Biology and Life Sciences

Abstract: Tobacco mosaic virus (TMV) poses a serious threat to global agricultural production due to its extremely stable infectious nature, broad host range, and widespread distribution across diverse agroecosystems. In the context of TMV management, plant-derived metabolites have emerged as promising, eco-friendly antiviral agents. This review comprehensively summarizes the diversity of anti-TMV mechanisms triggered by natural and plant-sourced semisynthetic compounds exhibiting anti-TMV activity. These metabolites mainly include alkaloids, flavonoids, terpenoids, phenylpropanoids, and glycosides, which act through either directly targeting virus particles or indirectly by eliciting host immunity. Together, these mechanisms form an integrated defence network that restricts viral replication and movement within the host. Their understanding will be essential for the rational development of sustainable and effective plant derived antiviral agents.

Abstract: Mechanisms for maintenance of chronic viruses are poorly understood, particularly for archaeal viruses. Here, we identify the product of Sulfolobus spindle-shaped virus 1 (SSV1) ORF a291 as a virally-encoded toxin required for growth inhibition but dispensable for viral replication and virion production. Viruses lacking ORF a291 replicated their genomes and formed morphologically normal spindle-shaped particles yet failed to inhibit growth of uninfected Saccharolobus solfataricus. Substitution of residues at a predicted N-terminal signal peptide cleavage site abolished growth suppression without affecting replication, suggesting that secretion is essential for toxin function. Despite primary sequence divergence among fusellovirus toxin candidates, analysis of protein structure predictions revealed a conserved hydrolase-like fold across SSV1, SSV9 and SSV10 toxins. These findings demonstrate functional separation of viral replication and host growth suppression and support a model in which chronic archaeal viruses modulate host competition through antagonistic factors. This work expands the known diversity of viral toxins and suggests that fuselloviruses employ conserved strategies to promote persistence in extreme environments. Impact Statement: This work identifies a virally-encoded toxin, the product of ORF a291, in Sulfolobus spindle-shaped virus 1. Unlike most toxins, this toxin appears to be secreted and only affects uninfected cells. Our findings expand the known diversity of viral toxins and suggest that Fuselloviruses broadly employ these mechanisms to promote their persistence in extreme environments.

Abstract: Neglected arboviruses dengue (DENV), Zika (ZIKV), yellow fever (YFV), Japanese encephalitis (JEV), and chikungunya collectively affect hundreds of millions of people annually, yet no specific antiviral drug has been approved for any of them. Alkaloids, nitrogen-containing specialized me-tabolites produced by diverse plant families, have emerged as a promising source of broad-spectrum antiviral scaffolds. This review compiles and critically analyzes ~100 alkaloid antiviral activities across several RNA virus families, providing a comparative mechanistic analysis. Lycorine, narciclasine, emetine, and berbamine, among others, exhibit potent activity against phylogenetically distant viruses, with the most potent interactions reported against fla-viviruses (narciclasine: EC₅₀ 0.02 µM against DENV, ZIKV, YFV, and JEV; pancratistatine: 0.0063 µM against ZIKV). Structure-activity analysis of multiple alkaloid classes identifies key pharma-cophoric features, including the phenanthridone nucleus (lycorine derivatives) and the bis-benzylisoquinoline scaffold (tetrandrine, berbamine), as determinants of antiviral potency, se-lectivity, and broad-spectrum activity. Genetic resistance data and replicon experiments challenge the widely accepted model of lycorine as a nucleoside inhibitor of flaviviruses, instead indicating that the membrane-associated NS4A-2K-NS4B replication complex is the actual functional target. Converging structural, biochemical, and transcriptomic evidence suggests that ribosome-mediated translational stress may represent an additional host-directed mechanism for isoquinoline-type alkaloids, though this hypothesis requires formal validation. The present analysis highlights that in vivo validation remains limited to a few compound-virus combinations. Unbiased target de-convolution and formal testing of the ribosome/integrated stress response hypothesis stand out as essential research priorities.

