Antiviral immune responses in human organoid models of emerging viral infections: A systematic review

Antiviral immune responses in human organoid models of emerging viral infections: A systematic review | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Systematic Review Antiviral immune responses in human organoid models of emerging viral infections: A systematic review Arnaw Kishore, Shailendra Chauhan, Madhumati Bathala This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9351966/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Human organoid models have emerged as powerful tools for studying viral pathogenesis and host immune responses in physiologically relevant human tissues. These three-dimensional systems provide opportunities to investigate virus–host interactions that are difficult to replicate in traditional cell culture models. However, a comprehensive synthesis of antiviral immune responses across different organoid systems and viral families remains limited. A systematic review was conducted in accordance with PRISMA guidelines to evaluate studies investigating antiviral immune responses in human organoid models. Literature searches were performed across major scientific databases for studies published between 2010- January 2026. After removal of duplicates and screening of titles, abstracts, and full texts based on predefined inclusion criteria, 23 studies were included in the final qualitative synthesis. Data were extracted on organoid origin, virus type, immune signaling pathways, and reported immune responses. The included studies investigated viruses from seven families, including Coronaviridae , Flaviviridae , Orthomyxoviridae , Picornaviridae , Filoviridae , Poxviridae , and Togaviridae . Organoid models primarily represented neural, respiratory, intestinal, and hepatic tissues derived from human embryonic stem cells, induced pluripotent stem cells, or adult stem cells. Across studies, viral infection commonly activated innate immune pathways involving pattern-recognition receptors such as Toll-like receptors and RIG-I–like receptors, leading to downstream activation of NF-κB and interferon regulatory factor signaling. These pathways induced production of type I and type III interferons, interferon-stimulated genes, and pro-inflammatory cytokines including IL-6, TNF-α, CXCL10, and CCL5. While several viruses triggered strong interferon-mediated antiviral responses, others demonstrated attenuated immune activation, suggesting virus-specific mechanisms of immune modulation or evasion. Human organoid models provide physiologically relevant platforms for studying antiviral immune responses across diverse viral infections and tissue types. The evidence highlights conserved innate immune pathways alongside virus- and tissue-specific differences in immune activation. These systems hold significant potential for advancing our understanding of viral pathogenesis, immune regulation, and therapeutic development. Organoids Innate Immunity Interferons Communicable Diseases Emerging Virus Diseases Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 1. Background Emerging and re-emerging infectious diseases (EIDs) remain one of the most significant global health challenges of the twenty-first century, driven by pathogen evolution, antimicrobial resistance, ecological disruptions, and globalization [ 1 , 2 ]. Outbreaks of Avian influenza, Chikungunya, Crimean-Congo haemorrhagic fever, Dengue (DENV), Ebola virus (EBOV) disease, Hantavirus, Marburg virus (MARV), Hand, foot and mouth disease, Japanese encephalitis (JEV), Nipah virus, novel human coronavirus, Rabies, Rift Valley fever, Viral hepatitis, SARS, Lassa fever, Swine flu, Zika virus (ZIKV) and COVID-19 have demonstrated the vulnerability of modern societies to novel pathogens, posing immense threats to health, economies, and global security [ 1 , 3 , 4 ]. Understanding the mechanisms underlying human immune responses to infection is therefore critical for the development of effective preventive and therapeutic interventions. The study of host-pathogen interactions and immune mechanisms has historically relied on traditional two-dimensional (2D) cell culture systems and animal models, both of which present significant limitations in recapitulating human-specific physiological responses. Conventional 2D cultures fail to reproduce the complex three-dimensional architecture, cellular diversity, and dynamic microenvironmental signals present in native tissues [ 5 ]. Animal models, while valuable, often exhibit species-specific differences in immune responses and tissue organization and are further constrained by ethical considerations, limited throughput, and reduced translational relevance [ 6 ]. These limitations have driven the development of advanced three-dimensional (3D) in vitro platforms that more accurately model the complexity of human physiological systems and immune responses. Such systems more closely mimic in vivo tissue architecture and provide improved platforms for studying human organ physiology, microenvironmental dynamics, and host–pathogen interactions [ 7 , 8 ]. In recent years, organoids, organ-on-chip technologies, multicellular spheroids, and bioprinted or explant-based models have become popular for modeling the architecture, multicellularity, and microenvironment of human tissues [ 9 , 10 ]. Specifically, organoid technology has emerged as a transformative approach, utilizing self-organizing, stem cell-derived 3D structures that recapitulate the cellular composition and architectural complexity of native organs [ 11 ]. These systems preserve genetic and epigenetic features of their tissue of origin, making them particularly valuable for patient-specific disease modeling. However, conventional organoid cultures present their own challenges, particularly the enclosed luminal architecture that limits access for pathogen exposure and the absence of dynamic mechanical forces present in vivo [ 12 ]. Furthermore, organ-on-a-chip (OOC) technologies have been developed, integrating microfluidic systems with tissue engineering to recreate physiologically relevant flow, mechanical strain, and multi-tissue interfaces [ 10 , 13 ]. These models offer valuable opportunities to study innate and adaptive immune mechanisms under controlled, human-specific conditions [ 13 , 14 ]. Specifically, immune organoids have been instrumental in modeling and analyzing human adaptive immunity and infectious diseases [ 15 – 17 ]. Recent advances have enabled the incorporation of both innate immune cells, including macrophages, dendritic cells (DCs), and neutrophils, and adaptive immune components such as T cells and B cells into these platforms [ 18 ]. At the same time, organ-on-chip systems, which integrate human cells into microfluidic devices to simulate organ-level physiology under continuous flow and mechanical forces, offer enhanced assay complexity and reproduction of tissue microenvironments. They are also used to engineer the immune microenvironment for toxicology, cancers, inflammatory disorders, infections, and immunotherapies [ 19 – 21 ]. Among these models, human-derived organoids have significantly advanced the understanding of emerging viral infections and immune responses [ 15 – 17 ]. However, a systematic synthesis of organoid-based studies investigating emerging viral infections and their corresponding immune responses remains limited. While individual studies report robust interferon and cytokine responses, a comparative evaluation across viral families, tissue origins, and organoid architectures remains unexplored. Such synthesis is essential to identify the strengths, limitations, and translational relevance of these systems in modeling human antiviral immunity. Therefore, this systematic review aims to critically evaluate and synthesize published research employing human organoid models to study emerging and re-emerging viral infections. The review specifically focuses on (i) the ability of organoid systems to replicate innate and adaptive immune responses, (ii) the influence of organoid origin and architecture on antiviral signaling, and (iii) the comparative immune patterns elicited by different viral families. By consolidating these findings, this review establishes an evidence-based framework for optimizing organoid use in infectious disease modeling and enhancing the predictive value of preclinical research. 2. Materials and methods 2.1. Study design and framework This systematic review employed a structured, multi-tiered methodology designed to capture, appraise, and synthesize existing evidence on human organoid-based 3D in vitro systems that model immune mechanisms in EIDs. The methodological framework was developed in accordance with the 2020 guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) [ 22 ]. The review emphasizes two principal aspects: (i) the technological diversity of human organoid systems used to study infectious diseases and (ii) their immunological relevance in elucidating human host–pathogen interactions. The protocol of the full systematic review is available in PROSPERO (CRD420261299053) 2.2. Research objectives This systematic review aimed to critically evaluate the application of human organoids in modeling emerging and re-emerging viral infections, with a focus on their capacity to recapitulate host immune responses. 2.3. Literature search strategy A comprehensive literature search was conducted using the scientific databases PubMed/MEDLINE, Web of Science, and Scopus. The search strategy combined three main thematic domains: (1) Organoids; (2) immune mechanisms; and (3) viral infectious diseases or emerging viral pathogens (Supplementary Table 1). The full set of search terms used was as follows: (“organoid” OR “Human organoid model”) AND (“immune system” OR “immune mechanism” OR “immune response” OR “innate immunity” OR “adaptive immunity” OR “cytokine” OR “chemokine” OR “immune signaling” OR “immunopathogenesis”) AND (“infectious disease” OR “viral infection” OR “emerging virus” OR “SARS-CoV-2” OR “COVID-19” OR “influenza” OR “Zika” OR “, Nipah virus” OR “Swine flu” OR “Ebola” OR “MERS-CoV” OR “Mpox virus ” OR “Japanese Encephalitis Virus” OR “Chikungunya virus ” OR “Dengue Virus” OR “Marburg” OR “Enteroviruses” OR “Hepatitis Virus” OR “Dengue Virus” OR “Marburg” OR "Rift Valley fever OR "Crimean-Congo hemorrhagic fever" OR "Hantavirus" ). The search was limited to publications from January 2010 to January 2026. 2.4. Eligibility criteria This review included original experimental studies that used human organoid models to investigate immune responses to emerging viral infectious diseases as categorised by WHO [ 1 , 23 – 25 ]. Only peer-reviewed articles published between 2010 and January 2026 were considered. Only studies that reported measurable immune outcomes were included. Studies were included if they: utilized human-derived organoid models, investigated viral infections classified as emerging or re-emerging viral pathogens, reported measurable immune outcomes, including cytokine, chemokine, interferon, or immune signaling responses. Studies comparing viral strains, disease states, or organoid types were also eligible if they provided quantitative or qualitative evidence of immune modulation. Exclusion criteria included studies relying solely on 2D cell cultures or animal models, and 3D systems other than human organoids. Additionally, reviews, theses, editorials, conference abstracts, and computational-only studies were not considered. Research focusing on non-infectious diseases, such as cancer, neurodegeneration, or metabolic disorders, was omitted unless the model was explicitly designed to incorporate infectious or immune components. Studies that lacked immune readouts, such as those limited to toxicology, pharmacokinetics, or metabolism, were also excluded. 2.5 Study Selection All records identified through database searches and additional sources were imported into a reference management software for duplicate removal. Two reviewers independently screened titles and abstracts to assess eligibility based on the predefined inclusion and exclusion criteria. Studies considered potentially relevant were retrieved for full-text review. Full texts were independently assessed by the same two reviewers to determine final inclusion in the review. Discrepancies between reviewers were resolved through discussion and consensus. No automation tools were used during the screening process. 2.6 Data Collection Process Data extraction was performed independently by two reviewers using a standardized data extraction form developed for this study. Data from all eligible studies were systematically extracted using a standardized matrix developed in Microsoft Excel. The results were tabulated and displayed visually in structured tables and figures. The extracted information included details on the model type, as well as the target tissue or organ modelled, infectious pathogen type, and its associated host-pathogen infection mechanism. Information on the immune components integrated was also collected. Technological characteristics and data on translational outcomes were extracted to determine the applied relevance of each model. Extracted data were cross-checked to ensure accuracy and consistency. Any disagreements between reviewers were resolved through discussion and, where necessary, consultation with a third reviewer. When information was unclear or incomplete, the study was reviewed in detail to extract the most relevant available data. 2.7. Quality appraisal and risk of bias assessment All included studies were appraised using a modified version of the Joanna Briggs Institute (JBI) Critical Appraisal Checklist for Experimental Studies, adapted for in vitro human organoid models of viral infection [ 26 ]. The ten appraisal domains evaluated methodological clarity, organoid derivation and validation, infection protocol transparency, inclusion of mock or uninfected controls, biological replication, quantification of immune responses, assay validation, statistical analysis, reproducibility, and data transparency. Studies with incomplete reporting of infection models, immune readouts, or culture conditions were considered to have a higher risk of bias. Two reviewers independently assessed each study to ensure objectivity and consistency in evaluation. Any discrepancies in scoring or interpretation were resolved through discussion, and when consensus could not be reached, a third reviewer provided arbitration to finalize the quality rating. 2.8 Certainty of evidence The certainty of evidence was assessed qualitatively, recognizing that conventional grading tools such as GRADE are not directly applicable to preclinical in vitro data [ 27 ]. Confidence in the evidence was determined by examining the consistency, reproducibility, and physiological relevance of findings, as well as the transparency of reporting and support from translational or human data. Studies demonstrating reproducible outcomes and strong biological plausibility were rated as high certainty, whereas those with incomplete immune characterization or limited replication were rated low certainty. This approach ensured a contextual and transparent appraisal of the overall strength of the evidence base. 2.9. Evidence synthesis and data analysis Due to the methodological and biological diversity of included studies, quantitative meta-analysis was not feasible. Instead, a narrative synthesis approach was employed to integrate findings across different parameters used to synthesize this systematic review. 3. Results 3.1 Study selection The literature search identified 986 records from electronic databases, including PubMed (n = 345), Scopus (n = 310), and Web of Science (n = 331). After duplicate removal, 107 unique articles remained. Titles and abstracts were screened, resulting in 104 articles being assessed for full-text eligibility; three records were excluded because the full text could not be accessed. An additional 10 records were identified through citation tracking. In total, 114 studies published between January 2010 and January 2026 were assessed for eligibility. During full-text assessment, several studies were excluded based on predefined criteria. Specifically, 44 studies were excluded because they did not involve a selected virus or viral infection model or instead investigated vaccine responses. A further 35 studies were removed because they employed alternative 3D or 2D systems that did not meet the structural or functional definition of organoids. Additionally, 12 studies utilized non-human organoid models (e.g., bat-derived organoids) and were excluded to maintain human biological relevance. After applying predefined inclusion and exclusion criteria, 23 studies met the eligibility criteria and were included in the final qualitative synthesis (Fig. 1 ). 