or host molecules. In this study, we use one- and two-color Number and Brightness fluorescence microscopy approaches to quantitatively characterize the interactions between orthohantavirus glycoproteins and the nucleoprotein in transfected cells. Our results indicate that orthohantavirus nucleoprotein homo-interactions are strongly affected by the host environment. Furthermore, we report evidence of Gc–nucleoprotein interactions, based on (i) the high fluorescence cross-correlation between these two proteins and (ii) the increased Gc-Gc interactions observed in the presence of nucleoprotein. Finally, experiments on a Gc deletion mutant suggest that the observed protein–protein interactions are mediated by the cytoplasmic tail of Gc. In conclusion, this study provides new insights into the role of the interactions between orthohantavirus glycoproteins and nucleoprotein in the context of viral assembly. Full article

Watermelon is one of the most important fruits in China, accounting for more than 70% of the world’s total output. Fusarium wilt of watermelon is the most common and serious disease in the cultivation of watermelon. It is mainly caused by Fusarium oxysporum f. sp. niveum (FoN), which has caused serious damage to the watermelon-planting industry. Some mycoviruses can reduce the pathogenicity of host pathogens and have the potential for biocontrol, so their application potential in the biological control of plant fungal diseases has attracted much attention. In this study, high-throughput sequencing was performed on 150 FoN strains isolated from three major watermelon-production areas (northern semi-arid area, northwestern arid area, and southern humid area) to detect the diversity of mycoviruses and to uncover new mycoviruses. The analysis identified 25 partial or complete genome segments representing eight previously undescribed mycoviruses. The existence of six mycoviruses was verified via RT-PCR. The southern humid area had the highest diversity of mycoviruses, with 15 species identified. Among these, 40% are dsRNA viruses and 33.3% belong to the family Chrysoviridae, representing the predominant viral type and family. In the northern semi-arid area, a total of 12 viral species were identified, among these 41.7% were +ssRNA viruses and 25% belonged to the family Mymonaviridae, constituting the main viral types and family. The northwestern arid area showed relatively low viral diversity, only containing three species. Two of these were +ssRNA viruses classified under the Mitoviridae and Potyviridae families. Notably, only one virus, Fusarium oxysporum f. sp. niveum Potyvirus 1 (FoNPTV1), was shared across all three areas. These findings reveal significant regional differences in the mycoviral species composition and distribution, highlighting the complex interactions between mycoviruses and FoN in different environments. By uncovering new mycoviruses associated with FoN, this study provides valuable resources for the potential biocontrol of Fusarium wilt in watermelon, contributing to sustainable disease management and improving the quality and safety of watermelon production in China. Full article

Active and passive surveillance, followed by gene sequencing, continue to be used to identify a diverse range of novel bacteria, viruses, and other microorganisms in ticks with the potential to cause disease in vertebrate hosts following tick bite. In this study, we describe the isolation and characterization of a novel virus from Bothriocroton hydrosauri ticks collected from a blotched blue-tongue, Tiliqua nigrolutea. In an attempt to isolate rickettsia, the inoculation of Vero cell cultures with tick extracts led to the isolation of a virus, identified as a novel tick Orthomyxovirus by electron microscopy and gene sequencing. Transmission electron microscopic analysis revealed that B. hydrosauri tick virus-1 (BHTV-1) is a spherical orthomyxovirus, 85 nm in size. Multiple developmental stages of the virus were evident in vitro. Analysis of putative BHTV-1 amino acid sequences derived from a genomic analysis of virus-infected host cell extracts revealed the presence of six putative RNA segments encoding genes, sharing the closest sequence similarity to viral sequences belonging to the arthropod-borne Thogotovirus genus within the Orthomyxoviridae. Thogotoviruses are an emerging cause of disease in humans and animals following tick bite. The detection of this new thogotovirus, BHTV-1, in B. hydrosauri, a competent vector for human tick-borne infectious diseases, warrants follow-up investigation to determine its prevalence, host range, and pathogenic potential. Full article

