Search Results (359)

Background: The continuous emergence of SARS-CoV-2 variants represents a major public health concern. Next-generation sequencing (NGS) enables genomic surveillance, facilitating the detection and monitoring of mutations that impact viral evolution. Methods: In this study, full-length SARS-CoV-2 genomes were analyzed between February 2022 and March 2024 as part of routine genomic surveillance conducted in Verona, Italy. Mutations in the envelope (E), membrane (M), and nucleocapsid (N) structural proteins were investigated. Only substitutions with a total prevalence of greater than 1% in the study dataset were considered. Results: A total of 178 mutations were identified across the three proteins (E: 16; M: 33; N: 129), of which 18 met the inclusion threshold (E: 3; M: 5; N: 10). Mutations were classified according to temporal dynamics as fixed, emerging, or transient. Throughout the study period, fixed mutations were consistently prevalent, emerging mutations appeared later but persisted with an ascending trend, while transient mutations displayed a single frequency peak before disappearing. Several mutations were reported with potential structural or functional relevance based on the existing literature, while others remain of unknown significance. Conclusions: The mutational patterns detected in this study broadly reflect global evolutionary trends of SARS-CoV-2. These findings emphasize the importance of continued genomic surveillance and underline the need for integrated experimental approaches to clarify the biological and epidemiological impact of poorly characterized mutations. Full article

Background/Objectives: Postbiotics derived from lactic acid bacteria are emerging as promising antimicrobial agents due to their antibacterial, antibiofilm, and immunomodulatory properties. Among their metabolites, lactic acid (LA) is thought to play a major role in antimicrobial activity. This study investigated the proteomic response of Pseudomonas aeruginosa and Staphylococcus aureus to Lacticaseibacillus rhamnosus cell-free supernatant (CFS) and compared it with that elicited by LA alone. Methods: Overnight bacterial cultures were exposed to sub-MIC LA or CFS (1:10 for P. aeruginosa and 1:8 for S. aureus; ~12.5–15.6 mM LA) for 6 h at 37 °C. Intracellular proteins were harvested and subsequently quantified and purified to be analysed by HPLC–MS/MS, for quantitative label-free proteomics. Results: Proteomic analysis revealed clear separation of treated samples from controls, with largely overlapping responses to CFS and LA. Hallmark acid-stress adaptations were observed, including urease-mediated pH buffering, confirming that part of the response was driven by mild organic acid. In P. aeruginosa, treatments suppressed virulence pathways (phenazines, T3SS), while shifting metabolism toward lactate utilisation and reinforcing the outer membrane (lipid A, polyamine). In S. aureus, decreased abundance of the SaeRS-regulated immune-evasion factor Sbi, together with changes in envelope, ROS and translation-related proteins, suggested a bacteriostatic-like state. S. aureus differences between CFS and LA were more pronounced; CFS uniquely increased cell-wall defences, oxidative stress (SodA, SodM) and chaperone expression (GroS, GrpE), suggesting stress beyond acidification alone. Conclusions: These findings shed light on the molecular mechanisms underlying bacterial adaptation to CFS and highlight their potential as a novel antimicrobial approach. 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

The human papillomavirus (HPV) is a small, non-enveloped virus with a circular double-stranded DNA genome. The HPV genome encodes the E2 activator protein, which is required for viral transcription. R-loops are triple-stranded nucleic acid structures that occur when newly synthesized single-stranded RNA anneals to duplex DNA. These structures form during papillomavirus transcription. We and others have demonstrated that resolution of viral R loops is crucial for HPV episomal maintenance. ZPR1 is a zinc finger protein that can recruit SETX to mammalian R-loops to mediate resolution. E2 binds to and recruits SETX, an R-loop helicase, to the viral promoter. We observed E2 in complex with SETX and ZPR1. However, we found that ZPR1 depletion decreased viral R-loops while enhancing cellular R-loops. ZPR1 depletion also increased SETX binding to the viral promoter. These data suggest that ZPR1 is not required for HPV R-loop resolution, in contrast to what has been observed in mammalian cells. We detected the E2 protein associated with R-loops and found that E2 overexpression increases cell-derived R-loop formation. Analysis of TCGA datasets revealed that ZPR1, but not SETX, mRNA expression is significantly reduced in HPV-positive cervical and head and neck cancers. Together, these findings indicate that while E2 mediates HPV R-loop resolution, it also promotes R-loop accumulation in the host genome, likely through SETX sequestration. Full article

