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Avian influenza A viruses (IAVs) pose a persistent threat to the poultry industry, causing substantial economic losses. Although traditional vaccines have helped reduce the disease burden, they typically rely on multivalent antigens, emphasize humoral immunity, and require intensive production. This study aimed to establish a genetically matched host–cell system to evaluate antigen-specific immune responses and identify conserved CD8+ T cell epitopes in avian influenza viruses. To this end, we developed an MHC class I genotype (B21)-matched host (Lohmann VALO SPF chicken) and cell vector (DF-1 cell line) model. DF-1 cells were engineered to express the hemagglutinin (HA) gene of clade 2.3.4.4b H5N1 either transiently or stably, and to stably express the matrix 1 (M1) and nucleoprotein (NP) genes of A/chicken/South Korea/SL20/2020 (H9N2, Y280-lineage). Following prime-boost immunization with HA-expressing DF-1 cells, only live cells induced strong hemagglutination inhibition (HI) and virus-neutralizing (VN) antibody titers in haplotype-matched chickens. Importantly, immunization with DF-1 cells transiently expressing NP induced stronger IFN-γ production than those expressing M1, demonstrating the platform’s potential for differentiating antigen-specific cellular responses. CD8+ T cell epitope mapping by mass spectrometry identified one distinct MHC class I-bound peptide from each of the HA-, M1-, and NP-expressing DF-1 cell lines. Notably, the identified HA epitope was conserved in 97.6% of H5-subtype IAVs, and the NP epitope in 98.5% of pan-subtype IAVs. These findings highlight the platform’s utility for antigen dissection and rational vaccine design. While limited by MHC compatibility, this approach enables identification of naturally presented epitopes and provides insight into conserved, functionally constrained viral targets.

H9N2 avian influenza A viruses (AIVs) cause economic losses in the poultry industry and provide internal genomic segments for the evolution of H5N1 and H7N9 AIVs into more detrimental strains for poultry and humans. In addition to the endemic Y439/Korea-lineage H9N2 viruses, the Y280-lineage spread to Korea since 2020. Conventional recombinant H9N2 vaccine strains, which bear mammalian pathogenic internal genomes of the PR8 strain, are pathogenic in BALB/c mice. To reduce the mammalian pathogenicity of the vaccine strains, the PR8 PB2 was replaced with the non-pathogenic and highly productive PB2 of the H9N2 vaccine strain 01310CE20. However, the 01310CE20 PB2 did not coordinate well with the hemagglutinin (HA) and neuraminidase (NA) of the Korean Y280-lineage strain, resulting in a 10-fold lower virus titer compared to the PR8 PB2. To increase the virus titer, the 01310CE20 PB2 was mutated (I66M-I109V-I133V) to enhance the polymerase trimer integrity with PB1 and PA, which restored the decreased virus titer without causing mouse pathogenicity. The reverse mutation (L226Q) of HA, which was believed to decrease mammalian pathogenicity by reducing mammalian receptor affinity, was verified to increase mouse pathogenicity and change antigenicity. The monovalent Y280-lineage oil emulsion vaccine produced high antibody titers for homologous antigens but undetectable titers for heterologous (Y439/Korea-lineage) antigens. However, this defect was corrected by the bivalent vaccine. Therefore, the balance of polymerase and HA/NA activities can be achieved by fine-tuning PB2 activity, and a bivalent vaccine may be more effective in controlling concurrent H9N2 viruses with different antigenicities.

Efficient replication of influenza A viruses (IAVs) requires balanced activities of hemagglutinin (HA), neuraminidase (NA), and the RNA polymerase complex, whose functions are strongly influenced by PB2 mutations. We previously revealed three distinct evolutionary pathways for PB2 mutations, with two pathways leading to the emergence of viral strains responsible for human seasonal infections and the 2009 pandemic, and a third pathway giving rise to H5Nx highly pathogenic avian influenza viruses (HPAIVs) defined by a triad of mutations (I147T, K339T, and A588T) that occasionally spill over to humans. Here, we investigated the zoonotic risk posed by this triad and elucidated its evolutionary relationship with HA, NA, and vaccination. Recombinant PR8 and clade 2.3.2.1c H5N1 viruses carrying the triad replicated efficiently in embryonated chicken eggs and had moderate replication efficiency in mammalian cells; moreover, mice infected with these viral strains exhibited milder weight loss and lower lung titers than those infected with the E627K-carrying strain. Sequence analysis of H5Nx viruses revealed early emergence and long-term persistence of the triad across diverse genotypes, which was closely linked to HA glycosylation and NA-stalk truncation. However, the prevalence of these viral strains declined significantly after successive H5 poultry-vaccination campaigns. These data indicate that the triad provides a replication advantage compatible with both poultry and mammalian hosts but confers only moderate mammalian pathogenicity and that sustained vaccination can restrain the spread of viral strains with these mutations. Continuous molecular surveillance of PB2 alongside HA and NA remains essential for preventing H5Nx zoonotic threats.Please check and confirm that the authors and their respective affiliations have been correctly identified and amend if necessary.I have checked and modifed the email addresses of the corresponding authors. I confirm the information of other authors are correct.

