Search Results (7,049)

Background/Objectives: Serial passage in embryonated eggs is widely used to attenuate the infectious bronchitis virus (IBV) for vaccine production; however, the evolutionary processes underlying attenuation and immunogenicity remain incompletely understood. Here, we analyzed genome-wide viral evolution during serial passages to investigate how mutations emerge, persist, are lost, or become fixed over time and how these dynamics relate to changes in pathogenicity and immunogenicity. Methods: Deep sequencing was performed on 11 representative serial passages (P2–P79) of the UY/11/CA/18 strain, including two derivative lineages: P7 VIR (virulent) and P53 VAC (attenuated and immunogenic). Results: This study identified an early adaptive phase characterized by a limited set of mutations potentially associated with genome replication, viral RNA processing, and virion assembly, including a key change in non-structural protein 14 and variants in M and 3c (E). This phase was followed by a broader expansion of the variant spectrum across replicase genes and delayed accumulation of Spike protein variants. Most Spike changes emerged during later passages and exhibited transient dynamics, and only a subset reached a high frequency after the establishment of early replicase- and structural-associated changes. Consistent with these dynamics, P7 VIR diverged before the late accumulation of Spike variants and retained a pathogenic phenotype, whereas P53 VAC diverged after the emergence of early high-frequency variants but before the extensive late-stage Spike variation observed in P79, which was associated with reduced immunogenicity. Conclusions: These findings support a multi-step model of IBV attenuation in which progressive filtering of genome-wide variation shapes distinct evolutionary outcomes during serial passages. This evolutionary framework provides insight into the relationship between attenuation and immunogenicity and may help guide the rational design of live attenuated vaccines. Full article

In this review, we examine the occurrence of two independent, single recombination events which occurred between human enteroviruses (Picornaviridae, Enterovirus, Enterovirus betacoxsackie). These recombination events contributed to the emergence of two viruses which adapted to pigs. These viruses have caused epizootics of swine vesicular disease (SVD) for many years. As was shown previously, the classical SVD virus (SVDV-1) originated from human coxsackievirus B5. The strain T75 (SVDV-2) emerged from human coxsackievirus B4 in the Tambov region of Russia, where it circulated from 1975 to 1977. A high percentage of similarity between both types of the SVD virus was found in the 3D protein coding region (88%). In our previous work, analysis of the VP1 gene dates the appearance of the SVDV-2 precursor to between 1954 and 1975. In this work, the origin of the genome region encoding non-structural proteins was analyzed and is believed to be a result of multiple recombination events between human enteroviruses (hypothetically, E1, E9, E11 and coxsackievirus A9). The recombination breakpoint between the region of structural CVB4 proteins and non-structural T75 proteins is located in region 2A. This mini-review also represents the historical research of SVDV-1 and SVDV-2 strains (O72(USS/6/72) and T75, respectively) isolated in the former Soviet Union. Full article

Cotton is recognized as the primary source of essential natural fibers for the global textile industry, supporting its sustainability and development. However, adverse environmental conditions such as drought severely constrain cotton production; thus, developing stress-tolerant cultivars via molecular breeding is essential for maintaining yield stability. Here, a comprehensive functional dissection was conducted on GhGA2ox15, a gibberellin 2-oxidase gene derived from Gossypium hirsutum L. This gene encodes a key catabolic enzyme implicated in the deactivation of endogenous bioactive GAs and the modulation of stress adaptation. We characterized GhGA2ox15, a GA2ox gene from upland cotton that modulates endogenous bioactive GA levels and abiotic stress tolerance. Bioinformatics and sequence analyses confirmed that GhGA2ox15 is a canonical C₂₀-GA2ox subfamily member, with conserved DIOX_N and 2OG-FeII_Oxy domains and marked similarity to orthologs in Arabidopsis and rice. Tobacco subcellular localization assays indicated that GhGA2ox15 resides in both the nucleus and the cytoplasm. In transgenic Arabidopsis and Oryza sativa lines, GhGA2ox15 overexpression was shown to increase drought tolerance, while virus-induced gene silencing (VIGS) of GhGA2ox15 yielded significantly compromised drought resistance. Physiological assays linked GhGA2ox15 silencing to impaired reactive oxygen species (ROS) detoxification. The suppressed lines displayed markedly lower antioxidant enzyme activities, concomitant ROS accumulation in leaves, and attenuated transcription of drought-responsive marker genes. Our findings delineate the mechanistic role of GhGA2ox15 in drought adaptation and highlight its potential utility in breeding drought-tolerant cotton. Full article