Zika virus (ZIKV) caused Zika outbreaks and continues to post threats to public health. ZIKV infection may cause congenital abnormalities during pregnancy and neurological manifestations in adults. The recurrent public health threat of Zika in various geographical areas demonstrates a need for the development of effective therapeutics. Currently, there are no approved therapies for Zika. ZIKV is a single-stranded, positive-sense RNA virus, whose genome encodes three structural proteins and seven non-structural proteins. The surface envelope (E) protein is essential for host–cell recognition and viral entry; therefore, inhibition of E-mediated viral entry is a key strategy underlying antiviral treatments. Here, molecular docking-based virtual screening was used to screen small-molecule compound libraries to identify potential ZIKV entry inhibitors. Among the compounds identified, Pyrimidine-Der1 exhibited efficient inhibition of reporter ZIKV infection. The microscale thermophoresis assay confirmed its binding with the ZIKV E protein. This compound has effective inhibition of authentic ZIKV infection in a plaque inhibition assay against R103451, PAN2016, and FLR human strains (IC₅₀: ~3–5 μM). Additionally, it efficiently inhibited ZIKV infection at viral entry and fusion steps of the virus life cycle in a time-of-addition assay. Overall, Pyrimidine-Der1 is a promising ZIKV entry inhibitor, warranting further optimization and evaluation. Full article

Gene duplication, a major source of new genes in evolution, often occurs via reverse transcription of mRNA, leading to the integration of a retrocopy into a new genomic locus. Here, we performed an in-depth analysis of the evolutionary history of the e(y)2 gene in Metazoa. The E(y)2 protein is a shared subunit of two highly conserved complexes involved in transcription regulation (the DUB module of the SAGA complex) and mRNA transport (TREX-2). In Deuterostomes, the e(y)2 gene has undergone multiple independent retropositions, often giving rise to functional retrogenes. In contrast, among Protostomes, duplications of e(y)2 were identified only in Drosophilinae and a member of the Lepidoptera family (Manduca sexta). In Drosophila, the retrocopy e(y)2 acquired an almost ubiquitous expression pattern and compensates for the function of the parental gene in all tissues except the testes. The parental gene, e(y)2b, evolved a testis-specific expression pattern, lost the ability to incorporate into the DUB module, but retained nuclear envelope localization and the capacity to assemble into the TREX-2 complex. Knockout of the D. melanogaster e(y)2b gene resulted in reduced male fertility. Overall, our study highlights distinct evolutionary trajectories of the e(y)2 gene in Deuterostomes and Protostomes. Full article

Xenotransplantation using pig cells, tissues or organs may be associated with the transmission of porcine zoonotic or xenozoonotic microorganisms. Porcine endogenous retroviruses (PERVs) pose a special risk for xenotransplantation as these viruses can infect human cells and are integrated in multiple copies in the genome of all pigs and, therefore, they cannot be eliminated as other viruses can. To prevent PERV transmission to the recipient, several strategies have been developed: PERV-C-free animals, siRNA and genomic editing. Another strategy is the generation of vaccines based on neutralizing antibodies in order to protect the recipient. To investigate whether a protective vaccine is feasible in the case of PERV, the recombinant transmembrane (p15E) and the surface envelope (gp70) protein of PERV were cloned, produced, purified and used to immunize rats. For the first time, an adjuvant type that is approved for human use was used. In all cases we obtained virus binding antibodies as shown in Western blot assays and neutralizing antibodies as shown in neutralization assays, indicating the potential for a protective vaccine. The epitopes recognized by the antisera against p15E were determined using overlapping peptides. Two main epitopes were found in the sequence of p15E, one in the membrane proximal external region (MPER) and one in the fusion peptide proximal region (FPPR). The epitopes correspond to epitopes determined previously when immunizing different animal species with p15E of PERV. Antibodies against these epitopes block the conformational changes in the transmembrane envelope proteins that are required for membrane fusion, thereby inhibiting infection. The epitope in the MPER is related by sequence and location to an epitope in the transmembrane envelope protein of the human immunodeficiency virus-1 (HIV-1) recognized by a broadly neutralizing antibody from infected patients. Full article

