Search Results (625)

Background. The highly mutable influenza virus causes severe annual infections worldwide and results in substantial socioeconomic losses. The spread of infection could be effectively controlled by cross-protective vaccines and universal diagnostic test systems based on the nucleoprotein (NP) as one of the most conserved viral antigens. However, NP also undergoes slow evolutionary changes, and little is known about the influence of these mutations on its antigenicity and immunogenicity. Methods. We expressed the full-length recombinant 6xHis-tagged NPs of ten evolutionary distant influenza A strains of different subtypes in E. coli BL21(DE3) cells and purified these proteins by immobilized metal affinity chromatography. The obtained antigens were identified by mass spectrometry and serological methods. NPs served as antigens for three immunizations of BALB/c mice (15 µg/animal at 14-day interval) and as capturing proteins in ELISA at 2 µg/mL, in order to study the effect of adaptive mutations on the antigenic and immunogenic properties of NPs. Results. A pronounced cross-reactivity of anti-NP antibodies induced in mice by immunization with different NPs was revealed. At the same time, we observed the differences in the humoral immunogenicity of NP, which are in line with the accumulation of evolutionarily driven NP mutations. In general, antibody affinity to heterologous NPs was reduced, indicating the differences in the specificity of anti-NP immunoglobulins, which may be caused by evolutionarily determined variability of immunogenic epitopes leading to the emergence of escape mutations. Conclusions. Overall, our results reflect the slightly evolving nature of the NP antigen, which influences the specificity spectrum of anti-NP antibodies and should be considered as a limitation for the development of NP-based cross-protective vaccines and test systems. Full article

Objective: The aim of this study was to characterize the epidemiological features and whole-genome characteristics of H5 subtype avian influenza viruses circulating in Jining City during 2024–2025, and to provide scientific evidence for avian influenza prevention and control. Methods: A total of 748 poultry-related environmental samples were collected in March, June, September, and December of 2024–2025. Reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) was used to detect influenza A virus and H5 subtype viral RNA. H5-positive samples were subjected to whole-genome sequencing and analyzed using bioinformatics tools. Results: Among the 748 samples, the positivity rate of influenza A virus was 16.04% (120/748), and that of the H5 subtype was 8.16% (61/748). The H5 positivity rate in 2025 (11.88%) was significantly higher than that in 2024 (5.37%). Higher positivity rates were observed in March and December compared to June and September. Twelve complete H5 genomes were obtained, including nine H5N1 and three H5N6 strains. All HA genes belonged to clade 2.3.4.4b. Key mutations related to antigenic drift, replication and adaptation were detected in multiple viral proteins. Conclusions: The positivity rate of H5 subtype avian influenza viruses in Jining City showed an increasing trend during 2024–2025, with higher prevalence in winter and spring. The circulating strains predominantly belonged to clade 2.3.4.4b. Antigenic drift-associated mutations in the HA protein were identified in some strains, which may affect vaccine matching. Enhanced surveillance of H5 viruses and regular evaluation of antigenic compatibility between vaccine and circulating strains are recommended to mitigate potential risks posed by viral genetic variation. Full article

Background/Objectives: Current prophylactic human papillomavirus (HPV) vaccines rely on major capsid proteins (L1). Although highly immunogenic, L1-based immunity is clade-restricted owing to the hypervariability of HPV strains across different geographic regions. This restricts cross-protection against diverse, localized, and non-vaccine viral strains circulating in specific areas, leaving these populations vulnerable to regional genotypes. Methods: We aimed to design a cross-protective vaccine tailored to local viral diversity through evolutionary and immunoinformatic analyses of circulating HPV strains in Thailand. Both major (L1) and minor (L2) capsid proteins were analyzed to evaluate selective evolutionary pressures, structural sequence conservation, and cross-strain promiscuity of predicted B- and T-cell epitopes using the IEDB database. The predicted immunogenic profile of the combined L1/L2 proteins was further assessed using in silico immune response simulations. Results: Evolutionary analysis confirmed that although the L1 protein is under strict purifying selection, it exhibits high regional interclade variability. L1-only epitopes demonstrated restricted cross-strain conservation, creating structural blind spots against divergent regional variants. The minor capsid protein (L2) harbored highly conserved dual-action core peptides that are evolutionarily conserved across multiple HPV type. Incorporation of conserved L2 regions alongside L1 sequences may broaden the predicted epitope coverage and help address limitations associated with L1 variability. The proposed multi-targeted L1/L2 construct therefore represents a computational framework for the development of candidate cross-reactive HPV vaccines relevant to circulating Thai genotypes. However, experimental validation remains necessary to determine immunogenicity, cross-neutralization potential, and protective efficacy. Conclusion: Our findings highlight these conserved HPV epitopes as potential targets for future development of next-generation cross-subtype prophylactic vaccines with broader population coverage. Full article