Abstract: Porcine epidemic diarrhea virus (PEDV) continues to undergo persistent genetic evolution and remains highly prevalent in pig herds worldwide. The resulting porcine epidemic diarrhea (PED) causes substantial economic losses to the global commercial swine industry. In this study, 296 clinical specimens were collected from diarrheic piglets across nine districts and counties of Chongqing between 2022–2024 and were screened using RT-qPCR. PEDV-positive specimens were detected in all sampling regions, with an overall positive rate of 48.31% (143/296), indicating widespread circulation and endemic persistence of PEDV throughout Chongqing. Phylogenetic analysis of the S gene from 15 representative field isolates revealed that all strains clustered within the G2c sublineage, implying that G2c has become the predominant epidemic lineage circulating in this region in recent years. Sequence analysis showed that the nucleotide identities of the S gene ranged from 93.37%–94.09% compared with the classic CV777 strain and from 96.79%–97.67% compared with the variant AJ1102 strain. Corresponding amino acid similarities were 92.88%–93.56% and 97.25%–98.05%, respectively. Notably, clear recombination footprints were identified in 11 sequenced isolates, all exhibiting highly identical recombination patterns, likely resulting from crossover events between the major parental strain FR/001/2014 and the minor parental strain CH/GDGZ/2012. Furthermore, ten distinct amino acid substitutions including F536L, D566E and L573S were identified within the COE antigenic domain of the S protein, whereas the SS2, SS6 and 2C10 domains remained highly conserved. Four isolates possessed four novel potential N-glycosylation motifs, including 300 NKTI and 787 NFSV, while two isolates concurrently lost the conserved 341 NLSF glycosylation site. These genetic alterations may influence viral pathogenicity and immune evasion capacity, thereby potentially contributing to the continued predominance and spread of the G2c sublineage in China. Together, this study expands current epidemiological knowledge of PEDV in inland Southwest China, and confirms G2c strains as the dominant circulating variants in local pig populations. These findings provide important molecular insights into the epidemiological trends and evolutionary dynamics of PEDV and offer a valuable reference for the development of more effective prevention and control strategies.

Abstract: Porcine sapelovirus (PSV), an emerging picornavirus, is increasingly recognized for its wide distribution and impact on swine health. While often subclinical, PSV can cause multisystemic disease and is frequently detected in co-infections with other porcine pathogens. However, the emergence and evolutionary dynamics of PSV in China are still not well characterized. This review consolidates recent progress on the origin and genetic evolution of PSV, with emphasis on genomic surveillance and recombination events. Studies reveal extensive genetic diversity and continuous adaptive evolution, driven largely by frequent recombination across the genome, with the 2A gene region identified as a key hotspot. This synthesis provides a timely theoretical foundation for understanding PSV evolution and informs future surveillance strategies. We emphasize the necessity of sustained genomic monitoring and call for focused research on the pathogenicity of circulating recombinants and their roles in co-infections, which is essential for developing effective countermeasures.

Abstract: Bovine viral diarrhea (BVD) is a globally prevalent infectious disease in cattle caused by bovine viral diarrhea virus (BVDV) and poses a serious threat to the livestock industry. Clinical manifestations of BVD suggest that inflammatory responses are involved in the pathogenesis of BVDV, whereas the underlying molecular mechanisms remain unclear. As a key signaling hub of innate immunity, inflammasomes activate Caspase-1, thereby facilitating the cleavage of Gasdermin D (GSDMD), promoting membrane pore formation and triggering pyroptosis, thereby contributing critically to host antiviral immunity and viral pathogenesis. This study used Madin-Darby bovine kidney (MDBK) cells as a model to compare infection responses between the cytopathic BVDV NADL strain and the non-cytopathic TC strain. The results showed that both strains upregulate the expression of IL-1β and IL-18 and promote the assembly of the NLRP3 inflammasome, indicating activation of upstream inflammasome signaling; however, only the NADL strain markedly induced Gasdermin D (GSDMD) cleavage, membrane pore formation, and pyroptosis. Further mechanistic studies revealed that core protein C (from the NADL strain) interacts with the inflammasome adaptor protein ASC and promotes NLRP3 inflammasome activation, thereby enhancing the secretion of inflammatory cytokines. In summary, this study provides the molecular mechanism by which cytopathic BVDV activates NLRP3 inflammasome-mediated pyroptosis in an ASC-dependent manner through the core protein C, providing new insights into the inflammation-related pathogenic process of BVDV and the differences in infection outcomes of different viral biotypes.

