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Antiviral innate immunity is a complicated system initiated by the induction of type I interferon (IFN-I) and downstream interferon-stimulated genes (ISGs) and is finely regulated by numerous positive and negative factors at different signaling adaptors. During this process, posttranslational modifications, especially ubiquitination, are the most common regulatory strategy used by the host to switch the antiviral innate signaling pathway and are mainly controlled by E3 ubiquitin ligases from different protein families. A comprehensive understanding of the regulatory mechanisms and a novel discovery of regulatory factors involved in the IFN-I signaling pathway are important for researchers to identify novel therapeutic targets against viral infectious diseases based on innate immunotherapy. In this section, we use the E3 ubiquitin ligase as an example to guide the identification of a protein belonging to the RING Finger (RNF) family that regulates the RIG-I-mediated IFN-I pathway through ubiquitination.

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Antiviral innate immunity is the first line of defence against viruses. The interferon (IFN) signaling pathway, the DNA damage response (DDR), apoptosis, endoplasmic reticulum (ER) stress, and autophagy are involved in antiviral innate immunity. Viruses abrogate the antiviral immune response of cells to replication in various ways. Viral genes/proteins play a key role in evading antiviral innate immunity. Here, we will discuss the interference of viruses with antiviral innate immunity and the strategy for identifying viral gene/protein immune evasion.

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Transcriptomics is an extremely important area of molecular biology and is a powerful tool for studying all RNA molecules in an organism. Conventional transcriptomic technologies include microarrays and RNA sequencing, and the rapid development of single-cell sequencing and spatial transcriptomics in recent years has provided an enormous scope for research in this field. This chapter describes the application, significance, and experimental procedures of a variety of transcriptomic technologies in antiviral natural immunity.

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With the rapid development of CRISPR-Cas9 technology, gene editing has become a powerful tool for studying gene function. Specifically, in the study of the mechanisms by which natural immune responses combat viral infections, gene knockout mouse models have provided an indispensable platform. This article describes a detailed protocol for constructing gene knockout mice using the CRISPR-Cas9 system. This field focuses on the design of single-guide RNAs (sgRNAs) targeting the antiviral immune gene cGAS, embryo microinjection, and screening and verification of gene editing outcomes. Furthermore, this study provides methods for using cGAS gene knockout mice to analyze the role of specific genes in natural immune responses. Through this protocol, researchers can efficiently generate specific gene knockout mouse models, which not only helps in understanding the functions of the immune system but also offers a powerful experimental tool for exploring the mechanisms of antiviral innate immunity.

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Antiviral innate immunity plays a critical role in the defense against viral infections, yet its complex interactions with viruses have been challenging to study using traditional models. Organoids, three-dimensional (3D) tissue-like structures derived from stem cells, have emerged as powerful tools for modeling human tissues and studying the complex interactions between viruses and the host innate immune system. This chapter summarizes relevant applications of organoids in antiviral innate immunity studies and provides detailed information and experimental procedures for using organoids to study antiviral innate immunity.

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Zebrafish is a widely used model organism in genetics, developmental biology, pathology, and immunology research. Due to their fast reproduction, large numbers, transparent early embryos, and high genetic conservation with the human genome, zebrafish have been used as a model for studying human and fish viral diseases. In particular, the ability to easily perform forward and reverse genetics and lacking a functional adaptive immune response during the early period of development establish the zebrafish as a favored option to assess the functional implication of specific genes in the antiviral innate immune response and the pathogenesis of viral diseases. In this chapter, we detail protocols for the antiviral innate immunity analysis using the zebrafish model, including the generation of gene-overexpression zebrafish, generation of gene-knockout zebrafish by clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, methods of viral infection in zebrafish larvae, analyzing the expression of antiviral genes in zebrafish larvae using qRT-PCR, Western blotting and transcriptome sequencing, and in vivo antiviral assays. These experimental protocols provide effective references for studying the antiviral immune response in the zebrafish model.

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Innate immunity is an important defense barrier for the human body. After viral pathogen-associated molecular patterns (PAMPs) are detected by host-pathogen recognition receptors (PRRs), the associated signaling pathways trigger the activation of the interferon (IFN) regulatory factor (IRF) family members and the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). However, any gene defects among the signaling adaptors will compromise innate immune efficiency. Therefore, investigating genetic defects in the antiviral innate immune signaling pathway is important. We summarize the commonly used research methods related to antiviral immune gene defects and outline the relevant research protocols, which will help investigators study antiviral innate immunity.