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (bla_CTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four bla_CTX-M subtypes were identified. bla_CTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the bla_CTX-M gene, and 96.29% of strains successfully transferred the bla_CTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of bla_CTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework. Full article

Background: Hemagglutinin (HA) is the primary surface protein of the influenza A virus, determining its subtype and antigenic properties. Traditional subtype classification methods rely on DNA or amino acid sequence analysis, which does not account for protein spatial folding. Methods: In this work, we propose EpitopeGNN—a graph neural network (GNN) that constructs a residue interaction network (RIN) from the 3D structure of HA and classifies the virus subtype. The model was trained on 249 structures from the Protein Data Bank (PDB), containing H1N1, H3N2, H5N1, and other subtypes. Results: After rigorous sequence redundancy reduction (92% identity), the model maintained 95–100% accuracy on non-redundant data, significantly outperforming sequence-only baselines (the best baseline achieved 85% for multi-class and 92.3% for binary classification). A significant correlation was found between the obtained structural embeddings and phylogenetic distances (r = 0.38, p < 0.001), confirming their biological relevance and opening opportunities for structural monitoring of virus evolution, as well as rapid analog searching for novel strains. Conclusions: We developed a new graph neural network that classifies influenza A virus subtypes directly from the 3D structure of hemagglutinin using residue interaction networks and physicochemical features, which can serve as a foundation for predicting influenza virus receptor specificity and epitope immunogenicity. Full article

H5 subtype avian influenza virus (AIV) can infect both chickens and ducks, leading to substantial economic losses. Nevertheless, certain strains cause silent infections in ducks. In this study, a goose-origin clade 2.3.4.4h H5N6 AIV was isolated, which caused high mortality in mixed-gender white leghorn chickens but no deaths in mixed-gender mallard ducks. After independent serial in vitro passage in duck embryo fibroblasts (DEFs) and in vivo passage in specific-pathogen-free (SPF) ducks, the DEF-passage 10 (P10) virus induced markedly higher mortality rates and viral loads in SPF ducks compared to the DEF-P1 virus and the original parental virus prior to passage. Similarly, the in vivo-passaged P3 and P4 viruses exhibited significantly higher mortality rates than the P1 virus in SPF ducks, with 100% mortality and markedly increased viral titers in the organs. A whole-genome SNP analysis identified seven high-frequency mutations in the M1, NA and NS1 proteins. The NS1-F161L substitution virus exhibited significantly increased mortality rates, viral loads in multiple tissues, and a robustly induced innate immune response in ducks. Furthermore, dynamic evolutionary variations in the NS1 protein among global H5 avian influenza viruses revealed that the NS1-F161L substitution became dominant in clade 2.3.4.4b viruses in 2021 and subsequent years. Collectively, our findings demonstrate that host-driven adaptation can rapidly increase the pathogenicity of H5N6 AIVs in ducks and identify NS1-F161L as a critical virulence marker. These results offer novel insights relevant to the molecular surveillance, virulence prediction, and risk assessment of circulating H5 AIVs in waterfowl. Full article