3.2 Study characteristics After all screening and eligibility phases, we found 23 studies, published between 2016 and 2025, were included in the final qualitative synthesis [ 28 – 50 ]. These studies represented diverse human organoid systems derived from induced pluripotent stem cells (hiPSCs; n = 9; 39.1%), adult stem cells (ASCs; n = 7; 30.4%), human embryonic stem cells (hESCs; n = 4; 17.4%), and human pluripotent stem cells (hPSCs; n = 3; 13%). A total of seven viral families were represented across the included studies, with Coronaviridae (SARS-CoV-2, MERS-CoV) being the most frequently investigated (n = 8; 34.8%), followed by Flaviviridae such as ZIKV, DENV, HCV, and JEV (n = 7; 30.5%). Orthomyxoviridae (Influenza A subtypes) accounted for three studies (13.0%), while Picornaviridae (Enteroviruses; n = 2; 8.7%) and Poxviridae (Mpox; n = 2; 8.7%) were less common. Studies involving Filoviridae (Ebola, Marburg), Togaviridae (Chikungunya) were limited to a single report each (4.3%), highlighting a research focus primarily on coronaviruses and flaviviruses in organoid-based infection models (Fig. 2 ). The studies represented four major tissue systems: neural (n = 9), respiratory (n = 6), intestinal (n = 6), and hepatic (n = 2) (Fig. 3 ). One study employed tumor-derived or diseased tissue organoids, while another integrated immune cells within a multi-lineage co-culture model [ 43 , 44 ]. Collectively, these studies provided quantitative and qualitative data on cytokine, chemokine, and interferon responses following viral infection, enabling comparative synthesis of host immune mechanisms across organoid systems. Fifteen studies examined viral infection and immunity, while seven focused primarily on organoid model characterization (Table 1 ). Table 1 Characteristics of Included Studies Investigating Antiviral Immune Responses in Human Organoid Models S.N. Study (Author, Year) Stem Cell Source Organoid Model Virus (Family) Key Immune Response 1 Dang et al., 2016 [ 28 ] hESC Cerebral organoids Zika virus (Flaviviridae) Activation of TLR3-mediated innate immune signaling. 2 Hui et al., 2018 [ 29 ] Adult stem cell–derived Airway organoids Influenza A virus (H1N1, H5N1, H7N9, H5N6) (Orthomyxoviridae) H5N1 induced higher IL-6, IFN-β, RANTES, and MCP-1 compared with other subtypes. 3 Muffat et al., 2018 [ 30 ] hiPSC Neural organoids Dengue virus (Flaviviridae) Strong upregulation of CXCL10, CCL5, IL-1β, and TNF-α. 4 Zhang et al., 2018 [ 31 ] hPSC Cortical organoids Japanese encephalitis virus (Flaviviridae) Activation of ISG15, ISG56, OAS1, and IFN-β signaling pathways. 5 Xu et al., 2019 [ 32 ] hESC Brain organoids Zika virus (Flaviviridae) Activation of TLR3 and RNA interference–mediated antiviral immunity. 6 Jacob et al., 2020 [ 33 ] hiPSC Choroid plexus and brain organoids SARS-CoV-2 (Coronaviridae) Upregulation of inflammatory cytokines including CCL7, IL-32, IL-18, and IL-8. 7 Yang et al., 2020 [ 34 ] hPSC Liver organoids SARS-CoV-2 (Coronaviridae) Upregulation of CXCL and CCL chemokines with activation of NF-κB and TNF signaling. 8 Yang et al., 2020 [ 34 ] hPSC Cholangiocyte organoids SARS-CoV-2 (Coronaviridae) Similar CXCL and CCL chemokine induction with NF-κB and TNF pathway activation. 9 Han et al., 2021 [ 35 ] hPSC Lung organoids SARS-CoV-2 (Coronaviridae) Upregulation of CXCL2, CCL2, IL1A, IL1B, and CXCL8; activation of NF-κB, TNF, and IL-17 pathways. 10 Han et al., 2021 [ 35 ] hPSC Colonic organoids SARS-CoV-2 (Coronaviridae) Differential cytokine and chemokine expression indicating active innate immune signaling. 11 Pei et al., 2021 [ 36 ] hESC Airway organoids SARS-CoV-2 (Coronaviridae) Induction of ISGs (IFITM3, MX1, ATF3, GEM) and activation of NF-κB signaling. 12 Tiwari et al., 2021 [ 37 ] hiPSC Lung organoids SARS-CoV-2 (Coronaviridae) Strong IFN-β induction with elevated IL-6, IL-8, CCL5, and CXCL10. 13 Zhao et al., 2021 [ 38 ] Adult stem cell–derived Intestinal organoids Coxsackievirus A16 (Picornaviridae) Weak induction of IFN-λ and inflammatory cytokines compared with EV-A71. 14 Zhao et al., 2021 [ 38 ] Adult stem cell–derived Intestinal organoids Enterovirus A71 (Picornaviridae) Robust IFN-λ1/λ3 and ISG activation (OAS1, MX1, IFIT1) with IL-6 and TNF-α production. 15 Zhao et al., 2021 [ 38 ] Adult stem cell–derived Intestinal organoids SARS-CoV (Coronaviridae) Minimal induction of IFN or interferon-stimulated genes. 16 Zhao et al., 2021 [ 38 ] Adult stem cell–derived Intestinal organoids SARS-CoV-2 (Coronaviridae) Strong IFN-λ signaling and ISG activation with elevated IL-6. 17 Krenn et al., 2021 [ 39 ] hESC Brain organoids Zika virus (Flaviviridae) Upregulation of ISGs with moderate IFN-β activation. 18 Schultz et al., 2021 [ 40 ] hiPSC Cerebral organoids Chikungunya virus (Togaviridae) Upregulation of IL-6, IL-10, CCL2, CCL3, and CXCL10; stronger response in Parkinson’s-derived organoids. 19 Tsang et al., 2021 [ 41 ] Adult stem cell–derived Small intestinal organoids Enterovirus A71 (Picornaviridae) Increased TNF-α, IP-10, MCP-1, and RANTES with IFN-λ2/3 and ISG induction. 20 Salgueiro et al., 2022 [ 42 ] Adult stem cell–derived 3D lung organoids Influenza A virus (Orthomyxoviridae) Strong innate immune activation with IL-6, IFN-β, IL-29, CXCL10, and CXCL9 induction. 21 Natarajan et al., 2022 [ 43 ] Adult stem cell–derived Liver organoids with CD8⁺ T-cell coculture Hepatitis C virus (Flaviviridae) Activation of CD8⁺ T cells with strong IFN-γ secretion. 22 Flores et al., 2025 [ 44 ] hiPSC Intestinal organoids Ebola virus (Filoviridae) Elevated IL-6, TNF-α, and CCL5 with modest IFNB1 and MX1 induction. 23 Flores et al., 2025 [ 44 ] hiPSC Intestinal organoids Marburg virus (Filoviridae) Strong MX1, IFNB1, CXCL10, IL-6, TNF-α, and CCL5 activation. 24 Flores et al., 2025 [ 44 ] hiPSC Colonic organoids Ebola virus (Filoviridae) Moderate cytokine induction with mild interferon response. 25 Flores et al., 2025 [ 44 ] hiPSC Colonic organoids Marburg virus (Filoviridae) Higher IFN-β and ISG activation compared with Ebola infection. 26 Xu et al., 2025 [ 45 ] Adult stem cell–derived Macrophage-augmented intestinal organoids SARS-CoV-2 (Coronaviridae) Strong ISG activation (MX1, ISG15, IFIT1, STAT1) and cytokine production (IL-1β, IL-6, TNF-α). 27 Nakata et al., 2025 [ 46 ] hiPSC Lung organoids Mpox virus (Poxviridae) Minimal immune activation with limited cytokine or interferon induction. 28 Schultz-Pernice et al., 2025 [ 47 ] hiPSC Neural organoids Mpox virus (Poxviridae) Weak innate immune response with mild IFN-β, IL-6, IL-8, and CXCL10 upregulation. 29 Choo et al., 2025 [ 48 ] hiPSC Cerebral organoids Zika virus (Flaviviridae) Induction of type I interferons and ISGs including IFI44, IFIT1, DDX58, and OAS3. 30 Rothan et al., 2025 [ 49 ] Adult stem cell–derived Airway organoids H5N1 influenza virus (Orthomyxoviridae) Robust IFN and NF-κB activation with increased IL-6, IL-8, TNF-α, and CXCL10. 31 Chiok et al., 2025 [ 50 ] hiPSC Lung organoids SARS-CoV-2 (Coronaviridae) Upregulation of IFIT1, MX1, OAS1, STAT1, and RSAD2 with strong IFN-β activation. 32 Chiok et al., 2025 [ 50 ] hiPSC Lung organoids MERS-CoV (Coronaviridae) Attenuated interferon signaling with elevated IL-1β-mediated inflammatory responses. The heat map further illustrated that the Coronaviridae were the most extensively studied viral family, spanning multiple organoid systems, particularly respiratory and intestinal models, reflecting their broad tissue tropism. Flaviviridae infections were modeled mainly in neural organoids, consistent with their neurotropic infection patterns. Orthomyxoviridae were primarily studied in respiratory organoids, aligning with their pulmonary pathogenesis. In contrast, Picornaviridae and Filoviridae were predominantly modeled in intestinal organoids, while Poxviridae and Togaviridae showed limited but diverse representation across neural and respiratory systems. This distribution highlights how organoid selection closely mirrors the tissue specificity of viral infection and disease (Fig. 4 ). 3.3 Chronological evolution and application of human-derived organoids in viral immunology Human-derived organoid technology, first established in the early 2010s, revolutionized in vitro modeling of tissue physiology and disease. These three-dimensional structures have since evolved to replicate complex tissue architecture and elements of immune competence. The earliest application in viral pathogenesis was reported by Dang et al. (2016), who used hESC-derived cerebral organoids to model ZIKV infection, revealing Toll-like receptor 3 (TLR3) activation and neuronal depletion, establishing brain organoids as a relevant platform for neurotropic viruses [ 28 ]. Between 2018 and 2019, studies by Hui et al. [ 29 ], Muffat et al. [ 30 ], Zhang et al. [ 31 ], and Xu et al. [ 32 ] extended organoid use to model influenza, DENV, and JEV infections. These confirmed canonical interferon (IFN) and cytokine responses, particularly Type I and Type III IFNs, and highlighted tissue-specific susceptibility to viral infection. The COVID-19 pandemic (2020–2021) marked a rapid expansion in organoid-based SARS-CoV-2 research. Studies such as Jacob et al. [ 33 ] and Yang et al. [ 34 ] employed hiPSC- and hPSC-derived organoids from the choroid plexus, liver, and cholangiocytes, revealing activation of NF-κB and TNF pathways and increased IL-6, IL-8, and TNF-α. Han et al. [ 35 ] and Pei et al. [ 36 ] used lung and colonic organoids to demonstrate robust interferon-stimulated gene (ISG) responses and chemokine activation. Adult stem cell–derived intestinal organoids-maintained tissue-specific antiviral mechanisms characterized by IFN-λ induction and ISG activation [ 38 ]. Organoid models were also applied to investigate virus-specific host responses and neurological outcomes, including studies demonstrating differential responses to Zika virus and herpes simplex virus infections as well as disease-specific susceptibility in cerebral organoids [ 39 , 40 ]. This chronological illustration shows early studies primarily focused on Flaviviridae viruses, whereas Coronaviridae became the most studied family after 2020. Recent studies increasingly target diverse viral families to analyse innate antiviral signaling across tissues (Fig. 5 ). 3.4 Antiviral immune responses The systematic review identified 32 antiviral immune responses across studies. Most studies investigated a single viral pathogen; however, several studies compared two viral species [ 28 – 50 ]. The review noted that antiviral immune responses in human organoid models varied substantially depending on the viral family and summarized in Table 2 . Across studies, antiviral responses were primarily characterized by activation of type I and type III interferon pathways, induction of interferon-stimulated genes (ISGs), and increased production of pro-inflammatory cytokines and chemokines including IL-6, TNF-α, CXCL10, and CCL5. Distinct tissue-specific immune profiles were also observed. For example, neural organoids frequently exhibited TLR3-mediated antiviral signaling and apoptosis, airway organoids showed strong interferon and cytokine responses, and intestinal organoids demonstrated epithelial IFN-λ–dominated antiviral signaling. Table 2 Summary of Antiviral Immune Responses by Virus Family No. Virus Family Representative Viruses (Studies) Organoid Model Key Immune Pathways Major Immune Mediators (Upregulated) Biological Outcome 1 Flaviviridae Zika virus (ZIKV) [ 28 , 30 , 32 , 39 , 48 ]; Dengue virus (DENV) [ 30 ]; Japanese encephalitis virus (JEV) [ 31 ]; Hepatitis C virus (HCV) [ 43 ] Neural, cerebral, cortical organoids; liver organoids TLR3/TLR7 activation; RIG-I–like receptor signaling; Type I interferon pathway; antigen presentation IFN-α/β, OAS1, MX1, IFIT1, IFITM3, CXCL10, IL-6, TNF-α Strong Type I IFN activation and ISG expression; neuronal apoptosis and progenitor depletion; neuroinflammation; immune–epithelial interaction modeling 2 Coronaviridae SARS-CoV-2 [ 33 – 38 , 50 ]; MERS-CoV [ 50 ]; SARS-CoV [ 38 ]; HCV-OC43 [ 38 ] Lung, airway, colonic, hepatic, intestinal, macrophage-augmented intestinal organoids Type I (IFN-β) and Type III (IFN-λ) interferon signaling; NF-κB and TNF pathways IFITM3, MX1, OAS1, ISG15, CXCL10, IL-6, TNF-α, IL-1β, CCL5 Strong antiviral and inflammatory signaling; tissue-specific IFN responses (IFN-λ dominant in gut, IFN-β in lung); cytokine storm–like responses 3 Orthomyxoviridae Influenza A virus (H1N1, H5N1, H7N9) [ 29 , 42 , 49 ] Airway and lung organoids Type I interferon–NF-κB signaling; cytokine–chemokine receptor pathways IFN-β, IL-6, TNF-α, MCP-1, CXCL10, CXCL9, IL-29 Robust cytokine and chemokine release; epithelial inflammation; attenuated antiviral responses in tumor-derived organoids 4 Filoviridae Ebola virus (EBOV); Marburg virus (MARV) [ 44 ] Intestinal and colonic organoids Type I interferon signaling; proinflammatory cytokine pathways IFNB1, MX1, CXCL10, IL-6, TNF-α, CCL5 MARV induces stronger IFN and ISG activation than EBOV; high inflammatory responses consistent with hemorrhagic viral infection 5 Poxviridae Mpox virus (MPXV) [ 46 , 47 ] Lung and neural organoids Weak interferon induction; partial NF-κB activation IFN-β, IL-6, IL-8, CXCL10 Limited innate activation in lung models; mild cytokine induction in neural organoids suggesting viral immune evasion 6 Togaviridae Chikungunya virus (CHIKV) [ 40 ] Cerebral organoids NF-κB and pro-inflammatory cytokine signaling IL-6, IL-10, CCL2, CCL3, CXCL10 Neuroinflammatory responses; exaggerated cytokine signaling in Parkinson’s disease–derived organoids indicating host susceptibility 7 Picornaviridae Enterovirus A71 (EV-A71); Coxsackievirus A16 (CVA16) [ 38 , 41 ] Intestinal and small intestinal organoids Type III interferon (IFN-λ1/λ3) signaling; epithelial antiviral responses IFN-λ1, IFN-λ3, IFI44L, IFIT3, HERC5, IL-6, TNF-α, IP-10, RANTES Strong IFN-λ–mediated antiviral response; moderate inflammation; CVA16 induces weaker IFN signaling than EV-A71 3.4.1 Influence of organoid origin and architecture The origin and structural architecture of human organoid systems represent critical determinants of antiviral immune responses. Across the reviewed studies, organoid derivation from pluripotent stem cells (hPSCs, hESCs, or iPSCs) or adult stem cells (ASCs), together with differences in tissue differentiation and structural complexity (e.g., three-dimensional organization or immune cell co-culture), influenced the magnitude and dynamics of antiviral immune signaling following infection. Organoids derived from pluripotent stem cells generally exhibited a more immunologically “primed” phenotype, characterized by rapid interferon induction and strong activation of interferon-stimulated genes. Studies using hPSC-derived lung, colonic, and hepatic organoids demonstrated activation of NF-κB, TNF, and IL-17 signaling pathways, accompanied by increased expression of chemokines including CXCL8, CCL2, and CXCL10 following SARS-CoV-2 infection [ 34 , 35 ]. Similarly, hESC-derived airway and alveolar organoids displayed strong type I and type III interferon responses with upregulation of antiviral genes such as IFITM3, MX1, ATF3, and RELB, together with increased cytokine production (IL-6, TNF, CXCL10) [ 36 ]. In contrast, adult stem cell–derived intestinal and hepatic organoids typically showed more restrained interferon responses but increased inflammatory cytokine production. For example, ASC-derived intestinal organoids infected with EBOV or MARV demonstrated moderate IFN-β induction but substantial release of inflammatory mediators such as IL-6, TNF-α, and CCL5 [ 44 ]. Organoid architecture further influenced infection dynamics and immune responses. Three-dimensional epithelial organization preserves tissue polarity, receptor distribution, and multicellular interactions, all of which are essential for physiologic viral entry and innate immune signaling. In lung organoid models, air–liquid interface (ALI) cultures that preserved apical–basal polarity demonstrated enhanced viral replication and stronger interferon responses compared with organoid-derived monolayers lacking structural polarity [ 50 ]. Incorporation of additional cell types also enhanced immune fidelity. Macrophage-augmented intestinal organoids (MaugOs) produced amplified cytokine and interferon responses, including IL-1β, IL-6, TNF-α, MX1, and ISG15, highlighting the importance of immune–epithelial crosstalk in antiviral defense [ 45 ]. Conversely, tumor-derived lung organoids exhibited reduced interferon signaling and impaired antiviral gene induction, likely reflecting oncogenic reprogramming and epigenetic suppression of innate immune pathways [ 42 ]. Immune responses were additionally influenced by tissue lineage and developmental maturity. Barrier tissues such as respiratory and intestinal organoids predominantly activated type I and type III interferon pathways, whereas neural organoids relied more heavily on TLR-mediated viral sensing mechanisms and displayed comparatively restricted cytokine responses [ 28 , 38 , 41 , 48 ]. Developmental maturity also affected antiviral competence; immature organoids often showed increased viral permissiveness and reduced interferon signaling. For instance, early-stage cortical organoids infected with JEV failed to induce IFN-β and exhibited extensive cell death, whereas more mature organoids (> 8 weeks) activated robust RIG-I–STAT1–ISG pathways, limiting viral replication [ 31 ]. Additionally, within the respiratory lineage, alveolar-type organoids showed stronger antiviral and apoptotic signatures than less differentiated airway counterparts, reflecting the acquisition of cell-type–specific immune identity with maturation [ 36 ]. 