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42 pages, 1287 KiB  
Review
Antimicrobial Potential of Bee-Derived Products: Insights into Honey, Propolis and Bee Venom
by Agnieszka Grinn-Gofroń, Maciej Kołodziejczak, Rafał Hrynkiewicz, Filip Lewandowski, Dominika Bębnowska, Cezary Adamski and Paulina Niedźwiedzka-Rystwej
Pathogens 2025, 14(8), 780; https://doi.org/10.3390/pathogens14080780 - 6 Aug 2025
Abstract
Bee products, in particular honey, propolis and bee venom, are of growing scientific interest due to their broad spectrum of antimicrobial activity. In the face of increasing antibiotic resistance and the limitations of conventional therapies, natural bee-derived substances offer a promising alternative or [...] Read more.
Bee products, in particular honey, propolis and bee venom, are of growing scientific interest due to their broad spectrum of antimicrobial activity. In the face of increasing antibiotic resistance and the limitations of conventional therapies, natural bee-derived substances offer a promising alternative or support for the treatment of infections. This paper summarizes the current state of knowledge on the chemical composition, biological properties and antimicrobial activity of key bee products. The main mechanisms of action of honey, propolis and bee venom are presented, and their potential applications in the prevention and treatment of bacterial, viral and fungal infections are discussed. Data on their synergy with conventional drugs and prospects for use in medicine and pharmacology are also included. The available findings suggest that, with appropriate standardization and further preclinical and clinical analyses, bee products could become an effective support for the treatment of infections, especially those caused by pathogens resistant to standard therapies. Full article
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17 pages, 972 KiB  
Article
SARS-CoV-2 Main Protease Dysregulates Hepatic Insulin Signaling and Glucose Uptake: Implications for Post-COVID-19 Diabetogenesis
by Praise Tatenda Nhau, Mlindeli Gamede, Andile Khathi and Ntethelelo Sibiya
Pathophysiology 2025, 32(3), 39; https://doi.org/10.3390/pathophysiology32030039 - 4 Aug 2025
Viewed by 129
Abstract
Background: There is growing evidence suggesting that SARS-CoV-2 may contribute to metabolic dysfunction. SARS-CoV-2 infection is associated with systemic inflammation, oxidative stress, and metabolic dysregulation, all of which may impair liver function and promote glucose intolerance. This study investigated the role of SARS-CoV-2, [...] Read more.
Background: There is growing evidence suggesting that SARS-CoV-2 may contribute to metabolic dysfunction. SARS-CoV-2 infection is associated with systemic inflammation, oxidative stress, and metabolic dysregulation, all of which may impair liver function and promote glucose intolerance. This study investigated the role of SARS-CoV-2, specifically its Main Protease (Mpro), in accelerating insulin resistance and metabolic dysfunction in HepG2 cells in vitro. Methods: HepG2 cells were treated with varying concentrations of Mpro (2.5, 5, 10, 20, 40, 80, and 160 nmol/mL) for 24 h to assess cytotoxicity and glucose uptake. Based on initial findings, subsequent assays focused on higher concentrations (40, 80, and 160 nmol/mL). The effects of Mpro on cell viability, protein kinase B (AKT) expression, matrix metallopeptidase-1 (MMP1), dipeptidyl peptidase 4 (DPP4), interleukin-6 (IL-6) expression, and lipid peroxidation were investigated. Results: Our findings reveal that the SARS-CoV-2 Mpro treatment led to a concentration-dependent reduction in glucose uptake in HepG2 cells. Additionally, the Mpro treatment was associated with reduced insulin-stimulated AKT activation, particularly at higher concentrations. Inflammatory markers such as IL-6 were elevated in the extracellular medium, while DPP4 expression was decreased. However, extracellular soluble DPP4 (sDPP4) levels did not show a significant change. Despite these changes, cell viability remained relatively unaffected, suggesting that the HepG2 cells were able to maintain overall metabolic functions under Mpro exposure. Conclusions: This study demonstrated the concentration-dependent impairment of hepatic glucose metabolism, insulin signaling, and inflammatory pathways in HepG2 cells acutely exposed to the SARS-CoV-2 Mpro. These findings warrant further investigation to explore the long-term metabolic effects of SARS-CoV-2 and its proteases in the liver and to develop potential therapeutic approaches for post-viral metabolic complications. Full article
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33 pages, 4412 KiB  
Review
CRISPR-Cas Gene Editing Technology in Potato
by Zagipa Sapakhova, Rakhim Kanat, Khanylbek Choi, Dias Daurov, Ainash Daurova, Kabyl Zhambakin and Malika Shamekova
Int. J. Mol. Sci. 2025, 26(15), 7496; https://doi.org/10.3390/ijms26157496 - 3 Aug 2025
Viewed by 168
Abstract
Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food [...] Read more.
