Search Results (729)

H5N1 Influenza A virus continues to pose a significant zoonotic threat, with increasing evidence of interspecies transmission and genetic adaptation. Previous studies primarily focused on avian or human isolates, with limited comprehensive analysis of H5N1 evolution across multiple mammalian hosts. Existing molecular surveillance often lags behind viral evolution; this study underscores the necessity for real-time monitoring of ongoing mutations affecting pathogenicity and transmissibility. Our goals are (1) to retrieve and analyze HA, NP and NA gene sequences of H5N1 Influenza A virus from diverse hosts, including humans, poultry and multiple mammalian species, to assess genetic diversity and evolutionary patterns and (2) to evaluate positive selection sites across the three major genes (HA, NP and NA) to determine adaptive mutations linked to host adaptation and viral survival. To achieve these goals, in this study, we considered (78 HA), (62 NP) and (61 NA) gene sequences from diverse hosts, including humans, poultry and multiple mammalian species, retrieved from the NCBI database. Phylogenetic analysis revealed distinct clade formations, indicating regional spread and cross-species transmission events, particularly from avian sources to mammals and humans. Selection pressure analysis identified positive selection across all three genes, suggesting adaptive mutations contributing to host adaptation and viral survival. Homology modeling and molecular dynamics simulations were performed to generate high-quality structural models of HA, NP and NA proteins, which were subsequently validated using multiple stereochemical parameters. Domain analysis confirmed conserved functional motifs, while protein–ligand docking demonstrated stable interactions at conserved binding sites, despite observed residue substitutions in recent isolates. Earlier research concentrated on HA alone; this study integrates HA, NP and NA genes for a broader understanding of viral evolution and adaptation. These findings highlight ongoing evolutionary changes in H5N1 genes that may enhance viral adaptability and pathogenicity, underscoring the need for continuous molecular surveillance and updated antiviral strategies. Full article

The 2022 global mpox outbreak, caused by clade IIb of the monkeypox virus (MPXV), prompted emergency use authorisation of the Modified Vaccinia Ankara–Bavarian Nordic (MVA-BN) vaccine, previously approved for smallpox prevention. Understanding immune responses to the MVA-BN vaccine is critical to inform both current and future mpox vaccine policy, particularly amid reports of breakthrough infections in vaccinated persons, uncertainty about the durability of vaccine-induced protection, and the emergence of further outbreaks of mpox from different viral clades, including the clade I-driven public health emergency of international concern. MVA-BN elicits binding and neutralising antibody, memory B cells, and T cell responses. Immune responses vary by host factors, prior orthopoxvirus exposure, and dosing regimens. While seroconversion is generally robust, circulating antibody titres often wane rapidly, particularly in vaccinia-naïve and/or immunocompromised individuals, including people with HIV. Vaccine-induced neutralising antibody responses to MPXV are frequently lower than to vaccinia virus, and their role in protection remains ill-defined. In contrast, T cell responses appear more sustained and may support long-term immunity in the absence of persistent antibody titres. This narrative review synthesises current evidence on the immunogenicity and durability of MVA-BN vaccination, highlights challenges in assay interpretation, and outlines key research priorities, including the need to explore correlates of protection, booster strategies, and next-generation vaccine design. Full article

Background/Objectives: The continued evolution and cross-species transmission of clade 2.3.4.4b H5Nx highly pathogenic avian influenza (HPAI) viruses underscores the need for broadly protective vaccines in swine, a key intermediary host. This study aimed to evaluate systemic and mucosal immune responses elicited by adenoviral-vectored (Ad) vaccines encoding a centralized consensus hemagglutinin antigen (H5CC) in mice and swine. Methods: We constructed H5CC-based vaccines that were delivered using replication-defective (Ad5 and Ad6) and replication-competent (Ad28 and Ad48) human adenoviral vectors. Using a serotype-switched prime-boost strategy, vaccines were delivered intramuscularly (IM) or intranasally (IN) in mice and swine. We determined humoral, mucosal, and cell-mediated immune responses by hemagglutination inhibition (HI), microneutralization assay (MNA), ELISA, and IFN-γ ELISpot. Protective efficacy was evaluated by lethal H5N1 challenge in mice. Results: All vaccine strategies and routes induced significant levels of anti-H5 immunity. Ad5/Ad6 IM immunization elicited strong systemic IgG and MNA titers and robust T cell responses. IN delivery with Ad5/Ad6 induced superior mucosal IgA levels in lungs and nasal secretion. In swine, Ad5/Ad6 IM conferred the highest MNA titer and T cell responses, while the IN route enhanced mucosal IgA. The Ad28/Ad48 vaccines induced immunity in a similar pattern as compared to the Ad5/Ad6 strategy, but to a slightly lesser degree, in general. The commercial H1/H3 swine influenza vaccine failed to elicit cross-protective immunity. All H5CC vaccinated mice survived lethal H5N1 challenge without weight loss. Conclusions: Adenoviral-vectored H5CC vaccines elicit broad, cross-clade immunity with route-dependent immune profiles. IM vaccination is optimal for systemic and cellular responses, while IN delivery enhances mucosal immunity. These findings support the advancement of adenoviral platforms for influenza control in swine and pandemic preparedness. Full article

