Search Results (587)

The family Flaviviridae has been expanded to include the highly divergent flavi-like viruses into three new families, Flaviviridae, Pestiviridae, and Hepaciviridae, in the order Amarillovirales. Classical flavivirids are small, enveloped viruses with positive-sense ssRNA genomes lacking a 3′ poly(A) tail and ~9.0–13.0 kb in length, with a single open reading frame (ORF) encoding structural proteins at the N-terminus and nonstructural proteins at the C-terminus. Members infect a wide range of mammals, birds, and insects, and many are host-specific and pathogenic. Although the RNA-directed RNA polymerase (RdRP) gene sequences of the flavi-like viruses group phylogenetically with those of classical flavivirids, flavi-like viruses often encode larger polyproteins and possess substantially longer genomes of up to ~40 kb, and some have a 3′ poly(A) tail. Their host range extends across the whole animal kingdom and angiosperm plants. This review describes the reported flavi-like viruses of aquatic animals, providing a meaningful update on all three new families in Amarillovirales that have been discovered using metagenomics in fish, crustaceans, mollusks, and echinoderms. These amarilloviruses include pathogenic viruses of aquatic animals, such as Cyclopterus lumpus virus (CLuV) detected in moribund lumpfish, and infectious precocity virus (IPV) found in iron prawn syndrome (IPS)-affected farmed giant freshwater prawns. Full article

Pleurotus ostreatus, a globally cultivated oyster mushroom, is susceptible to viral infections that threaten yield and quality. This study reports the identification and characterization of three novel viruses from a symptomatic P. ostreatus strain K3: Pleurotus ostreatus deltaflexivirus 2, 3, and 4 (PoDFV2, PoDFV3, PoDFV4). Complete genome sequencing revealed that they are single-stranded, positive-sense RNA viruses with lengths of 7809 nt, 7771 nt, and 7786 nt, encoding 5, 2, and 4 open reading frames (ORFs), respectively. The largest open reading frame (ORF1) encodes a putative replication-associated polyprotein (RP) containing three conserved domains—viral RNA methyltransferase (Mtr), viral RNA helicase (Hel), and RNA-dependent RNA polymerase (RdRp). Based on genomic sequence analysis, multiple sequence alignments, and phylogenetic analysis, PoDFV2–4 were identified as novel viruses of the genus Deltaflexivirus within the family Deltaflexiviridae. PoDFV2–4 had no significant effects on mycelial growth rate, plate mycelial biomass, or laccase activity. However, they significantly inhibited mycelial cellulase activity and resulted in malformed fruiting bodies, as well as a substantial reduction in yield. Full article

Potyvirus genomes are expressed as a single large open reading frame, which is translated into a polyprotein that is post-translationally cleaved by three virus-encoded proteases into 10 functional proteins. Several of these potyviral proteins, including nuclear inclusion protein b (NIb), are multifunctional. Here, using the classic GFP silencing in Nicotiana benthamiana gfp-transgenic plants, we show that potato virus Y (PVY) NIb, in addition to its canonical role as the viral RNA-dependent RNA polymerase (RdRP), functions as a suppressor of RNA silencing. Mutational analyses reveal a previously unreported NIb nuclear localization signal (NLS) consisting of a triple-lysine motif. NIb suppression of RNA silencing activity was lost when the NLS was mutated, suggesting that nuclear localization is required for NIb suppression of RNA silencing activity. Analysis of sequenced GFP siRNAs revealed three reproducible hotspot regions at ≈175 nt, ≈320–330 nt, and a broader 3′-proximal region spanning ≈560–700 nt that contains multiple local maxima. These data show differences in the positional distribution of siRNAs between samples expressing NIb and those expressing NIb^Del3×2, the NIb null mutant that does not suppress RNA silencing. However, the positional distribution of GFP-derived small RNAs across the transgene differed modestly between NIb and NIb^Del3×2, while both treatments showed the same three reproducible hotspot regions. Furthermore, NIb was found to interact with four key RNA silencing pathway proteins—AGO4, HSP70, HSP90, and SGS3. Except for HSP90, each of these proteins showed degradation products that were absent in NIb mutants that did not suppress RNA silencing. These findings support a role for NIb in countering host defense during virus infection. Full article