Potato (Solanum tuberosum L.) is one of the most important food crops in the world, ranking fourth after rice, maize, and wheat. Potatoes are exposed to biotic and abiotic environmental factors, which lead to economic losses and increase the possibility of food security threats in many countries. Traditional potato breeding faces several challenges, primarily due to its genetic complexity and the time-consuming nature of the process. Therefore, gene editing—CRISPR-Cas technology—allows for more precise and rapid changes to the potato genome, which can speed up the breeding process and lead to more effective varieties. In this review, we consider CRISPR-Cas technology as a potential tool for plant breeding strategies to ensure global food security. This review summarizes in detail current and potential technological breakthroughs that open new opportunities for the use of CRISPR-Cas technology for potato breeding, as well as for increasing resistance to abiotic and biotic stresses, and improving potato tuber quality. In addition, the review discusses the challenges and future perspectives of the CRISPR-Cas system in the prospects of the development of potato production and the regulation of gene-edited crops in different countries around the world. Full article
(This article belongs to the Section Molecular Plant Sciences)
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24 pages, 6999 KiB  
Article
Plasmid DNA Delivery to Cancer Cells with Poly(L-lysine)-Based Copolymers Bearing Thermally Sensitive Segments: Balancing Polyplex Tightness, Transfection Efficiency, and Biocompatibility
by Mustafa Kotmakci, Natalia Toncheva-Moncheva, Sahar Tarkavannezhad, Bilge Debelec Butuner, Ivaylo Dimitrov and Stanislav Rangelov
Pharmaceutics 2025, 17(8), 1012; https://doi.org/10.3390/pharmaceutics17081012 - 2 Aug 2025
Viewed by 334
Abstract
Background/Objectives. Efficient nucleic acid delivery into target cells remains a critical challenge in gene therapy. Due to its advantages in biocompatibility and safety, recent research has increasingly focused on non-viral gene delivery. Methods. A series of copolymers—synthesized by integrating thermally sensitive poly(N-isopropylacrylamide) [...] Read more.
Background/Objectives. Efficient nucleic acid delivery into target cells remains a critical challenge in gene therapy. Due to its advantages in biocompatibility and safety, recent research has increasingly focused on non-viral gene delivery. Methods. A series of copolymers—synthesized by integrating thermally sensitive poly(N-isopropylacrylamide) (PNIPAm), hydrophilic poly(ethylene glycol) (PEG) grafts, and a polycationic poly(L-lysine) (PLL) block of varying lengths ((PNIPAm)77-graft-(PEG)9-block-(PLL)z, z = 10–65)—were investigated. Plasmid DNA complexation with the copolymers was achieved through temperature-modulated methods. The resulting polyplexes were characterized by evaluating complex strength, particle size, zeta potential, plasmid DNA loading capacity, resistance to anionic stress, stability in serum, and lysosomal membrane destabilization assay. The copolymers’ potential for plasmid DNA delivery was assessed through cytotoxicity and transfection studies in cancer cell lines. Results. Across all complexation methods, the copolymers effectively condensed plasmid DNA into stable polyplexes. Particle sizes (60–90 nm) ranged with no apparent correlation to copolymer type, complexation method, or N/P ratio, whereas zeta potentials (+10–+20 mV) and resistance to polyanionic stress were dependent on the PLL length and N/P ratio. Cytotoxicity analysis revealed a direct correlation between PLL chain length and cell viability, with all copolymers demonstrating minimal cytotoxicity at concentrations required for efficient transfection. PNL-20 ((PNIPAm)77-graft-(PEG)9-block-(PLL)20) exhibited the highest transfection efficiency among the tested formulations while maintaining low cytotoxicity. Conclusions. The study highlights the promising potential of (PNIPAm)77-graft-(PEG)9-block-(PLL)z copolymers for effective plasmid DNA delivery to cancer cells. It reveals the importance of attaining the right balance between polyplex tightness and plasmid release to achieve improved biocompatibility and transfection efficiency. Full article
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18 pages, 6860 KiB  
Article
Molecular Characterization and Antiviral Function Against GCRV of Complement Factor D in Barbel Chub (Squaliobarbus curriculus)
by Yu Xiao, Zhao Lv, Yuling Wei, Mengyuan Zhang, Hong Yang, Chao Huang, Tiaoyi Xiao and Yilin Li
Fishes 2025, 10(8), 370; https://doi.org/10.3390/fishes10080370 - 2 Aug 2025
Viewed by 171
Abstract
The barbel chub (Squaliobarbus curriculus) exhibits remarkable resistance to grass carp reovirus (GCRV), a devastating pathogen in aquaculture. To reveal the molecular basis of this resistance, we investigated complement factor D (DF)—a rate-limiting serine protease governing alternative complement pathway activation. Molecular [...] Read more.
