Viruses-Basel最新文献

Retinoic acid-inducible gene I (RIG-I) is a crucial pattern recognition receptor for detecting viral RNA and initiating an immune response against influenza A viruses (IAVs). The activation of RIG-I in mammalian cells requires ubiquitination by two E3 ubiquitin ligases: TRIM25 and RIPLET. Using dual luciferase assays, we demonstrate that duck RIPLET enhances the activation of RIG-I, driving the IFN-β promoter activity in chicken DF-1 fibroblasts. qPCR analyses show that the co-expression of duck RIG-I and RIPLET significantly upregulates key immune genes and reduces viral RNA transcripts in DF-1 cells challenged with low pathogenic avian influenza (LPAI) H6N2. Co-immunoprecipitation and confocal microscopy studies suggest the interaction and confirm the colocalization of duck RIG-I and RIPLET in the cytoplasm. Further, we show that the non-structural protein 1 (NS1) of IAV, known for its role in immune evasion, suppression, and pathogenicity, from five different strains of IAV (PR8, BC500, CA431, D4AT, and VN1203) can all inhibit duck RIPLET activation of RIG-I, with NS1 from avian strains showing the greatest decrease in IFN-β promoter activity in chicken DF-1 cells. Overall, our research provides valuable insight into the E3 ubiquitin ligases required for RIG-I activation and susceptibility of this pathway to IAV interference across species.

Foot-and-mouth disease virus (FMDV) is a highly contagious pathogen of cloven-hoofed livestock. Recombination is one of the mechanisms that contribute to genetic diversity of FMDV and facilitate the generation of new viral lineages, or recombinant forms. While the general patterns of recombination in FMDV are well-known, the temporal dynamics of this process remain unexplored. This study systematically analyzed recombination across 1485 publicly available complete genome sequences of FMDV, collected from 1934 to 2024. In addition to the well-known general recombination pattern with hotspots on the borders of the genome region that encodes capsid proteins VP2-VP3-VP1, we identified serotype-specific recombination patterns. A significant temporal signal required to analyze temporal dynamics was found in serotypes A, Asia1, O, and SAT1 in the VP2-VP3-VP1 genome region. To assess the lifetimes of FMDV recombinant forms, we compared these time-scaled phylogenetic trees with phylogenies for other genomic regions exchanged by recombination events. The median lifetimes of FMDV recombinant forms ranged from 2 to 18 years, depending on the serotype and the nonstructural genomic region involved in recombination. These timescales are comparable to human (+)RNA viruses, such as enteroviruses and caliciviruses. In distinct serotypes, recombination could be more frequent on the 5' or 3' border of the capsid-encoding genome region, without a uniform pattern.

Human Pegivirus (HPgV) is an understudied flavivirus that is highly prevalent and often persists in the blood and tissues of humans. HPgV-infected brain tissue from individuals with Parkinson's disease has shown significant transcriptomic and immune signaling differences compared to non-infected Parkinson's brains. The HPgV genome is similar to Hepatitis C Virus (HCV), a well-characterized flavivirus with multiple approved small-molecule therapeutics. Here, we used HCV crystal structures to create homology models for two HPgV non-structural (NS) proteins, the serine protease (NS3) and the RNA-dependent RNA polymerase (NS5B), and performed molecular dynamic simulations. HCV and HPgV proteins had minimal structural differences, as seen by the Root Mean Square Deviation (RMSD) difference between NS3 (1.00 Å) and NS5B (1.26 Å). FDA-approved small molecules were then docked in silico to the NS3 and NS5B subunits of HCV and HPgV. HCV had weak to moderate correlated docking scores with HPgV NS3 (R² = 0.21, p < 0.001) and NS5B (R² = 0.58, p < 0.001). The predicted protein-ligand interactions showed potential binding between HCV antivirals and conserved residues of HPgV, including the catalytic triad for NS3 or the GDD motif for NS5B. Together, these results provide structural insights for key HPgV proteins and highlight possibilities for therapeutic repurposing of HCV antivirals.

In the field of antiviral peptide (AVP) design, one of the most prominent limiting factors is the time and material cost required to perform the initial screening of novel AVPs. In particular, traditional target identification as well as traditional preclinical screening of novel drug candidates can be a very lengthy and expensive process. In recent decades, target identification and initial screening of AVPs has been increasingly carried out using machine learning (ML). The use of ML to initially screen potential interactions reduces the financial cost and lengthy time scale of preclinical AVP development, allowing for candidate peptides to be identified and screened faster, at a lower cost to both manufacturer and consumer. Additionally, the use of ML in generating and screening AVP candidates allows a more diverse chemical space to be explored than high-throughput screening methodologies allow. In silico generation and validation of AVP candidates also limits researcher contact with high BSL-rated viruses, thereby increasing the safety and accessibility of AVP design. This review seeks to provide a broad overview of the current uses of ML in early-stage AVP design, and to shed some light on the future direction of the field.