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PURPOSE OF REVIEW: Viruses are the most common etiological agents of diarrhea in children. Despite rotavirus vaccine introduction, rotavirus remains as the leading cause of death globally, followed by norovirus, which represents a diagnostic challenge. Here, we describe new advances in the diagnosis and management of viral diarrheas. RECENT FINDINGS: Although immunoassays are widely used for their fast turnaround time and low cost, molecular techniques have become the most reliable diagnostic method due to their high sensitivity and capacity to analyze multiple pathogens in gastrointestinal panels. Isothermal nucleic acid amplification assays (LAMP and RPA) are promising techniques since they do not require sophisticated equipment and can be used as point-of-care testing. CRISPR/Cas nucleic acid detection systems are new diagnostic methods with great potential. Several recent published articles describe the role of human intestinal enteroids to characterize norovirus infection, to test new drugs, and for vaccine development. The interaction between the human gut microbiota and gastrointestinal viral infections has been extensively reviewed and offers some innovative mechanisms for therapeutic and preventive measures. SUMMARY: Although important advances have been made, more research is needed to address remaining challenges and further improve diagnostic capabilities and better management strategies for this critical infectious disease.

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Mitochondria are vital for most cells' functions. Viruses hijack mitochondria machinery for misappropriation of energy supply or to bypass defense mechanisms. Many of these mitochondrial dysfunctions persist after recovery from treated or untreated viral infections, particularly when mitochondrial DNA is permanently damaged. Quantitative defects and structural rearrangements of mitochondrial DNA accumulate in post-mitotic tissues as recently reported long after SARS-CoV-2 or HIV infection, or following antiviral therapy. These observations are consistent with the "hit-and-run" concept proposed decades ago to explain viro-induced cell transformation and it could apply to delayed post-viral onsets of symptoms and advocate for complementary supportive care. Thus, according to this concept, following exposure to viruses or antiviral agents, mitochondrial damage could evolve into an autonomous clinical condition. It also establishes a pathogenic link between communicable and non-communicable chronic diseases.

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Viral lower respiratory tract infections (LRTIs), including rhinovirus and respiratory syncytial virus during early childhood, have been linked to subsequent asthma. However, the impact of other respiratory viruses remains unclear. We analyzed nationwide Korean data from January 1, 2008, to December 31, 2018, utilizing the national health insurance database. Our study focused on 19 169 meticulously selected children exposed to severe respiratory infections requiring hospitalization with documented viral pathogens, matched with 191 690 unexposed children at a ratio of 1:10 using incidence density sampling. Our findings demonstrate that asthma exacerbation rates were higher among the exposed cohort than the unexposed cohort over a mean follow-up of 7.8 years. We observed elevated risks of asthma exacerbation and newly developed asthma compared to the unexposed cohort. Hospitalization due to rhinovirus, respiratory syncytial virus, influenza, metapneumovirus, and adenovirus was related to increased asthma exacerbations. Notably, we found a stronger association in cases of multiple LRTI hospitalizations. In conclusion, our study shows that early childhood respiratory viral infections are related to subsequent asthma exacerbations and new asthma diagnoses.

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Inflammatory syndromes, including those caused by infection, are a major cause of hospital admissions among children and are often misdiagnosed because of a lack of advanced molecular diagnostic tools. In this study, we explored the utility of circulating cell-free RNA (cfRNA) in plasma as an analyte for the differential diagnosis and characterization of pediatric inflammatory syndromes. We profiled cfRNA in 370 plasma samples from pediatric patients with a range of inflammatory conditions, including Kawasaki disease (KD), multisystem inflammatory syndrome in children (MIS-C), viral infections, and bacterial infections. We developed machine learning models based on these cfRNA profiles, which effectively differentiated KD from MIS-C-two conditions presenting with overlapping symptoms-with high performance [test area under the curve = 0.98]. We further extended this methodology into a multiclass machine learning framework that achieved 80% accuracy in distinguishing among KD, MIS-C, viral, and bacterial infections. We further demonstrated that cfRNA profiles can be used to quantify injury to specific tissues and organs, including the liver, heart, endothelium, nervous system, and the upper respiratory tract. Overall, this study identified cfRNA as a versatile analyte for the differential diagnosis and characterization of a wide range of pediatric inflammatory syndromes.