The barbel chub (Squaliobarbus curriculus) exhibits remarkable resistance to grass carp reovirus (GCRV), a devastating pathogen in aquaculture. To reveal the molecular basis of this resistance, we investigated complement factor D (DF)—a rate-limiting serine protease governing alternative complement pathway activation. Molecular cloning revealed that the barbel chub DF (ScDF) gene encodes a 1251-bp cDNA sequence translating into a 250-amino acid protein. Crucially, bioinformatic characterization identified a unique N-glycosylation site at Asn139 in ScDF, representing a structural divergence absent in grass carp (Ctenopharyngodon idella) DF (CiDF). While retaining a conserved Tryp_SPc domain harboring the catalytic triad (His61, Asp109, and Ser204) and substrate-binding residues (Asp198, Ser219, and Gly221), sequence and phylogenetic analyses confirmed ScDF’s evolutionary conservation, displaying 94.4% amino acid identity with CiDF and clustering within the Cyprinidae. Expression profiling revealed constitutive ScDF dominance in the liver, and secondary prominence was observed in the heart. Upon GCRV challenge in S. curriculus kidney (SCK) cells, ScDF transcription surged to a 438-fold increase versus uninfected controls at 6 h post-infection (hpi; p < 0.001)—significantly preceding the 168-hpi response peak documented for CiDF in grass carp. Functional validation showed that ScDF overexpression suppressed key viral capsid genes (VP2, VP5, and VP7) and upregulated the interferon regulator IRF9. Moreover, recombinant ScDF protein incubation induced interferon pathway genes and complement C3 expression. Collectively, ScDF’s rapid early induction (peaking at 6 hpi) and multi-pathway coordination may contribute to barbel chub’s GCRV resistance. These findings may provide molecular insights into the barbel chub’s high GCRV resistance compared to grass carp and novel perspectives for anti-GCRV breeding strategies in fish. Full article
(This article belongs to the Special Issue Molecular Design Breeding in Aquaculture)
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37 pages, 1469 KiB  
Review
Oncolytic Therapies for Glioblastoma: Advances, Challenges, and Future Perspectives
by Omar Alomari, Habiba Eyvazova, Beyzanur Güney, Rana Al Juhmani, Hatice Odabasi, Lubna Al-Rawabdeh, Muhammed Edib Mokresh, Ufuk Erginoglu, Abdullah Keles and Mustafa K. Baskaya
Cancers 2025, 17(15), 2550; https://doi.org/10.3390/cancers17152550 - 1 Aug 2025
Viewed by 741
Abstract
Glioblastoma (GBM) remains one of the most aggressive and treatment-resistant brain tumors, necessitating novel therapeutic approaches. Oncolytic treatments, particularly oncolytic viruses (OVs), have emerged as promising candidates by selectively infecting and lysing tumor cells while stimulating anti-tumor immunity. Various virus-based therapies are under [...] Read more.