3.4.2 Influence of virus type on antiviral immune responses Flaviviridae infections were the most frequently modeled in early organoid studies (2016–2019), primarily using neural organoids derived from hESCs or hiPSCs. ZIKV infection consistently triggered strong type I interferon responses and activation of interferon-stimulated genes, including OAS1, MX1, and IFITM3, often accompanied by neuronal apoptosis and depletion of progenitor populations [ 28 , 32 , 39 , 48 ]. Dengue virus infection produced a comparatively stronger pro-inflammatory cytokine profile, including CXCL10, CCL5, IL-1β, and TNF-α, indicating virus-specific differences in immune activation within similar organoid systems [ 30 ]. Japanese encephalitis virus induced canonical interferon signaling pathways involving IFN-β, ISG15, and OAS1, consistent with the establishment of antiviral cellular states [ 31 ]. From 2020 onward, Coronaviridae infections dominated organoid-based viral immunology studies. SARS-CoV-2 infection across lung, intestinal, hepatic, and macrophage-augmented organoids consistently induced interferon responses and chemokine production, including upregulation of MX1, IFITM3, CXCL10, and IL-6 [ 35 – 38 ]. Activation of NF-κB, TNF, and IL-17 signaling pathways was observed in both respiratory and gastrointestinal organoids [ 34 , 35 ]. Intestinal organoids also demonstrated stronger IFN-λ responses to SARS-CoV-2 than to SARS-CoV, highlighting tissue-specific differences in antiviral signaling [ 38 ]. In contrast, MERS-CoV infection produced a relatively weaker interferon response but increased IL-1β expression, suggesting a more inflammatory immune profile [ 50 ]. Influenza virus infections in airway and lung organoids demonstrated typical type I interferon and NF-κB activation patterns [ 29 , 42 , 49 ]. Highly pathogenic influenza strains such as H5N1 induced higher levels of inflammatory mediators, including IL-6, IFN-β, and MCP-1 compared with seasonal strains [ 29 ]. Some studies also reported activation of TGF-β signaling and elevated IL-6 and TNF-α expression, suggesting involvement of inflammatory and fibrotic pathways during severe infection [ 49 ]. Filoviridae infections in intestinal organoids revealed strong but differential immune activation. Both EBOV and MARV induced cytokines such as IL-6, TNF-α, and CCL5 together with interferon-stimulated genes including MX1 and IFNB1, although MARV elicited stronger interferon responses than EBOV [ 44 ]. Other viruses demonstrated more restricted immune activation patterns. Mpox virus infection in lung organoids resulted in minimal cytokine induction, whereas neural organoids showed modest increases in IFN-β, IL-6, and CXCL10 [ 46 , 47 ]. Chikungunya virus infection of cerebral organoids induced neuroinflammatory cytokines including IL-6, IL-10, CCL2, and CXCL10 [ 40 ]. Enterovirus infections in intestinal organoids elicited strong type III interferon responses, accompanied by ISG activation and inflammatory cytokine production [ 38 , 41 ]. Finally, a microfluidic co-culture system combining liver organoids with CD8⁺ T cells demonstrated enhanced IFN-γ production and T-cell activation during hepatitis C virus infection, representing a model capable of recapitulating both innate and adaptive immune responses [ 43 ]. 3.4.3. Influence of organoid type on antiviral immune responses The type of organoid used strongly influenced the magnitude and nature of antiviral immune responses, reflecting intrinsic tissue-specific immune properties and viral tropism. Neural organoids were the most frequently employed system, particularly for neurotropic viruses such as ZIKV, JEV, Chikungunya virus, and Mpox virus. Flavivirus infections typically induced strong type I interferon signaling and ISG activation, often leading to apoptosis of neural progenitor cells [ 28 , 31 , 32 ]. Additional studies reported upregulation of antiviral sensors including IFI44, DDX58, and TRIM22, reflecting activation of TLR3 and RIG-I pathways in cerebral organoids [ 39 , 48 ]. In contrast, Mpox and Chikungunya infections produced more moderate cytokine responses dominated by IL-6 and CXCL10, consistent with the immune-privileged environment of neural tissues [ 40 , 47 ]. Respiratory organoids exhibited the most robust antiviral immune responses across organoid systems. SARS-CoV-2 infection consistently induced strong type I and III interferon signaling together with NF-κB-mediated cytokine production, including IL-6, CXCL10, TNF-α, and CCL5 [ 35 – 37 , 50 ]. In contrast, MERS-CoV produced attenuated IFN signaling but elevated IL-1β, implying a preferential pro-inflammatory response [ 50 ]. Similar patterns were observed during influenza virus infection, whereas tumor-derived lung organoids exhibited blunted antiviral signaling [ 29 , 42 ]. Intestinal and colonic organoids displayed antiviral responses dominated by type III interferon (IFN-λ) signaling, reflecting the physiological antiviral barrier of the gastrointestinal epithelium. Enterovirus infections triggered strong ISG activation and cytokine production, whereas SARS-CoV-2 infection induced potent IFN-λ responses and antiviral gene expression [ 38 , 41 ]. More complex systems, such as macrophages, further amplified inflammatory signaling and interferon responses, illustrating the importance of immune–epithelial interactions in mucosal antiviral defense [ 45 ]. EBOV and MARV induced high levels of IL-6, TNF-α, CCL5, and IFNB1, with MARV exhibiting a stronger IFN-driven signature than Ebola [ 44 ]. Hepatic organoids demonstrated integrated antiviral and metabolic immune responses. SARS-CoV-2 infection of liver and cholangiocyte organoids activated NF-κB, TNF, and IL-17 pathways together with chemokine induction [ 34 ]. In contrast, hepatitis C virus infection modeled using liver organoid–T cell co-cultures produced strong IFN-γ responses and T-cell activation, highlighting the potential of these systems for studying chronic viral infections and adaptive immune interactions [ 43 ]. 3.5 Quality Appraisal and Risk of Bias Assessment Overall, the methodological quality of the included literature was generally high across studies. Out of 23 studies, all scored between 9 and 10 points on the modified Joanna Briggs Institute appraisal scale, meeting the threshold for high methodological quality and low risk of bias. Six studies demonstrated minor reporting limitations, primarily related to the specification of biological replicates and the availability of raw data. These studies were therefore scored slightly lower (9.0–9.5 points) but remained within the high-quality range. No study met the criteria for exclusion due to poor methodological quality or unclear reporting. However, some variability in reporting standards was observed, particularly regarding experimental replication and detailed methodological descriptions. The overall quality assessment is summarized in Supplementary Table 2. 3.6 Certainty of Evidence for Organoid-Based Viral Infection Studies Overall, the body of evidence demonstrated high to moderate certainty, supported by generally strong methodological quality, reproducibility across studies, and consistent immunological outcomes reported in multiple laboratories. Studies investigating SARS-CoV-2, Influenza A, ZIKV, and filoviruses (Ebola and Marburg) provided the most robust evidence, demonstrating reproducible activation of interferon signaling pathways and cytokine responses across several independent organoid systems. In contrast, moderate certainty was assigned to studies involving MERS-CoV, Mpox virus, and Chikungunya virus, primarily due to the limited number of available studies and narrower range of organoid models used. The overall certainty assessment is summarized in Supplementary Table 3. 4. Discussion This systematic review provides a comprehensive synthesis of current evidence on human organoid–based models for studying emerging viral infections and host immune responses. Although three-dimensional tissue culture predates the modern term organoid, the advent of human-induced pluripotent stem cell (hiPSC) technology in 2007 marked a transformative milestone in regenerative biology and infection modeling [ 51 , 52 ]. Between 2007 and 2015, most studies were devoted to establishing proof-of-concept and elucidating the mechanisms underlying organoid formation [ 53 ]. The ability to reprogram adult somatic cells into pluripotent states created new opportunities to derive human cell populations capable of differentiating into multiple tissue types, thereby facilitating advanced in vitro disease modeling [ 54 ]. From approximately 2015 onward, the field transitioned from early experimental systems toward human organoid platforms derived from pluripotent and adult stem cells [ 55 ]. During this period, improved differentiation protocols enabled the generation of organoids that closely replicate the physiological and pathological processes of their organ of origin while retaining human genetic and immunological characteristics [ 54 , 55 ]. Consequently, all studies included in this review were published between 2016 and 2025, despite our search extending back to 2010, reflecting the relatively recent expansion of organoid-based infectious disease research. Advances in stem cell biology have enabled the development of diverse organoid systems, including neural, hepatic, respiratory, renal, and gastrointestinal models [ 56 , 57 ]. Our synthesis identified studies employing organoids derived from pluripotent, embryonic, and adult stem cells to model infections caused by seven viral families: Coronaviridae, Flaviviridae, Orthomyxoviridae, Filoviridae, Togaviridae, Poxviridae, Picornaviridae. Collectively, these studies demonstrate that human organoids are capable of recapitulating virus-specific cellular tropism, interferon-mediated innate immune signaling, and cytokine-driven inflammatory responses, closely resembling host responses observed in vivo. Compared with conventional two-dimensional (2D) cell culture systems, organoids provide a more physiologically relevant microenvironment, preserving cellular heterogeneity, tissue polarity, and spatial receptor distribution [ 5 , 60 ]. These structural features allow improved modeling of viral entry, replication, and host immune signaling. For example, lung organoid models reproduce interferon and cytokine responses to SARS-CoV-2 infection that closely resemble those observed in human airway tissues, whereas commonly used cell lines such as Vero E6 or A549 exhibit markedly reduced interferon responses [ 35 , 40 , 61 ]. Similarly, cerebral organoids infected with ZIKV reproduce neuroinflammatory and apoptotic responses observed in human fetal brain tissue—responses that are not captured in conventional neural progenitor cultures [ 28 , 32 ]. Human organoid models also provide advantages over animal systems by enabling the study of viral pathogenesis within a human genetic and immunological context, thereby avoiding species-specific immune differences. For example, ZIKV induces TLR3-mediated neuronal apoptosis in human cerebral organoids but not in murine brains unless interferon signaling is experimentally suppressed [ 28 , 62 , 63 ]. Non-human primate organoids exhibit partial overlap in interferon-stimulated gene expression but lack the magnitude of TLR3 activation observed in human-derived models [ 64 ]. These findings highlight the importance of human-specific tissue systems for investigating viral neurotropism and host immune responses. Similarly, lung and intestinal organoids demonstrate robust activation of type I and type III interferon pathways in response to SARS-CoV-2 infection, whereas many conventional cell culture models display limited or dysregulated antiviral signaling [ 37 , 40 , 65 , 66 ]. Studies using bat-derived organoids, although limited, further demonstrate species-specific differences in viral replication kinetics and interferon responses [ 67 – 71 ]. In contrast, widely used cell lines such as Vero E6 permit efficient viral replication but lack functional type I interferon responses, limiting their utility for studying host antiviral immunity [ 72 , 73 ]. Organoid models have also proven valuable for studying additional viral pathogens. For example, influenza virus infection in human airway organoids reproduces viral replication dynamics together with cytokine responses resembling those observed in severe respiratory infections, including elevated IL-6, IL-8, and IFN-β levels [ 29 , 50 ]. Similarly, intestinal organoid systems have demonstrated differential immune responses to EBOV and MARV infection, with MARV eliciting stronger interferon activation than EBOV [ 44 ]. In addition to modeling viral infection, organoid platforms have provided insights into viral immune evasion strategies. Mpox virus, for example, employs multiple mechanisms to suppress innate immune signaling, including inhibition of cytokine pathways, complement activation, and inflammasome signaling [ 78 ]. In human lung and neural organoids, Mpox infection produced relatively attenuated interferon responses, which may contribute to its ability to establish persistent infection. Such findings highlight the potential of organoid systems to elucidate mechanisms of viral immune modulation and host susceptibility. Collectively, the evidence synthesized in this review indicates that human organoids provide physiologically relevant experimental platforms that bridge the gap between oversimplified cell culture systems and species-limited animal models. By preserving human tissue architecture and immune signaling networks, organoids offer valuable tools for investigating viral pathogenesis, antiviral immunity, and preclinical therapeutic strategies. 5. Limitations Several limitations should be considered when interpreting the findings of this review. Although a comprehensive search strategy was applied, some relevant studies may not have been identified, particularly unpublished data or studies reported in non-indexed sources. Additionally, the included studies exhibited methodological heterogeneity, including differences in stem cell sources, differentiation protocols, organoid maturation stages, and infection models. Such variability may influence immune responsiveness and complicate direct comparison across studies. Variations in experimental design were also observed in the measurement and reporting of immune outcomes, including cytokine assays, transcriptomic analyses, and viral replication metrics. The absence of standardized protocols for organoid infection experiments, therefore, limits cross-study comparability. Another potential limitation is publication bias, as studies demonstrating successful infection models or significant immune responses are more likely to be published than studies reporting negative or inconclusive findings. Finally, although organoid models provide valuable human-specific insights, they still lack certain physiological components present in vivo , including fully developed vascular networks, systemic immune interactions, and long-term tissue remodeling processes. These limitations highlight the need for continued development of immune-integrated and vascularized organoid platforms. 