SARS-CoV-2 persists worldwide, driving the demand for effective antivirals that inhibit replication and limit the emergence of resistant variants. Lycorine, a non-nucleoside inhibitor of SARS-CoV-2 RNA-dependent RNA polymerase, exhibits antiviral activity without direct mutagenic effects. Here, we examine the occurrence of single-nucleotide variants (SNVs) and insertions/deletions (indels) in SARS-CoV-2 B.1.499 strain during serial passages in Vero cells, comparing lycorine-treated cultures (2.5 and 5 µg/mL) with untreated controls. Whole-genome sequencing was used to assess mutation patterns and frequencies. Lycorine-treated passages displayed greater variant diversity than controls, with fixed mutations mainly affecting non-structural proteins (Nsp3-F1375A, Nsp5-L50F, and Nsp14-G265D) and the envelope protein (E-S6L). A 15-nucleotide deletion in the spike gene (QTQTN motif) occurred in both groups but became fixed only in untreated passages, suggesting negative selection under lycorine pressure. Notably, the L50F mutation in Nsp5, previously linked to nirmatrelvir resistance, was found exclusively in lycorine-treated passages. Additionally, a 1-nucleotide deletion in the accessory gene ORF8, detected only under lycorine treatment, resulted in a frameshift mutation that added four amino acids, potentially altering the protein’s function. Overall, lycorine induces a distinct mutation profile, favoring replication-related variants while suppressing deleterious deletions. These findings suggest potential mechanisms of cross-resistance and highlight the importance of monitoring resistance during clinical use. Full article

Chikungunya virus (CHIKV) is an arthritogenic alphavirus transmitted primarily via Aedes aegypti and Aedes albopictus mosquitoes. Since its identification, CHIKV remained confined to parts of Africa and Asia until the early 2000s, when it expanded to other continents, causing epidemics. Structurally, it is an enveloped virus with a positive-single-stranded RNA genome, which encodes four non-structural proteins (nsP1-nsP4), responsible for viral replication, and five structural proteins (C, E3, E2, 6K, and E1), which form the capsid and envelope. Of these proteins, glycoproteins E1 and E2 are essential for cell recognition and membrane fusion, determining infectivity and viral tropism. CHIKV replication occurs in the cytosol of different cell types, triggering an intense inflammatory and immune response, which manifests clinically as Chikungunya fever (CHIKF). Despite its epidemiological impact, current treatment is limited to symptomatic approaches, including the use of analgesics and anti-inflammatories, as no specific antiviral therapies are available. In response, promising advances are being made, including the development of vaccines, targeted antivirals, and immunotherapies. This article aims to review the main aspects of viral biology, epidemiology, and immunopathogenesis of CHIKV infection, in addition to discussing the main advances in the development of new therapeutic approaches for its control. Full article

The genus Orthoflavivirus (family Flaviviridae) comprises several important pathogens that are widespread across the globe, often co-circulating in many regions. In Austria, the closely related mosquito-borne West Nile (WN) and Usutu (USU) viruses have been detected since the early 2000s. Orthoflavivirus-neutralizing antibodies primarily target the major envelope protein E. However, due to their antigenic relationship, recurring contacts with different orthoflaviviruses can lead to the induction of broadly cross-reactive E-specific antibodies. These can pose a problem in the diagnosis and differentiation of orthoflavivirus infections. Therefore, we established immunological assays based on the non-structural protein 1 (NS1) to differentiate infections caused by WN and USU viruses. The NS1 protein is secreted during acute infection, and NS1-specific antibodies have been reported to be less cross-reactive than those against E. Using sera from individuals with a confirmed WN or USU virus infection, it was possible to distinguish between the two virus infections with high accuracy, specifically when IgM and IgG results were combined. Full article

Fibrinogen (FIB), a key component of the coagulation cascade, is traditionally recognized for its role in hemostasis and tissue repair. However, due to its high plasma abundance and susceptibility to proteolytic cleavage during inflammation, it may also represent a previously unrecognized source of bioactive peptides. This study presents, for the first time, a comprehensive analysis of the antimicrobial, anti-inflammatory, and antiviral properties of six cationic antimicrobial peptides (AMPs) deriving from the C-terminal extremities of the three subunits of human fibrinogen (FIBα, FIBβ, and FIBγ), identified using a scoring function developed by our group. Antibacterial assays against Gram-positive and Gram-negative pathogens revealed different antimicrobial activity profile depending on their parent protein. Selected peptides displayed additive or synergistic effects when combined with conventional antibiotics or the thrombin-derived peptide (P)GKY20, highlighting their potential for combination therapies. Hemolytic assay confirmed the biocompatibility of fibrinogen-derived cryptic peptides with erythrocytes. Furthermore, the peptides significantly reduced LPS-induced nitric oxide release in murine macrophages Raw 264.7 cells, indicating anti-inflammatory activity. Notably, antiviral activity was observed against enveloped viruses (HCoV-229E and HSV-1) under various treatment conditions, while no activity was detected against the non-enveloped virus CVB3. Overall, these findings reveal human fibrinogen as a source of multifunctional cryptic peptides with broad-spectrum antimicrobial, antiviral, and immunomodulatory activities, supporting their potential as part of the innate immune system. Full article

