RNA-dependent RNA Polymerase Research Articles

TRIM56 restricts Coxsackievirus B infection by mediating the ubiquitination of viral RNA-dependent RNA polymerase 3D.

Coxsackievirus B (CVB) is the major causative pathogen for severe diseases such as viral myocarditis, meningitis, and pancreatitis. There is no effective antiviral therapy currently available for CVB infection primarily due to that the pathogenesis of CVB has not been completely understood. Viruses are obligate intracellular pathogens which subvert cellular processes to ensure viral replication. Dysregulation of ubiquitination has been implicated in CVB infection. However, how ubiquitination is involved in CVB infection remains unclear. Here we found that the 3D protein of CVB3, the RNA-dependent RNA polymerase, was modified at K220 by K48-linked polyubiquitination which promoted its degradation through proteasome. Proteomic analysis showed that the E3 ligase TRIM56 was upregulated in CVB3-infected cells, while the majority of TRIMs remained unchanged. Pull-down and immunoprecipitation analyses showed that TRIM56 interacted with CVB3 3D. Immunofluorescence observation showed that viral 3D protein was colocalized with TRIM56. TRIM56 overexpression resulted in enhanced ubiquitination of CVB3 3D and decreased virus yield. Moreover, TRIM56 was cleaved by viral 3C protease in CVB3-infected cells. Taken together, this study demonstrated that TRIM56 mediates the ubiquitination and proteasomal degradation of the CVB3 3D protein. These findings demonstrate that TRIM56 is an intrinsic cellular restriction factor against CVB infection, and enhancing viral protein degradation could be a potential strategy to control CVB infection.

Recent Advancements in the Delivery of Therapeutic Agents Targeting RNA-dependent RNA Polymerase of SARS-CoV-2.

This study aimed to undertake a complete evaluation and analysis of all known data on RNA-dependent RNA polymerase (RdRp) inhibitors, concentrating on their safety, efficacy, and current improvements in the delivery of therapeutic drugs targeting RdRp of SARS-CoV-2. The work has attempted to emphasise the necessity for future research into the development of nanocarrier-based targeted drug delivery methods for RdRp inhibitors in the treatment of COVID-19. In December 2019, a novel SARS-- CoV-2 strain was discovered in Wuhan, China. SARS-CoV-2 is transferable among humans and has caused a global pandemic. The rapid global outbreak of SARS-CoV-2 and numerous deaths caused because of coronavirus disease (COVID-19) prompted the World Health Organization to announce a pandemic on March 12, 2020. COVID-19 is becoming a key concern that has a significant impact on an individual's life status. RdRp inhibitors are major pharmaceutical agents used in the treatment of COVID-19, which have various undesirable side effects, a greater risk of recurrence, lower bioavailability, as well as a lack of targeted therapy. Hence, the present article has provided a review on all known data on RdRp inhibitors, safety, and efficacy, and recent advances in the delivery of therapeutic agents targeting RdRp of SARS-CoV-2. An analysis has been done using a scientific data search engine, such as the National Center for Biotechnology Information (NCBI/PubMed), Science Direct, Google Scholar, WIPO, Lens, etc. The information has emphasized the need for more research into the safety, efficacy, and development of nanocarrier-based targeted drug delivery systems for RdRp inhibitors in the treatment of COVID-19.

Efficacy of favipiravir in COVID-19: A retrospective two center comparative study.