6. Implications and Future Research The results of this review highlight the value of human organoid models for studying emerging viral infections and host immune responses. For research practice, organoid systems offer a more physiologically relevant experimental platform than conventional cell lines, enabling improved investigation of viral tropism, host immune signaling, and antiviral drug responses. In translational and clinical research contexts, organoid models hold considerable promise for patient-specific disease modeling and therapeutic screening, supporting the development of precision medicine approaches for infectious diseases. The integration of standardized organoid methodologies into regulatory and ethical frameworks could enhance reproducibility and reduce dependence on animal models. Collaboration between research institutions and policy agencies is essential to promote data sharing and protocol harmonization. Future research should focus on several key priorities. These include the development of immune-competent organoid models incorporating innate and adaptive immune cells, the integration of vascular and stromal components to better mimic tissue physiology, and the establishment of standardized protocols for viral infection assays and immune response measurements. In addition, multicenter collaborations and shared experimental platforms will be essential to improve reproducibility, protocol harmonization, and data comparability across laboratories. Such efforts will strengthen the evidence base supporting organoid technologies and facilitate their translation into preclinical antiviral research and therapeutic development. 7. Conclusion Over the past decade, human organoid models have emerged as powerful and physiologically relevant tools for studying viral pathogenesis and innate immunity. Across diverse tissue systems and viral families, organoids consistently replicate human-specific interferon and cytokine signaling, providing critical insights into host–virus interactions. The evolution from early neural organoids to advanced immune-cocultured constructs reflects the field’s transition toward functional complexity and translational relevance. Collectively, these findings position human organoids at the forefront of preclinical virology, bridging experimental and clinical domains in the study of emerging infectious diseases. Abbreviations ASCs Adult Stem Cells DCs Dendritic Cells DENV Dengue Virus EBOV Ebola Virus EIDs Emerging and Re-emerging Infectious Diseases hESCs Human Embryonic Stem Cells hiPSCs Induced Pluripotent Stem Cells hPSCs Human Pluripotent Stem Cells JEV Japanese Encephalitis Virus MARV Marburg Virus OOC Organ-on-a-Chip SARS Severe Acute Respiratory Syndrome TLR3 Toll-Like Receptor 3 ZIKV Zika Virus Declarations Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare that they have no competing interests Funding: Nil Author Contribution Conceptualization, A.K.; methodology, A.K. and M.B.; software, A.K. and M.B; validation, A.K., S.C., and M.B.; formal analysis, S.C.; investigation, A.K. and S.C.; data curation, AK.; writing original draft preparation, AK. Writing, review, and editing, A.K., S.C., and M.B.; visualization, A.K.; supervision, S.C. and M.B; project administration, A.K. All authors have read and agreed to the published version of the manuscript. Acknowledgement We acknowledge Dr. Deepti Srivastava, Ph.D., Nimble Scholars, India, for providing support in scientific editing and formatting the manuscript. Availability of data and materials: The datasets used and/or analysed during the current study are available from the corresponding author. References World Health Organization (2016) Regional Office for South-East Asia. A brief guide to emerging infectious diseases and zoonoses. WHO-SEARO, New Delhi, pp 3–48 Wang S, Li W, Wang Z, Yang W, Li E, Xia X et al (2024) Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduct Target Ther 9(1):223 Banik A, Basu S (2025) Drivers and consequences of viral zoonoses: public health and economic perspectives. Zoonotic Dis 5(4):32 Ristori MV, Guarrasi V, Soda P, Petrosillo N, Gurrieri F, Longo UG et al (2024) Emerging microorganisms and infectious diseases: one health approach for health shared vision. Genes 15(7):908 Al-Kabani A, Huda B, Haddad J, Yousuf M, Bhurka F, Ajaz F et al (2025) Exploring experimental models of colorectal cancer: a critical appraisal from 2D cell systems to organoids, humanized mouse avatars, organ-on-chip, CRISPR engineering, and AI-driven platforms. Cancers 17(13):2163 Adesina PA, Ooka M, TeKrony C, Xia M (2025) Emerging advances in intestinal models for in vitro preclinical research. Am J Physiol Gastrointest Liver Physiol. ;329(3) Pun S, Haney LC, Barrile R (2021) Modelling human physiology on-chip: historical perspectives and future directions. Micromachines (Basel) 12(10):1250 Mittal R, Woo FW, Castro CS et al (2019) Organ-on-chip models: implications in drug discovery and clinical applications. J Cell Physiol 234:8352–8380 Bassi G, Grimaudo MA, Panseri S, Montesi M (2021) Advanced multi-dimensional cellular models as emerging reality to reproduce in vitro the human body complexity. Int J Mol Sci 22(3):1195 Gouveia Z, Özkan A, Giannobile WV, Santerre JP, Wu DT (2025) Oral tissue spheroid, organoid, and organ-on-chip microphysiological modeling strategies towards enhanced emulation of health and disease. Bioeng Transl Med Zhang X, Liu H, Cheng H, Cui Y, Wang J, Yao Q et al (2025) In vitro biomimetic models for respiratory diseases: progress in lung organoids and lung-on-a-chip. Stem Cell Res Ther 16(1):415 Majorova D, Atkins E, Martineau H, Vokral I, Oosterhuis D, Olinga P et al (2021) Use of precision-cut tissue slices as a translational model to study host-pathogen interaction. Front Vet Sci 8:686088 Hammel JH, Cook SR, Belanger MC, Munson JM, Pompano RR (2021) Modeling immunity in vitro: slices, chips, and engineered tissues. Annu Rev Biomed Eng 23:461–491 Cherne MD, Sidar B, Sebrell TA, Sanchez HS, Heaton K, Kassama FJ et al (2021) A synthetic hydrogel improves immune cell-epithelial interactions in a tissue chip co-culture model of human gastric organoids and dendritic cells. Front Pharmacol 12:707891 Aguilar C, Alves da Silva M, Saraiva M, Neyazi M, Olsson IA, Bartfeld S (2021) Organoids as host models for infection biology: a review of methods. Exp Mol Med 53(10):1471–1482 Iakobachvili N, Peters PJ (2017) Humans in a dish: the potential of organoids in modeling immunity and infectious diseases. Front Microbiol 8:2402 Li T, Peng D, Yao M, Li M, Wang Y, Li S et al (2025) Immune organoids: emerging platforms for modeling and analyzing human adaptive immunity. Front Immunol 16:1632117 Li X, Xiao H, Zhou M, Yang C, Yang X, Cheng T et al (2025) Organoids in respiratory virus research: advances and perspectives. Mol Biomed 6(1):100 Ramadan Q, Hazaymeh R, Zourob M (2023) Immunity-on-a-chip: integration of immune components into organ-on-chip systems. Adv Biol 7(12):2200312 Li L, Xu Q, Zhao J, Qu Y, Luo Y, Zhang X (2025) Engineering immune microenvironments for organoid-on-a-chip systems. Med Mat. :10–97 Alonso-Roman R, Mosig AS, Figge MT, Papenfort K, Eggeling C, Schacher FH et al (2024) Organ-on-chip models for infectious disease research. Nat Microbiol 9(4):891–904 Moher D, Liberati A, Tetzlaff J, Altman DG (2009) Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. ;6 World Health Organization (2011) Asia Pacific strategy for emerging diseases. WHO-SEARO, New Delhi World Health Organization (2023) Emerging zoonotic diseases and the One Health approach: an overview [Internet]. WHO, Geneva. [cited 2026 Jan 15] World Health Organization. WHO launches global framework for understanding the origins of new or re-emerging pathogens [Internet] (2024) [cited 2026 Jan 15] Aromataris E, Fernandez R, Godfrey C, Holly C, Khalil H, Tungpunkom P (2015) Summarizing systematic reviews: methodological development, conduct and reporting of an umbrella review approach. Int J Evid Based Healthc 13(3):132–140 Guyatt GH, Oxman AD, Vist GE, Kunz R, Falck-Ytter Y, Alonso-Coello P et al (2008) GRADE: an emerging consensus on rating quality of evidence and strength of recommendations. BMJ 336(7650):924–926 Dang J, Tiwari SK, Lichinchi G, Qin Y, Patil VS, Eroshkin AM et al (2016) Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3. Cell Stem Cell 19(2):258–265. 10.1016/j.stem.2016.04.014 Hui KPY, Ching RHH, Chan SKH, Nicholls JM, Sachs N, Clevers H et al (2018) Tropism, replication competence, and innate immune responses of influenza virus: an analysis of human airway organoids and ex vivo bronchus cultures. Lancet Respir Med 6(11):846–854. 10.1016/S2213-2600(18)30236-0 Muffat J, Li Y, Omer A, Durbin A, Bosch I, Bakiasi G et al (2018) Human induced pluripotent stem cell-derived glial cells and neural progenitors display divergent responses to Zika and dengue infections. Proc Natl Acad Sci U S A 115(27):7117–7122. 10.1073/pnas.1719266115 Zhang B, He Y, Xu Y, Mo F, Mi T, Shen QS et al (2018) Differential antiviral immunity to Japanese encephalitis virus in developing cortical organoids. Cell Death Dis 9(7):719. 10.1038/s41419-018-0763-y Xu YP, Qiu Y, Zhang B, Chen G, Chen Q, Wang M et al (2019) Zika virus infection induces RNAi-mediated antiviral immunity in human neural progenitors and brain organoids. Cell Res 29(4):265–273. 10.1038/s41422-019-0152-9 Jacob F, Pather SR, Huang WK, Zhang F, Wong SZH, Zhou H et al (2020) Human pluripotent stem cell-derived neural cells and brain organoids reveal SARS-CoV-2 neurotropism predominates in choroid plexus epithelium. Cell Stem Cell 27(6):937–50e9. 10.1016/j.stem.2020.09.016 Yang L, Han Y, Nilsson-Payant BE, Gupta V, Wang P, Duan X et al (2020) A human pluripotent stem cell-based platform to study SARS-CoV-2 tropism and model virus infection in human cells and organoids. Cell Stem Cell 27(1):125–36e7. 10.1016/j.stem.2020.06.015 Han Y, Duan X, Yang L, Nilsson-Payant BE, Wang P, Duan F et al (2021) Identification of SARS-CoV-2 inhibitors using lung and colonic organoids. Nature 589(7841):270–275. 10.1038/s41586-020-2901-9 Pei R, Feng J, Zhang Y, Sun H, Li L, Yang X et al (2021) Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection. Stem Cell Rep 16(3):437–445. 10.1016/j.stemcr.2021.02.005 Tiwari SK, Wang S, Smith D, Carlin AF, Rana TM (2021) Revealing tissue-specific SARS-CoV-2 infection and host responses using human stem cell-derived lung and cerebral organoids. Stem Cell Rep 16(3):437–445. 10.1016/j.stemcr.2021.02.005 Zhao X, Fu Y, Liu J, Shi Y (2021) Human intestinal organoids recapitulate enteric infections of enterovirus and coronavirus. Stem Cell Rep 16(3):493–504. 10.1016/j.stemcr.2021.02.006 Krenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A et al (2021) Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Cell Stem Cell 28(8):1362–79e7. 10.1016/j.stem.2021.03.004 Schultz EM, Jones TJ, Xu S, Dean DD, Zechmann B, Barr KL (2021) Cerebral organoids derived from a Parkinson’s patient exhibit unique pathogenesis from Chikungunya virus infection when compared to a non-Parkinson’s patient. Pathogens 10(7):913. 10.3390/pathogens10070913 Tsang JO, Zhou J, Zhao X, Li C, Zou Z, Yin F et al (2021) Development of three-dimensional human intestinal organoids as a physiologically relevant model for characterizing the viral replication kinetics and antiviral susceptibility of enteroviruses. Biomedicines 9(1):88. 10.3390/biomedicines9010088 Salgueiro L, Kummer S, Sonntag-Buck V, Weiss A, Schneider MA, Kraeusslich HG et al (2022) Generation of human lung organoid cultures from healthy and tumor tissue to study infectious diseases. J Virol 96(7):e00098–e00022. 10.1128/jvi.00098-22 Natarajan V, Simoneau CR, Erickson AL, Meyers NL, Baron JL, Cooper S et al (2022) Modelling T-cell immunity against hepatitis C virus with liver organoids in a microfluidic coculture system. Open Biol 12(3):210320. 10.1098/rsob.210320 Flores EY, Hume AJ, Olejnik J, Mithal A, D’Amico A, Yang M et al (2025) Filovirus infection disrupts epithelial barrier function and ion transport in human iPSC-derived gut organoids. PLoS Pathog 21(11):e1013698. 10.1371/journal.ppat.1013698 Xu G, Zhou J, Liu K, Zhang P, Zhang Y, Wang Y et al (2025) Macrophage-augmented intestinal organoids model virus–host interactions in enteric viral diseases and facilitate therapeutic development. Nat Commun 16:4475. 10.1038/s41467-025-59639-9 Nakata Y, Uriu K, Hashimoto R, Yamamoto T, Saito A, Sato K et al (2025) Mpox virus replicates in lung organoids without significantly affecting their cellular function. Biochem Biophys Rep 44:102326. 10.1016/j.bbrep.2025.102326 Schultz-Pernice I, Fahmi A, Brito F, Behrens G, Krahling V, Schwemmle M (2025) Monkeypox virus spreads from cell-to-cell and leads to neuronal death in human neural organoids. Nat Commun 16:5376. 10.1038/s41467-025-61134-0 Choo YY, Tan TZ, Zhang SL, Chen MS, Chua ML, Tan NH et al (2025) Comparison of human cerebral organoids infected with wild-type Zika versus attenuated DN-2 virus strains uncovers differences in host immune responses. Cell Commun Signal 23(1):5888. 10.1186/s12964-025-02588-z Rothan H, Mostafa A, Bayoumi M, Ye C, Barre RS, Allué-Guardia A et al (2025) Emerging highly pathogenic H5N1 influenza triggers fibrotic remodeling in human airway organoids. Emerg Microbes Infect 14(1):2532684. 10.1080/22221751.2025.2532684 Chiok KL, Jenik K, Fenton M, Falzarano D, Dhar N, Banerjee A (2025) MERS-CoV and SARS-CoV-2 infection in diverse human lung organoid-derived cultures. J Virol 99(10):e01098–e01025. 10.1128/jvi.01098-25 Simian M, Bissell MJ (2017) Organoids: a historical perspective of thinking in three dimensions. J Cell Biol 216(1):31–40 Liu X, Zhou Z, Zhang Y, Zhong H, Cai X, Guan R (2025) Recent progress on organoids: techniques, advantages and applications. Biomed Pharmacother 185:117942 Jusop AS, Thanaskody K, Tye GJ, Dass SA, Wan Kamarul Zaman WS, Nordin F (2023) Development of brain organoid technology derived from iPSC for neurodegenerative disease modelling. Front Mol Neurosci 16:1173433 Doss MX, Sachinidis A (2019) Current challenges of iPSC-based disease modeling and therapeutic implications. Cells 8(5):403 Kim J, Koo BK, Knoblich JA (2020) Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol 21(10):571–584 Schutgens F, Clevers H (2020) Human organoids: tools for understanding biology and treating diseases. Annu Rev Pathol 15:211–234 Novelli G, Spitalieri P, Murdocca M, Centanini E, Sangiuolo F (2023) Organoid factory: the recent role of human induced pluripotent stem cells in precision medicine. Front Cell Dev Biol 10:1059579 Tang XY, Wu S, Wang D, Chu C, Hong Y, Tao M et al (2022) Human organoids in basic research and clinical applications. Signal Transduct Target Ther 7(1):168 Zhu S, Chen D, Yang X, Yang L, Han Y (2025) Organoid models to study human infectious diseases. Cell Prolif Fontoura JC, Viezzer C, Dos Santos FG, Ligabue RA, Weinlich R, Puga RD, Antonow D, Severino P, Bonorino C (2020) Comparison of 2D and 3D cell culture models for cell growth, gene expression and drug resistance. Mater Sci Engineering: C 107:110264 Geerling E, Pinski AN, Stone TE, DiPaolo RJ, Zulu MZ, Maroney KJ, Brien JD, Messaoudi I, Pinto AK Roles of antiviral sensing and type I interferon signaling in the restriction of SARS-CoV-2 replication. Iscience. 21;25(1):103553 Cugola FR, Fernandes IR, Russo FB et al (2016) The Brazilian Zika virus strain causes birth defects in experimental models. Nature 534(7606):267–271 Li C, Xu D, Ye Q et al (2016) Zika virus disrupts neural progenitor development. Cell Stem Cell 19(1):120–126 Qian X, Nguyen HN, Song MM et al (2018) Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165(5):1238–1254 Blanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, Møller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT (2020) Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181(5):1036–1045 Liu X, Li C, Wan Z, Chiu MC, Huang J, Yu Y, Zhu L, Cai JP, Rong L, Song YQ, Chu H (2022) Analogous comparison unravels heightened antiviral defense and boosted viral infection upon immunosuppression in bat organoids. Signal Transduct Target therapy 7(1):392 Zhou J, Li C, Liu X et al (2020) Infection of bat and human intestinal organoids by SARS-CoV-2. Nat Med 26(7):1077–1083 Ardestani A, Maedler K, Commentary (2020) A Human Pluripotent Stem Cell-Based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids. Front Endocrinol (Lausanne) 11:585922. 10.3389/fendo.2020.585922 Hashimi M, Sebrell TA, Hedges JF, Snyder D, Lyon KN, Byrum SD, Mackintosh SG, Crowley D, Cherne MD, Skwarchuk D, Robison A (2023) Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection. Nat Commun 14(1):6882 Han Y, Yang L, Lacko LA, Chen S (2022) Human organoid models to study SARS-CoV-2 infection. Nat Methods 19(4):418–428 Lamers MM, van der Vaart J, Knoops K et al (2020) Human airway and intestinal organoids as models of SARS-CoV-2 infection. Nat Med 26(7):1077–1083 Vicenti I, Boccuto A, Giannini A, Dragoni F, Saladini F, Zazzi M (2018) Comparative analysis of different cell systems for Zika virus (ZIKV) propagation and evaluation of anti-ZIKV compounds in vitro. Virus Res 244:64–70 Lui VC, Hui KP, Babu RO, Yue H, Chung PH, Tam PK, Chan MC, Wong KK (2022) Human liver organoid derived intra-hepatic bile duct cells support SARS-CoV-2 infection and replication. Sci Rep 12(1):5375 Punyadarsaniya D, Liang CH, Winter C, Petersen H, Rautenschlein S, Hennig-Pauka I, Schwegmann-Wessels C, Wu CY, Wong CH, Herrler G (2011) Infection of differentiated porcine airway epithelial cells by influenza virus: differential susceptibility to infection by porcine and avian viruses. PLoS ONE 6(12):e28429 Shokouhi H, Gholizadeh F, Sokhandan H, Sisakht MM, Mehrbod P (2025) From monolayer to spheroid: assessing influenza a virus infection in 2D and 3D cell culture of A549 and HEK293. Virol J 22(1):309 Kuzmin IV, Schwarz TM, Ilinykh PA, Jordan I, Ksiazek TG, Sachidanandam R, Basler CF, Bukreyev A (2017) Innate Immune Responses of Bat and Human Cells to Filoviruses: Commonalities and Distinctions. J Virol 91(8):e02471–e02416 Widerspick L, Steffen JF, Tappe D, Muñoz-Fontela C (2023) Animal Model Alternatives in Filovirus and Bornavirus Research. Viruses 15(1):158. 