Glioblastoma (GBM) remains one of the most aggressive and treatment-resistant brain tumors, necessitating novel therapeutic approaches. Oncolytic treatments, particularly oncolytic viruses (OVs), have emerged as promising candidates by selectively infecting and lysing tumor cells while stimulating anti-tumor immunity. Various virus-based therapies are under investigation, including genetically engineered herpes simplex virus (HSV), adenovirus, poliovirus, reovirus, vaccinia virus, measles virus, and Newcastle disease virus, each exploiting unique tumor-selective mechanisms. While some, such as HSV-based therapies including G207 and DelytactTM, have demonstrated clinical progress, significant challenges persist, including immune evasion, heterogeneity in patient response, and delivery barriers due to the blood–brain barrier. Moreover, combination strategies integrating OVs with immune checkpoint inhibitors, chemotherapy, and radiation are promising but require further clinical validation. Non-viral oncolytic approaches, such as tumor-targeting bacteria and synthetic peptides, remain underexplored. This review highlights current advancements while addressing critical gaps in the literature, including the need for optimized delivery methods, better biomarker-based patient stratification, and a deeper understanding of GBM’s immunosuppressive microenvironment. Future research should focus on enhancing OV specificity, engineering viruses to deliver therapeutic genes, and integrating OVs with precision medicine strategies. By identifying these gaps, this review provides a framework for advancing oncolytic therapies in GBM treatment. Full article
(This article belongs to the Section Cancer Immunology and Immunotherapy)
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68 pages, 2838 KiB  
Review
Unravelling the Viral Hypothesis of Schizophrenia: A Comprehensive Review of Mechanisms and Evidence
by Mădălina Georgeta Sighencea and Simona Corina Trifu
Int. J. Mol. Sci. 2025, 26(15), 7429; https://doi.org/10.3390/ijms26157429 - 1 Aug 2025
Viewed by 374
Abstract
Schizophrenia is a challenging multifactorial neuropsychiatric disease that involves interactions between genetic susceptibility and environmental insults. Increasing evidence implicates viral infections as significant environmental contributors, particularly during sensitive neurodevelopmental periods. This review synthesises current findings on the viral hypothesis of schizophrenia, encompassing a [...] Read more.
Schizophrenia is a challenging multifactorial neuropsychiatric disease that involves interactions between genetic susceptibility and environmental insults. Increasing evidence implicates viral infections as significant environmental contributors, particularly during sensitive neurodevelopmental periods. This review synthesises current findings on the viral hypothesis of schizophrenia, encompassing a wide array of neurotropic viruses, including influenza viruses, herpesviruses (HSV-1 and 2, CMV, VZV, EBV, HHV-6 and 8), hepatitis B and C viruses, HIV, HERVs, HTLV, Zika virus, BoDV, coronaviruses (including SARS-CoV-2), and others. These pathogens can contribute to schizophrenia through mechanisms such as direct microinvasion, persistent central nervous system infection, immune-mediated neuroinflammation, molecular mimicry, and the disturbance of the blood–brain barrier. Prenatal exposure to viral infections can trigger maternal immune activation, resulting in cytokine-mediated alterations in the neurological development of the foetus that persist into adulthood. Genetic studies highlight the role of immune-related loci, including major histocompatibility complex polymorphisms, in modulating susceptibility to infection and neurodevelopmental outcomes. Clinical data also support the “mild encephalitis” hypothesis, suggesting that a subset of schizophrenia cases involve low-grade chronic neuroinflammation. Although antipsychotics have some immunomodulatory effects, adjunctive anti-inflammatory therapies show promise, particularly in treatment-resistant cases. Despite compelling associations, pathogen-specific links remain inconsistent, emphasising the need for longitudinal studies and integrative approaches such as viromics to unravel causal relationships. This review supports a “multi-hit” model in which viral infections interfere with hereditary and immunological susceptibilities, enhancing schizophrenia risk. Elucidating these virus–immune–brain interactions may facilitate the discovery of biomarkers, targeted prevention, and novel therapeutic strategies for schizophrenia. Full article
(This article belongs to the Special Issue Schizophrenia: From Molecular Mechanism to Therapy)
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16 pages, 1803 KiB  
Article
Degradation of Poliovirus Sabin 2 Genome After Electron Beam Irradiation
by Dmitry D. Zhdanov, Anastasia N. Shishparenok, Yury Y. Ivin, Anastasia A. Kovpak, Anastasia N. Piniaeva, Igor V. Levin, Sergei V. Budnik, Oleg A. Shilov, Roman S. Churyukin, Lubov E. Agafonova, Alina V. Berezhnova, Victoria V. Shumyantseva and Aydar A. Ishmukhametov
Vaccines 2025, 13(8), 824; https://doi.org/10.3390/vaccines13080824 - 31 Jul 2025
Viewed by 282
Abstract
Objectives: Most antiviral vaccines are created by inactivating the virus using chemical methods. The inactivation and production of viral vaccine preparations after the irradiation of viruses with accelerated electrons has a number of significant advantages. Determining the integrity of the genome of the [...] Read more.