Since 2022, global outbreaks of monkeypox virus (MPXV) have been repeatedly designated by the World Health Organization (WHO) as a public health emergency of international concern (PHEIC), underscoring the urgent need to elucidate the multidimensional mechanisms underlying viral evolution and transmission. Current understanding remains largely focused on genomic variation, while the critical role of epigenetic regulation has been considerably overlooked. To address this gap, this study integrates high-throughput evolutionary genomic analysis with whole-genome DNA methylation profiling. Using parallel Illumina and Nanopore sequencing platforms, we comprehensively characterized two clinically derived MPXV isolates collected locally. The results revealed that both isolates belonged to the C.1.1 ancestral lineage, diverging into distinct clades (E.3 and E.4, respectively, supporting the presence of at least two independent viral introduction events into the region, each followed by limited local transmission. They had accrued a considerable number of single-nucleotide polymorphisms (SNPs), with APOBEC3-associated substitutions constituting 84.8% and 77.6% of all observed mutations. Furthermore, both 5-hydroxymethylcytosine (5hmC) and N6-methyladenine (6mA) modifications were identified and found to be preferentially enriched within the inverted terminal repeats (ITRs) regions of MPXV genome in both viral strains; moreover, the E.4 lineage viral strain exhibits a markedly more intricate and compositionally diversified modification landscape, a pattern that indicates appreciable epigenetic heterogeneity among MPXV lineages. Our study furnishes a multi-omics framework that presents a systematic evolutionary feature of two clinical MPXV isolates and their genomic DNA 5hmC and 6mA modification topologies, and enhances our understanding of MPXV viral adaptation and diversification.

To establish a rapid, sensitive, and reproducible method for evaluating the immunogenic performance of Tembusu virus (TMUV) vaccines, we developed and optimized a blocking enzyme-linked immunosorbent assay (bELISA) using the TMUV envelope (E) protein as the coating antigen. By systematically screening the coating antigen concentration, mAb dilution, serum dilution, and chromogenic reaction time, we determined the optimal reaction conditions for this assay. The results showed that bELISA exhibited high specificity, yielding positive reactions only with TMUV-positive sera and no cross-reactivity with sera against other common duck viruses; the cutoff value for positivity was 48.89%, and the lowest detectable serum dilution was 1:10. Neutralization assays confirmed that the TMUV E-specific mAb significantly inhibited viral replication, supporting the functional relevance and reliability of the established bELISA. In a comparative investigation, this assay was used to assess five TMUV vaccines, including both inactivated and attenuated variants, in Cherry Valley ducks. The DF2 inactivated vaccine was found to elicit the highest antibody levels and blocking rates. This was followed by the WF100 attenuated vaccine, which also demonstrated a strong immune response. The TC2B inactivated vaccine, although effective, showed a comparatively lower response, whereas the FX2010-180P strain and mosquito cell-derived WF100 attenuated vaccine showed weaker immunogenicity. Neutralization assays further confirmed that the TMUV E-specific mAb significantly inhibited viral replication, supporting the functional relevance and reliability of the established bELISA. In summary, the bELISA described here demonstrates high specificity, sensitivity, and reproducibility and is suitable for evaluating the immune efficacy of different TMUV vaccines, providing a reliable technical platform for vaccine immunology studies and optimization of immunization strategies.

Flaviviruses are arthropod-borne RNA viruses associated with significant human diseases globally. There are no effective direct-acting antivirals approved to treat these viral infections. Given its critical role in viral replication, the RNA-dependent RNA polymerase (RdRp) is a logical target for antiviral drug development. Remdesivir (formerly GS-5734), a 1'-cyano modified C-adenosine monophosphate prodrug, was the first US Food and Drug Administration (FDA) approved antiviral for coronavirus disease 2019 (COVID-19) and was also shown to inhibit flavivirus replication. GS-7682, a 4'-cyano modified C-adenosine prodrug, exhibits a broad-spectrum antiviral activity. Here, we determined the anti-flavivirus potency of both remdesivir and GS-7682 and characterized their active triphosphate forms, GS-443902 and GS-646939, respectively, against a panel of purified flavivirus RdRps. These include dengue, Japanese encephalitis, West Nile, yellow fever, and Zika. Enzyme kinetics demonstrate efficient RNA incorporation of GS-443902 and GS-646939. GS-646939 acts as an immediate chain terminator. Conversely, GS-443902 acts through a template-dependent inhibition mechanism by impeding the incorporation of the complementary UTP. Both mechanisms correlate with anti-flavivirus activity, although remdesivir is generally superior. The data demonstrate that immediate chain termination is not necessarily a preferred mechanism of action of nucleotide analogs. Template-dependent inhibition should also be considered, especially for viruses lacking intrinsic proofreading activities.