During the 2009 H1N1 pandemic (pdm09), the poor replication of PR8-derived vaccine strains in embryonated chicken eggs (ECEs) delayed vaccine production, necessitating costly adjuvants. To improve egg-based yield, we generated PB2-substituted H1N1 strains via reverse genetics, replacing PR8 PB2 with a PB2 lacking mammalian-adaptive mutations (dtxPB2), cognate pdm09 PB2 (19PB2), or avian PB2. All PB2-substituted strains achieved over tenfold higher titers than the conventional PR8 PB2-containing strain (rGD19), with rGD19/dtxPB2 and rGD19/19PB2 exhibiting significantly higher titers and reduced murine virulence. Among these, rGD19/19PB2 produced the highest hemagglutinin (HA) yield and, when administered intranasally as a binary ethyleneimine (BEI)-inactivated whole-virion vaccine, elicited a significantly stronger broncho-alveolar IgA response than rGD19. Both rGD19 and rGD19/19PB2 provided comparable protection against a homologous H1N1 challenge, yet only rGD19/19PB2 conferred full survival protection after a lethal heterologous H3N2 challenge. These findings show that incorporation of cognate PB2 enhances H1N1 replication in ECEs and antigen yield, reduces murine virulence, and confers robust homo- and heterosubtypic protection via intranasal immunization, underscoring the promise of PB2-modified H1N1 strains as inactivated mucosal whole-virion vaccines for future vaccine development.

Recent advances in reverse genetics techniques make it possible to manipulate the genome of RNA viruses such as Newcastle disease virus (NDV). Several NDV vaccine strains have been used as vaccine vectors in poultry, mammals, and humans to express antigens of different pathogens. The safety, immunogenicity, and protective efficacy of these NDV-vectored vaccines have been evaluated in pre-clinical and clinical studies. The vaccines are safe in mammals, humans, and poultry. Bivalent NDV-vectored vaccines against pathogens of economic importance to the poultry industry have been developed. These bivalent vaccines confer solid protective immunity against NDV and other foreign antigens. In most cases, NDV-vectored vaccines induce strong local and systemic immune responses against the target foreign antigen. This review summarizes the development of NDV-vectored vaccines and their potential use as a base for designing other effective vaccines for veterinary and human use.

Various chimeric lysins have been developed as efficacious antibiotics against multidrug-resistant bacteria, but direct comparisons of their antibacterial activities have been difficult due to the preparation of multiple recombinant chimeric lysins. Previously, we reported an Escherichia coli cell-free expression method to better screen chimeric lysins against Staphylococcus aureus, but we still needed to increase the amounts of expressed proteins enough to be able to detect them non-isotopically for quantity comparisons. In this study, we improved the previous cell-free expression system by adding a previously reported artificial T7 terminator and reversing the different nucleotides between the T7 promoter and start codon to those of the T7 phage. The new method increased the expressed amount of chimeric lysins enough for us to detect them using Western blotting. Therefore, the qualitative comparison of activity between different chimeric lysins has become possible via the adjustment of the number of variables between samples without protein purification. We applied this method to select more active chimeric lysins derived from our previously reported chimeric lysin (ALS2). Finally, we compared the antibacterial activities of our selected chimeric lysins with reported chimeric lysins (ClyC and ClyO) and lysostaphin and determined the rank orders of antibacterial activities on different Staphylococcus aureus strains in our experimental conditions.

is an opportunistic Gram-positive bacterium that causes necrotic enteritis and other severe infections in animals, as well as food poisoning in humans. In this study, we introduce a framework consisting of sequence typing (RSTing) and network analysis to investigate the evolutionary trajectories of . By analyzing 319 sequences-300 from public databases and 19 newly sequenced isolates from chicken and cattle sources-we identified 84 sequence types (RSTs). Among them, the early emerging RST 1-1 was the most prevalent (21.3%), while the putative ancestral type, RST 0, was the fifth most common (4.7%). The high RST diversity and the predominance of RST 1-1, mainly from chickens, suggest that chickens may serve as an important reservoir. By integrating virulence gene profiling, MLST, and comparative genomics, we separated identical RSTs into distinct genotypes and uncovered genomic evidence of possible interspecies transmission between chickens and cattle, two major food-producing species. These findings indicate that RSTing provides a useful complementary approach to investigating the evolutionary and epidemiological dynamics of .