The continuous emergence of SARS-CoV-2 variants, especially the Omicron strain with its heightened transmissibility, has posed ongoing challenges to the efficacy of existing vaccine and drug regimens. This situation highlights the pressing demand for antiviral drugs employing novel mechanisms of action. Pentacyclic triterpenoids (PTs), a structurally varied group of compounds derived from plants, exhibit both antiviral and anti-inflammatory activities, making them attractive candidates for further therapeutic development. These natural products, along with their saponin derivatives, show broad-spectrum inhibitory effects against multiple SARS-CoV-2 variants (from Alpha to Omicron) via interactions with multiple targets, such as the spike protein, main protease (Mpro), RNA-dependent RNA polymerase (RdRp), and inflammatory signaling pathways. This review consolidates recent findings on PTs and their saponins, emphasizing their influence on the key structural features required for inhibiting viral attachment, membrane fusion, reverse transcription, and protease function. We systematically summarized the structure–activity relationships and their antiviral results of PTs based on different target proteins in existing studies. Furthermore, this work points toward new strategies for designing multi-target PT-based inhibitors with improved efficacy against Omicron and future variants. Full article

Retinitis pigmentosa (RP), an inherited retinal disorder, leads to progressive photoreceptor degeneration and irreversible blindness, with limited treatment options available. Emerging evidence implicates microRNAs (miRNAs) in the pathogenesis of retinal disease, yet understanding of their specific roles in RP remains incomplete. In this study, we employed high-throughput RNA sequencing to profile miRNA expression in a rd1 RP mouse model at postnatal day 14. Our analysis revealed 40 upregulated and 27 downregulated miRNAs in rd1 retinas compared to controls. Notably, miR-142a-5p, miR-223-3p, and miR-653-5p were significantly elevated, while miR-25-3p was downregulated. Given miR-142a-5p’s established roles in apoptosis and inflammation, we investigated its contribution to retinal degeneration. Knockdown of miR-142a-5p in rd1 mice improved retinal function and preserved outer nuclear layer thickness, suggesting a protective effect against photoreceptor loss. These findings highlight miR-142a-5p as a key regulator of RP progression and a promising therapeutic target for mitigating vision loss in retinal degenerative diseases. Full article

(1) Background: Modifications of histone methylation could alter chromatin structure and thereby have an impact on gene expressions. (2) Methods: To investigate whether ORY-1001 delay retinal photoreceptor degeneration, rd10 mice were intraperitoneally injected with ORY-1001 (0.075 mg/kg) every second day from the 14th to the 24th day after birth. Full-field electroretinogram detection (ff ERG), optical coherence tomography (OCT), visual behavioral testing, retinal tissue morphology observation, and protein expression detection experiments were performed on the 25th day. Simultaneously, ATAC-seq and RNA-seq were used to test the mice’s retinal tissues, and metabolomics detection and quantitative real-time polymerase chain reaction (qRT-PCR) were carried out. (3) Results: Compared with the rd10 group, in the treatment group, the function in the electroretinogram response and the visual behavioral responses were improved, the nuclear layer morphology of retinal tissue was reserved more, and the protein expression of H3K4me2 and CoREST was increased. Conjoint analysis of our ATAC-seq and RNA-seq results showed that chromatin accessibility was changed, as was gene expression which was involved in metabolism changes. In addition, the effector gene in the retina was Gnat1. (4) Conclusions: ORY-1001 delays retinal photoreceptor degeneration by inhibiting H3K4me2 demethylation in rd10 mice, which suggests that ORY-1001, as a novel epigenetic modifier, has potential for treating RP. Full article