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The presence of transmissible disease in livestock has a major impact on welfare and economics in animal and public health. A lack of data enables the spread of diseases due to misinformed decision-making on prevention and control. Low-resource settings face challenges in providing data, turning data availability into a development issue. For this study, a large dataset (n = 997) was collected on prevalence and seroprevalence estimates on viral (n = 224), bacterial (n = 83) and parasitic (n = 690) diseases in backyard chickens in low- and middle-income countries (LMICs). These estimates originate from 306 studies identified during the screening phase of a systematic literature review. An attempt was made to classify the studies according to the Food and Agriculture Organization of the United Nations'classification system for family poultry production systems. Of the studies, 98.7% (302/306) focused on a single poultry production system, while 1.3% (4/306) targeted two different production systems. Within the group of studies that covered one production system, 85.4% (258/302) were classified as â€Ëœsmall extensive scavenging or extensive scavenging,'â€Ëœsmall extensive scavenging'and/or â€Ëœextensive scavenging'. In addition, 52% (159/306) of the studies did not report information on chicken breed type. No data were found on any relevant disease for 56.9% (78/137) of LMICs, signifying a potential data gap. Of the estimates on viral and bacterial diseases, 71.0% (218/307) corresponded to diseases notifiable to the World Organisation for Animal Health, highlighting a tendency to measure disease occurrence for diseases relevant to trade. The latter might not necessarily be priority diseases for the producers, however. Furthermore, 72.3% (222/307) of the estimates originate from random samples and could be used to estimate prevalence in backyard chickens using imputation methods, thus bridging the data gap.

Les maladies transmissibles affectant les animaux d'élevage ont un impact majeur sur la santé animale et la santé publique, avec des effets sur le bien-être et sur l'économie. L'absence de données favorise la propagation des maladies puisque les mesures de prévention et de contrôle reposent sur des décisions mal informées. Les contextes faiblement dotés en ressources se heurtent à la difficulté de produire des données, ce qui fait de la disponibilité des données un enjeu de développement. Pour les besoins de la présente étude, un vaste jeu de données (n = 997) a été constitué, regroupant les taux de prévalence et de séroprévalence estimés d'un certain nombre de maladies virales (n = 224), bactériennes (n = 83) et parasitaires (n = 690) affectant les poulets de basse-cour dans les pays à revenu faible et intermédiaire. Ces estimations sont extraites des 306 études retenues lors de la phase de sélection initiale d'un examen systématique de la littérature. Une tentative de classement de ces études a été réalisée en se basant sur la classification des systèmes d'aviculture familiale élaborée par l'Organisation des Nations Unies pour l'alimentation et l'agriculture. Au total, 98,7 % (302/306) des études portaient sur un système unique de production de volailles, les 1,3 % restantes (4/306) portant sur deux systèmes de production différents. Dans le groupe des études couvrant un seul système de production, 85,4 % des élevages étudiés (258/302) relevaient des catégories " petits systèmes extensifs en liberté ou systèmes extensifs en liberté ", " petits systèmes extensifs en liberté " et/ou " systèmes extensifs en liberté ". En outre, dans 52 % des études (159/306), la race des poulets n'était pas précisée. Aucune donnée n'a pu être trouvée concernant les maladies importantes des volailles dans 56,9 % (78/137) des pays à revenu faible ou intermédiaire, ce qui indique un déficit potentiel de données. S'agissant des maladies virales et bactériennes, 71,0 % des estimations (218/307) correspondaient à des maladies à déclaration obligatoire à l'Organisation mondiale de la santé animale, ce qui souligne la tendance à signaler la survenue des maladies ayant une incidence sur les échanges internationaux. Toutefois, ce ne sont pas nécessairement ces maladies qui sont prioritaires pour les éleveurs. D'autre part, 72,3 % (222/307) des estimations provenaient d'échantillons aléatoires et pourraient donc servir à estimer la prévalence chez les poulets de basse-cour en appliquant des méthodes d'imputation, ce qui permettrait de combler les écarts.