Favipiravir (FVP) is an antiviral, targeting RNA-dependent RNA polymerase. We aimed to evaluate the efficacy of FVP as a treatment for COVID-19. We conducted a retrospective study in two centers (San Martino University Hospital in Genova, Italy, and Marmara University Pendik Training and Research Hospital, Turkey). Adult patients (inpatients) diagnosed with COVID-19 between March and June 2020 were included. All patients in the Italian center received the standard of care (SoC) treatment, while in the Turkish center patients received FVP in addition to SoC. Six hundred-nineteen patients were analyzed (225 from Turkey, all treated with FVP, and 394 from Italy, none treated with FVP). Propensity score-matching was done in 142 patients (71 from the SoC group vs. 71 from the SoC + FVP group). A Higher requirement of NIV/CPAP (n = 38; 53.5%) was registered in the SoC group compared to the SoC + FVP group (n = 9; 12.7%). A higher frequency of intubation was registered in the SoC + FVP group (n = 25; 35.2% vs n = 13, 18.3%). There was a trend towards better survival in SoC + FVP treated patients with HR = 0.64 (95% CI 0.30-1.34). At 28 days the OS was, respectively, 70.3% (95% CI: 53.2-82.1) vs 80.3% (95% CI: 69.0-87.8). The addition of FVP to SoC did not show a significant difference in survival and invasive and noninvasive (CPAP/NIMV) mechanical ventilation compared to standard of care in moderate and severe COVID-19-infected patients.

From RNA to DNA: Emergence of reverse transcriptases from an ancestral RNA-dependent RNA polymerase

The transition from RNA as the informational molecule of primordial biological systems to the DNA genomes of modern organisms represents one of the greatest evolutionary transitions in the history of life. One way to understand this transition is to comprehend the origin of the enzymes responsible for the metabolism of nucleic acid polymers. In the present work, we reconstructed the ancestral sequence of RNA-dependent DNA polymerase (RdDp) and modeled its structure. The data demonstrate that, in terms of primary sequence, the ancestral sequences exhibit characteristic elements of RdDp; however, structurally, they are more similar to RNA-dependent RNA polymerase (RdRp). The presented data suggest that RdDp may have originated through modifications and neofunctionalization from an RdRp-like ancestor.

Non-Nucleoside Lycorine-Based Analogs as Potential DENV/ZIKV NS5 Dual Inhibitors: Structure-Based Virtual Screening and Chemoinformatic Analysis.

Dengue (DENV) and Zika (ZIKV) virus continue to pose significant challenges globally due to their widespread prevalence and severe health implications. Given the absence of effective vaccines and specific therapeutics, targeting the highly conserved NS5 RNA-dependent RNA polymerase (RdRp) domain has emerged as a promising strategy. However, limited efforts have been made to develop inhibitors for this crucial target. In this study, we employed an integrated in silico approach utilizing combinatorial chemistry, docking, molecular dynamics simulations, MM/GBSA, and ADMET studies to target the allosteric N-pocket of DENV3-RdRp and ZIKV-RdRp. Using this methodology, we designed lycorine analogs with natural S-enantiomers (LYCS) and R-enantiomers (LYCR) as potential inhibitors of non-structural protein 5 (NS5) in DENV3 and ZIKV. Notably, 12 lycorine analogs displayed a robust binding free energy (<-9.00 kcal/mol), surpassing that of RdRp-ribavirin (<-7.00 kcal/mol) along with promising ADMET score predictions (<4.00), of which (LYCR728-210, LYCS728-210, LYCR728-212, LYCS505-214) displayed binding properties to both DENV3 and ZIKV targets. Our research highlights the potential of non-nucleoside lycorine-based analogs with different enantiomers that may present different or even completely opposite metabolic, toxicological, and pharmacological profiles as promising candidates for inhibiting NS5-RdRp in ZIKV and DENV3, paving the way for further exploration for the development of effective antiviral agents.

First Report of Citrus Leaf Blotch Virus on Nagami Kumquat in Turkey.