Abstract: This study was conducted to understand the reinfection pattern of cocoa swollen shoot disease (CSSD) in rehabilitation pilot plots in the cocoa landscape on Nawa region (Soubre) in Côte d’Ivoire. For that, the monitoring of CSSD was carried out on a ran-domly selected representative sample size of rehabilitating trials over time by assessing the epidemiological parameters of the disease through field observations combined with molecular samples analysis on-farm and at landscape level. Results showed that the reinfection appeared earlier than expected with high speed of incidence estimated to 6.95 % from 2020 to 2022. Grafting technology with clones on matures cocoa trees seems more susceptible to reinfection compared to grafting on seedling and hybrids. The use of PCR as molecular diagnostic indicated some miss infections in the removal strategy when considering the buffer zone recommended in the cutting out process currently in force. Recommendations for an efficient protection of rehabilitated farms after the cutting out campaigns were highlighted.

Abstract: Rising clinical interest in phage therapy and the exponential growth of metagenomic sequence catalogues have driven a rapid expansion of bacteriophage bioinformatics. More than 80 dedicated tools, mostly published since 2020, now span identification, assembly, annotation, taxonomy, lifestyle prediction, defence-system detection and host prediction. Aimed at experienced practitioners and developers, this review synthesizes the field through the lens of three successive computational paradigms: sequence homology, bounded by database completeness; machine learning, constrained by labelled training data; and foundation models, which now achieve Matthews correlation coefficients above 0.95 for identification via structure-informed prediction. Furthermore, we map the upstream components, namely gene callers, homology engines, protein language models, and structural search tools, that underpin most downstream pipelines, exposing shared infrastructure and ecosystem-level fragility when dependencies change. To translate this into practice, we propose web-based and command-line reference workflows calibrated to user expertise and sample types. Finally, we set an agenda for the next wave of tool development. Roughly half of phage genes still resist functional annotation despite structural methods; no broadly generalisable strain-level host predictor exists for phage therapy; varying true positive rates (0% to 97%) underscore the absence of standardised community benchmarks analogous to CASP or CAMI. As generative genome models begin designing synthetic phages, progress will depend less on producing standalone tools than on rigorous evaluation, interoperable infrastructure, and clinically meaningful prediction targets.

Abstract: The World Health Organization recognizes mosquito-borne viruses as a global public health threat with pandemic potential and has called on countries to prepare for the next pandemic. ZIKV is an important mosquito-borne virus with pandemic potential. Its unique neurotropism and vertical transmission capacity constitute special pathogenic and transmission risks. The prevention and control of ZIKV faces significant challenges due to the lack of vaccines and therapeutics. ZIKV entry into host cells is the initial step in establishing infection, and research on its entry mechanisms provides the fundamental theoretical basis for the development of anti-ZIKV entry inhibitory drugs. This review will summarize recent research findings from the perspectives of ZIKV receptor selection, membrane fusion mechanisms, and entry inhibitor research, aiming to provide concise information for a deeper understanding of ZIKV entry mechanisms.

Abstract: Since its emergence in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected a wide range of animal species, including wildlife. Although SARS-CoV-2 infection has been widely reported in wildlife, particularly in white-tailed deer (WTD; Odocoileus virginianus) across the United States, data on viral circulation in New England wildlife remain limited. Here, we evaluated SARS-CoV-2 infection and serological evidence of previous exposure in free-ranging wildlife from the northeastern United States. We examined samples from 1,646 animals representing 28 wildlife species, collected through wildlife rehabilitation centers, clinics, and hunter harvests in New England and Virginia between 2022 and 2025. SARS-CoV-2 RNA was detected in three WTD from Massachusetts and Vermont. Phylogeographic analysis of Vermont WTD sequences indicated a human SARS-CoV-2 lineage as the most likely source, consistent with a single human-to-deer spillover event followed by subsequent circulation within deer. Serological screening using ELISA detected SARS-CoV-2 antibodies in 12 individ-uals from three species, including Eastern cottontail (Sylvilagus floridanus), Eastern coyote (Canis latrans), and raccoon (Procyon lotor), although neutralizing antibodies were found in only one Eastern cottontail. Overall, these findings reveal ongoing but limited SARS-CoV-2 circulation in northeastern wildlife and highlight the importance of continued surveillance to detect spillover events, monitor viral evolution, and evaluate potential risks posed by wildlife.