The non-structural protein 1 (NS1) of dengue virus (DENV) plays a multifaceted role in viral pathogenesis and immune modulation. Although vaccine strategies have traditionally focused on neutralizing antibodies against the envelope (E) protein, recent evidence highlights the protective potential of anti-NS1 antibodies—particularly those that mediate Fc-dependent effector functions. These functions include antibody-dependent cellular cytotoxicity (ADCC), antibody-dependent cellular phagocytosis (ADCP), and complement-dependent cytotoxicity (CDC), which collectively bridge adaptive antibody responses with innate immune activation. However, the outcomes of anti-NS1 responses are context-dependent: certain antibody specificities confer protection, while others may contribute to immunopathology. In this review, I synthesize current evidence on the roles of anti-NS1 antibodies in modulating Fc receptor engagement, subclass-specific responses, glycosylation patterns, and their effector functions. Understanding these mechanisms is essential for guiding rational vaccine design and the development of antibody-based diagnostics and therapeutics. By integrating the findings from both innate and adaptive immunology, this review emphasizes the importance of NS1 as a multifunctional immune determinant in dengue virus infection. Full article

Dengue is a rapidly spreading mosquito-borne viral infection, with increasing reports of outbreaks globally. According to the World Health Organization (WHO), by 30 April 2024, over 7.6 million dengue cases were reported, including 3.4 million confirmed cases, more than 16,000 severe cases, and over 3000 deaths. As dengue remains endemic in many regions, there is a critical need for the development of new vaccines and manufacturing processes that are efficient, cost-effective, and capable of meeting growing demand. In this study, we explore an alternative process development pathway for the future manufacturing of a dengue vaccine, utilizing Komagataella phaffii (Pichia pastoris) as the host organism, one of the most promising candidates for the expression of heterologous proteins in vaccine development. It combines the speed and ease of highly efficient prokaryotic platforms with some key capabilities of mammalian systems, making it ideal for scalable and cost-effective production. The key outcomes of our research include (i) demonstrating the versatility of the Komagataella phaffii platform in the production of dengue viral-like particles (VLPs); (ii) optimizing the culture process using Design of Experiments (DoE) approaches in small-scale bioreactors; (iii) developing a novel purification platform for enveloped VLPs (eVLPs), and (iv) establishing alternative biophysical characterization methods for the dengue vaccine prototype. These findings provide a promising foundation for efficient and scalable production of dengue vaccines, addressing both technical and operational challenges in vaccine manufacturing. Full article

The cellular envelope of Gram-negative bacteria is a space where processes that are extremely important for the proper functioning of bacteria and determining their virulence take place. The extracytoplasmic protein quality control system, which includes chaperones, protein-folding catalysts, and proteases, is responsible for maintaining homeostasis in this cellular compartment. This system has been well studied in the model bacterium Escherichia coli, but little is known about its function in other bacteria. In bacteria evolutionarily distant from Enterobacteriaceae, the protein quality control system appears to function differently. For example, in the phylum Campylobacterota, a number of homologs of folding factors and proteases, whose functions are important for maintaining homeostasis in the periplasm of E. coli, have not been identified. Instead, there are quality control components that have no similar counterparts in the Enterobacteriaceae. In this review, we present the current state of knowledge on the extracytoplasmic protein quality control system in the model Campylobacterota, C. jejuni and H. pylori. Full article

Schmallenberg virus (SBV) is a negative-sense RNA virus transmitted by insect vectors, causing arthrogryposis-hydranencephaly syndrome in newborn ruminants. Since its discovery in Germany and the Netherlands in 2011, SBV has rapidly spread across multiple European countries, resulting in significant economic losses in the livestock industry. With the increasing global animal trade and the expanded range of insect transmission, the risk of SBV introduction into non-endemic regions is also rising. As the gold standard for serological testing, the virus neutralization test (VNT) is crucial for tracking the spread of SBV and evaluating the efficacy of vaccines. However, in non-endemic regions, the lack of local viral strains and the biosafety risks associated with introducing foreign strains pose challenges to the implementation of VNT. In this study, we employed reverse genetics techniques using vesicular stomatitis virus (VSV) to substitute the VSV G protein with the envelope glycoproteins of SBV, thereby successfully generating and rescuing the recombinant virus rVSVΔG-eGFP-SBVGPC. The recombinant virus was then thoroughly characterized in terms of SBV Gc protein expression, viral morphology, and growth kinetics. Importantly, rVSVΔG-eGFP-SBVGPC exhibited SBV-specific cell tropism and was capable of reacting with SBV-positive serum, enabling the measurement of neutralizing antibody titers. The results suggest that this recombinant virus can serve as a feasible alternative for SBV neutralization tests, with promising potential for application in serological screening and vaccine evaluation. Full article