Kumquat, known as the smallest of citrus fruits, has seen an increase in the number of commercial orchards in recent years. In May of 2022, a PCR-based survey for citrus virus diseases was conducted in commercial Nagami kumquat (Fortunella margarita (Lour.) Swingle) orchards in the Cukurova region of Turkey. During the survey, five trees with bud union disorder symptoms were found in two different kumquat orchards in the Erdemli district of Mersin province. Young leaf samples from the five trees showing bud union disorder symptoms and two symptomless trees were collected from 6-year-old kumquat. Common citrus viruses and viroids, such as citrus psorosis virus, citrus exocortis viroid, and hop stunt viroid, were not detected in PCR tests performed on all collected samples. The samples were also tested for citrus leaf blotch virus (CLBV; genus Citrivirus, family Betaflexiviridae), a virus associated with a bud union crease in kumquat (Vives et al.2001). Total RNA was isolated from collected leaf samples using the RNeasy Plant Mini Kit (Qiagen, USA). In the RT-PCR assay, two separate specific primer pairs were used to determine the presence of CLBV. The coat protein gene (CP), was amplified with primers KU-18 (5'-TTAAGATTACAGACACGAAGG- 3') and KU-19 (5' CTGTTTTTGAATTTTGCTCG-3'), and the RNA-dependent RNA polymerase gene (RdRp) was amplified with KU-27(5'-GATGCAAGCCAGGATGAATAC-3') and KU-15 (5'-CAGACACTCCAAGACCTTTCC-3') primers (Vives et al. 2002). All of symptomatic samples yielded amplicons of the expected size (456-bp RdRp and 438-bp CP). No amplicons were obtained from symptomless samples. Two PCR products were sequenced to confirm their identity by direct sequencing (GenBank accession no: OQ718432, OQ718433, PP726107, PP726108). Consensus sequences of these two genes showed 96% and 97% nt identity with CP and RdRP genes of the CLBV sequence in GenBank (MT038390, EU857539), respectively. For biological indexing, four RT-PCR-positive samples were used as inoculum sources. Four of Etrog citron (C. medica) and four of Dweet tangor (C. tangerina) seedlings were graft-inoculated for each source, and two seedlings for each cultivar were used as a negative control. Two months later, chlorotic blotching symptoms were observed on Dweet tangor leaves. Six months later, Etrog citron exhibited stem pitting symptoms. None of the negative control seedlings developed any symptoms. RT-PCR was performed to confirm the presence of CLBV in the virus-inoculated seedlings, and amplicons of the expected sizes (456-bp RdRp and 438-bp CP) were obtained. To the best of our knowledge, this is the first report of the CLBV infection in citrus in Turkey. CLBV is thought to have originated from infected grafting material in the country, although it is not known where it may have originated. Further research is needed to determine the distribution of CLBV and its potential to impact commercial citrus production in Turkey.

Limited Short-Term Evolution of SARS-CoV-2 RNA-Dependent RNA Polymerase under Remdesivir Exposure in Upper Respiratory Compartments.

The extent of the SARS-CoV-2 short-term evolution under Remdesivir (RDV) exposure and whether it varies across different upper respiratory compartments are not fully understood. Patients hospitalized for COVID-19, with or without RDV therapy, were enrolled and completed up to three visits, in which they provided specimens from four respiratory compartments. Near full-length genome SARS-CoV-2 sequences were obtained from viral RNA, standard lineage and variant assignments were performed, and viral mutations in the RNA-dependent RNA polymerase (RdRp) region-the RDV target gene-were detected and compared between participants with and without RDV, across the four compartments, within participants across visits, and versus a larger sequence dataset. The statistical analysis used a generalized linear mixed-effects model. A total of 139 sequences were obtained from 37 out of the 44 (84%) enrolled participants. The genotyping success varied across respiratory compartments, which ranged from 42% with oropharyngeal specimens to 67% with nasopharyngeal specimens and showed improvement with higher viral loads. No RdRp mutations known to be associated with RDV resistance were identified, and for 34 detected mutations at 32 amino acid positions that are not known as RDV-associated, there was no evidence of any associations with the RDV exposure, respiratory compartment, or time. At least 1 of these 34 mutations were detected in all participants, and some differed from the larger sequence dataset. This study highlighted the SARS-CoV-2 short-term genomic stability within hosts and across upper respiratory compartments, which suggests a lack of evolution of RDV resistance over time. This contributes to our understanding of SARS-CoV-2 genomic dynamics.

Binding Mechanism of the Active Form of Molnupiravir to RdRp of SARS-CoV-2 and Designing Potential Analogues: Insights from Molecular Dynamics Simulations.