Objectives: Most antiviral vaccines are created by inactivating the virus using chemical methods. The inactivation and production of viral vaccine preparations after the irradiation of viruses with accelerated electrons has a number of significant advantages. Determining the integrity of the genome of the resulting viral particles is necessary to assess the quality and degree of inactivation after irradiation. Methods: This work was performed on the Sabin 2 model polio virus. To determine the most sensitive and most radiation-resistant part, the polio virus genome was divided into 20 segments. After irradiation at temperatures of 25 °C, 2–8 °C, −20 °C, or −70 °C, the amplification intensity of these segments was measured in real time. Results: The best correlation between the amplification cycle and the irradiation dose at all temperatures was observed for segment 3D, left. Consequently, this section of the poliovirus genome is the least resistant to the action of accelerated electrons and is the most representative for determining genome integrity. The worst dependence was observed for the VP1 right section, which, therefore, cannot be used to determine genome integrity during inactivation. The electrochemical approach was also employed for a comparative assessment of viral RNA integrity before and after irradiation. An increase in the irradiation dose was accompanied by an increase in signals indicating the electrooxidation of RNA heterocyclic bases. The increase in peak current intensity of viral RNA electrochemical signals confirmed the breaking of viral RNA strands during irradiation. The shorter the RNA fragments, the greater the peak current intensities. In turn, this made the heterocyclic bases more accessible to electrooxidation on the electrode. Conclusions: These results are necessary for characterizing the integrity of the viral genome for the purpose of creating of antiviral vaccines. Full article
(This article belongs to the Special Issue Recent Scientific Development of Poliovirus Vaccines)
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14 pages, 290 KiB  
Article
Patterns of Reverse Transcriptase Inhibitor Resistance Mutations in People Living with Human Immunodeficiency Virus in Libreville, Gabon
by Guy Francis Nzengui-Nzengui, Gaël Mourembou, Euloge Ibinga, Ayawa Claudine Kombila-Koumavor, Hervé M’boyis-Kamdem, Edmery Muriel Mpouho-Ntsougha, Alain Mombo-Mombo and Angélique Ndjoyi-Mbiguino
Trop. Med. Infect. Dis. 2025, 10(8), 216; https://doi.org/10.3390/tropicalmed10080216 - 30 Jul 2025
Viewed by 269
Abstract
Objective: To characterize the profiles of resistance mutations to HIV reverse transcriptase inhibitors in Gabon. Design: Cross-sectional study conducted over 37 months, from October 2019 to October 2022, at the IST/HIV/AIDS Reference Laboratory, a reference center for the biological monitoring of people living [...] Read more.
Objective: To characterize the profiles of resistance mutations to HIV reverse transcriptase inhibitors in Gabon. Design: Cross-sectional study conducted over 37 months, from October 2019 to October 2022, at the IST/HIV/AIDS Reference Laboratory, a reference center for the biological monitoring of people living with the human immunodeficiency virus (PWHIV) in Gabon. Methods: Plasma from 666 PWHIV receiving antiretroviral treatment was collected, followed by RNA extraction, amplification, and reverse transcriptase gene sequencing. Statistical analyses were performed using Stata® 14.0 software (USA). Results: Six hundred and sixty-six (666) PWHIV plasma collected from 252 male and 414 female patients were analyzed and 1654 mutations were detected in 388 patients, including 849 (51.3%) associated with nucleoside reverse transcriptase inhibitors (NRTIs) and 805 (48.7%) with non-nucleoside reverse transcriptase inhibitors (NNRTIs). Three of the most prescribed treatment regimens were associated to the appearance of both NRTIs and NNRTIs resistance mutations: TDF + 3TC + EFV (24.02%; 160/666); TDF + FTC + EFV) (17.2%; 114/666) and AZT + 3TC + EFV (14.6%; 97/666). Additionally, stage 3 of CD4 T-lymphocyte deficiency, the higher viral load, and treatment duration are risk factors influencing the appearance of virus mutations. Also, treatment containing TDF-3TC + DTG is more protective against mutations. Conclusions: Drug resistance mutations are common in Gabon and compromise the efficacy of ART. Further study must search for other causes of therapeutic failure in Gabon in PWHIV. Full article
(This article belongs to the Special Issue HIV Testing, Prevention and Care Interventions, 2nd Edition)
24 pages, 1024 KiB  
Review
SARS-CoV-2 Infection and Antiviral Strategies: Advances and Limitations
by Vinicius Cardoso Soares, Isabela Batista Gonçalves Moreira and Suelen Silva Gomes Dias
Viruses 2025, 17(8), 1064; https://doi.org/10.3390/v17081064 - 30 Jul 2025
Viewed by 510
Abstract
Since the onset of the COVID-19 pandemic, remarkable progress has been made in the development of antiviral therapies for SARS-CoV-2. Several direct-acting antivirals, such as remdesivir, molnupiravir, and nirmatrelvir/ritonavir, offer clinical benefits. These agents have significantly contributed to reducing the viral loads and [...] Read more.