La presencia de enfermedades transmisibles en los animales de granja tiene importantes repercusiones en el bienestar y la economía tanto en el ámbito de la sanidad animal como en el de la salud pública. La falta de datos favorece la propagación de enfermedades debido a la toma de decisiones en materia de prevención y control basada en información mal fundada. En los entornos de bajos recursos existen dificultades para el suministro de información, lo que convierte la disponibilidad de datos en un problema de desarrollo. Para este estudio, se recopiló un amplio conjunto de datos (n = 997) sobre estimaciones de prevalencia y seroprevalencia de enfermedades víricas (n = 224), bacterianas (n = 83) y parasitarias (n = 690) en pollos de traspatio en países de ingresos medios y bajos (PIMB). Estas estimaciones provienen de 306 estudios encontrados durante la fase de selección de una revisión bibliográfica sistemática. Se intentó clasificar los estudios según la clasificación de sistemas de producción avícola familiar de la Organización de las Naciones Unidas para la Alimentación y la Agricultura. El 98,7 % de los estudios (302/306) se centraron en un único sistema de producción avícola, mientras que el 1,3 % (4/306) se centraron en dos sistemas de producción diferentes. Dentro del grupo de estudios que abarcaban un solo sistema de producción, el 85,4 % (258/302) se clasificaron como sistema "extensivo de escarbado pequeño o extensivo de escarbado", "extensivo de escarbado pequeño" o "extensivo de escarbado". Además, en el 52 % (159/306) de los estudios no se proporcionó información sobre el tipo de raza de los pollos. No se encontraron datos sobre ninguna enfermedad pertinente para el 56,9 % (78/137) de los PIMB, lo que indica una posible carencia de datos. De las estimaciones sobre enfermedades víricas y bacterianas, el 71,0 % (218/307) correspondían a enfermedades de declaración obligatoria a la Organización Mundial de Sanidad Animal, lo que evidencia una tendencia a medir la aparición de enfermedades pertinentes para el comercio. Sin embargo, estas podrían no ser necesariamente enfermedades prioritarias para los productores. Por otro lado, el 72,3 % (222/307) de las estimaciones proceden de muestras aleatorias y podrían utilizarse para estimar la prevalencia en los pollos de traspatio utilizando métodos de imputación, lo que permitiría subsanar la carencia de datos.

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The endoplasmic reticulum (ER) is a unique organelle responsible for protein synthesis and processing, lipid synthesis in eukaryotic cells, and the replication of many animal viruses is closely related to ER. A considerable number of viral proteins are synthesised during viral infection, resulting in the accumulation of unfolded and misfolded proteins in ER, which in turn induces endoplasmic reticulum stress (ERS). ERS further drives three signalling pathways (PERK, IRE1, and ATF6) of the cellular unfolded protein response (UPR) to respond to the ERS. In numerous studies, ERS has been shown to mediate autophagy, a highly conserved cellular degradation mechanism to maintain cellular homeostasis in eukaryotic cells, through the UPR to restore ER homeostasis. ERS-mediated autophagy is closely linked to the occurrence and development of numerous viral diseases in animals. Host cells can inhibit viral replication by regulating ERS-mediated autophagy, restoring the ER's normal physiological process. Conversely, many viruses have evolved strategies to exploit ERS-mediated autophagy to achieve immune escape. These strategies include the regulation of PERK-eIF2α-Beclin1, PERK-eIF2α-ATF4-ATG12, IRE1α-JNK-Beclin1, and other signalling pathways, which provide favourable conditions for the replication of animal viruses in host cells. The ERS-mediated autophagy pathway has become a hot topic in animal virological research. This article reviews the most recent research regarding the regulatory functions of ERS-mediated autophagy pathways in animal viral infections, emphasising the underlying mechanisms in the context of different viral infections. Furthermore, it considers the future direction and challenges in the development of ERS-mediated autophagy targeting strategies for combating animal viral diseases, which will contribute to unveiling their pathogenic mechanism from a new perspective and provide a scientific reference for the discovery and development of new antiviral drugs and preventive strategies.