Molnupiravir, an FDA-approved nucleoside prodrug for treating COVID-19, converts into N4-hydroxycytidine triphosphate (NHC-TP), which integrates into SARS-CoV-2 RNA by its RNA-dependent RNA polymerase (RdRp) causing lethal mutations in viral proteins. Due to the risk of RdRp-mediated drug resistance and potential off-target effects on host polymerases (e.g., human polymerase II/HPolII), it is crucial to understand NHC-TP interactions at polymerase active sites for developing new, resistance-proof treatments. In this study, we used molecular dynamics (MD) simulations to probe key interactions between NHC-TP and SARS-CoV-2 RdRp and designed novel NHC-TP analogues with greater selectivity for SARS-CoV-2 RdRp over HPolII by a virtual screening workflow. We docked NHC-TP to a modified SARS-CoV-2 RdRp-Remdesivir triphosphate structure (PDB ID: 7BV2) and generated 71 NHC-TP analogues with bulky substituents to increase the interaction with RdRP and to reduce HPolII incorporation. MD simulations assessed the stability, binding affinity, and site interactions of these analogues. The top 7 candidates, with favorable ADMET properties, likely inhibit replication via potential dual mechanisms (the replicative stalling and the induction of lethal mutations) while maintaining selectivity for SARS-CoV-2 RdRp.

Optimization of Bangladesh and Malaysian genotype recombinant reporter Nipah viruses for in vitro antiviral screening and in vivo disease modeling

Nipah virus (NiV) causes near-annual outbreaks of fatal encephalitis and respiratory disease in South Asia with a high mortality rate (∼70%). Since there are no approved therapeutics for NiV disease in humans, the WHO has designated NiV and henipaviral diseases priority pathogens for research and development. We generated a new recombinant green fluorescent reporter NiV of the circulating Bangladesh genotype (rNiV-B-ZsG) and optimized it alongside our previously generated Malaysian genotype reporter counterpart (rNiV-M-ZsG) for antiviral screening in primary-like human respiratory cell types. Validating our platform for rNiV-B-ZsG with a synthetic compound library directed against viral RNA-dependent RNA polymerases, we identified a hit compound and confirmed its sub-micromolar activity against wild-type NiV, green fluorescent reporter, and the newly constructed bioluminescent red fluorescent double reporter (rNiV-B-BREP) NiV. We furthermore demonstrated that rNiV-B-ZsG and rNiV-B-BREP viruses showed pathogenicity comparable to wild-type NiV-B in the Syrian golden hamster model of disease, supporting additional use of these tools for both pathogenesis and advanced pre-clinical studies in vivo.

Bioprospection for antiviral compounds from selected medicinal plants against RNA polymerase of rotavirus A using molecular modelling and density functional theory

Rotavirus A (RVA) infection remains a significant global health challenge, especially in developing countries, causing severe dehydrating diarrhoea in children under five years of age. Despite the availability of four World Health Organization (WHO) pre-qualified vaccines, their availability, particularly in low-income countries, pose significant challenges. Currently, there are no specific anti-rotaviral medications hence, the urgency to develop novel therapeutics against rotavirus infection. Thus, this study explored the potential of secondary metabolites of Spondias mombin, Macaranga barteri and Dicerocaryum eriocarpum as novel inhibitors of the RNA-dependent RNA polymerase (VP1) of rotavirus A using computational techniques. Pharmacokinetics parameters were adopted to screen the top 20 metabolites with high affinity for the target, initially identified through a docking study. Furthermore, the ability of the resulting compounds to modulate the investigated target was assessed using molecular dynamics (MD) simulation, while density functional theory (DFT) calculations were conducted to predict the molecular properties of the top-ranked compounds. Except for ellagic acid hexoside (-33.14 kcal/mol), all the leads had higher binding free energy values relative to sofosbuvir (-36.58 kcal/mol) following a 120 ns MD simulation. Overall, the resulting complexes with the lead compounds demonstrated acceptable stability, reduced flexibility and compactness, with spiraeoside (-51.02 kcal/mol) displaying more favourable thermodynamics metrics, albeit with a lesser binding free energy relative to chrysoeriol 7-glucuronide (-58.36 kcal/mol). The binding free energy and thermodynamic parameters of the top-hit compounds could be attributed to their respective bond interactions and molecular orbital properties except chrysoeriol 7-glucuronide, with a need for additional structural adjustment to enhance its thermodynamic properties. Thus, these findings indicate the potential modulatory ability of the lead compounds against the VP1 protein of RVA, underscoring the importance of further in vitro and in vivo studies to validate the predicted activity, and ongoing efforts are being made to pursue this line of investigation.