Since the onset of the COVID-19 pandemic, remarkable progress has been made in the development of antiviral therapies for SARS-CoV-2. Several direct-acting antivirals, such as remdesivir, molnupiravir, and nirmatrelvir/ritonavir, offer clinical benefits. These agents have significantly contributed to reducing the viral loads and duration of the illness, as well as the disease’s severity and mortality. However, despite these advances, important limitations remain. The continued emergence of resistant SARS-CoV-2 variants highlights the urgent need for adaptable and durable therapeutic strategies. Therefore, this review aims to provide an updated overview of the main antiviral strategies that are used and the discovery of new drugs against SARS-CoV-2, as well as the therapeutic limitations that have shaped clinical management in recent years. The major challenges include resistance associated with viral mutations, limited treatment windows, and unequal access to treatment. Moreover, there is an ongoing need to identify novel compounds with broad-spectrum activity, improved pharmacokinetics, and suitable safety profiles. Combination treatment regimens represent a promising strategy to increase the efficacy of treating COVID-19 while minimizing the potential for resistance. Ideally, these interventions should be safe, affordable, and easy to administer, which would ensure broad global access and equitable treatment and enable control of COVID-19 cases and preparedness for future threats. Full article
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12 pages, 1028 KiB  
Article
Clone-Specific Variation in Myzus persicae Influences Transmission of BMYV and BYV and Associated Feeding Behavior
by Grégoire Noël, Lallie Glacet, Christiane Then and Frédéric Francis
Insects 2025, 16(8), 784; https://doi.org/10.3390/insects16080784 - 30 Jul 2025
Viewed by 254
Abstract
Sugar beet (Beta vulgaris ssp. vulgaris) is a vital crop, contributing to nearly a quarter of global sugar production, but faces significant challenges from biotic stressors, particularly aphids, which transmit damaging yellowing viruses such as Beet Yellow Virus (BYV) and Beet [...] Read more.
Sugar beet (Beta vulgaris ssp. vulgaris) is a vital crop, contributing to nearly a quarter of global sugar production, but faces significant challenges from biotic stressors, particularly aphids, which transmit damaging yellowing viruses such as Beet Yellow Virus (BYV) and Beet Mild Yellowing Virus (BMYV). Following the partial ban of neonicotinoids in Europe, viral infections in sugar beet have surged, highlighting the need for a deeper understanding of aphid-mediated virus transmission mechanisms. This study aims to evaluate the transmission efficiency of BYV and BMYV through different clones of the aphid vector Myzus persicae from sugar beet seed companies across Europe, and to analyze the feeding behaviors of efficient clones to identify factors influencing virus transmission. The transmission rates of yellowing viruses by M. persicae clones ranged from 52% to 79% for BMYV (mean 65%) and 7% to 96% for BYV (mean 47%). While no significant differences in BMYV transmission efficiency were observed among clones, a significant difference was detected between two BYV-carrying clones. Moreover, the BYV-carrying clone exhibited prolonged penetration activities during its feeding phase compared to the BMYV-carrying clone, suggesting a potential behavioral influence on transmission efficiency. This study highlights the importance of considering aphid clone influence in the development of sugar beet resistance. Full article
(This article belongs to the Special Issue Protecting Field Crops from Economically Damaging Aphid Infestation)
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20 pages, 732 KiB  
Review
AI Methods Tailored to Influenza, RSV, HIV, and SARS-CoV-2: A Focused Review
by Achilleas Livieratos, George C. Kagadis, Charalambos Gogos and Karolina Akinosoglou
Pathogens 2025, 14(8), 748; https://doi.org/10.3390/pathogens14080748 - 30 Jul 2025
Viewed by 430
Abstract
Artificial intelligence (AI) techniques—ranging from hybrid mechanistic–machine learning (ML) ensembles to gradient-boosted decision trees, support-vector machines, and deep neural networks—are transforming the management of seasonal influenza, respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptom-based [...] Read more.