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Combining different drugs synergistically is an essential aspect of developing effective treatments. Although there is a plethora of research on computational prediction for new combination therapies, there is limited to no research on combination therapies in the treatment of viral diseases. This paper proposes AI-based models for predicting novel antiviral combinations to treat virus diseases synergistically. To do this, we assembled a comprehensive dataset comprising information on viral strains, drug compounds, and their known interactions. As far as we know, this is the first dataset and learning model on combination therapy for viruses. Our proposal includes using a random forest model, an SVM model, and a deep model to train viral combination therapy. The machine learning models showed the highest performance, and the predicted values were validated by a t-test, indicating the effectiveness of the proposed methods. One of the predicted combinations of acyclovir and ribavirin has been experimentally confirmed to have a synergistic antiviral effect against herpes simplex type-1 virus, as described in the literature.

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BACKGROUND: Routine screening for viral infections at blood donation is important to avoid transfusion-transmitted infections. It also offers an opportunity to detect an asymptomatic infection. OBJECTIVE: To study changes in serology positivity for viral infections (B and C hepatitis, HTLV-1/2, and HIV) at blood donation in a blood bank from Southern Brazil, comparing two periods of 5 years: the period from 2013 to 2017 with the period from 2018 to 2022. In addition, data on the donor fidelity rate during the studied period were sought. METHODS: Retrospective study using data from 2013 to 2022 from a single blood center electronic database from Curitiba, Southern Brazil. RESULTS: A significant drop in positive serology for all studied viruses was observed: highest in HIV (OR=0.39; 95% CI=0.27-0.57) and lowest in total anti HBc (0.56; 95 CI=0.50-0.63). Anti HBc serology became more commonly seen in women in the period of 2018-2022 when compared to men. No changes in the distribution of positive serology according to donors' ages were observed. Loyalty rates had a median of 70%, with the lowest being 60% in 2013, while the highest was 73% in 2018 and 2022. CONCLUSION: A significant reduction in discarded blood bags due to viral serology was observed when the period of 2013-2017 was compared to 2018-2022 on this blood bank; the highest reduction was observed in HIV serology and the lowest in HBc serology, which became more common in women in the second period. High rates of donor fidelity were observed during the period studied.

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Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system possess a broad range of applications for genetic modification, diagnosis and treatment of infectious as well as non-infectious disease. The CRISPR-Cas system is found in bacteria and archaea that possess the Cas protein and guide RNA (gRNA). Cas9 and gRNA forms a complex to target and cleave the desired gene, providing defense against viral infections. Human immunodeficiency virus (HIV), hepatitis B virus (HBV), herpesviruses, human papillomavirus (HPV), and severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) cause major life threatening diseases which cannot cure completely by drugs. This chapter describes the present strategy of CRISPR-Cas systems for altering the genomes of viruses, mostly human ones, in order to control infections.

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Viruses utilize host cells at all stages of their life cycle, from the transcription of genes and translation of viral proteins to the release of viral copies. The human immune system counteracts viruses through a variety of complex mechanisms, including both innate and adaptive components. Viruses have an ability to evade different components of the immune system and affect them, leading to disruption. This review covers contemporary knowledge about the virus-induced complex interplay of molecular interactions, including regulation of transcription and translation in host cells resulting in the modulation of immune system functions. Thorough investigation of molecular mechanisms and signaling pathways that are involved in modulating of host immune response to viral infections can help to develop novel approaches for antiviral therapy. In this review, we consider new therapeutic approaches for antiviral treatment. Modern therapeutic strategies for the treatment and cure of human immunodeficiency virus (HIV) are considered in detail because HIV is a unique example of a virus that leads to host T lymphocyte deregulation and significant modulation of the host immune response. Furthermore, peculiarities of some promising novel agents for the treatment of various viral infections are described.

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Neurotropic viruses, characterized by their capacity to invade the central nervous system, present a considerable challenge to public health and are responsible for a diverse range of neurological disorders. This group includes a diverse array of viruses, such as herpes simplex virus, varicella zoster virus, poliovirus, enterovirus and Japanese encephalitis virus, among others. Some of these viruses exhibit high neuroinvasiveness and neurovirulence, while others demonstrate weaker neuroinvasive and neurovirulent properties. The clinical manifestations of infections caused by neurotropic viruses can vary significantly, ranging from mild symptoms to severe life-threatening conditions. Extracellular vesicles (EVs) have garnered considerable attention due to their pivotal role in intracellular communication, which modulates the biological activity of target cells via the transport of biomolecules in both health and disease. Investigating EVs in the context of virus infection is crucial for elucidating their potential role contribution to viral pathogenesis. This is because EVs derived from virus-infected cells frequently transfer viral components to uninfected cells. Importantly, EVs released by virus-infected cells have the capacity to traverse the blood-brain barrier (BBB), thereby impacting neuronal activity and inducing neuroinflammation. In this review, we explore the roles of EVs during neurotropic virus infections in either enhancing or inhibiting viral pathogenesis. We will delve into our current comprehension of the molecular mechanisms that underpin these roles, the potential implications for the infected host, and the prospective diagnostic applications that could arise from this understanding.