Complete genome sequence of lima bean endornavirus 1: a putative new member of the genus Alphaendornavirus (family Endornaviridae).

In this study, we completely sequenced the genome of a new member of the genus Alphaendornavirus, family Endornaviridae, from lima bean (Phaseolus lunatus), for which we propose the name "lima bean endornavirus 1" (LbEV1). The complete genome of LbEV1 consists of 15,265 nucleotides, including a stretch of 12 cytosine residues at its 3' end, and contains a long single open reading frame (ORF) coding for a 4980-aa-long polyprotein. Analysis of the polyprotein sequence revealed the presence of four conserved functional domains (in order from the N- to C-terminus): viral helicase 1, peptidase _C97, glycosyltransferase_GTB-type, and viral RNA-dependent RNA polymerase (RdRP). The LbEV1 polyprotein showed the highest amino acid sequence similarity (63% identity and 98% coverage) to Phaseolus vulgaris endornavirus 3 (PvEV3) and also showed 42% identity (95% coverage) to Geranium carolinianum endornavirus. Phylogenetic analysis based on the viral RdRp domain showed that LbEV1 belongs to a subclade within the genus Alphaendornavirus that includes three other viruses infecting plants of the genus Phaseolus.

Development of targeted whole genome sequencing approaches for Crimean-Congo haemorrhagic fever virus (CCHFV)

Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, with a reported case fatality rate of 30 % or higher. The virus contains a tri-segmented, negative-sense RNA genome consisting of the small (S), medium (M) and large (L) segments encoding respectively the nucleoprotein (NP), the glycoproteins precursor (GPC) and the viral RNA-dependent RNA polymerase (RDRP). CCHFV is one of the most genetically diverse arboviruses, with seven distinct lineages named after the region they were first reported in and based on S segment phylogenetic analysis.Due to the high genetic divergence of the virus, a single targeted tiling PCR strategy to enrich for viral nucleic acids prior to sequencing is difficult to develop, and previously we have developed and validated a tiling PCR enrichment method for the Europe 1 genetic lineage.We have developed a targeted, probe hybridisation capture method and validated its performance on clinical as well as cell-cultured material of CCHFV from different genetic lineages, including Europe 1, Europe 2, Africa 2 and Africa 3. The method produced over 95 % reference coverages with at least 10x sequencing depth. While we were only able to recover a single complete genome sequence from the tested Europe 1 clinical samples with the capture hybridisation protocol, the data provides evidence of its applicability to different CCHFV genetic lineages.CCHFV is an important tick-borne human pathogen with wide geographical distribution. Environmental as well as anthropogenic factors are causing increased CCHFV transmission. Development of strategies to recover CCHFV sequences from genetically diverse lineages of the virus is of paramount importance to monitor the presence of the virus in new areas, and in public health responses for CCHFV molecular surveillance to rapidly detect, diagnose and characterise currently circulating strains.

The roles of rabies virus structural proteins in immune evasion and implications for vaccine development.

Rabies is a zoonotic infectious disease that targets the nervous system of human and animals and has about 100% fatality rate without treatment. Rabies virus is a bullet-like viral particle composed of five structural proteins, including nucleoprotein (N), phosphorylated protein (P), matrix protein (M), glycoprotein (G), and large subunit (L) of RNA-dependent RNA polymerase. These multifunctional viral proteins also play critical roles in the immune escape by inhibiting specific immune responses in the host, resulting in massive replication of the virus in the nervous system and abnormal behaviors of patients such as brain dysfunction and hydrophobia, which ultimately lead to the death of patients. Herein, the role of five structural proteins of rabies virus in the viral replication and immune escape and its implication for the development of vaccines were systemically reviewed, so as to shed light on the understanding of pathogenic mechanism of rabies virus.