Hepatitis E virus (HEV) is a zoonotic pathogen of global concern that circulates in both domestic and wild swine populations. Understanding its presence and dynamics in wildlife reservoirs is crucial for assessing spillover risks and designing One Health surveillance strategies. This study investigated the occurrence, genetic diversity, and evolutionary relationships of HEV in wild boars from mainland Portugal. A total of 120 animals from seven districts were tested, with HEV RNA detected in four cases (3.3%), all from the Évora district near the Spanish border. One positive sample was successfully sequenced, and phylogenetic analysis based on the complete genome classified it within the HEV-3m subtype, clustering with predominantly human-derived sequences from Spain and France, which highlights its zoonotic potential. A second phylogenetic analysis based on a partial genomic fragment, including sequences from domestic pigs in Portugal, revealed the co-circulation of subtypes 3e, 3f, and 3m without clear spatial or temporal patterns. Phylogeographic analysis suggested that the identified strain was most likely introduced from Spain, supporting the hypothesis of cross-border transmission through wild boar movement. No recombination events were detected in the sequence obtained in this study. These findings provide the first molecular evidence of HEV-3m circulation in wild boars in Portugal, offering valuable insight into the HEV strain circulation in European wildlife populations. The zoonotic potential of HEV and the likelihood of interspecies transmission highlight the need for coordinated cross-border surveillance and integrated One Health strategies. Full article

Birds serve as the primary natural reservoirs for avian influenza viruses (AIVs), harboring nearly all known AIV subtypes. The seasonal migratory movements of wild birds play a significant role in the transmission and dissemination of AIVs. Jianhu Lake in Dali, Yunnan Province, serves as a vital congregation point along avian migratory routes, providing an ideal habitat for birds. In this study, a total of 619 avian samples were collected from the Jianhu area, from which four H6N2 subtype AIV strains were successfully isolated. Among these, A/grey heron/Jianhu/JH-89/2024 (hereafter referred to as JH-89) and A/grey heron/Jianhu/JH-91/2024 (JH-91) were isolated from grey herons (Ardea cinerea); A/mareca penelope/Jianhu/JH-2-11/2025 (JH-2-11) from a Eurasian wigeon (Mareca penelope); and A/duck/Jianhu/JH-1-1/2025 (JH-1-1) from a domestic duck (Anas platyrhynchos domesticus). Genomic analyses revealed that these four H6N2 isolates belong to the Eurasian lineage, with all eight gene segments originating from complex reassortment events among diverse Asian isolates. In vitro assays demonstrated that the representative strain JH-2-11 replicated efficiently in various human- and animal-derived cell lines. In vivo infection models revealed that, without prior adaptation, the JH-2-11 strain successfully infected BALB/c mice, resulting in suppressed body weight gain and severe pathological lesions in the respiratory tract (nasal turbinates, trachea, and lungs), without causing mortality or extrapulmonary dissemination. Collectively, although these H6N2 viruses evolve primarily within avian hosts, they exhibit potential for mammalian adaptation and require continuous epidemiological monitoring. Full article