Shiga toxin-producing Escherichia coli (STEC) are genetically diverse foodborne pathogens of major global public health concerns. Serogroup-level identification is critical for effective surveillance and outbreak control; however, it is often challenged by STEC’s genome plasticity and frequent recombination. In this study, we employed a standardized pangenomic pipeline integrating Roary ILP Bacterial Core Annotation Pipeline (RIBAP) and Panaroo to analyze 160 complete, high-quality STEC genomes representing eight major serogroups at a 95% sequence identity threshold. Candidate serogroup-specific markers were identified using gene presence/absence profiles from RIBAP and Panaroo. Our analysis revealed several high-confidence markers, including metabolic genes (dgcE, fcl_2, dmsA, hisC) and surface polysaccharide-related genes (capD, rfbX, wzzB). Comparative pangenomic evaluation showed that RIBAP predicted a larger pangenome size than Panaroo. Additionally, some genomes from the O104:H1, O145:H28, and O45:H2 serotypes clustered outside their expected clades, indicating sporadic serotype misplacements in phylogenetic reconstructions. Functional annotation suggested that most candidate markers are involved in critical processes such as glucose metabolism, lipopolysaccharide biosynthesis, and cell surface assembly. Notably, approximately 22.9% of the identified proteins were annotated as hypothetical. Overall, this study highlights the utility of pangenomic analysis for potential identification of clinically relevant STEC serogroups markers and phylogenetic interpretation. We also note that pangenome analysis could guide the development of more accurate diagnostic and surveillance tools. Full article

Background: While enteroviruses (EVs) are recognized causes of diverse illnesses, little is known about the epidemiology and molecular characteristics of uncommon enterovirus C (EV-C) types, including EV-C104, EV-C105, and EV-C109. Methods: We conducted genomic surveillance of EVs at the Johns Hopkins Health System between 2018 and 2024 (a total of 3715 samples), identifying EV-C104, EV-C105, and EV-C109 in respiratory samples. VP4-VP2 and whole-genome sequencing were used to assess genetic diversity and intra-host evolution. Results: Five EV-C105 infections were identified primarily in pediatric patients, presenting with a range of clinical features including fever, gastrointestinal symptoms, and cerebellitis. Prolonged EV-C104 and EV-C109 infections were identified in two immunocompromised adults. EV-C104 persisted for over five months and showed evidence of viral genomic changes (intra-host evolution). EV-C109 was detected over a four-month period. Phylogenetic analysis revealed a novel EV-C105 clade (C3) closely related to recent USA strains. EV-C104 genomes aligned with genotype B sequences from the USA and Europe, while EV-C109 sequences were similar to 2014–2015 strains from the Netherlands. Conclusions: These findings highlight the emergence, persistence, and genetic evolution of uncommon EV-C types in Maryland, especially among immunocompromised hosts, emphasizing the importance of continued genomic surveillance and clinical correlations. Full article

Citrus tristeza virus (CTV) is an important pathogen threatening the global citrus industry, but its evolution and transmission mechanism in wild citrus has not been clarified. Most of the existing studies are based on CTV-specific gene fragments, lacking genome-wide analysis. There is especially a lack of understanding of CTV transmission dynamics in wild citrus, which needs further investigation. In this study, wild citrus samples from three provinces of China were collected, virus genome data were obtained by high-throughput sequencing (HTS) technology and combined with public database data, and Bayesian phylogeographic inference was used to analyze virus composition characteristics in wild citrus, as well as the population genetic structure, temporal dynamic evolution, and spatial transmission mode of CTV. The results showed that Yunnan wild citrus samples contained the most abundant virus components, including CTV, Citrus Exocortis Viroid (CEVd), Citrus associated Ampelovirus 1 (CaAV-1), and Citrus Virus B (CiVB), while Jiangxi and Hunan samples only contained CTV and CEVd, with all samples showing mixed infection. Phylogenetic analysis showed that nine wild citrus CTV isolates were scattered in different evolutionary clades, and only 9.27% of genetic variation existed between the populations, while 90.72% of genetic variation existed within the populations, indicating little effect of geographic isolation on gene flow. The time to the most recent common ancestor (tMRCA) of CTV was estimated at 1360 CE, with subsequent divergence into two lineages, with population size stabilizing after a rapid increase in 1980–1990. Asia has been identified as the central source of CTV’s global spread, with key migration events including Asia to North America (1746), Asia to Oceania (1829), and Asia to South America (1965), coinciding with global maritime trade and the expansion of the citrus industry. Full article