Artificial intelligence (AI) techniques—ranging from hybrid mechanistic–machine learning (ML) ensembles to gradient-boosted decision trees, support-vector machines, and deep neural networks—are transforming the management of seasonal influenza, respiratory syncytial virus (RSV), human immunodeficiency virus (HIV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptom-based triage models using eXtreme Gradient Boosting (XGBoost) and Random Forests, as well as imaging classifiers built on convolutional neural networks (CNNs), have improved diagnostic accuracy across respiratory infections. Transformer-based architectures and social media surveillance pipelines have enabled real-time monitoring of COVID-19. In HIV research, support-vector machines (SVMs), logistic regression, and deep neural network (DNN) frameworks advance viral-protein classification and drug-resistance mapping, accelerating antiviral and vaccine discovery. Despite these successes, persistent challenges remain—data heterogeneity, limited model interpretability, hallucinations in large language models (LLMs), and infrastructure gaps in low-resource settings. We recommend standardized open-access data pipelines and integration of explainable-AI methodologies to ensure safe, equitable deployment of AI-driven interventions in future viral-outbreak responses. Full article
(This article belongs to the Section Viral Pathogens)
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36 pages, 539 KiB  
Review
Genomic Adaptation, Environmental Challenges, and Sustainable Yak Husbandry in High-Altitude Pastoral Systems
by Saima Naz, Ahmad Manan Mustafa Chatha, Qudrat Ullah, Muhammad Farooq, Tariq Jamil, Raja Danish Muner and Azka Kiran
Vet. Sci. 2025, 12(8), 714; https://doi.org/10.3390/vetsci12080714 - 29 Jul 2025
Viewed by 215
Abstract
The yak (Bos grunniens) is a key species in high-altitude rangelands of Asia. Despite their ecological and economic importance, yak production faces persistent challenges, including low milk yields, vulnerability to climate changes, emerging diseases, and a lack of systematic breeding programs. [...] Read more.
The yak (Bos grunniens) is a key species in high-altitude rangelands of Asia. Despite their ecological and economic importance, yak production faces persistent challenges, including low milk yields, vulnerability to climate changes, emerging diseases, and a lack of systematic breeding programs. This review presents the genomic, physiological, and environmental dimensions of yak biology and husbandry. Genes such as EPAS1, which encodes hypoxia-inducible transcription factors, underpin physiological adaptations, including enlarged cardiopulmonary structures, elevated erythrocyte concentrations, and specialized thermoregulatory mechanisms that enable their survival at elevations of 3000 m and above. Copy number variations (CNVs) and single nucleotide polymorphisms (SNPs) present promising markers for improving milk and meat production, disease resistance, and metabolic efficiency. F1 and F2 generations of yak–cattle hybrids show superior growth and milk yields, but reproductive barriers, such as natural mating or artificial insemination, and environmental factors limit the success of these hybrids beyond second generation. Infectious diseases, such as bovine viral diarrhea and antimicrobial-resistant and biofilm-forming Enterococcus and E. coli, pose risks to herd health and food safety. Rising ambient temperatures, declining forage biomass, and increased disease prevalence due to climate changes risk yak economic performance and welfare. Addressing these challenges by nutritional, environmental, and genetic interventions will safeguard yak pastoralism. This review describes the genes associated with different yak traits and provides an overview of the genetic adaptations of yaks (Bos grunniens) to environmental stresses at high altitudes and emphasizes the need for conservation and improvement strategies for sustainable husbandry of these yaks. Full article
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24 pages, 4103 KiB  
Article
SARS-CoV-2 Remdesivir Exposure Leads to Different Evolutionary Pathways That Converge in Moderate Levels of Drug Resistance
by Carlota Fernandez-Antunez, Line A. Ryberg, Kuan Wang, Long V. Pham, Lotte S. Mikkelsen, Ulrik Fahnøe, Katrine T. Hartmann, Henrik E. Jensen, Kenn Holmbeck, Jens Bukh and Santseharay Ramirez
Viruses 2025, 17(8), 1055; https://doi.org/10.3390/v17081055 - 29 Jul 2025
Viewed by 424
Abstract
Various SARS-CoV-2 remdesivir resistance-associated substitutions (RAS) have been reported, but a comprehensive comparison of their resistance levels is lacking. We identified novel RAS and performed head-to-head comparisons with known RAS in Vero E6 cells. A remdesivir escape polyclonal virus exhibited a 3.6-fold increase [...] Read more.