Norovirus (NoV) and sapovirus (SaV) are major viral pathogens causing acute gastroenteritis (AGE) in both children and adults in developed countries and are also responsible for large-scale outbreaks. However, in Quebec, Canada, there are limited and updated data with respect to the genotypes circulating and implicated in outbreaks, particularly for SaV. This study aimed to investigate the genetic diversity and genotype predominance of NoVs and SaVs associated with AGE outbreaks in Quebec, Canada. Confirmed NoV and SaV outbreaks from long-term care facilities and hospital settings between September 2011 and April 2016 were investigated (n = 252). NoVs and SaVs were genetically diverse: 21 RdRp-capsid combinations were identified, of which 10 are recombinants. NoV GII.4 New Orleans[P4 NewOrleans] was the predominant genotype from 2011 to 2013, and GII.4 Sydney[P31] was the predominant genotype from 2013 to 2015. In 2015–2016, no single genotype predominated; instead, GII.17[P17], GII.4 Sydney[P16], GII.4 Sydney[P31], and SaV GI.2 strains were co-circulating at similar frequencies. Notably, emerging global genotypes including GII.17[P17], GII.4 Sydney[P16], GII.2[P16], and GII.4 San Francisco[P31] were detected for the first time in Quebec. These findings may contribute to an enhanced understanding of NoV and SaV infection and spread, and to the development of candidate vaccines. Full article

Various microbial agents have been found in the feces of both humans and animals, especially in newborns. While some of these agents are recognized as causing diarrhea, the role of others, specifically bopiviruses of the family Picornaviridae, in diarrhea remains uncertain. In this study, we conducted an analysis of 214 fecal samples from cattle (n = 114), sheep (n = 82), and goats (n = 18) with diarrhea, collected from farms across 17 different provinces in Türkiye. All samples were tested using RT-PCR targeting the 3D^(RdRp) region of bopiviruses, and two samples from sheep (2.4%) tested positive. The 7303 nt-long complete coding sequence of Bopivirus/Sheep/KS-1M/2024/TUR and partial 3D^(RdRp), VP3, and 2A-2C sequences of Bopivirus/Sheep/ANK-K30/2017/TUR were determined by additional RT-PCR, 3′RACE-PCR reactions and Sanger sequencing. Both strains show close sequence and phylogenetic relationship to members of species “Bopivirus B” of genus Bopivirus. Bopivirus/Sheep/KS-1M/2024/TUR is most closely related to a sheep Bopivirus B strain (sheep/14-73/2018/ITA) from Italy, but the phylogenetic separation, the low sequence identities and high p-distance values in VP1 to existing genotypes of “B1” and “B2” suggest that both strains could belong to novel genotypes (“B3” and “B4”) in species “Bopivirus B”, although additional closely related sequences are necessary for proper typing. Full article

The GI.3 norovirus is the most detected and recombinant-rich genotype within genogroup I, yet the mechanistic basis for its epidemiological success remains poorly understood. This study integrates Bayesian evolutionary analysis with in vitro enzymology to investigate the link between RdRp function and the evolutionary dynamics of GI.3 NoV. We analyzed 831 GI.3 sequences, finding that prevalent strains (GI.3[P3] and GI.3[P13]) exhibited significantly higher evolutionary rates in both the RdRp and VP1 genes than non-prevalent strains (GI.3[P10] and GI.3[P14]). While the RdRp gene displayed a strong molecular clock signal, the VP1 gene’s evolution was more complex, showing cluster-specific trends. Functionally, the RdRps from prevalent strains demonstrated superior enzymatic activity and substrate affinity (K_m: GI.3[P13] = 0.092 mM; GI.3[P3] = 0.176 mM) compared to non-prevalent strains (K_m: GI.3[P14] = 0.273 mM). Notably, GI.3 RdRp required higher manganese ion concentrations for optimal activity than previously reported for GII strains, suggesting a potential biochemical constraint. Our findings demonstrate a clear correlation between RdRp enzymatic efficiency, evolutionary rate, and strain prevalence. We propose that a highly active RdRp may potentially accelerate VP1 evolution and confer a replicative advantage, underpinning the dominance of specific GI.3 lineages. This work provides crucial experimental evidence linking viral polymerase function to evolutionary and epidemiological outcomes. Full article