Over the decades, cattle have not been considered primary hosts for influenza A viruses (IAV), and their role in influenza epidemiology has been largely unrecognized. While bovines are known reservoirs for influenza D virus, the recent emergence of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in U.S. dairy cattle marks an alarming shift in influenza ecology. Since March 2024, this virus has affected thousands of dairy cows, causing clinical signs such as fever, reduced feed intake, drastic declines in milk production, and abnormal milk appearance. Evidence suggests that the virus may be replicated within mammary tissue, raising urgent concerns about milk safety, foodborne transmission, and occupational exposure. This review highlights the unprecedented expansion of viruses into bovine populations, exploring the potential for host adaptation, and interconnected roles of pets, peridomestic animals, and human exposure within shared environments. The potential impacts on dairy production, food safety, and zoonotic spillover highlight the urgent need for integrated One Health surveillance to stay ahead of this evolving threat. Full article

The presently used vaccines do not offer solid immunity/protection against the currently circulating strains of the H5N1 viruses. We aim to design a pan-H5N1 vaccine that protects birds against the presently circulating clade 2.3.4.4b in chickens. We used AI tools, including epitope mapping, molecular docking, and immune simulation, to design a multiepitope DNA vaccine including the top-ranked B and T cell epitopes within four major proteins (HA, NA, NP, and M2) of H5N1 clade 2.3.4.4b. We selected the top-ranked 12 epitopes and linked them together using linkers. The designed vaccine is linked to IL-18 as an adjuvant. The molecular docking results showed a high binding affinity of those predicted epitopes from the MHC I and MHC II classes of molecules with chicken alleles. The immune simulation results showed that the designed vaccine has the potential to stimulate the host immune response, including antibody and cell-mediated immunity in chickens and other birds. We believe this vaccine is going to be a universal vaccine that offers good protection against HPAI-H5N1 clade 2.3.4.4b. We are reporting the successful molecular cloning of a recombinant multiepitope-based vaccine spanning some key epitopes within some key proteins of the currently circulating H5N1 clade 2.3.4.4b. These designed vaccines could be a great positive impact on the protection of birds and various species of animals, as well as humans, against the HP-H5N1 influenza virus. Further studies are required to validate this vaccine candidate in chickens. Full article

The genus Raiamas currently comprises 18 valid species, only 2 of which occur in Asia; the remaining 16 are endemic to Africa. Raiamas harmandi was originally described by Sauvage in 1880 as Bola harmandi, which is distributed in the Great Lakes, Cambodia, the Mekong River Basin. It was considered a synonym of R. guttatus by later researchers. In this study, we examined 49 Raiamas individuals from the Mekong, Irrawaddy, and Salween river basins, recording both meristic counts and morphometric measurements. Based on the morphological evidence, we revised the taxonomy of Raiamas in the Mekong River Basin, confirming R. harmandi as a valid species and providing a comprehensive redescription. Raiamas harmandi can be distinguished from R. guttatus mainly by having more predorsal scales (25–28 vs. 21–23) and a different color pattern on the lateral body. Utilizing a total of 44 aligned COI and Cyt b sequences—including eight newly sequenced individuals of Raiamas from three river basins—we reconstructed its phylogenetic relationships. The analysis strongly supported four R. harmandi individuals from the Mekong River Basin forming a distinct clade, which was the sister to the clade comprising five R. guttatus individuals from the Irrawaddy and Salween river basins. Genetic distances between R. harmandi and R. guttatus ranged from 14.0 to 14.9% for COI and 16.1 to 17.0% for Cyt b. Distributionally, R. harmandi occurs throughout the Mekong River Basin, as evidenced by combined voucher specimens and molecular sequence data. Full article