Background/Objectives: Marine-derived bioactive compounds have attracted increasing interest due to their potential antiviral properties. This study investigated in vitro antiviral activity of oil extracted from the green-lipped mussel (Perna canaliculus, GLM) and low-molecular-weight (LMW) fucoidan from Undaria pinnatifida against three human viruses in mammalian cell systems. herpes simplex virus-1 (HSV-1), respiratory syncytial virus (RSV), and SARS-CoV-2. These marine compounds were selected with the longer-term aim of evaluating their combination as a potential synergistic antiviral strategy. Methods: Antiviral efficacy was assessed using complementary assay platforms, including plaque reduction assays in mammalian cell systems and a lentiviral pseudovirus system delivering a bioluminescent reporter gene in HEK293/ACE2 cells pseudotyped with the SARS-CoV-2 spike glycoprotein. Cytotoxicity was assessed in parallel, and the selectivity index (SI) was calculated as the ratio of CC₅₀ to IC₅₀ for each compound and virus tested. Results: GLM oil showed potential antiviral activity against SARS-CoV-2 pseudovirus (SI > 6.20), with limited activity against RSV (SI > 3.48) and HSV-1 (SI > 2.28). In contrast, LMW fucoidan did not demonstrate antiviral activity against any of the tested viruses. Conclusions: These findings support further investigation of GLM-derived bioactive compounds as potential antiviral agents, including studies to elucidate their mechanisms of action and in vivo studies to confirm their antiviral efficacy. Combination studies were not pursued in the present work as both compounds require further optimisation individually; however, future studies should evaluate their combined antiviral potential, as synergistic or additive effects remain plausible. Full article

The global emergence of the avian influenza virus (AIV) H5N1 clade 2.3.4.4B since 2016 has caused substantial losses in wild bird and poultry populations, along with heightened risks of transmission to humans and other mammals. Vaccination of poultry has been a key strategy to curb the virus’s spread and mitigate its socioeconomic impact. This report describes an outbreak of high pathogenicity avian influenza virus (HPAIV) H5N1 clade 2.3.4.4B in a flock of 15,000 brown layer chickens (170 days old), all of which had received a four-dose vaccination regimen with H5N1/H5N8 commercial vaccines at 17, 50, 100, and 125 days of age. Despite this vaccination history, H5N1 infection was confirmed approximately seven weeks post-vaccination. H5N1 infection was confirmed by RT-qPCR, virus isolation, and full genome sequencing covering all eight gene segments, followed by phylogenetic and molecular analyses. Clinical signs included reduced feed intake, decreased egg production, and a cumulative mortality rate of 35% over 52 days. Hemagglutination inhibition (HI) testing with various H5 antigens revealed inconsistent antibody titers (geometric mean: 4.0 to 9.1 log2). Genetic analysis of the full-length HA and NA gene sequences further revealed strong similarity to contemporaneous H5N1 clade 2.3.4.4B strains circulating in Egypt, with multiple mutations in the HA head domain, particularly near immunogenic epitopes and receptor binding sites. These findings highlight the limitations of current vaccination strategies under conditions of antigenic mismatch and complex immunization schedules, emphasizing the need for improved vaccine matching and continuous molecular surveillance. To improve outbreak management in poultry, enhanced vaccination protocols, stringent biosecurity measures, and rigorous monitoring practices are critical. Full article

Transposable elements (TEs) are increasingly recognized as modulators of innate immunity, yet their antiviral functions remain poorly understood outside mammals and dipterans. Here, we identify a long terminal repeat retrotransposon, LmGypsy, as a key regulator of antiviral defense in Locusta migratoria. The infection of Acrididae reovirus (ARV) induces rapid upregulation of LmGypsy, and its inhibition compromises antiviral resistance. Mechanistically, LmGypsy promotes viral-derived DNA (vDNA) production, which drives Dicer-2-dependent biogenesis of virus-derived small interfering RNAs (vsiRNAs) to enhance RNA interference-mediated viral clearance. Notably, vDNA persists throughout infection, suggesting a role in sustaining antiviral responses. In parallel, LmGypsy activity is positively associated with induction of cyclic GMP-AMP synthase (cGAS)-like receptors (LmcGAS1/2/4) and their downstream effector Stimulator of Interferon Genes (STING). Together, these findings support a dual-layer antiviral strategy and indicate that TE-mediated immunity represents a widespread antiviral mechanism across taxa. Full article