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BACKGROUND: Emerging evidence suggests that viral infections may contribute to Alzheimer's disease (AD) onset and/or progression. However, the extent of their involvement and the mechanisms through which specific viruses increase AD susceptibility risk remain elusive. METHODS: We used an integrative systems bioinformatics approach to identify viral-mediated pathogenic mechanisms, by which Herpes Simplex Virus 1 (HSV-1), Human Cytomegalovirus (HCMV), Epstein-Barr virus (EBV), Kaposi Sarcoma-associated Herpesvirus (KSHV), Hepatitis B Virus (HBV), Hepatitis C Virus (HCV), Influenza A Virus (IAV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) could facilitate AD pathogenesis via virus-host protein-protein interactions (PPIs). We also explored potential synergistic pathogenic effects resulting from herpesvirus reactivation (HSV-1, HCMV, and EBV) during acute SARS-CoV-2 infection, potentially increasing AD susceptibility. RESULTS: Herpesviridae members (HSV-1, EBV, KSHV, HCMV) impact AD-related processes like amyloid-ß (Aß) formation, neuronal death, and autophagy. Hepatitis viruses (HBV, HCV) influence processes crucial for cellular homeostasis and dysfunction, they also affect microglia activation via virus-host PPIs. Reactivation of HCMV during SARS-CoV-2 infection could potentially foster a lethal interplay of neurodegeneration, via synergistic pathogenic effects on AD-related processes like response to unfolded protein, regulation of autophagy, response to oxidative stress, and Aß formation. CONCLUSIONS: These findings underscore the complex link between viral infections and AD development. Viruses impact AD-related processes through shared and distinct mechanisms, potentially influencing variations in AD susceptibility.

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BACKGROUND: Metagenomics is a powerful approach for the detection of unknown and novel pathogens. Workflows based on Illumina short-read sequencing are becoming established in diagnostic laboratories. However, high sequencing depth requirements, long turnaround times, and limited sensitivity hinder broader adoption. We investigated whether we could overcome these limitations using protocols based on untargeted sequencing with Oxford Nanopore Technologies (ONT), which offers real-time data acquisition and analysis, or a targeted panel approach, which allows the selective sequencing of known pathogens and could improve sensitivity. METHODS: We evaluated detection of viruses with readily available untargeted metagenomic workflows using Illumina and ONT, and an Illumina-based enrichment approach using the Twist Bioscience Comprehensive Viral Research Panel (CVRP), which targets 3153 viruses. We tested samples consisting of a dilution series of a six-virus mock community in a human DNA/RNA background, designed to resemble clinical specimens with low microbial abundance and high host content. Protocols were designed to retain the host transcriptome, since this could help confirm the absence of infectious agents. We further compared the performance of commonly used taxonomic classifiers. RESULTS: Capture with the Twist CVRP increased sensitivity by at least 10-100-fold over untargeted sequencing, making it suitable for the detection of low viral loads (60 genome copies per ml (gc/ml)), but additional methods may be needed in a diagnostic setting to detect untargeted organisms. While untargeted ONT had good sensitivity at high viral loads (60,000 gc/ml), at lower viral loads (600-6000 gc/ml), longer and more costly sequencing runs would be required to achieve sensitivities comparable to the untargeted Illumina protocol. Untargeted ONT provided better specificity than untargeted Illumina sequencing. However, the application of robust thresholds standardized results between taxonomic classifiers. Host gene expression analysis is optimal with untargeted Illumina sequencing but possible with both the CVRP and ONT. CONCLUSIONS: Metagenomics has the potential to become standard-of-care in diagnostics and is a powerful tool for the discovery of emerging pathogens. Untargeted Illumina and ONT metagenomics and capture with the Twist CVRP have different advantages with respect to sensitivity, specificity, turnaround time and cost, and the optimal method will depend on the clinical context.

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