Background: The Dirigent (DIR) gene family is pivotal for lignin polymerization and stress adaptation in plants, yet its systematic characterization in Sorghum bicolor (S. bicolor), a critical bioenergy crop, remains underexplored. Methods: Leveraging the S. bicolor genome database, we conducted a genome-wide identification, phylogenetic classification, and expression profiling of the DIR gene family. Evolutionary dynamics, gene structure variations, promoter cis-regulatory elements, and spatiotemporal transcriptome patterns were analyzed using bioinformatics and experimental validation (RT-qPCR). Results: A total of 53 SbDIR genes were systematically identified, exhibiting uneven chromosomal distribution. Phylogenetic analysis clustered them into five clades (DIR-a, DIR-b/d, DIR-c, DIR-e, DIR-f), with subfamily-specific exon number variations suggesting functional divergence. Evolutionary studies revealed tandem duplication (TD) as the primary driver of family expansion, accompanied by strong purifying selection. Promoter analysis highlighted abundant hormone- and stress-responsive cis-elements. Tissue-specific RNA-seq data revealed root-enriched expression of SbDIR2/4/18/39/44/53, implicating their roles in root development. Notably, SbDIR39 and SbDIR53 were significantly upregulated (2.8- and 5-fold, respectively) under 150 mM NaCl stress, underscoring their stress-responsive functions. Conclusions: This study provides the first comprehensive atlas of the DIR gene family in S. bicolor, elucidating its evolutionary mechanisms and tissue-specific/stress-induced expression profiles. Key candidates (SbDIR39/53) were identified as promising targets for molecular breeding or CRISPR-based editing to enhance stress resilience in S. bicolor. These findings lay a foundation for translating genomic insights into agronomic improvements. Full article

Kobuvirus is a new genus of viruses in the Picornaviridae family causing diarrhea in animals. Porcine kobuvirus (PKV) is an important pathogen with a high rate of infection in pig herds. In this study, a total of 10,990 fecal swabs and tissue samples were collected from different areas of Guangxi province in southern China during 2021–2025 and then tested for PKV using RT-qPCR. The results showed a 19.19% (2109/10,990) PKV positivity rate. Sixty-two PKV-positive samples, which were selected according to sampling regions, sampling seasons, and detection Ct values, were used for PCR amplification and gene sequencing. A sequence comparison showed that the nucleotide and amino acid identities of VP1, 2B, and 3D genes were 78.6–99.5% and 83.5–100%, 77.7–99.8% and 80.9–100%, and 90.9–99.8% and 94.9–99.9%, respectively, indicating that the 3D gene was more conserved than the VP1 and 2B genes. The phylogenetic trees based on these three genes revealed that the PKV VP1 gene sequences from different countries could be classified into two groups (Groups I and II), and the PKV VP1 gene sequences obtained from Guangxi province were distributed in Groups I and II and formed independent clades. The 2B and 3D gene sequences could also be classified into two groups (Groups I and II). Bayesian analysis indicated a state of population growth for PKV strains from the time of their discovery until 2009, at which point it began to decline. Amino acid sequence analysis of the VP1 gene identified mutations and insertions in the obtained PKV strains. Recombinant analysis showed that no recombinant event was found in the VP1, 2B, and 3D genes of the obtained strains. The results indicated the geographically specific inheritance and variation in PKV, provided more information on the prevalence and genetic evolution of PKV in Guangxi province, Southern China, and emphasized the importance of regularly monitoring genetic variation in PKV for better comprehension of PKV. Full article

The GLABROUS1 Enhancer Binding Protein (GeBP) gene family plays a crucial role in plant growth, development, and stress responses. In this study, 28 GeBP genes were identified in Brassica oleracea using HMMER and validated through multiple conserved domain databases. A phylogenetic tree was constructed based on the GeBP protein sequences from B. oleracea, Arabidopsis thaliana, Brassica rapa, and Brassica napus, dividing them into four evolutionary clades (A–D), which revealed a close evolutionary relationship within the genus Brassica. Conserved motif and gene structure analyses showed clade-specific features, while physicochemical property analysis indicated that most BoGeBP proteins are hydrophilic, nuclear-localized, and structurally diverse. Gene duplication and chromosomal localization analyses suggested that both segmental and tandem duplication events have contributed to the expansion of this gene family. Promoter cis-element analysis revealed a dominance of light-responsive and hormone-responsive elements, implying potential roles in photomorphogenesis and stress signaling pathways. Notably, the protein encoded by BolC01g019630.2J possesses both a transmembrane domain and characteristics of the Major Facilitator Superfamily (MFS) transporter family, and it is predicted to localize to the plasma membrane. This suggests that it may act as a molecular bridge between environmental signal perception and transcriptional regulation, potentially representing a novel signaling mechanism within the GeBP family. This unique feature implies its involvement in transmembrane signal perception and downstream transcriptional regulation under environmental stimuli, providing valuable insights for further investigation of its role in stress responses and metabolic regulation. Overall, this study provides a theoretical foundation for understanding the evolutionary patterns and functional diversity of the GeBP gene family in B. oleracea and lays a basis for future functional validation and breeding applications. Full article