Background/Objectives: Klebsiella pneumoniae (K. pneumoniae) is a leading cause of serious hospital-acquired and community-acquired infections, with limited treatment options, especially for immunocompromised and critically ill patients. No licensed vaccine is currently available. The FimA antigen, a key fimbrial subunit essential for bacterial adhesion and invasion, represents a promising vaccine target. However, little is known about the immunodominant antibody responses against invasive K. pneumoniae. This study aimed to evaluate the immunogenicity and protective efficacy of recombinant FimA protein, to fine-map its immunodominant linear B-cell epitopes, and to assess the individual and combined protective capacity of these epitopes against both standard and clinically isolated K. pneumoniae strains. Methods: A murine model of lethal K. pneumoniae challenge was used. Recombinant FimA protein was administered to evaluate immunogenicity and protective efficacy. Immunodominant linear B-cell epitopes were identified by overlapping peptide ELISA using immune antisera. The identified epitopes were synthesized and conjugated to keyhole limpet hemocyanin (KLH). Mice were immunized with individual epitope-KLH conjugates or a mixture of all four, then challenged with the standard strain ATCC700721 or with multiple clinical isolates of distinct multilocus sequence types (MLST). Epitope-specific antibody responses (total IgG and IgG subclasses) and survival rates were measured. Results: Immunization with full-length recombinant FimA conferred 90% protection against lethal challenge with the standard strain ATCC700721 and induced robust IgG1-dominant antibody responses. Four novel immunodominant linear B-cell epitopes were identified: FimA_97–114, FimA_103–120, FimA_109–126, and FimA_145–160. Structural mapping revealed that the first three epitopes reside within the α-helical region, while FimA_145–160 is located in the β-sheet domain. These epitopes are highly conserved, exhibiting 100% sequence identity across 36 diverse K. pneumoniae strains. Among individual epitope-KLH conjugates, FimA_109–126-KLH induced the highest epitope-specific antibody titers, followed by FimA_103–120-KLH. Immunization with a mixture of all four epitope-KLH conjugates elicited significant cross-protection against multiple clinical isolates, achieving survival rates of 60%, 50%, 50%, and 40% against strains 10CYZ, 13LGY, 19ZXQ, and 22CZY, respectively. Protective immunity was primarily associated with IgG1 subtype responses. Conclusions: This study provides the first fine-mapping and protective evaluation of immunodominant linear B-cell epitopes within K. pneumoniae FimA. The identification of highly conserved, functionally relevant B-cell epitopes and the demonstration of cross-protection conferred by a multi-epitope formulation underscore the potential of FimA-based epitope-driven vaccines. These findings offer a promising strategy for the development of broadly protective vaccines against K. pneumoniae infections. Full article

Avian influenza infections cause substantial economic losses in the poultry industry and raise public health concerns due to viral adaptation and cross-species transmission. The frequent antigenic drift of influenza viruses further complicates the prevention and treatment of avian respiratory infections. In this study, we generated high-affinity heavy-chain variable domain (VHH) nanobodies from naïve alpaca/camelid VHH libraries using phage display combined with H9N2 influenza A virus (IAV)-infected Madin-Darby Canine Kidney (MDCK) cells. Based on binding affinity and neutralization potential, we identified seven hemagglutinin (HA)-specific and two neuraminidase (NA)-specific VHHs. Molecular docking predicted the interaction sites of HA-specific VHHs (L1-2, L1-4, A5) and NA-specific VHHs (L1-3, L2-2), providing mechanistic insights. Notably, the three HA-specific VHHs (L1-2, L1-4, A5) showed cross-reactivity to representative HA subtypes (H1, H3, and influenza B), indicating recognition of conserved epitopes across divergent influenza strains. For the first time, these camelid nanobodies were fused to the chicken IgY Fc domain, and the expression cassette was integrated into the Saccharomyces cerevisiae genome, achieving a secretion yield of 15–20 mg/L of VHH-Fc antibodies. Experimental validation confirmed that the three HA-specific VHHs-Fc constructs effectively blocked viral infection, while the two NA-specific VHH-Fc constructs (L1-3, L2-2) inhibited NA activity, demonstrating the functional efficacy of the yeast-secreted VHH–IgY Fc platform. This novel IgY Fc fusion approach offers a scalable platform with enhanced stability, extended circulation potential, and applicability in poultry. Full article

Background/Objectives: This retrospective study investigates the prevalence and distribution of HCV genotypes among 233 genotyped patients from the Epirus region of Northwestern Greece from 2014 to 2024. Methods: Genotypes were detected by molecular diagnostic assays, and their association with demographic parameters and viral load was analyzed. Results: The most prevalent subtype was 3a (50.2%), especially among younger and male patients, followed by subtypes 1b and 1a. A statistically significant association was found between genotype and both age and sex, while genotype distribution did not significantly differ by national origin. Furthermore, subtype 6c-I was found only in a non-native case, suggesting a possible introduction of this rare strain. Viral load showed no significant difference by sex, genotype, or age group. A notable decline in HCV cases was documented during the COVID-19 pandemic, underscoring the impact of the public health crisis on HCV diagnosis. Despite the decreasing need for genotyping in the direct-acting antiviral (DAA) era, our findings support the continued molecular surveillance of circulating HCV strains. Conclusions: This is the first study to longitudinally assess HCV genotype dynamics over a full decade (2014–2024) in the Epirus region of Northwestern Greece, capturing trends during the COVID-19 era and documenting the emergence of rare genotypes. It contributes to the evolving knowledge of HCV epidemiology in Southeastern Europe. Full article