Tuberculosis remains one of the leading infectious causes of morbidity and mortality worldwide, disproportionately affecting women of reproductive age, particularly in low- and middle-income countries. Tuberculosis during pregnancy represents a major clinical challenge, as physiological and immunological changes associated with pregnancy may obscure symptoms, delay diagnosis, and contribute to adverse maternal and perinatal outcomes. This narrative review provides an updated and clinically oriented overview of tuberculosis during pregnancy, with particular emphasis on diagnostic challenges, imaging strategies, microbiological testing, maternal–fetal complications, and therapeutic management. Key topics include symptom-based screening, tuberculin skin test and interferon gamma release assays, as well as molecular diagnostic methods such as GeneXpert Mycobacterium tuberculosis/Rifampicin (MTB/RIF) and Xpert MTB/RIF Ultra, chest radiography, computed tomography, and emerging biomarkers. We also discuss the impact of tuberculosis on pregnancy outcomes, including prematurity, low birth weight, maternal morbidity, and neonatal complications, as well as the particular challenges posed by human immunodeficiency virus HIV coinfection and multidrug-resistant tuberculosis. Current treatment strategies, preventive approaches, postpartum care, neonatal management, and Bacille Calmette–Guérin vaccination are reviewed in light of contemporary evidence and international recommendations. Finally, we highlight practical diagnostic algorithms, current evidence gaps, and priorities for future research aimed at improving maternal and neonatal outcomes in both high- and low-resource settings. Full article

Background/Objectives: In 2020, the world found itself in the midst of the SARS-CoV-2 pandemic. The virus has spread globally, resulting in over 779 million cases worldwide. In response to this crisis, there arose a critical need for diagnostic techniques capable of meeting the overwhelming global demand, including RT-qPCR as the gold standard due to its high sensitivity and specificity. However, RT-qPCR has its limitations, including susceptibility to factors such as inadequate sample collection, variations in viral load, and insufficient clinical validation, all of which can lead to false negatives. Consequently, this study aims to evaluate the clinical performance of four commercial RT-qPCR kits for detecting SARS-CoV-2. Methods: The study utilized 200 nasopharyngeal swab samples collected in January 2022, comparing kits from Qiagen, Seegene, Bio-Manguinhos, and IBMP. Results: Results indicated significant differences in kit performance, with 66% of samples showing consistent results across all kits, and 34% showing discrepancies. Ct values were also analyzed, and statistical tests highlighted varying sensitivities among the kits, ranging from 100% to 86.82%. Conclusions: The study underscores how extraction and purification processes, kit quality, and target gene adequacy critically influence kit performance, influencing the occurrence of false positives and negatives. Full article

Plant viruses need to use many host factors to establish infection. During the viral cycle, intracellular transport is fundamental to reach the plasmodesmata to enable cell-to-cell transport. Cucumovirus CMV (cucumber mosaic virus, CMV) can infect plants from most economically important crops. To identify additional host proteins involved in CMV movement in melon, we used the MP as a bait to screen a Yeast two-hybrid cDNA library from CMV-infected plants and identified a Niemann-Pick C1 (NPC1) protein as a novel MP interactor. NPC1 is a transmembrane protein involved in cholesterol transport in animal cells, but also in the infection by several viruses of different families. The identified clone from the melon NPC1 gene spans from exons 25 to 28 and includes two introns. Notably, deletion of the two introns and exon 28 does not impair the interaction capacity of the remaining peptide. The identified CmNPC1 gene maps to chromosome 11. In addition, the melon genome encodes a second copy of NPC1 in chromosome 7 (CmNPC1-C7), highly similar. Functional assays revealed that the interaction domain of CmNPC1-C7 also interacts with CMV MP, suggesting that both genes could have a role in CMV infection. This study represents the first report linking NPC1 to the infection process of a plant virus, expanding our understanding of plant–virus interactions. Full article