Co-infection of Orientia tsutsugamushi and influenza A virus complicates diagnosis and treatment in endemic regions because of overlapping clinical features and potential synergistic inflammation. We describe a 68-year-old woman from Hainan, China, who presented with five days of high fever (39.2 °C), nonproductive cough, eschar formation, lymphadenopathy, cytopenias, elevated liver enzymes, and raised inflammatory markers. On the day of admission, influenza A was confirmed by rapid antigen test and Orientia tsutsugamushi IgM/IgG was detected via colloidal-gold immunochromatography, prompting concurrent oseltamivir and doxycycline therapy. Quantitative PCR on day 2 measured an Orientia tsutsugamushi load of 2.85 × 10⁴ copies/mL (Cq 28.86), and targeted next-generation sequencing on day 3 revealed a high H1N1pdm09 viral burden (>1 × 10⁶ copies/mL) with low-level human herpesvirus 1 co-detection. Nested PCR and Sanger sequencing assigned Orientia tsutsugamushi to the Karp_A lineage and influenza A to clade 6B.1A.5a.2a. The patient defervesced by hospital day 2, laboratory indices normalized by day 3, and radiographic abnormalities resolved by day 6. This first documented Orientia tsutsugamushi–influenza A co-infection in China highlights the value of integrating rapid serology, qPCR quantification, nested PCR genotyping, and tNGS for early, precise dual-pathogen identification. Systematic multi-pathogen screening during overlapping transmission seasons is recommended to guide timely combination therapy and enhance epidemiological surveillance. Full article

Novel waterfowl reoviruses (nWRVs) have been reported in several countries, but their circulation and genetic characteristics in Vietnam remain poorly understood. In this study, we investigated nWRVs in northern Vietnam through molecular detection, virus isolation, experimental infection in ducklings, and molecular analysis of the sigma C-encoding (sC) gene. We also applied immunoinformatic tools to explore the antigenic and structural features of the sC protein. nWRVs were detected in 15.6% of tested samples across ten provinces. Three isolates were successfully recovered, all showing a characteristic cytopathic effect—syncytium formation—in Vero cells. When tested in ducklings (n = 72), the isolates caused disease of varying severity, but all induced characteristic gross and microscopic lesions, particularly ecchymotic hemorrhages and large necrotic foci in the liver and spleen. Phylogenetic analysis based on sC sequences placed the Vietnamese isolates (n = 14) within the nWRV clade, with evidence of two genetically distinct groups. Our immunoinformatic analysis identified four predicted B-cell epitopes located in the head and body domains of the sC protein, with little variation. Full article

The genus Blanus (Amphisbaenia: Blanidae) comprises fossorial, limbless reptiles with cryptic external morphology, making species delimitation particularly challenging. This study presents a comprehensive comparative osteological and geometric morphometric investigation of three Blanus species distributed in Türkiye—B. alexandri, B. aporus, and B. strauchi. Using both dry and cleared-and-stained specimens, diagnostic variations in cranial and postcranial skeletal elements, especially elements within the nasal, maxilla, vomer, squamosal, dentary, and coronoid bones, as well as vertebral counts were identified. A geometric morphometric analysis of the dorsal and ventral cranial morphology revealed distinct shape differences, particularly separating B. alexandri from the other two species along principal component axes. A phylogenetic analysis based on 45 discrete osteological characters supported the monophyly of the eastern Blanus clade, with B. alexandri forming a distinct lineage from B. aporus and B. strauchi. These findings emphasize the significance of skeletal morphology for resolving phylogenetic relationships and highlight the role of osteological characters in refining species boundaries within cryptic reptilian taxa. The integrative approach employed here underscores the evolutionary distinctiveness of Anatolian Blanus and enhances our understanding of morphological evolution in amphisbaenians. Full article