Various SARS-CoV-2 remdesivir resistance-associated substitutions (RAS) have been reported, but a comprehensive comparison of their resistance levels is lacking. We identified novel RAS and performed head-to-head comparisons with known RAS in Vero E6 cells. A remdesivir escape polyclonal virus exhibited a 3.6-fold increase in remdesivir EC50 and mutations throughout the genome, including substitutions in nsp12 (E796D) and nsp14 (A255S). However, in reverse-genetics infectious assays, viruses harboring both these substitutions exhibited only a slight decrease in remdesivir susceptibility (1.3-fold increase in EC50). The nsp12-E796D substitution did not impair viral fitness (Vero E6 cells or Syrian hamsters) and was reported in a remdesivir-treated COVID-19 patient. In replication assays, a subgenomic replicon containing nsp12-E796D+nsp14-A255S led to a 16.1-fold increase in replication under remdesivir treatment. A comparison with known RAS showed that S759A, located in the active site of nsp12, conferred the highest remdesivir resistance (106.1-fold increase in replication). Nsp12-RAS V166A/L, V792I, E796D or C799F, all adjacent to the active site, caused intermediate resistance (2.0- to 11.5-fold), whereas N198S, D484Y, or E802D, located farther from the active site, showed no resistance (≤2.0-fold). In conclusion, our classification system, correlating replication under remdesivir treatment with RAS location in nsp12, shows that most nsp12-RAS cause moderate resistance. Full article
(This article belongs to the Special Issue Viral Resistance)
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Article
Deciphering Cowpea Resistance to Potyvirus: Assessment of eIF4E Gene Mutations and Their Impact on the eIF4E-VPg Protein Interaction
by Fernanda Alves de Andrade, Madson Allan de Luna-Aragão, José Diogo Cavalcanti Ferreira, Fernanda Freitas Souza, Ana Carolina da Rocha Oliveira, Antônio Félix da Costa, Francisco José Lima Aragão, Carlos André dos Santos-Silva, Ana Maria Benko-Iseppon and Valesca Pandolfi
Viruses 2025, 17(8), 1050; https://doi.org/10.3390/v17081050 - 28 Jul 2025
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Abstract
Cowpea (Vigna unguiculata) is a crop of significant socioeconomic importance, particularly in the semi-arid regions of Africa and America. However, its productivity has been adversely affected by viral diseases, including the cowpea aphid-borne mosaic virus (CABMV), a single-stranded RNA virus. It [...] Read more.
Cowpea (Vigna unguiculata) is a crop of significant socioeconomic importance, particularly in the semi-arid regions of Africa and America. However, its productivity has been adversely affected by viral diseases, including the cowpea aphid-borne mosaic virus (CABMV), a single-stranded RNA virus. It is known that the VPg protein interacts with the host’s translation initiation factor (eIF4E), promoting viral replication. This study aimed to investigate the relationship between mutations in the cowpea eIF4E gene and resistance to CABMV. Twenty-seven cultivars were screened by PCR and bioassays for presence/absence of mutations associated with resistance or susceptibility to Potyviruses. Of the cultivars with mutations previously associated with susceptibility, 88.24% exhibited viral symptoms, while 62.5% associated with resistance remained asymptomatic. The in silico analyses revealed that non-synonymous mutations (Pro68Arg, Gly109Arg) alter the structure of the eIF4E protein, reducing its affinity to VPg. Molecular dynamics simulations also pointed to an enhanced structural stability of eIF4E in resistant cultivars and reinforced, for the first time, key mutations and the functional role of the eIF4E gene in resistance to CABMV in cowpea. Our results offer valuable insights for virus disease management and for genetic improvement programs for this important crop. Full article
(This article belongs to the Special Issue Viral Manipulation of Plant Stress Responses)
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