The innate immune system, particularly the retinoic acid-inducible gene I (RIG-I)-like receptor (RLR) signaling pathway, is a major early defense barrier against influenza A virus infection. However, excessive immune responses can trigger lethal cytokine storms and severe immune-mediated pathology. In this study, we performed a genome-wide CRISPR/dCas9 gene activation screen in human lung epithelial (A549) cells by using an A/Puerto Rico/8/1934 (H1N1) reporter virus, and identified the ubiquitin-specific protease USP17L13 as a novel negative regulator of innate immunity that promotes influenza virus replication. Overexpression of USP17L13 significantly enhanced the replication of multiple subtypes of influenza viruses in A549 cells, including a human pandemic H1N1 virus, seasonal H3N2 viruses, as well as a globally circulating clade, 2.3.4.4b, of the highly pathogenic avian H5N1 virus. Transcriptomic analysis demonstrated that USP17L13 suppresses host antiviral defenses by downregulating nuclear factor kappa B (NF-κB) signaling and arachidonic acid metabolism, while upregulating pathways associated with ribosomal translation and oxidative phosphorylation to facilitate viral production. Mechanistically, USP17L13 attenuates the host interferon (IFN) response by promoting the degradation of the key viral RNA sensors, RIG-I, and melanoma differentiation-associated protein 5 (MDA5). Further analysis revealed that USP17L13 is inducible by type I and type II interferons as well as inflammatory cytokines, suggesting that it may act as a negative-feedback regulator to limit excessive inflammation. Collectively, our findings identify USP17L13 as a previously unrecognized proviral host factor and provide new insight into how host deubiquitinases shape influenza virus-host interactions, with potential implications for host-directed approaches to controlling excessive inflammation during viral infection and improving influenza vaccine production. Full article

Gammaherpesviruses are oncogenic viruses that reprogram host cell metabolism to support viral production. Among these, murine herpesvirus 68 (MHV-68) serves as a model system for studying lytic gammaherpesvirus infection and associated host cell changes. To characterize host transcriptional alterations induced throughout lytic gammaherpesvirus infection and identify novel host pathways that may be therapeutically targeted, we performed temporal bulk RNA-sequencing of mock- and MHV-68-infected NIH 3T3 cells at various timepoints throughout the lytic cycle. Our analysis revealed widespread and progressive host gene expression changes, including robust innate immune pathways and extensive remodeling of metabolic gene expression. We further identified a strong activation of the pentose phosphate pathway (PPP) genes, accompanied by increased abundance in PPP metabolic intermediates. Pharmacological inhibition of the PPP with 6-aminonicotinamide (6-AN) reduced infectious virus production. Moreover, at the intersection of metabolic and transcriptional reprogramming, we identified infection-associated gene expression changes in chromatin-modulating enzymes, including Tet2, and their metabolite co-factors, such as α-KG. Pharmacological inhibition of Ten-Eleven Translocation (TET) enzymatic activity led to a marked decrease in infectious MHV-68 production. Collectively, these findings define a novel metabolic–epigenetic crosstalk that supports productive gammaherpesvirus replication and identifies host pathways that can be targeted to treat lytic gammaherpesvirus infections. Full article

The first yellow-leafed crabapple variety developed in China is Malus ‘Duojiao’. The light level affects its leaf color. (1) Background: Plants are frequently shaded by photovoltaic panels and green buildings. It is unknown how genetic regulation and partial shadowing regulate leaf color. (2) Methods: Four 28-day shading treatments were used for ‘Duojiao’ crabapple and its maternal ‘Xifu’ crabapple. Virus-induced gene silencing (VIGS), overexpression transgenic validation experiments, and physiological index analysis were employed to identify the expression levels of significant candidate genes. (3) Results: Improvements in chlorophyll synthesis, mineral metabolism, and antioxidant status were observed. The net photosynthetic rate was 39.29% higher under double-layer shade than in the control. (4) Conclusions: Partial double-layer shading exhibited the optimal effect. MsCPOX was the key gene controlling leaf color. Our results provide a theoretical basis for analyzing light responses and determining genes regulating leaf color in crabapple. Full article