10.3390/v15010158.https://doi.org/10.3390/v15010158 Wicherska-Pawłowska K, Wróbel T, Rybka J (2021) Toll-Like Receptors (TLRs), NOD-like receptors (NLRs), and RIG-I-like receptors (RLRs) in innate immunity. TLRs, NLRs, and RLRs ligands as immunotherapeutic agents for hematopoietic diseases. Int J Mol Sci 22(24):13397 Ekchariyawat P, Hamel R, Bernard E, Wichit S, Surasombatpattana P, Talignani L, Thomas F, Choumet V, Yssel H, Desprès P, Briant L (2015) Inflammasome signaling pathways exert antiviral effect against Chikungunya virus in human dermal fibroblasts. Infect Genet Evol 32:401–408 Sepulveda-Crespo D, Resino S, Martinez I (2020) Innate immune response against hepatitis C virus: targets for vaccine adjuvants. Vaccines 8(2):313 Additional Declarations No competing interests reported. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-9351966","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Systematic Review","associatedPublications":[],"authors":[{"id":619909033,"identity":"a33e2ed9-0ffc-4c20-80ad-74f37fc63cde","order_by":0,"name":"Arnaw Kishore","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA9UlEQVRIiWNgGAWjYBACCWYGNiRuBRAzMzeQouUMSAsjAS0MyFoY28Akfi2S7ezPHnzcY8PAP/vswc+882qj+duBWn5UbMOpRZqZx9xwxrM0BolzecnSvNuO5844zNjA2HPmNk4tcsw8bNI8Bw4DvcFjIJ277VhuA1ALM2MbPi3sz4Ba/jPIn+Ex/p0751jufEJapJkZzIBaDjAYnOExk85tqMndQEiLZDOPmeSMA8k8hkAt1n+OHcjdCNRyEJ9fJM4ffybx4YCdnBzQYTdn1NTlzjt/+OCDHxW4tcAAD5Q+DCYPEFSPBOpIUTwKRsEoGAUjBAAAN3VS2JeXbZEAAAAASUVORK5CYII=","orcid":"","institution":"East Point College of Medical Sciences and Research Centre","correspondingAuthor":true,"prefix":"","firstName":"Arnaw","middleName":"","lastName":"Kishore","suffix":""},{"id":619909040,"identity":"c07795a7-16f8-4e2e-a631-495f5e88bc71","order_by":1,"name":"Shailendra Chauhan","email":"","orcid":"","institution":"The University of Texas Medical Branch at Galveston","correspondingAuthor":false,"prefix":"","firstName":"Shailendra","middleName":"","lastName":"Chauhan","suffix":""},{"id":619909058,"identity":"50c4dc68-d059-469b-a0c2-ec224f183a7e","order_by":2,"name":"Madhumati Bathala","email":"","orcid":"","institution":"East Point College of Medical Sciences and Research Centre","correspondingAuthor":false,"prefix":"","firstName":"Madhumati","middleName":"","lastName":"Bathala","suffix":""}],"badges":[],"createdAt":"2026-04-08 05:38:49","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-9351966/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-9351966/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":106476309,"identity":"91bd7a96-65e0-4bcc-81cc-92bcbe013a97","added_by":"auto","created_at":"2026-04-09 03:20:18","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":173673,"visible":true,"origin":"","legend":"\u003cp\u003ePRISMA Flow Diagram\u003c/p\u003e","description":"","filename":"image1.png","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/3e25a4a4dc10137a1120c9d3.png"},{"id":106724423,"identity":"a1ae2441-1c12-41be-8bfd-0078f58da040","added_by":"auto","created_at":"2026-04-12 18:27:59","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":13587,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of studies based on virus classification\u003c/p\u003e","description":"","filename":"image2.png","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/05d6b4fdaefdd0195a90b75e.png"},{"id":106476311,"identity":"4363f3a4-6f99-4d4c-b59c-fce6518ed485","added_by":"auto","created_at":"2026-04-09 03:20:18","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":30055,"visible":true,"origin":"","legend":"\u003cp\u003ePercent distribution of studies based on the organ used to form the organoids\u003c/p\u003e","description":"","filename":"image3.png","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/78bd8c42e6127aea3ec1b05f.png"},{"id":106724497,"identity":"3b308044-8a12-487b-abd4-ce8b7ad553bf","added_by":"auto","created_at":"2026-04-12 18:28:19","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":134211,"visible":true,"origin":"","legend":"\u003cp\u003eDistribution of organoid systems across the virus families\u003c/p\u003e","description":"","filename":"image4.png","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/1afc8d1cb6536161664c9325.png"},{"id":106724539,"identity":"0d157c3a-8133-4967-a16e-81e85f711c9a","added_by":"auto","created_at":"2026-04-12 18:28:31","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":245953,"visible":true,"origin":"","legend":"\u003cp\u003eChronological distribution of studies based on virus classification and organoid\u003c/p\u003e","description":"","filename":"image5.png","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/0ae8fa9bc303a5a6bd5d35c3.png"},{"id":107771575,"identity":"c9114ba1-b2f3-431d-aebc-699aebcf5fc7","added_by":"auto","created_at":"2026-04-25 04:39:51","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":1081403,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/2349a955-f927-4513-a2a4-35bec9e5716c.pdf"},{"id":106476313,"identity":"bcdd854a-ba6b-48e9-9951-25233ac62e57","added_by":"auto","created_at":"2026-04-09 03:20:18","extension":"docx","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":27563,"visible":true,"origin":"","legend":"","description":"","filename":"Supplementarydata.docx","url":"https://assets-eu.researchsquare.com/files/rs-9351966/v1/7506e71d047557761bbcc8bc.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"Antiviral immune responses in human organoid models of emerging viral infections: A systematic review","fulltext":[{"header":"1. Background","content":"\u003cp\u003eEmerging and re-emerging infectious diseases (EIDs) remain one of the most significant global health challenges of the twenty-first century, driven by pathogen evolution, antimicrobial resistance, ecological disruptions, and globalization [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. Outbreaks of Avian influenza, Chikungunya, Crimean-Congo haemorrhagic fever, Dengue (DENV), Ebola virus (EBOV) disease, Hantavirus, Marburg virus (MARV), Hand, foot and mouth disease, Japanese encephalitis (JEV), Nipah virus, novel human coronavirus, Rabies, Rift Valley fever, Viral hepatitis, SARS, Lassa fever, Swine flu, Zika virus (ZIKV) and COVID-19 have demonstrated the vulnerability of modern societies to novel pathogens, posing immense threats to health, economies, and global security [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Understanding the mechanisms underlying human immune responses to infection is therefore critical for the development of effective preventive and therapeutic interventions. The study of host-pathogen interactions and immune mechanisms has historically relied on traditional two-dimensional (2D) cell culture systems and animal models, both of which present significant limitations in recapitulating human-specific physiological responses. Conventional 2D cultures fail to reproduce the complex three-dimensional architecture, cellular diversity, and dynamic microenvironmental signals present in native tissues [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Animal models, while valuable, often exhibit species-specific differences in immune responses and tissue organization and are further constrained by ethical considerations, limited throughput, and reduced translational relevance [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. These limitations have driven the development of advanced three-dimensional (3D) \u003cem\u003ein vitro\u003c/em\u003e platforms that more accurately model the complexity of human physiological systems and immune responses. Such systems more closely mimic \u003cem\u003ein vivo\u003c/em\u003e tissue architecture and provide improved platforms for studying human organ physiology, microenvironmental dynamics, and host\u0026ndash;pathogen interactions [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e, \u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. In recent years, organoids, organ-on-chip technologies, multicellular spheroids, and bioprinted or explant-based models have become popular for modeling the architecture, multicellularity, and microenvironment of human tissues [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e, \u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Specifically, organoid technology has emerged as a transformative approach, utilizing self-organizing, stem cell-derived 3D structures that recapitulate the cellular composition and architectural complexity of native organs [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. These systems preserve genetic and epigenetic features of their tissue of origin, making them particularly valuable for patient-specific disease modeling. However, conventional organoid cultures present their own challenges, particularly the enclosed luminal architecture that limits access for pathogen exposure and the absence of dynamic mechanical forces present in vivo [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. Furthermore, organ-on-a-chip (OOC) technologies have been developed, integrating microfluidic systems with tissue engineering to recreate physiologically relevant flow, mechanical strain, and multi-tissue interfaces [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e, \u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eThese models offer valuable opportunities to study innate and adaptive immune mechanisms under controlled, human-specific conditions [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. Specifically, immune organoids have been instrumental in modeling and analyzing human adaptive immunity and infectious diseases [\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. Recent advances have enabled the incorporation of both innate immune cells, including macrophages, dendritic cells (DCs), and neutrophils, and adaptive immune components such as T cells and B cells into these platforms [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e]. At the same time, organ-on-chip systems, which integrate human cells into microfluidic devices to simulate organ-level physiology under continuous flow and mechanical forces, offer enhanced assay complexity and reproduction of tissue microenvironments. They are also used to engineer the immune microenvironment for toxicology, cancers, inflammatory disorders, infections, and immunotherapies [\u003cspan additionalcitationids=\"CR20\" citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. Among these models, human-derived organoids have significantly advanced the understanding of emerging viral infections and immune responses [\u003cspan additionalcitationids=\"CR16\" citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. However, a systematic synthesis of organoid-based studies investigating emerging viral infections and their corresponding immune responses remains limited. While individual studies report robust interferon and cytokine responses, a comparative evaluation across viral families, tissue origins, and organoid architectures remains unexplored. Such synthesis is essential to identify the strengths, limitations, and translational relevance of these systems in modeling human antiviral immunity. Therefore, this systematic review aims to critically evaluate and synthesize published research employing human organoid models to study emerging and re-emerging viral infections. The review specifically focuses on (i) the ability of organoid systems to replicate innate and adaptive immune responses, (ii) the influence of organoid origin and architecture on antiviral signaling, and (iii) the comparative immune patterns elicited by different viral families. By consolidating these findings, this review establishes an evidence-based framework for optimizing organoid use in infectious disease modeling and enhancing the predictive value of preclinical research.\u003c/p\u003e"},{"header":"2. Materials and methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003e2.1. Study design and framework\u003c/h2\u003e \u003cp\u003eThis systematic review employed a structured, multi-tiered methodology designed to capture, appraise, and synthesize existing evidence on human organoid-based 3D \u003cem\u003ein vitro\u003c/em\u003e systems that model immune mechanisms in EIDs. The methodological framework was developed in accordance with the 2020 guidelines of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e]. The review emphasizes two principal aspects: (i) the technological diversity of human organoid systems used to study infectious diseases and (ii) their immunological relevance in elucidating human host\u0026ndash;pathogen interactions. The protocol of the full systematic review is available in PROSPERO (CRD420261299053)\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003e2.2. Research objectives\u003c/h2\u003e \u003cp\u003eThis systematic review aimed to critically evaluate the application of human organoids in modeling emerging and re-emerging viral infections, with a focus on their capacity to recapitulate host immune responses.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003e2.3. Literature search strategy\u003c/h2\u003e \u003cp\u003eA comprehensive literature search was conducted using the scientific databases PubMed/MEDLINE, Web of Science, and Scopus. The search strategy combined three main thematic domains: (1) Organoids; (2) immune mechanisms; and (3) viral infectious diseases or emerging viral pathogens (Supplementary Table\u0026nbsp;1). The full set of search terms used was as follows: (\u0026ldquo;organoid\u0026rdquo; OR \u0026ldquo;Human organoid model\u0026rdquo;) AND (\u0026ldquo;immune system\u0026rdquo; OR \u0026ldquo;immune mechanism\u0026rdquo; OR \u0026ldquo;immune response\u0026rdquo; OR \u0026ldquo;innate immunity\u0026rdquo; OR \u0026ldquo;adaptive immunity\u0026rdquo; OR \u0026ldquo;cytokine\u0026rdquo; OR \u0026ldquo;chemokine\u0026rdquo; OR \u0026ldquo;immune signaling\u0026rdquo; OR \u0026ldquo;immunopathogenesis\u0026rdquo;) AND (\u0026ldquo;infectious disease\u0026rdquo; OR \u0026ldquo;viral infection\u0026rdquo; OR \u0026ldquo;emerging virus\u0026rdquo; OR \u0026ldquo;SARS-CoV-2\u0026rdquo; OR \u0026ldquo;COVID-19\u0026rdquo; OR \u0026ldquo;influenza\u0026rdquo; OR \u0026ldquo;Zika\u0026rdquo; OR \u0026ldquo;, Nipah virus\u0026rdquo; OR \u0026ldquo;Swine flu\u0026rdquo; OR \u0026ldquo;Ebola\u0026rdquo; OR \u0026ldquo;MERS-CoV\u0026rdquo; OR \u0026ldquo;Mpox virus \u0026rdquo; OR \u0026ldquo;Japanese Encephalitis Virus\u0026rdquo; OR \u0026ldquo;Chikungunya virus \u0026rdquo; OR \u0026ldquo;Dengue Virus\u0026rdquo; OR \u0026ldquo;Marburg\u0026rdquo; OR \u0026ldquo;Enteroviruses\u0026rdquo; OR \u0026ldquo;Hepatitis Virus\u0026rdquo; OR \u0026ldquo;Dengue Virus\u0026rdquo; OR \u0026ldquo;Marburg\u0026rdquo; OR \"Rift Valley fever OR \"Crimean-Congo hemorrhagic fever\" OR \"Hantavirus\" ). The search was limited to publications from January 2010 to January 2026.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec6\" class=\"Section2\"\u003e \u003ch2\u003e2.4. Eligibility criteria\u003c/h2\u003e \u003cp\u003eThis review included original experimental studies that used human organoid models to investigate immune responses to emerging viral infectious diseases as categorised by WHO [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan additionalcitationids=\"CR24\" citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. Only peer-reviewed articles published between 2010 and January 2026 were considered. Only studies that reported measurable immune outcomes were included. Studies were included if they: utilized human-derived organoid models, investigated viral infections classified as emerging or re-emerging viral pathogens, reported measurable immune outcomes, including cytokine, chemokine, interferon, or immune signaling responses. Studies comparing viral strains, disease states, or organoid types were also eligible if they provided quantitative or qualitative evidence of immune modulation.