Coronavirus disease-2019 (COVID-19), attributed to the severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2), has posed global health challenges since it first emerged in 2019, and its impact continues to persist. The neurotropic nature of SARS-CoV-2 remains undisclosed, though researchers are proposing hypotheses on how the virus is transmitted to the central nervous system. One of the prevailing hypotheses is that SARS-CoV-2 travels through the olfactory nerve system via the olfactory epithelium (OE). Using a K18-human angiotensin converting-enzyme 2 (hACE2) transgenic mouse model with impaired olfactory sensory neurons (OSNs) induced by zinc sulfate, we examined the role of the olfactory nerve in the brain invasion by SARS-CoV-2. Mice lacking OSNs exhibited reduced levels of viral transmission to the brain, leading to significantly improved outcomes following SARS-CoV-2 infection. Moreover, a positive correlation was observed between viral persistence in the OE and brain infection. These results indicate that early inhibition of the olfactory nerve pathway effectively prevents viral invasion of the brain in K18-hACE2 mice. Our study underscores the significance of the olfactory nerve pathway in the transmission of SARS-CoV-2 to the brain.

The global spread, frequent antigenic changes, and pandemic potential of clade 2.3.4.4b highly pathogenic avian influenza H5N1 underscore the urgent need for robust cross-protective vaccines. Here, we developed a clade 2.3.4.4b H5N1 whole inactivated virus (WIV) vaccine strain with improved structural stability, productivity, and safety. By analyzing the evolutionary trends of clade 2.3.4.4b H5N1 viruses, we identified a key mutation (R90K) that increases heat stability while preserving antigenicity. Additionally, the PB2 gene of PR8 was replaced with a prototypical avian PB2 gene to increase replication efficiency in embryonated chicken eggs and reduce replication efficiency in mammalian cells, thereby improving productivity and biosafety. We found that our optimized clade 2.3.4.4b H5N1 vaccine strain (22W_KY), inactivated with binary ethylenimine (BEI), had superior antigen internalization into respiratory epithelial cells compared to those inactivated with formaldehyde or beta-propiolactone. Following intranasal administration to mice, the BEI-inactivated 22W_KY also elicited significantly stronger systemic IgG, mucosal IgA, and T-cell responses, especially in the lungs. Protective efficacy studies revealed that the BEI-inactivated 22W_KY vaccine provided complete protection against heterologous viral challenges and significant protection against heterosubtypic viral challenges, with no weight loss and complete suppression of the viral load in the respiratory tract in 2 of 3 mice. These results indicate that the BEI-inactivated 22W_KY vaccine could serve as a promising candidate for a safe, stable, cost-efficient, and broadly protective intranasal influenza vaccine against zoonotic and pandemic threats.

Translational regulation in tissue environments during in vivo viral pathogenesis has rarely been studied due to the lack of translatomes from virus-infected tissues, although a series of translatome studies using in vitro cultured cells with viral infection have been reported. In this study, we exploited tissue-optimized ribosome profiling (Ribo-seq) and severe-COVID-19 model mice to establish the first temporal translation profiles of virus and host genes in the lungs during SARS-CoV-2 pathogenesis. Our datasets revealed not only previously unknown targets of translation regulation in infected tissues but also hitherto unreported molecular signatures that contribute to tissue pathology after SARS-CoV-2 infection. Specifically, we observed gradual increases in pseudoribosomal ribonucleoprotein (RNP) interactions that partially overlapped the trails of ribosomes, being likely involved in impeding translation elongation. Contemporaneously developed ribosome heterogeneity with predominantly dysregulated 5 S rRNP association supported the malfunction of elongating ribosomes. Analyses of canonical Ribo-seq reads (ribosome footprints) highlighted two obstructive characteristics to host gene expression: ribosome stalling on codons within transmembrane domain-coding regions and compromised translation of immunity- and metabolism-related genes with upregulated transcription. Our findings collectively demonstrate that the abrogation of translation integrity may be one of the most critical factors contributing to pathogenesis after SARS-CoV-2 infection of tissues. SARS-CoV-2 infection: disruption of translation integrity This study reveals that SARS-CoV-2 exhibits distinct profiles of viral gene expression in tissue microenvironments, with lower levels of subgenomic RNAs and subdued expansion compared to cell lines. Researchers discovered pseudoribosomal ribonucleoprotein (RNP) interactions developing in the lungs during SARS-CoV-2 pathogenesis, which may contribute to the accumulation of small Ribo-seq reads and affect translation elongation. Ribosome heterogeneity with compromised 5 S rRNP association was also observed, suggesting a potential strategy for coping with SARS-CoV-2 pathogenesis by resolving RBP complexes. The findings provide valuable insights into the molecular mechanisms underlying SARS-CoV-2 infection and potential therapeutic targets for COVID-19 treatment.