Abstract: Poxviruses are large double-stranded DNA (dsDNA) viruses that cause important human and animal diseases, including smallpox and mpox. Poxviruses have also been identified in diverse bat populations; however, their potential for zoonotic transmission and adaptation to other mammalian hosts remains poorly understood. Poxviruses encode numerous immunomodulatory proteins that contribute to virulence, immune evasion, and host range. In this study, we performed a comparative genomic analysis of two bat-associated poxviruses belonging to the genus Vespertilionpoxvirus: hypsugopox virus (HYPV) and eptesipox virus (EPTV). We identified 24 and three previously unannotated putative open reading frames (ORFs) in HYPV, and EPTV, respectively, substantially expanding the predicted coding capacity of these viruses. Comparative analyses further revealed gene duplication and fragmentation events affecting several virulence and host range factors, as well as other unusual genomic features, including the presence of two divergent E3L homologs in EPTV. Together, our findings provide new insights into the genome evolution and potential host adaptation of bat-associated poxviruses and establish a foundation for future functional studies of Vespertilionpoxvirus biology, host-virus interactions, and zoonotic potential.

Abstract: Background/Objectives: African Swine Fever (ASF) represents one of the most serious threats to animal health and global food security. The causative agent of ASF is the African swine fever virus (ASFV), a DNA virus belonging to the Asfarviridae family. Here, we describe ex vivo results for an original anti-ASFV vaccine approach based on the cellular immune response induced by extracellular vesicles (EVs) engineered to express four ASFV antigens. EV engineering was achieved by expressing a DNA vector encoding a biologically inactive HIV-1 Nef protein (Nef^mut), which exhibits unusually high efficiency of incorporation into EVs, even when fused to foreign proteins. Previous studies have demonstrated that intramuscular injection of Nef^mut-based vectors leads to the engineering of EVs spontaneously released by muscle cells and induction of antigen-specific CD8⁺ T cell immunity. Methods: We designed DNA vectors expressing the fusion products between Nef^mut and each of the four ASFV structural proteins p³⁰, p⁵⁴, pp⁶², and p⁷². Engineered EVs were molecularly characterized by western blot and nanotrack analysis, and their potential immunogenicity was assessed by priming and cross-presentation assays. Results: We assessed that the four antigens were successfully expressed in transfected mammalian cells, with the release of valuable amounts of engineered EVs. When immature swine dendritic cells were challenged with the engineered EVs and then co-cultivated with autologous peripheral blood lymphocytes in priming assays, lymphocyte subpopulations specifically reacting against each ASFV antigen were elicited, as detected by an IFN-γ ELISpot assay. In addition, we provide evidence that the Nef^mut-based fusion products incorporated into the engineered EVs can be cross-presented by professional antigen-presenting cells, leading to cross-priming of autologous lymphocytes. Conclusions: These results represent the best premise to go forward with experiments of immunogenicity and antiviral efficiency in pigs.

Abstract: The 2026 multinational outbreak of Andes virus (ANDV) linked to the cruise ship MV Hondius represents an unprecedented epidemiological event with established person-to-person transmission. As of mid-May 2026, 11 confirmed cases (with 2 probable) have been identified across multiple countries, with 3 documented fatalities (case fatality ratio 27%). This outbreak underscores urgent clinical need for novel therapeutics against ANDV-induced hantavirus cardiopulmonary syndrome (HCPS), for which no FDA-approved antivirals exist.This perspective synthesizes structural, genomic, and clinical evidence to support urgent investigation of remdesivir as a therapeutic candidate for ANDV infection.Key findings: (1) ANDV L protein (RdRp) shows 72% amino acid identity with HTNV, with 70–75% conservation of catalytic residues; (2) Remdesivir mechanism depends on nucleotide-binding pocket geometry, substantially conserved across hantavirus species; (3) New ANDV strain shows high genomic stability with selective constraints on RdRp evolution; (4) Meta-analysis of New World hantavirus mortality identifies urgent clinical prognostic markers; (5) Cross-species nucleoside analogues demonstrate efficacy against both Old-World and New-World hantaviruses.Conclusion: Combined structural, genomic, and clinical evidence provides compelling rationale for immediate experimental evaluation of remdesivir against ANDV.