\u003c/p\u003e \u003cp\u003eExclusion criteria included studies relying solely on 2D cell cultures or animal models, and 3D systems other than human organoids. Additionally, reviews, theses, editorials, conference abstracts, and computational-only studies were not considered. Research focusing on non-infectious diseases, such as cancer, neurodegeneration, or metabolic disorders, was omitted unless the model was explicitly designed to incorporate infectious or immune components. Studies that lacked immune readouts, such as those limited to toxicology, pharmacokinetics, or metabolism, were also excluded.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003e2.5 Study Selection\u003c/h2\u003e \u003cp\u003eAll records identified through database searches and additional sources were imported into a reference management software for duplicate removal. Two reviewers independently screened titles and abstracts to assess eligibility based on the predefined inclusion and exclusion criteria. Studies considered potentially relevant were retrieved for full-text review. Full texts were independently assessed by the same two reviewers to determine final inclusion in the review. Discrepancies between reviewers were resolved through discussion and consensus. No automation tools were used during the screening process.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003e2.6 Data Collection Process\u003c/h2\u003e \u003cp\u003eData extraction was performed independently by two reviewers using a standardized data extraction form developed for this study. Data from all eligible studies were systematically extracted using a standardized matrix developed in Microsoft Excel. The results were tabulated and displayed visually in structured tables and figures. The extracted information included details on the model type, as well as the target tissue or organ modelled, infectious pathogen type, and its associated host-pathogen infection mechanism. Information on the immune components integrated was also collected. Technological characteristics and data on translational outcomes were extracted to determine the applied relevance of each model. Extracted data were cross-checked to ensure accuracy and consistency. Any disagreements between reviewers were resolved through discussion and, where necessary, consultation with a third reviewer. When information was unclear or incomplete, the study was reviewed in detail to extract the most relevant available data.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec9\" class=\"Section2\"\u003e \u003ch2\u003e2.7. Quality appraisal and risk of bias assessment\u003c/h2\u003e \u003cp\u003eAll included studies were appraised using a modified version of the Joanna Briggs Institute (JBI) Critical Appraisal Checklist for Experimental Studies, adapted for \u003cem\u003ein vitro\u003c/em\u003e human organoid models of viral infection [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. The ten appraisal domains evaluated methodological clarity, organoid derivation and validation, infection protocol transparency, inclusion of mock or uninfected controls, biological replication, quantification of immune responses, assay validation, statistical analysis, reproducibility, and data transparency. Studies with incomplete reporting of infection models, immune readouts, or culture conditions were considered to have a higher risk of bias. Two reviewers independently assessed each study to ensure objectivity and consistency in evaluation. Any discrepancies in scoring or interpretation were resolved through discussion, and when consensus could not be reached, a third reviewer provided arbitration to finalize the quality rating.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003e2.8 Certainty of evidence\u003c/h2\u003e \u003cp\u003eThe certainty of evidence was assessed qualitatively, recognizing that conventional grading tools such as GRADE are not directly applicable to preclinical in vitro data [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Confidence in the evidence was determined by examining the consistency, reproducibility, and physiological relevance of findings, as well as the transparency of reporting and support from translational or human data. Studies demonstrating reproducible outcomes and strong biological plausibility were rated as high certainty, whereas those with incomplete immune characterization or limited replication were rated low certainty. This approach ensured a contextual and transparent appraisal of the overall strength of the evidence base.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003e2.9. Evidence synthesis and data analysis\u003c/h2\u003e \u003cp\u003eDue to the methodological and biological diversity of included studies, quantitative meta-analysis was not feasible. Instead, a narrative synthesis approach was employed to integrate findings across different parameters used to synthesize this systematic review.\u003c/p\u003e \u003c/div\u003e"},{"header":"3. Results","content":"\u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003e3.1 Study selection\u003c/h2\u003e \u003cp\u003eThe literature search identified 986 records from electronic databases, including PubMed (n\u0026thinsp;=\u0026thinsp;345), Scopus (n\u0026thinsp;=\u0026thinsp;310), and Web of Science (n\u0026thinsp;=\u0026thinsp;331). After duplicate removal, 107 unique articles remained. Titles and abstracts were screened, resulting in 104 articles being assessed for full-text eligibility; three records were excluded because the full text could not be accessed. An additional 10 records were identified through citation tracking. In total, 114 studies published between January 2010 and January 2026 were assessed for eligibility. During full-text assessment, several studies were excluded based on predefined criteria. Specifically, 44 studies were excluded because they did not involve a selected virus or viral infection model or instead investigated vaccine responses. A further 35 studies were removed because they employed alternative 3D or 2D systems that did not meet the structural or functional definition of organoids. Additionally, 12 studies utilized non-human organoid models (e.g., bat-derived organoids) and were excluded to maintain human biological relevance. After applying predefined inclusion and exclusion criteria, 23 studies met the eligibility criteria and were included in the final qualitative synthesis (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003e3.2 Study characteristics\u003c/h2\u003e \u003cp\u003eAfter all screening and eligibility phases, we found 23 studies, published between 2016 and 2025, were included in the final qualitative synthesis [\u003cspan additionalcitationids=\"CR29 CR30 CR31 CR32 CR33 CR34 CR35 CR36 CR37 CR38 CR39 CR40 CR41 CR42 CR43 CR44 CR45 CR46 CR47 CR48 CR49\" citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. These studies represented diverse human organoid systems derived from induced pluripotent stem cells (hiPSCs; n\u0026thinsp;=\u0026thinsp;9; 39.1%), adult stem cells (ASCs; n\u0026thinsp;=\u0026thinsp;7; 30.4%), human embryonic stem cells (hESCs; n\u0026thinsp;=\u0026thinsp;4; 17.4%), and human pluripotent stem cells (hPSCs; n\u0026thinsp;=\u0026thinsp;3; 13%). A total of seven viral families were represented across the included studies, with Coronaviridae (SARS-CoV-2, MERS-CoV) being the most frequently investigated (n\u0026thinsp;=\u0026thinsp;8; 34.8%), followed by Flaviviridae such as ZIKV, DENV, HCV, and JEV (n\u0026thinsp;=\u0026thinsp;7; 30.5%). Orthomyxoviridae (Influenza A subtypes) accounted for three studies (13.0%), while Picornaviridae (Enteroviruses; n\u0026thinsp;=\u0026thinsp;2; 8.7%) and Poxviridae (Mpox; n\u0026thinsp;=\u0026thinsp;2; 8.7%) were less common. Studies involving Filoviridae (Ebola, Marburg), Togaviridae (Chikungunya) were limited to a single report each (4.3%), highlighting a research focus primarily on coronaviruses and flaviviruses in organoid-based infection models (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe studies represented four major tissue systems: neural (n\u0026thinsp;=\u0026thinsp;9), respiratory (n\u0026thinsp;=\u0026thinsp;6), intestinal (n\u0026thinsp;=\u0026thinsp;6), and hepatic (n\u0026thinsp;=\u0026thinsp;2) (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). One study employed tumor-derived or diseased tissue organoids, while another integrated immune cells within a multi-lineage co-culture model [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e, \u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. Collectively, these studies provided quantitative and qualitative data on cytokine, chemokine, and interferon responses following viral infection, enabling comparative synthesis of host immune mechanisms across organoid systems. Fifteen studies examined viral infection and immunity, while seven focused primarily on organoid model characterization (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eCharacteristics of Included Studies Investigating Antiviral Immune Responses in Human Organoid Models\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"6\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eS.N.\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eStudy (Author, Year)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eStem Cell Source\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eOrganoid Model\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eVirus (Family)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eKey Immune Response\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eDang et al., 2016 [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehESC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCerebral organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eZika virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eActivation of TLR3-mediated innate immune signaling.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHui et al., 2018 [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAirway organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eInfluenza A virus (H1N1, H5N1, H7N9, H5N6) (Orthomyxoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eH5N1 induced higher IL-6, IFN-β, RANTES, and MCP-1 compared with other subtypes.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eMuffat et al., 2018 [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNeural organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDengue virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong upregulation of CXCL10, CCL5, IL-1β, and TNF-α.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZhang et al., 2018 [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCortical organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eJapanese encephalitis virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eActivation of ISG15, ISG56, OAS1, and IFN-β signaling pathways.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eXu et al., 2019 [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehESC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBrain organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eZika virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eActivation of TLR3 and RNA interference\u0026ndash;mediated antiviral immunity.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eJacob et al., 2020 [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChoroid plexus and brain organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of inflammatory cytokines including CCL7, IL-32, IL-18, and IL-8.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eYang et al., 2020 [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLiver organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of CXCL and CCL chemokines with activation of NF-κB and TNF signaling.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eYang et al., 2020 [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCholangiocyte organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eSimilar CXCL and CCL chemokine induction with NF-κB and TNF pathway activation.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHan et al., 2021 [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of CXCL2, CCL2, IL1A, IL1B, and CXCL8; activation of NF-κB, TNF, and IL-17 pathways.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eHan et al., 2021 [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eColonic organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDifferential cytokine and chemokine expression indicating active innate immune signaling.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e11\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePei et al., 2021 [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehESC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAirway organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInduction of ISGs (IFITM3, MX1, ATF3, GEM) and activation of NF-κB signaling.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e12\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTiwari et al., 2021 [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong IFN-β induction with elevated IL-6, IL-8, CCL5, and CXCL10.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZhao et al., 2021 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eCoxsackievirus A16 (Picornaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eWeak induction of IFN-λ and inflammatory cytokines compared with EV-A71.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZhao et al., 2021 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eEnterovirus A71 (Picornaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eRobust IFN-λ1/λ3 and ISG activation (OAS1, MX1, IFIT1) with IL-6 and TNF-α production.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e15\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZhao et al., 2021 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMinimal induction of IFN or interferon-stimulated genes.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e16\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eZhao et al., 2021 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong IFN-λ signaling and ISG activation with elevated IL-6.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eKrenn et al., 2021 [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehESC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eBrain organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eZika virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of ISGs with moderate IFN-β activation.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e18\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSchultz et al., 2021 [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCerebral organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eChikungunya virus (Togaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of IL-6, IL-10, CCL2, CCL3, and CXCL10; stronger response in Parkinson\u0026rsquo;s-derived organoids.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e19\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTsang et al., 2021 [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eSmall intestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eEnterovirus A71 (Picornaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIncreased TNF-α, IP-10, MCP-1, and RANTES with IFN-λ2/3 and ISG induction.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e20\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSalgueiro et al., 2022 [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e3D lung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eInfluenza A virus (Orthomyxoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong innate immune activation with IL-6, IFN-β, IL-29, CXCL10, and CXCL9 induction.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNatarajan et al., 2022 [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLiver organoids with CD8⁺ T-cell coculture\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eHepatitis C virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eActivation of CD8⁺ T cells with strong IFN-γ secretion.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e22\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlores et al., 2025 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eEbola virus (Filoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eElevated IL-6, TNF-α, and CCL5 with modest IFNB1 and MX1 induction.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlores et al., 2025 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMarburg virus (Filoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong MX1, IFNB1, CXCL10, IL-6, TNF-α, and CCL5 activation.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e24\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlores et al., 2025 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eColonic organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eEbola virus (Filoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eModerate cytokine induction with mild interferon response.