Rabies, The Administration of Vaccines and Public Health Concern, Neglected Challenges and Historical Perspective in China

Rabies virus is transmitted via contact of saliva of a rabid animal with a person ,s mucosa or a skin lesion. It is a fatal encephalomyelitis caused by members of expanding Lyssavirus genus, and the genus included 17 species. The aim of this literature review is to survey on rabies and vaccination in China, threats and challenges to eliminate it, especially in China. The information provided is obtained from randomized control experiments, review articles, and analytical observations and studies which were gathered from various literature sources such as Scopus, Google Scholar, PubMed, and Science Direct. The keywords were dogs, glycoprotein, lyssavirus, post-exposure prophylaxis, and rabies virus. Rabies virus is a bullet shaped enveloped virion, and the classical rabies virus and its field strains are discovered worldwide and induces to rabies in animals and humans. In recent years, China has made wonderful and significant achievements in rabies prevention and control, and currently, the mortality and incidence rate of human infection with rabies have decreased to the minimum level historically, which has caused a notable foundation for the ultimate elimination of human rabies. Generally, five proteins are available in mature rabies virus particles, phosphoprotein, nucleoprotein, glycoprotein, matrix protein, and RNA-dependent RNA polymerase. The main carriers of rabies in China are dogs which are accountable for most of the human rabies deaths in China. Most common way of entry of rabies virus into the body is both via infected neural tissue through open cuts in the skin and salvia. The most notable parameters which limit rabies vaccinations are limited laboratory-based surveillance, diminished community outreach and education, underestimation of the population at risk, irregular vaccine applications in space and time, inaccessible naïve free-ranging dogs, exclusion of puppies, cold chain failure, translocation of cases, effect of other species, including cats, wildlife, and livestock, accessibility to remote hotspots, competing priorities, lack of adequate resources, impact of poverty on responsible social ownership and routine animal health care, cultural disparities, Sisyphean fatigue, frustration and staff burn-out. Rabies remain a public health problem and continue to present health risks for both animals and human; It is important to improve access to PEP in endemic countries where human rabies deaths still happen, but the big problem is its costs that should be curtailed and surveillance strengthened for controlling and eliminating it.

RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories.

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of non-enveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoV) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent-RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.

Characterization of ACTN4 as a novel antiviral target against SARS-CoV-2

The various mutations in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pose a substantial challenge in mitigating the viral infectivity. The identification of novel host factors influencing SARS-CoV-2 replication holds potential for discovering new targets for broad-spectrum antiviral drugs that can combat future viral mutations. In this study, potential host factors regulated by SARS-CoV-2 infection were screened through different high-throughput sequencing techniques and further identified in cells. Subsequent analysis and experiments showed that the reduction of m6A modification level on ACTN4 (Alpha-actinin-4) mRNA leads to a decrease in mRNA stability and translation efficiency, ultimately inhibiting ACTN4 expression. In addition, ACTN4 was demonstrated to target nsp12 for binding and characterized as a competitor for SARS-CoV-2 RNA and the RNA-dependent RNA polymerase complex, thereby impeding viral replication. Furthermore, two ACTN4 agonists, YS-49 and demethyl-coclaurine, were found to dose-dependently inhibit SARS-CoV-2 infection in both Huh7 cells and K18-hACE2 transgenic mice. Collectively, this study unveils the pivotal role of ACTN4 in SARS-CoV-2 infection, offering novel insights into the intricate interplay between the virus and host cells, and reveals two potential candidates for future anti-SARS-CoV-2 drug development.

A novel ormycovirus isolated from the plant-pathogenic fungus Fusarium graminearum.

In this study, we identified a novel mycovirus, Fusarium graminearum ormycovirus 1 (FgOV1), from the pathogenic fungus Fusarium graminearum. The virus has two RNA segments, RNA1 and RNA2, with lengths of 2,591 and 1,801 nucleotides, respectively, excluding the polyA tail. Each segment contains a single open reading frame (ORF). The ORF in RNA1 encodes an RNA-dependent RNA polymerase, while the ORF in RNA2 encodes a hypothetical protein. Phylogenetic analysis showed that FgOV1 belongs to the gammaormycovirus clade, whose members are related to betaormycoviruses. To our knowledge, this is the first report of an ormycovirus in Fusarium graminearum.