Zika virus (ZIKV) remains a significant global public health concern, and growing resistance to existing antiviral drugs underscores the necessity of developing alternative therapeutic options. In this study, we investigated the inhibitory effects of ethyl gallate against ZIKV using antiviral activity evaluation, molecular docking, and molecular dynamic simulations. Treatment of ZIKV-infected Vero E6 cells with ethyl gallate resulted in dose-dependent suppression of viral infection without inducing cytotoxicity. In addition, ethyl gallate inhibited the increase in the expression of interferon-stimulated genes in ZIKV-infected cells. It also exhibited binding energies of −5.9868, −247.271, and −200.43 kcal/mol for ZIKV envelope, NS3, and RdRp proteins, respectively. Furthermore, the molecular dynamic simulation results showed that the ethyl gallate-NS3 and ethyl gallate-RdRp complexes were more stable than the ethyl gallate-envelope protein complex, suggesting that ethyl gallate has the potential to inhibit ZIKV replication. These findings position ethyl gallate as an antiviral agent with potential against Zika infection. Full article

Hendra virus (HeV) is a highly pathogenic zoonotic paramyxovirus that poses a serious threat to human and equine health, yet no approved antivirals or vaccines currently exist. RNA-dependent RNA polymerase (RdRp) of Hendra virus represents a critical and attractive target for antiviral drug development, given its essential role in both viral genome replication and mRNA transcription. Due to the lack of a human homolog, it is more druggable and less likely to cause host toxicity. Its sequence conservation among related paramyxoviruses further highlights its potential for the development of broad-spectrum inhibitors. This study offers the first comprehensive computational analysis of the Hendra virus RdRp, potentially promising FDA-approved drugs as possible inhibitors. A homology model of RdRp was generated in the absence of experimental three-dimensional (3D) structure, followed by virtual screening and molecular dynamics (MD) simulations to evaluate the drug binding and stability. Based on the highest energy, four FDA-approved drugs selected were menadiol diphosphate (−49.88 kcal/mol), masoprocol (−39.69 kcal/mol), pamidronic acid (−34.29 kcal/mol), and dinoprostone (−46.90 kcal/mol). Furthermore, these compounds exhibited significant interactions with the catalytic GDNE motif. With strong conformational stability and pharmacokinetic profile, masoprocol and menadiol diphosphate showed the most stable and energetically favorable interactions within the RdRp active site. These findings suggest their potential as repurposed therapeutic candidates against Hendra virus infection and they provide a structural basis for the development of broad-spectrum paramyxovirus inhibitors, justifying additional experimental confirmation. Full article

The COVID-19 outbreak has had a tremendous socioeconomic impact around the world, and although there are currently some drugs that have been granted authorization by the U.S. FDA for the treatment of COVID-19, there are still some restrictions on their use. As a result, it is still necessary to urgently carry out related drug development research. Deep generative models and cheminformatics were used in this study to design and screen novel candidates for potential anti-SARS-CoV-2 small molecule compounds. In this study, the small molecule structure of Molnupiravir which has been authorized by the U.S. FDA for emergency use was used to be a model in a similarity search based on the BIOVIA Available Chemicals Directory (BIOVIA ACD) database using the BIOVIA Discovery Studio (DS) software (version 2022). There were 61,480 similar structures of Molnupiravir, which were used as training dataset for the deep generative model, and then the reinforcement learning model was used to generate 6000 small molecule structures. To further confirm whether those molecule structures potentially possess the ability of anti-SARS-CoV-2, cheminformatics techniques were used to assess 38 small molecule compounds with potential anti-SARS-CoV-2 activity. The suitability of 38 small molecule structures was calculated using ADMET analysis. Finally, one compound structure, Molecule_36, passed ADMET and was unpatented. This study demonstrates that Molecule_36 may have better potential than Molnupiravir does in affinity with SARS-CoV-2 RdRp and ADMET. We provide a combination of generative deep neural networks and cheminformatics for developing new anti-SARS-CoV-2 compounds. However, additional chemical refinement and experimental validation will be required to determine its stability, mechanism of action, and antiviral efficacy. Full article