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e25\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlores et al., 2025 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eColonic organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMarburg virus (Filoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eHigher IFN-β and ISG activation compared with Ebola infection.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e26\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eXu et al., 2025 [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eMacrophage-augmented intestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eStrong ISG activation (MX1, ISG15, IFIT1, STAT1) and cytokine production (IL-1β, IL-6, TNF-α).\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e27\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eNakata et al., 2025 [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMpox virus (Poxviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMinimal immune activation with limited cytokine or interferon induction.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eSchultz-Pernice et al., 2025 [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNeural organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMpox virus (Poxviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eWeak innate immune response with mild IFN-β, IL-6, IL-8, and CXCL10 upregulation.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChoo et al., 2025 [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCerebral organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eZika virus (Flaviviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eInduction of type I interferons and ISGs including IFI44, IFIT1, DDX58, and OAS3.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e30\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eRothan et al., 2025 [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAdult stem cell\u0026ndash;derived\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAirway organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eH5N1 influenza virus (Orthomyxoviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eRobust IFN and NF-κB activation with increased IL-6, IL-8, TNF-α, and CXCL10.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e31\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChiok et al., 2025 [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eSARS-CoV-2 (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eUpregulation of IFIT1, MX1, OAS1, STAT1, and RSAD2 with strong IFN-β activation.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eChiok et al., 2025 [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003ehiPSC\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eMERS-CoV (Coronaviridae)\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eAttenuated interferon signaling with elevated IL-1β-mediated inflammatory responses.\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eThe heat map further illustrated that the Coronaviridae were the most extensively studied viral family, spanning multiple organoid systems, particularly respiratory and intestinal models, reflecting their broad tissue tropism. Flaviviridae infections were modeled mainly in neural organoids, consistent with their neurotropic infection patterns. Orthomyxoviridae were primarily studied in respiratory organoids, aligning with their pulmonary pathogenesis. In contrast, Picornaviridae and Filoviridae were predominantly modeled in intestinal organoids, while Poxviridae and Togaviridae showed limited but diverse representation across neural and respiratory systems. This distribution highlights how organoid selection closely mirrors the tissue specificity of viral infection and disease (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003e3.3 Chronological evolution and application of human-derived organoids in viral immunology\u003c/h2\u003e \u003cp\u003eHuman-derived organoid technology, first established in the early 2010s, revolutionized \u003cem\u003ein vitro\u003c/em\u003e modeling of tissue physiology and disease. These three-dimensional structures have since evolved to replicate complex tissue architecture and elements of immune competence. The earliest application in viral pathogenesis was reported by Dang et al. (2016), who used hESC-derived cerebral organoids to model ZIKV infection, revealing Toll-like receptor 3 (TLR3) activation and neuronal depletion, establishing brain organoids as a relevant platform for neurotropic viruses [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Between 2018 and 2019, studies by Hui et al. [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e], Muffat et al. [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e], Zhang et al. [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], and Xu et al. [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e] extended organoid use to model influenza, DENV, and JEV infections. These confirmed canonical interferon (IFN) and cytokine responses, particularly Type I and Type III IFNs, and highlighted tissue-specific susceptibility to viral infection.\u003c/p\u003e \u003cp\u003eThe COVID-19 pandemic (2020\u0026ndash;2021) marked a rapid expansion in organoid-based SARS-CoV-2 research. Studies such as Jacob et al. [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e] and Yang et al. [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e] employed hiPSC- and hPSC-derived organoids from the choroid plexus, liver, and cholangiocytes, revealing activation of NF-κB and TNF pathways and increased IL-6, IL-8, and TNF-α. Han et al. [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] and Pei et al. [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e] used lung and colonic organoids to demonstrate robust interferon-stimulated gene (ISG) responses and chemokine activation. Adult stem cell\u0026ndash;derived intestinal organoids-maintained tissue-specific antiviral mechanisms characterized by IFN-λ induction and ISG activation [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Organoid models were also applied to investigate virus-specific host responses and neurological outcomes, including studies demonstrating differential responses to Zika virus and herpes simplex virus infections as well as disease-specific susceptibility in cerebral organoids [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. This chronological illustration shows early studies primarily focused on Flaviviridae viruses, whereas Coronaviridae became the most studied family after 2020. Recent studies increasingly target diverse viral families to analyse innate antiviral signaling across tissues (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003e3.4 Antiviral immune responses\u003c/h2\u003e \u003cp\u003eThe systematic review identified 32 antiviral immune responses across studies. Most studies investigated a single viral pathogen; however, several studies compared two viral species [\u003cspan additionalcitationids=\"CR29 CR30 CR31 CR32 CR33 CR34 CR35 CR36 CR37 CR38 CR39 CR40 CR41 CR42 CR43 CR44 CR45 CR46 CR47 CR48 CR49\" citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. The review noted that antiviral immune responses in human organoid models varied substantially depending on the viral family and summarized in Table\u0026nbsp;\u003cspan refid=\"Tab2\" class=\"InternalRef\"\u003e2\u003c/span\u003e. Across studies, antiviral responses were primarily characterized by activation of type I and type III interferon pathways, induction of interferon-stimulated genes (ISGs), and increased production of pro-inflammatory cytokines and chemokines including IL-6, TNF-α, CXCL10, and CCL5. Distinct tissue-specific immune profiles were also observed. For example, neural organoids frequently exhibited TLR3-mediated antiviral signaling and apoptosis, airway organoids showed strong interferon and cytokine responses, and intestinal organoids demonstrated epithelial IFN-λ\u0026ndash;dominated antiviral signaling.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab2\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 2\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSummary of Antiviral Immune Responses by Virus Family\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNo.\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eVirus Family\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eRepresentative Viruses (Studies)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eOrganoid Model\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eKey Immune Pathways\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eMajor Immune Mediators (Upregulated)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eBiological Outcome\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFlaviviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eZika virus (ZIKV) [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e, \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e, \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]; Dengue virus (DENV) [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]; Japanese encephalitis virus (JEV) [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]; Hepatitis C virus (HCV) [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eNeural, cerebral, cortical organoids; liver organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eTLR3/TLR7 activation; RIG-I\u0026ndash;like receptor signaling; Type I interferon pathway; antigen presentation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFN-α/β, OAS1, MX1, IFIT1, IFITM3, CXCL10, IL-6, TNF-α\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eStrong Type I IFN activation and ISG expression; neuronal apoptosis and progenitor depletion; neuroinflammation; immune\u0026ndash;epithelial interaction modeling\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eCoronaviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eSARS-CoV-2 [\u003cspan additionalcitationids=\"CR34 CR35 CR36 CR37\" citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]; MERS-CoV [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]; SARS-CoV [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]; HCV-OC43 [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung, airway, colonic, hepatic, intestinal, macrophage-augmented intestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eType I (IFN-β) and Type III (IFN-λ) interferon signaling; NF-κB and TNF pathways\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFITM3, MX1, OAS1, ISG15, CXCL10, IL-6, TNF-α, IL-1β, CCL5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eStrong antiviral and inflammatory signaling; tissue-specific IFN responses (IFN-λ dominant in gut, IFN-β in lung); cytokine storm\u0026ndash;like responses\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eOrthomyxoviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eInfluenza A virus (H1N1, H5N1, H7N9) [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e, \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAirway and lung organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eType I interferon\u0026ndash;NF-κB signaling; cytokine\u0026ndash;chemokine receptor pathways\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFN-β, IL-6, TNF-α, MCP-1, CXCL10, CXCL9, IL-29\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eRobust cytokine and chemokine release; epithelial inflammation; attenuated antiviral responses in tumor-derived organoids\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eFiloviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eEbola virus (EBOV); Marburg virus (MARV) [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal and colonic organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eType I interferon signaling; proinflammatory cytokine pathways\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFNB1, MX1, CXCL10, IL-6, TNF-α, CCL5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eMARV induces stronger IFN and ISG activation than EBOV; high inflammatory responses consistent with hemorrhagic viral infection\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePoxviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eMpox virus (MPXV) [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e, \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eLung and neural organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eWeak interferon induction; partial NF-κB activation\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFN-β, IL-6, IL-8, CXCL10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eLimited innate activation in lung models; mild cytokine induction in neural organoids suggesting viral immune evasion\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003eTogaviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eChikungunya virus (CHIKV) [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eCerebral organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eNF-κB and pro-inflammatory cytokine signaling\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIL-6, IL-10, CCL2, CCL3, CXCL10\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eNeuroinflammatory responses; exaggerated cytokine signaling in Parkinson\u0026rsquo;s disease\u0026ndash;derived organoids indicating host susceptibility\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003ePicornaviridae\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eEnterovirus A71 (EV-A71); Coxsackievirus A16 (CVA16) [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eIntestinal and small intestinal organoids\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003eType III interferon (IFN-λ1/λ3) signaling; epithelial antiviral responses\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003eIFN-λ1, IFN-λ3, IFI44L, IFIT3, HERC5, IL-6, TNF-α, IP-10, RANTES\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003eStrong IFN-λ\u0026ndash;mediated antiviral response; moderate inflammation; CVA16 induces weaker IFN signaling than EV-A71\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cdiv id=\"Sec17\" class=\"Section3\"\u003e \u003ch2\u003e3.4.1 Influence of organoid origin and architecture\u003c/h2\u003e \u003cp\u003eThe origin and structural architecture of human organoid systems represent critical determinants of antiviral immune responses. Across the reviewed studies, organoid derivation from pluripotent stem cells (hPSCs, hESCs, or iPSCs) or adult stem cells (ASCs), together with differences in tissue differentiation and structural complexity (e.g., three-dimensional organization or immune cell co-culture), influenced the magnitude and dynamics of antiviral immune signaling following infection. Organoids derived from pluripotent stem cells generally exhibited a more immunologically \u0026ldquo;primed\u0026rdquo; phenotype, characterized by rapid interferon induction and strong activation of interferon-stimulated genes. Studies using hPSC-derived lung, colonic, and hepatic organoids demonstrated activation of NF-κB, TNF, and IL-17 signaling pathways, accompanied by increased expression of chemokines including CXCL8, CCL2, and CXCL10 following SARS-CoV-2 infection [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. Similarly, hESC-derived airway and alveolar organoids displayed strong type I and type III interferon responses with upregulation of antiviral genes such as IFITM3, MX1, ATF3, and RELB, together with increased cytokine production (IL-6, TNF, CXCL10) [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]. In contrast, adult stem cell\u0026ndash;derived intestinal and hepatic organoids typically showed more restrained interferon responses but increased inflammatory cytokine production. For example, ASC-derived intestinal organoids infected with EBOV or MARV demonstrated moderate IFN-β induction but substantial release of inflammatory mediators such as IL-6, TNF-α, and CCL5 [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOrganoid architecture further influenced infection dynamics and immune responses. Three-dimensional epithelial organization preserves tissue polarity, receptor distribution, and multicellular interactions, all of which are essential for physiologic viral entry and innate immune signaling. In lung organoid models, air\u0026ndash;liquid interface (ALI) cultures that preserved apical\u0026ndash;basal polarity demonstrated enhanced viral replication and stronger interferon responses compared with organoid-derived monolayers lacking structural polarity [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. Incorporation of additional cell types also enhanced immune fidelity. Macrophage-augmented intestinal organoids (MaugOs) produced amplified cytokine and interferon responses, including