Abstract: Avian metapneumovirus (aMPV) represents a serious respiratory pathogen of poultry and is associated with considerable economic losses in breeder flocks worldwide. Although horizontal transmission is well established, the contribution of vertical transmission remains poorly understood, especially under field conditions in chickens. In this study, we aimed to assess whether aMPV could be transmitted vertically in unvaccinated broiler breeder flocks that tested positive by PCR in Egypt. Therefore, 10 broiler breeder flocks (≥30 weeks) from seven Egyptian governorates were screened for aMPV subtypes A and B. From each flock, tracheal swabs were collected from breeder hens, along with 20 fertile eggs and 20 newly hatched chicks. All samples, including tracheal swabs, chicken tissues (trachea, lungs, reproductive tract, and spleen), eggshells, internal egg contents, and embryonic tissues were analyzed for aMPV RNA using subtype-specific RT-qPCR. All breeder flocks tested positive for aMPV subtype B, but not subtype A. No aMPV RNA was found in eggshells, internal egg contents, embryonic tissues, or tissues from newly hatched chicks. In conclusion, Despite PCR detection of aMPV in breeder hens, the absence of viral RNA in eggs and their progeny provides field evidence that vertical transmission of subtype B is unlikely to play a significant role in virus spread in commercial broiler breeder flocks. These results support horizontal transmission as the primary route of aMPV spread and highlight the need for further longitudinal and genomic studies to better elucidate aMPV transmission dynamics.

Abstract: Retroviruses induce immunosuppression in their infected hosts. This phenomenon is well described for the immunodeficiency viruses, with human immunodeficiency virus type 1 (HIV-1) representing the best-studied example, but it also occurs in other retroviral infec-tions. Immunosuppressive properties were first characterized in murine leukemia viruses (MuLV). Additional well-studied examples include feline leukemia virus (FeLV) and koala retrovirus (KoRV). Investigations into the mechanisms underlying retrovirus-induced immunosuppression revealed that not only inactivated viral particles, but also their purified transmembrane envelope (TM) proteins exhibit immunosuppressive activity. However, in certain retroviral infections, additional viral proteins contribute to the immunosup-pression in vivo. Within the TM proteins, a highly conserved region, designated the immunosuppressive (isu) domain, was identified. Synthetic peptides corresponding to this domain suppress a wide range of in vitro immune responses by regulating Ras-Raf-MEK-MAPK and PI3K-AKT-mTOR pathways. They modulate cytokine release and alter gene expression in immune cells, mirroring the activity of the corresponding TM protein. Mutations in the sequence abrogate the effect. Numerous TM proteins have demonstrated immunosuppressive activity in vivo, in a tumor rejection model, and muta-tions within the isu domain also abrogate this function. These studies have important implications for reproduction, particularly through the immunosuppressive syncytins in the placenta; for tumor development, where similar mechanisms may protect cancer cells from the host immune system; as well as for vaccine development and xenotransplantation. Notably, immunization with TM proteins carrying mutations in the isu domain elic-its stronger immune responses compared with the wild-type proteins. Finally, the potential of retroviral TM proteins to protect xenotransplants from immune rejection will be discussed.

Abstract: West Nile Virus (WNV) belongs to the orthoflavivirus genus and is part of the Flaviviridae family, which includes the Japanese encephalitis virus, Dengue virus, Zika virus, and yellow fever virus. WNV circulates among birds and mosquitoes, posing infection risks to humans and mammals. The significant rise in WNV's geographic spread and infection rates over the past five decades has prompted urgent public health concerns, driving the need for accelerated vaccine research. The development of a vaccine for WNV infection presents several challenges, primarily due to the virus's complex biology, the risk of cross-reactivity with other flaviviruses, safety concerns such as Antibody-dependent enhancement (ADE), and the economic and logistical hurdles in vaccine production. Despite significant research efforts, no human vaccine has been approved, although several candidates are in various stages of development. The current review offers a comprehensive summary of the latest progress and the concomitant challenges in the development of vaccines. It also discusses the role of host-pathogen interaction, host immunity, viral immune evasion, and disease pathogenesis in facilitating the advancement of vaccines.