Objectives: To characterize urodynamic findings after lower-level spinal cord injury (LSCI) and to evaluate a new pressure-based classification framework—the bladder–sphincter dyscoordination syndrome (BSDS)—for describing voiding patterns. We also introduce a descriptive “neurogenic bladder outlet obstruction” (NBOO) phenotype for straining-dependent voiding difficulty. Methods: We retrospectively analyzed the first urodynamic studies (December 2020–August 2024) in 81 men with LSCI (injury at T10 or below). Key urodynamic measures included detrusor and intravesical pressures during filling and voiding, bladder volumes (first desire to void and capacity), compliance, maximum flow rate (Q_max), post-void residual (PVR), voiding efficiency, and the ratio of detrusor to abdominal pressure rise (ΔPdet/ΔPabd). We compared cases with detrusor overactivity (DO) versus those without DO. Among those with voiding discoordination, we distinguished classical detrusor–sphincter dyssynergia (DSD) from a proposed NBOO phenotype (characterized by abdominal straining pressure ≥ 40 cmH₂O, detrusor pressure < 20 cmH₂O, incomplete emptying, and no anatomic obstruction). We further classified discoordination cases using the BSDS framework into four subtypes—dual high-pressure (DHP), detrusor-muscle predominant (DMP), dual low-pressure (DLP), and abdominal-pressure predominant (APP)—based on reference pressure thresholds (detrusor 20 cmH₂O; abdominal 40 cmH₂O). Results: Patients with DO (43.2%) showed significantly higher detrusor pressures during filling (at first desire to void and at capacity) and a lower first desire volume than non-DO patients, while maximum capacity was similar (p = 0.105). During voiding, DO cases had lower PVR and higher emptying rates, although the detrusor-vs-abdominal pressure contribution (ΔPdet/ΔPabd) was comparable between groups. Among 63 patients with voiding discoordination, 32 (50.8%) met NBOO criteria; these NBOO cases exhibited lower detrusor and intravesical voiding pressures but worse emptying (higher PVR) compared to classical DSD cases. Overall, 76 of 81 patients (93.8%) fit within the BSDS classification—distributed as 22 DHP, 13 DMP, 15 DLP, and 26 APP patterns. Conclusions: The BSDS framework (and the NBOO descriptor when conventional indices cannot be applied) offers a novel way to describe voiding patterns after LSCI. It links urodynamic observations to potential management strategies (by identifying whether the bladder or outlet is the primary issue). Prospective studies are needed to validate this framework against outcomes such as upper tract integrity, continence, and dependence on catheterization. Full article

Johne’s disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is endemic in Saudi Arabia and contributes to substantial production losses in small-ruminant herds. This study investigated MAP infection in 388 locally raised small ruminants (151 sheep and 237 goats) using IS900 real-time PCR (qPCR) on fecal samples and indirect ELISA on serum samples. Ziehl–Neelsen (ZN) staining and pathological assessment were applied as supportive tools in necropsied cases. Overall, qPCR detected MAP DNA in 135/388 animals (34.8%), with higher positivity in goats (100/237; 42.1%) than in sheep (35/151; 23.1%). ELISA detected MAP antibodies in 120/388 animals (30.9%), including 90/237 goats (37.9%) and 30/151 sheep (19.8%). Based on clinical examination (presence/absence of clinical signs), qPCR-positive animals were categorized as subclinical (n = 15; 10 goats and 5 sheep) or clinically progressed (n = 120; 90 goats and 30 sheep). Gross and histopathological findings were assessed in a necropsied subset (n = 20; 10 subclinical and 10 clinically progressed), revealing mild focal granulomatous enteritis with scant acid-fast bacilli in subclinical cases and diffuse lepromatous-type granulomatous lesions with abundant bacilli in clinically progressed animals. Genotyping and subtyping were performed on tissue-derived DNA from six necropsied cases using DMC, IS900, and F57 targets, and IS900 sequencing confirmed the circulation of both Type C/II and Type S/I MAP strains. Collectively, these findings demonstrate widespread MAP infection among small ruminants in Saudi Arabia, with higher detection rates and more pronounced pathology in goats, and highlight the genetic heterogeneity of circulating MAP strains. Full article