SARS-CoV-2 continues to evolve into immune-evasive variants, and although vaccination remains the cornerstone of prevention, the search for antiviral molecules targeting conserved viral enzymes remains essential. The RNA-dependent RNA polymerase (NSP12) is a central component of coronavirus replication, and natural polyphenols have been recurrently proposed as modulators of viral polymerases. Among these compounds, Fisetin has been reported to interact with multiple viral and cellular pathways, yet its direct antiviral activity against SARS-CoV-2 remained largely unexplored. Here, we first analyzed the interaction of Fisetin with the catalytic and NiRAN domains of NSP12 using molecular docking and molecular dynamics simulations, revealing stable and energetically favorable binding throughout a 100 ns simulation. Previous biochemical reports have shown that Fisetin inhibits the recombinant SARS-CoV-2 RdRp, supporting its potential to engage the polymerase. We then evaluated its antiviral activity in human A549 lung epithelial cells infected with the Omicron JN.1 variant. We observed a clear dose-dependent reduction in viral infection, achieving up to 91.9% inhibition at 3 μM while maintaining acceptable cell viability. In addition, Fisetin displayed a selectivity index superior to that of Lopinavir, the positive antiviral control used in this study. Altogether, our findings demonstrate that Fisetin possesses reproducible antiviral activity in a physiologically relevant human lung model and support its role as a natural scaffold for the rational development of polymerase-targeting antivirals against emerging SARS-CoV-2 variants. Full article

Porcine reproductive and respiratory syndrome virus (PRRSV) nonstructural protein 9 (NSP9), the viral RNA-dependent RNA polymerase (RdRp), is essential for viral replication but its comprehensive host interactome remains uncharacterized. This study employed co-immunoprecipitation coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to systematically identify NSP9-associated host proteins. We identified 222 high-confidence host interactors, with Gene Ontology and KEGG pathway analyses revealing significant enrichment in RNA/DNA-binding proteins, ubiquitin-proteasome pathways, metabolic regulators (amino acid/lipid biosynthesis), endoplasmic reticulum processing, and cell cycle components. Protein-protein interaction network analysis further delineated six functional modules involved in RNA processing, vesicular transport, and innate immunity. Crucially, validation studies confirmed direct binding between NSP9 and key candidates (CAPZ1, PSMA3, CDK1, USP48). Functional assessment demonstrated that CDK1 overexpression significantly inhibited PRRSV replication, implicating CDK1 as a host restriction factor. These findings collectively unveil the multifaceted role of NSP9 in subverting host machinery while identifying novel host defense mechanisms and potential targets for antiviral development against PRRSV. Full article

Noroviruses are a leading cause of acute gastroenteritis worldwide, with a particularly high burden among children under five years of age. We analyzed nationwide surveillance data from EnterNet-Korea collected between 2019 and 2024—covering both the pre- and post-COVID-19 pandemic periods—to assess norovirus detection rates and genotype distribution. Noroviruses were detected by RT-qPCR, and dual genotyping of capsid (G) and polymerase (P) types was performed by sequencing the ORF1–2 junction region. Among the 67,159 specimens tested, 8.4% (n = 5652) were norovirus-positive, with the highest prevalence observed in children aged 0–5 years (19.9%). In this age group, genotyping was successful in 72.4% (2633/3635) of positive cases, identifying 30 distinct genotypes (GI: 9; GII: 21). The most common strains were GII.4[P31] (38.1%), GII.4[P16] (27.1%), and GII.2[P16] (10.4%), with substantial year-to-year variation. Notably, the emergence of GII.17[P17] in late 2024 indicates shifting genotype dynamics, underscoring the need for strengthened surveillance and reconsideration of vaccine strain selection. To our knowledge, this is the first nationwide dual-typing study in Korea encompassing the COVID-19 pandemic era. These findings provide essential baseline data for integration into global surveillance systems and inform future vaccine development and public health strategies. Full article