Genomic surveillance is a cornerstone of pandemic response; it has helped guide public health interventions worldwide. However, North Africa stands between limited surveillance resources and efforts to address the data gap in this strategic geographic region that links sub-Saharan Africa and Europe. In this study, we present the first comprehensive evolutionary investigation of Algerian SARS-CoV-2 genomes, revealing their phylogeny, continuous phylogeography within the country, mutation analysis, and a super-spreading event through haplotype network analysis. We characterized the genetic diversity and unique mutation pattern of 449 Algerian sequences, revealing multiple independent introductions into the country since the first reported case on the 25th of February 2020 followed by numerous local transmissions that facilitated the virus's rapid propagation. This study highlights both the importance of molecular epidemiology and equitable access to resources in implementing genomic epidemiology and in increasing sequencing efforts to strengthen pandemic preparedness.

With the ongoing emergence of SARS-CoV-2 variants, continued surveillance of antiviral susceptibility remains critical for detecting resistance that could compromise treatment efficacy. This study evaluated the activity of 2 SARS-CoV-2 RNA-dependent RNA polymerase (Nsp12) inhibitors against emerging Omicron variants: remdesivir (RDV), an approved antiviral for the treatment of COVID-19, and obeldesivir (ODV), an oral prodrug that shares the same parent nucleoside as RDV. Both RDV and ODV were shown to retain antiviral activity against the Omicron subvariants BA.2.86.1, JN.1.7, KP.2, KP.3.1.1, KP.3.3, LP.8.1, NB.1.8.1, XBB.2, XEC, and XFG compared with wild-type reference strains. Only 1 new lineage-defining Nsp12 substitution, D284Y (detected in NB.1.8.1), was observed. Phenotypic analysis demonstrated that a replicon containing this substitution remained susceptible to both RDV and ODV. These findings are consistent with previous studies showing that RDV and ODV retain potent activity against previously identified Omicron variants, support the continued clinical use of RDV against circulating SARS-CoV-2 variants, and reinforce the potential of ODV as an oral antiviral therapeutic.

In recent years, wastewater (WW)-based epidemiology has been increasingly used for surveillance of SARS-CoV-2 and has emerged as a potential tool for monitoring other respiratory viruses. Most evidence on the use of WW for detecting multiple respiratory viruses comes from developed countries. In this study, we assessed the feasibility of multi-respiratory virus sewage surveillance in a middle-income country and explored signals that may be potentially used as early warning signs for Public Health authorities. We examined the presence of SARS-CoV-2, influenza virus, respiratory syncytial virus (RSV), and human metapneumovirus (hMPV) in 238 WW samples collected from three treatment plants in San Luis Potosí, Mexico, over one year. The weekly detection of each virus was compared with the weekly number of hospital admissions for respiratory infections caused by that virus in pediatric patients. SARS-CoV-2, influenza, hMPV, and RSV were detected in 152 (63.9%), 108 (45.4%), 95 (39.9%), and 24 (10.1%) samples, respectively. There was no significant correlation between viral detection in WW and the number of hospitalizations during that week. However, analyses of WW viral detection with hospitalizations in subsequent weeks showed an increasing correlation reaching a maximum correlation for a lag of 12 weeks for SARS-CoV-2 (r_s = 0.63, p = 0.001), 9 weeks for influenza (r_s 0.62, p = 0.0001), 2 weeks for RSV (r_s = 0.30, p = 0.05), and 3 weeks for hMPV (r_s = 0.39, p = 0.009). In addition, we identified time-periods of SARS-CoV-2, influenza, and RSV widespread circulation (several consecutive weeks in which viruses were detected in the three treatment plants); most hospitalizations caused by these viruses occurred after widespread circulation was detected in WW, suggesting this may be used as an early alert for public health systems. Overall, our results show that WW-based surveillance of multiple respiratory viruses is feasible and has potential applications as an early warning system in middle-income countries.