The global tilapia industry is threatened due to the mass die-off of farmed tilapia caused by an emerging virus, Tilapia Lake Virus (TiLV). The threat of TiLV disease demands for cost-effective diagnostics and preventive measures such as protein and antibody-based detection tools and even vaccines like protein subunit vaccines. In this study, we aimed to recombinantly express the entire S4 protein of TiLV in vitro and in vivo using an extended host-range baculovirus expression vector system (EHR-BEVS) and used the purified protein to generate polyclonal anti-S4 antibodies. The parental extended host-range ABM-eIF4E baculovirus previously developed in our laboratory was used to generate the recombinant ABM-eIF4E-S4-His baculovirus expression vector using homologous recombination and was purified through multiple rounds of plaque selection and end-point titration, eliminating the need for the use of antibiotic resistance gene selection marker. Different insect cell lines including Trichoplusia ni Hübner, 1802 larvae were infected with ABM-eIF4-S4-His to produce recombinant S4 protein. Western blotting was used to detect the recombinantly expressed S4 protein. We generated an antibiotic resistance gene-free EHR-BEV and observed the permissibility of all the insect cell lines tested including T. ni larvae to infection with the recombinant ABM-eIF4E-S4-His. Secondly, immunogenic S4 protein capable of eliciting rabbit polyclonal anti-S4 antibodies was recombinantly expressed in the infected insect cells and larvae. TiLV S4 protein was recombinantly expressed in vitro and in vivo using extended host-range ABM-eIF4E-S4-His baculovirus expression vector and was shown to induce rabbit antibody production that can recognize S4 protein supporting the potential of insect larvae as alternative biofactories in the production of recombinant TiLV protein subunit for the development of diagnostics and preventive vaccines against TiLV disease. Full article

Tomato is widely produced in Burkina Faso for its culinary, nutritional, and economic value. Tens of thousands of farmers are involved in its production throughout the country. However, they face significant biotic constraints that limit yields and income. In particular, tomato yellow leaf curl virus (TYLCV), a begomovirus transmitted by whiteflies (Bemisia tabaci), severely affects tomato production. This study evaluated the response of 13 tomato genotypes to tomato yellow leaf curl disease (TYLCD), including eight lines with different Ty resistance gene combinations; three local improved varieties, and two commercial varieties in western and central Burkina Faso. All genotypes developed TYLCD symptoms with considerable variability in genotypic responses. Four genotypes carrying a single gene, namely CLN4279O (Ty2), CLN4270I (Ty1/Ty3), CLN4270F (Ty1/Ty3), and CLN4018G (Ty2), exhibited the best field tolerance, with lower disease incidence and severity across sites. In contrast, genotype CLN4078A carrying two resistance genes (Ty1/Ty3 + Ty2), and the checks PETOMECH and ROMA VF were highly susceptible. Hierarchical clustering grouped the genotypes into four classes based on tolerance level and yield. These findings highlight the variability in resistance expression under field conditions and suggest possible interactions between host genotype, environmental factors, and virus populations. Broader multi-site evaluations, supported by molecular diagnostics to identify endemic TYLCV strains, are needed to refine the selection process. Full article

This study is a narrative review of natural killer (NK) cells in Behcet disease (BD). BD is an inflammatory disorder with manifestations in mucosal tissues. Unlike autoimmune diseases that generate autoantibodies, BD is believed to be an autoinflammatory disease triggered by innate immune cells rather than adaptive cells. Hyperactivation of neutrophils causes vasculitis and thrombosis, and they migrate into cutaneous and ocular lesions. Dominance of M1 macrophages promotes the differentiation of Th1 cells. Moreover, the cross-reaction of bacterial heat shock proteins induces production of cytokines such as IL-4 and IFN-γ in γδT cells, which alters the balance between Th1 and Th2 phenotypes. Nevertheless, NK cells play more critical roles in BD pathogenesis than other innate immune cells because not only is their activity precisely controlled by the interaction between ligands and receptors, but NK1 shift also elicits Th1 dominance. The genetic factors associated with BD are HLA-B51 and major histocompatibility complex class I-related chain A (MICA), which stimulate NK receptors as ligands. Improperly processed peptides dysregulate their interaction with NK receptors, triggering the inflammatory response. NK1 and NK2 subsets represent cytokine production in relapse and remission periods; however, the cytotoxicity of NK cells in relapse is lower than that in remission periods. It still remains unclear how NK cells are activated recurrently and expand cytokine production. This review highlights the regulation of gene expression encoding NK receptors, tissue-resident NK cells, and adaptive NK cells to discuss their potential for relapse. Splicing variants and readthrough genes encoding NK receptors easily alter cytokine production. Moreover, tissue-resident NK cells in mucosal tissues and adaptive NK cells that memorize the virus infection have the potential to trigger hyperactivation in relapse. Full article