In Silico Evaluation of HIV Protease and RNA Polymerase Inhibitors as Potential COVID-19 Therapeutics.

The COVID-19 coronavirus, also known as the acute respiratory syndrome coronavirus, emerged as a significant global health concern. First identified in Wuhan, China, in December 2019, the virus rapidly spread to over 187 countries due to its high transmissibility. Until an effective treatment or vaccine is developed, preventive measures remain the only mandatory strategy to curb person-to-person transmission. The study aimed to explore potential therapeutic options for COVID-19 by repurposing existing drugs. Specifically, the objective was to evaluate a library of clinically approved or investigational antiviral compounds through docking studies to identify candidates with high binding affinity to COVID-19 proteins. The study employed molecular docking techniques using the Maestro interface (Schrodinger Suite, LLC, NY) to assess the interaction of selected compounds with various COVID-19 protein targets. A total of 15 compounds were analyzed for their binding potential to multiple forms of the virus's proteins. The docking studies revealed that several compounds, particularly HIV protease inhibitors and RNA-dependent RNA polymerase inhibitors, demonstrated strong binding affinities to key COVID-19 enzymes. These interactions suggest their potential as therapeutic candidates for COVID-19 treatment. The findings from this drug repurposing study highlight the potential of certain existing antiviral agents in the treatment of COVID-19. The identified compounds could serve as promising candidates for further investigation in the ongoing battle against the coronavirus pandemic.

Characterization and genetic diversity of grapevine Pinot gris virus in Serbian vineyards

Sixty-five samples of grapevine from commercial vineyards in the Rasina district of Serbia were tested for the presence of grapevine Pinot gris virus (GPGV), using the reverse transcription-polymerase chain reaction. Fourteen samples of the grapevine varieties ‘Red Globe’, ‘Victoria’ and ‘Preobraženje’ were infected with GPGV. All the infected plants showed symptoms of leaf chlorotic mottling, puckering, and deformation, stunting, and reduced yields. The coding regions of the movement and coat protein (MP/CP) and a region of the RNA-dependent RNA polymerase (RdRP) domains of eight virus isolates were sequenced. Phylogenetic analyses of these genomic regions showed high nucleotide similarity among the Serbian GPGV isolates. This study is the first to describe genetic diversity of GPGV isolates in Serbia.

MMFA-DTA: Multimodal Feature Attention Fusion Network for Drug-Target Affinity Prediction for Drug Repurposing Against SARS-CoV-2.

The continuous emergence of novel infectious diseases poses a significant threat to global public health security, necessitating the development of small-molecule inhibitors that directly target pathogens. The RNA-dependent RNA polymerase (RdRp) and main protease (Mpro) of SARS-CoV-2 have been validated as potential key antiviral drug targets for the treatment of COVID-19. However, the conventional new drug R&D cycle takes 10-15 years, failing to meet the urgent needs during epidemics. Here, we propose a general multimodal deep learning framework for drug repurposing, MMFA-DTA, to enable rapid virtual screening of known drugs and significantly improve discovery efficiency. By extracting graph topological and sequence features from both small molecules and proteins, we design attention mechanisms to achieve dynamic fusion across modalities. Results demonstrate the superior performance of MMFA-DTA in drug-target affinity prediction over several state-of-the-art baseline methods on Davis and KIBA data sets, validating the benefits of heterogeneous information integration for representation learning and interaction modeling. Further fine-tuning on COVID-19-relevant bioactivity data enhances model predictions for critical SARS-CoV-2 enzymes. Case studies screening the FDA-approved drug library successfully identify etacrynic acid as the potential lead compound against both RdRp and Mpro. Molecular dynamics simulations further confirm the stability and binding affinity of etacrynic acid to these targets. This study proves the great potential and advantages of deep learning and drug repurposing strategies in supporting antiviral drug discovery. The proposed general and rapid response computational framework holds significance for preparedness against future public health events.