Dichorhavirus is a recently accepted plant virus genus within the family Rhabdoviridae. Species assigned to the genus consist of bi-segmented, negative sense, single-stranded RNA viruses and are transmitted by Brevipalpus spp. Currently, there are five recognized species and two unclassified members in the genus Dichorhavirus. Four out of seven-orchid fleck virus (OFV), citrus leprosis virus N, citrus chlorotic spot virus, and citrus bright spot virus-can infect citrus and produce leprosis disease-like symptoms. The E-probe Diagnostic for Nucleic Acid Analysis (EDNA) was developed to reduce computational effort and then integrated within Microbe-Finder (MiFi^®) online platform to design and evaluate e-probes in raw High Throughput Sequencing (HTS) data. During this study, Dichorhavirus genomes were downloaded from public databases and e-probes were designed using the MiProbe incorporated into the MiFi^® platform. Three different sizes of e-probes, 40, 60, and 80 nucleotides, were developed and selected based on whole genome comparisons with near-neighbor genomes. For curation, each e-probe was searched in the NCBI nucleotide sequence database using BLASTn. All the e-probes that had hits with non-target species with ≥90% identities were removed. The sensitivity and specificity of Dichorhavirus genus, species, strain, and variant-specific e-probes were validated in vivo using HTS meta-transcriptomic libraries generated from Dichorhavirus-suspected citrus, orchid, and ornamentals. Through downstream analysis of HTS data, EDNA not only detected the known hosts of OFV but also discovered an unknown host leopard plant (Farfugium japonicum), and the possible existence of a new ornamental strain of OFV in nature. Full article

Orthobunyaviruses are a diverse group of segmented RNA viruses with significant but underexplored public and veterinary health implications. This study provides a genomic, phylogenetic, and ecological analysis of neglected Orthobunyaviruses using next-generation sequencing and computational predictions. We identified unique phylogenetic relationships, with Tanga virus forming a distinct lineage linked to zoonotic, human-associated, or non-vertebrate viruses across segments. GC content analysis revealed segment-specific patterns: higher GC content in the S segment suggests genomic stability and immune evasion, while lower GC content in the L segment reflects host-vector adaptation. Phylogenetic ties to well-characterized pathogenic viruses, such as Ilesha virus with Cache Valley virus and Bwamba virus with California encephalitis virus, indicate potential neurotropism. Ingwavuma virus clustered with Oropouche virus, suggesting risks of systemic febrile illnesses. Within the Simbu serogroup, Sango and Sabo viruses show teratogenic risks to livestock. Vector and host predictions implicate rodents, artiodactyls, and primates in Orthobunyavirus transmission, emphasizing complex ecological dynamics and zoonotic potential. These findings advance the understanding of Orthobunyavirus diversity, linking genomic features to pathogenicity and ecological adaptation, while providing a foundation for future surveillance and intervention strategies targeting these neglected viruses. Full article

Rotavirus alphagastroenteritidis is the major causative agent of acute gastroenteritis in both children under the age of 5 and young mammals and birds globally. RVAs are non-enveloped viruses with a genome comprising 11 double-stranded RNA segments. In 2008, the Rotavirus Classification Working Group pioneered a comprehensive and complete RVA genome classification system, establishing a specific threshold, which measures the genetic distances between homologous genes. The aim of this study was to perform an updated systematic analysis of the genetic variability across all RVA genes. Our investigation involved assessing the established cutoff values for each RVA genome segment and determining the need for any updates. To achieve this objective, multiple sequence alignments were constructed for all 11 genes and one for each genotype with discrepancies. Also, pairwise distances along with their cutoff values were evaluated. The analyses provided insights into the current relevance of cutoff values, which remain applicable for the majority of genotypes. In conclusion, this study fortifies the current classification system by highlighting its robustness and accurate genotyping of Rotavirus alphagastroenteritidis. Full article