Human Immunodeficiency Virus Type 1 (HIV-1), the causative agent of the acquired immune deficiency syndrome (AIDS), originated from zoonotic transmissions of simian immunodeficiency viruses (SIVs) infecting African great apes, following complex cross-species transmission events and virus–host co-evolution. These processes were accompanied by multiple viral adaptations, particularly within structural and accessory genes, enabling evasion of host restriction factors and long-term viral persistence. In 1988, an antisense open reading frame (ORF) overlapping the env gene was proposed and subsequently confirmed by the identification of antisense transcripts and the antisense protein (ASP). An “intact” ASP ORF (defined as >150 codons) is predominantly conserved in pandemic HIV-1 group M viruses and shows evidence of positive selection, suggesting a selective advantage. Increasing evidence supports the hypothesis that the asp gene emerged de novo during the evolution of group M and contributed to viral adaptation and global spread in humans. This review combines a narrative review of the literature with original in silico analyses of HIV-1 and SIV sequences retrieved from the Los Alamos National Laboratory database. We systematically reassessed the distribution, length variability and conservation of the ASP ORF across HIV-1 groups (M, N, O, P), subtypes, circulating recombinant forms (CRFs), unique recombinant forms (URFs) and related SIV lineages. Our updated analyses confirmed the strong association between the presence of an “intact” ASP ORF and pandemic HIV-1 group M lineages, while revealing rare but notable antisense ORFs in selected SIVcpz and SIVgor strains. By integrating evolutionary, epidemiological and sequence-based evidence, we aim to clarify the origin and maintenance of the ASP ORF and to contextualize its emergence within the broader framework of overlapping gene evolution, de novo gene birth and the selective pressures shaping viral fitness and pandemic potential. Full article

Background/Objectives: Klebsiella pneumoniae is one of the major causes of severe infections in cancer patients. The rapid and accurate typing of isolates is essential for tracking transmission routes and implementing infection control measures. The IR Biotyper, an automated system based on Fourier transform infrared (FT-IR) spectroscopy, enables fast cluster analysis with reduced cost and turnaround time. The aim of this paper was to compare typing results obtained by the IR Biotyper and pulsed-field gel electrophoresis (PFGE) for the epidemiological surveillance of K. pneumoniae in an oncology hospital. Methods: A total of 137 isolates collected between 2020 and 2023 from both colonization and infection were retrospectively analyzed using PFGE and the IR Biotyper. The discriminatory power of both methods and their concordance were assessed. Results: Both methods demonstrated high discriminatory power. PFGE classified the strains into 59 distinct types (96 including subtypes), while the IR Biotyper differentiated 70 FT-IR types. Concordance between the methods was moderate (adjusted Wallace coefficient: 0.515). PFGE type B was the most prevalent, comprising 43 isolates and subdivided into 16 subtypes. The most frequent FT-IR types were 16 (17 isolates), 10 (8 isolates), and 14 (5 isolates), all corresponding to PFGE type B with different subtypes. The IR Biotyper successfully distinguished isolates within the long-standing PFGE type B clone. Conclusions: The IR Biotyper demonstrated good discriminatory capacity and was able to differentiate isolates within a dominant PFGE clone, supporting its potential as a rapid tool for monitoring clonal spread in oncology settings. However, the moderate concordance with PFGE highlights that further studies are needed to optimize performance and confirm its role as a complementary method for routine hospital epidemiological surveillance. Full article