Abstract: Non-invasive methods for monitoring the condition of laboratory animals play a key role in ensuring animal welfare and improving the reliability of scientific data. This study evaluates the effectiveness of two non-invasive approaches - daily body weight measurement and urine analysis by qPCR - for monitoring the health of BALB/c mice infected with tick-borne encephalitis virus (TBEV). Calculation of the first derivative of body weight change allowed precise determination of disease onset, which correlated with clinical symptoms and detection of viral RNA in urine. Mathematical analysis of body weight change dynamics (first derivative with type 2 cubic spline smoothing, rh = 1) showed that a derivative threshold value of ≤ −0.6 reliably distinguishes infected BALB/c mice from healthy ones (AUC = 1 in ROC analysis). Urine analysis by qPCR allowed for the detection of viral RNA as early as the second day after infection, with a peak on the seventh day. The mathematical model was further tested on C57BL/6, CBA, and BALB/c mice of different ages and proved to be suitable. The threshold values of the derivative were found to be dependent on the mouse strain. The proposed non-invasive methods offer a humane and accurate alternative to invasive procedures, contributing to higher ethical standards and quality of research in virology.

Abstract: A series of critical interactions within the viral core between the viral RNA (vRNA) and HIV-1 Integrase (IN) has previously been reported. In these studies, contact points between vRNA and IN were identified using RNA-seq and MS-based protein foot-printing approaches. Several IN amino acids located in its C-terminal domain (CTD) were found to be essential for vRNA binding and their alanine substitution severely impacted the correct morphogenesis of the matured viral core. Here, we have extended these studies by performing a comprehensive mapping of the IN-vRNA interaction by deploying RNA crosslinking and NMR methodologies. Together, these approaches were able to identify additional contacts points between the vRNA and IN. Our results reveal several new basic amino acids located in the IN CTD critical for the vRNA-IN interaction, viral replication and correct morphology of the matured viral core.

Abstract: Canine parvovirus (CPV) remains one of the most relevant viral pathogens affecting domestic dogs worldwide, particularly in young and unvaccinated populations, due to its high environmental resistance and rapid transmission. This study provides an updated and integrative overview of epidemiology, pathogenesis, diagnosis, and control of CPV through a systematic qualitative review conducted following PRISMA guidelines. A comprehensive literature search was carried out using major academic databases, including PubMed, SciELO, MDPI, and Google Scholar, considering studies published between 2020 and 2026. A total of 312 articles were initially identified, of which 70 met the inclusion criteria and were selected for detailed analysis. The results confirm the global circulation of multiple variants (CPV-2a, CPV-2b, and CPV-2c), as well as the persistence of the virus in diverse environments and its impact on susceptible populations. Molecular diagnostic techniques, particularly PCR and qPCR, remain the most reliable tools for early detection, although their availability is still uneven across regions. Despite advances in supportive therapy and emerging antiviral approaches, vaccination continues to represent the most effective preventive strategy. Continuous surveillance and improvements in diagnostic and immunization strategies are essential to reduce the impact of CPV infections.

Abstract: As a cornerstone of modern science, cell lines are the foundational platforms for key medical advances. They enable vaccinology (by propagating and attenuating viruses), gene therapy (by facilitating vector development), and biopharmaceutical production (through recombinant protein expression). Mammalian, avian, and insect cell expression systems like Vero, MDCK, HEK293, BHK21, CHO,PER.C6, EB66, are indispensable cellular platforms that produce enhanced biologic yields and quality biotherapeutics suited to regulatory and industrial requirements. Simultaneously, advances in cell biology ranging from engineering and optimization of cell culture media to designer cell lines, have enabled improved scalability, genetic stability, and biosafety of the end-product biologic. A critical shift is underway from serum-dependent media to serum-free, chemically defined, and xeno-free alternatives, which minimize culture media variability, reduce exogenous contamination risks, and align with Good Manufacturing Practice standards. This review emphasizes the far-reaching influence of cell culture systems as the expression powerhouse that sustains modern virology whilst focusing on recent cell-engineering methods and optimization strategies in culture media that facilitated this shift.