IL-1β, IL-6, TNF-α, MX1, and ISG15, highlighting the importance of immune\u0026ndash;epithelial crosstalk in antiviral defense [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. Conversely, tumor-derived lung organoids exhibited reduced interferon signaling and impaired antiviral gene induction, likely reflecting oncogenic reprogramming and epigenetic suppression of innate immune pathways [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eImmune responses were additionally influenced by tissue lineage and developmental maturity. Barrier tissues such as respiratory and intestinal organoids predominantly activated type I and type III interferon pathways, whereas neural organoids relied more heavily on TLR-mediated viral sensing mechanisms and displayed comparatively restricted cytokine responses [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e, \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. Developmental maturity also affected antiviral competence; immature organoids often showed increased viral permissiveness and reduced interferon signaling. For instance, early-stage cortical organoids infected with JEV failed to induce IFN-β and exhibited extensive cell death, whereas more mature organoids (\u0026gt;\u0026thinsp;8 weeks) activated robust RIG-I\u0026ndash;STAT1\u0026ndash;ISG pathways, limiting viral replication [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e]. Additionally, within the respiratory lineage, alveolar-type organoids showed stronger antiviral and apoptotic signatures than less differentiated airway counterparts, reflecting the acquisition of cell-type\u0026ndash;specific immune identity with maturation [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section3\"\u003e \u003ch2\u003e3.4.2 Influence of virus type on antiviral immune responses\u003c/h2\u003e \u003cp\u003eFlaviviridae infections were the most frequently modeled in early organoid studies (2016\u0026ndash;2019), primarily using neural organoids derived from hESCs or hiPSCs. ZIKV infection consistently triggered strong type I interferon responses and activation of interferon-stimulated genes, including OAS1, MX1, and IFITM3, often accompanied by neuronal apoptosis and depletion of progenitor populations [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e, \u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. Dengue virus infection produced a comparatively stronger pro-inflammatory cytokine profile, including CXCL10, CCL5, IL-1β, and TNF-α, indicating virus-specific differences in immune activation within similar organoid systems [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. Japanese encephalitis virus induced canonical interferon signaling pathways involving IFN-β, ISG15, and OAS1, consistent with the establishment of antiviral cellular states [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eFrom 2020 onward, Coronaviridae infections dominated organoid-based viral immunology studies. SARS-CoV-2 infection across lung, intestinal, hepatic, and macrophage-augmented organoids consistently induced interferon responses and chemokine production, including upregulation of MX1, IFITM3, CXCL10, and IL-6 [\u003cspan additionalcitationids=\"CR36 CR37\" citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Activation of NF-κB, TNF, and IL-17 signaling pathways was observed in both respiratory and gastrointestinal organoids [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e, \u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e]. Intestinal organoids also demonstrated stronger IFN-λ responses to SARS-CoV-2 than to SARS-CoV, highlighting tissue-specific differences in antiviral signaling [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. In contrast, MERS-CoV infection produced a relatively weaker interferon response but increased IL-1β expression, suggesting a more inflammatory immune profile [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eInfluenza virus infections in airway and lung organoids demonstrated typical type I interferon and NF-κB activation patterns [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e, \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]. Highly pathogenic influenza strains such as H5N1 induced higher levels of inflammatory mediators, including IL-6, IFN-β, and MCP-1 compared with seasonal strains [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. Some studies also reported activation of TGF-β signaling and elevated IL-6 and TNF-α expression, suggesting involvement of inflammatory and fibrotic pathways during severe infection [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eFiloviridae infections in intestinal organoids revealed strong but differential immune activation. Both EBOV and MARV induced cytokines such as IL-6, TNF-α, and CCL5 together with interferon-stimulated genes including MX1 and IFNB1, although MARV elicited stronger interferon responses than EBOV [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. Other viruses demonstrated more restricted immune activation patterns. Mpox virus infection in lung organoids resulted in minimal cytokine induction, whereas neural organoids showed modest increases in IFN-β, IL-6, and CXCL10 [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e, \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. Chikungunya virus infection of cerebral organoids induced neuroinflammatory cytokines including IL-6, IL-10, CCL2, and CXCL10 [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]. Enterovirus infections in intestinal organoids elicited strong type III interferon responses, accompanied by ISG activation and inflammatory cytokine production [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]. Finally, a microfluidic co-culture system combining liver organoids with CD8⁺ T cells demonstrated enhanced IFN-γ production and T-cell activation during hepatitis C virus infection, representing a model capable of recapitulating both innate and adaptive immune responses [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section3\"\u003e \u003ch2\u003e3.4.3. Influence of organoid type on antiviral immune responses\u003c/h2\u003e \u003cp\u003eThe type of organoid used strongly influenced the magnitude and nature of antiviral immune responses, reflecting intrinsic tissue-specific immune properties and viral tropism. Neural organoids were the most frequently employed system, particularly for neurotropic viruses such as ZIKV, JEV, Chikungunya virus, and Mpox virus. Flavivirus infections typically induced strong type I interferon signaling and ISG activation, often leading to apoptosis of neural progenitor cells [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e, \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. Additional studies reported upregulation of antiviral sensors including IFI44, DDX58, and TRIM22, reflecting activation of TLR3 and RIG-I pathways in cerebral organoids [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e, \u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e]. In contrast, Mpox and Chikungunya infections produced more moderate cytokine responses dominated by IL-6 and CXCL10, consistent with the immune-privileged environment of neural tissues [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e, \u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eRespiratory organoids exhibited the most robust antiviral immune responses across organoid systems. SARS-CoV-2 infection consistently induced strong type I and III interferon signaling together with NF-κB-mediated cytokine production, including IL-6, CXCL10, TNF-α, and CCL5 [\u003cspan additionalcitationids=\"CR36\" citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. In contrast, MERS-CoV produced attenuated IFN signaling but elevated IL-1β, implying a preferential pro-inflammatory response [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. Similar patterns were observed during influenza virus infection, whereas tumor-derived lung organoids exhibited blunted antiviral signaling [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIntestinal and colonic organoids displayed antiviral responses dominated by type III interferon (IFN-λ) signaling, reflecting the physiological antiviral barrier of the gastrointestinal epithelium. Enterovirus infections triggered strong ISG activation and cytokine production, whereas SARS-CoV-2 infection induced potent IFN-λ responses and antiviral gene expression [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e, \u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]. More complex systems, such as macrophages, further amplified inflammatory signaling and interferon responses, illustrating the importance of immune\u0026ndash;epithelial interactions in mucosal antiviral defense [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. EBOV and MARV induced high levels of IL-6, TNF-α, CCL5, and IFNB1, with MARV exhibiting a stronger IFN-driven signature than Ebola [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eHepatic organoids demonstrated integrated antiviral and metabolic immune responses. SARS-CoV-2 infection of liver and cholangiocyte organoids activated NF-κB, TNF, and IL-17 pathways together with chemokine induction [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]. In contrast, hepatitis C virus infection modeled using liver organoid\u0026ndash;T cell co-cultures produced strong IFN-γ responses and T-cell activation, highlighting the potential of these systems for studying chronic viral infections and adaptive immune interactions [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv id=\"Sec20\" class=\"Section2\"\u003e \u003ch2\u003e3.5 Quality Appraisal and Risk of Bias Assessment\u003c/h2\u003e \u003cp\u003eOverall, the methodological quality of the included literature was generally high across studies. Out of 23 studies, all scored between 9 and 10 points on the modified Joanna Briggs Institute appraisal scale, meeting the threshold for high methodological quality and low risk of bias. Six studies demonstrated minor reporting limitations, primarily related to the specification of biological replicates and the availability of raw data. These studies were therefore scored slightly lower (9.0\u0026ndash;9.5 points) but remained within the high-quality range. No study met the criteria for exclusion due to poor methodological quality or unclear reporting. However, some variability in reporting standards was observed, particularly regarding experimental replication and detailed methodological descriptions. The overall quality assessment is summarized in Supplementary Table\u0026nbsp;2.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec21\" class=\"Section2\"\u003e \u003ch2\u003e3.6 Certainty of Evidence for Organoid-Based Viral Infection Studies\u003c/h2\u003e \u003cp\u003eOverall, the body of evidence demonstrated high to moderate certainty, supported by generally strong methodological quality, reproducibility across studies, and consistent immunological outcomes reported in multiple laboratories. Studies investigating SARS-CoV-2, Influenza A, ZIKV, and filoviruses (Ebola and Marburg) provided the most robust evidence, demonstrating reproducible activation of interferon signaling pathways and cytokine responses across several independent organoid systems. In contrast, moderate certainty was assigned to studies involving MERS-CoV, Mpox virus, and Chikungunya virus, primarily due to the limited number of available studies and narrower range of organoid models used. The overall certainty assessment is summarized in Supplementary Table\u0026nbsp;3.\u003c/p\u003e \u003c/div\u003e"},{"header":"4. Discussion","content":"\u003cp\u003eThis systematic review provides a comprehensive synthesis of current evidence on human organoid\u0026ndash;based models for studying emerging viral infections and host immune responses. Although three-dimensional tissue culture predates the modern term organoid, the advent of human-induced pluripotent stem cell (hiPSC) technology in 2007 marked a transformative milestone in regenerative biology and infection modeling [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e, \u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. Between 2007 and 2015, most studies were devoted to establishing proof-of-concept and elucidating the mechanisms underlying organoid formation [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. The ability to reprogram adult somatic cells into pluripotent states created new opportunities to derive human cell populations capable of differentiating into multiple tissue types, thereby facilitating advanced in vitro disease modeling [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eFrom approximately 2015 onward, the field transitioned from early experimental systems toward human organoid platforms derived from pluripotent and adult stem cells [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e]. During this period, improved differentiation protocols enabled the generation of organoids that closely replicate the physiological and pathological processes of their organ of origin while retaining human genetic and immunological characteristics [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e, \u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e]. Consequently, all studies included in this review were published between 2016 and 2025, despite our search extending back to 2010, reflecting the relatively recent expansion of organoid-based infectious disease research.\u003c/p\u003e \u003cp\u003eAdvances in stem cell biology have enabled the development of diverse organoid systems, including neural, hepatic, respiratory, renal, and gastrointestinal models [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e, \u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e]. Our synthesis identified studies employing organoids derived from pluripotent, embryonic, and adult stem cells to model infections caused by seven viral families: Coronaviridae, Flaviviridae, Orthomyxoviridae, Filoviridae, Togaviridae, Poxviridae, Picornaviridae. Collectively, these studies demonstrate that human organoids are capable of recapitulating virus-specific cellular tropism, interferon-mediated innate immune signaling, and cytokine-driven inflammatory responses, closely resembling host responses observed in vivo.\u003c/p\u003e \u003cp\u003eCompared with conventional two-dimensional (2D) cell culture systems, organoids provide a more physiologically relevant microenvironment, preserving cellular heterogeneity, tissue polarity, and spatial receptor distribution [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e]. These structural features allow improved modeling of viral entry, replication, and host immune signaling. For example, lung organoid models reproduce interferon and cytokine responses to SARS-CoV-2 infection that closely resemble those observed in human airway tissues, whereas commonly used cell lines such as Vero E6 or A549 exhibit markedly reduced interferon responses [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e, \u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e]. Similarly, cerebral organoids infected with ZIKV reproduce neuroinflammatory and apoptotic responses observed in human fetal brain tissue\u0026mdash;responses that are not captured in conventional neural progenitor cultures [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eHuman organoid models also provide advantages over animal systems by enabling the study of viral pathogenesis within a human genetic and immunological context, thereby avoiding species-specific immune differences. For example, ZIKV induces TLR3-mediated neuronal apoptosis in human cerebral organoids but not in murine brains unless interferon signaling is experimentally suppressed [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e, \u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e, \u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e]. Non-human primate organoids exhibit partial overlap in interferon-stimulated gene expression but lack the magnitude of TLR3 activation observed in human-derived models [\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e]. These findings highlight the importance of human-specific tissue systems for investigating viral neurotropism and host immune responses.\u003c/p\u003e \u003cp\u003eSimilarly, lung and intestinal organoids demonstrate robust activation of type I and type III interferon pathways in response to SARS-CoV-2 infection, whereas many conventional cell culture models display limited or dysregulated antiviral signaling [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e, \u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e, \u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e, \u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e]. Studies using bat-derived organoids, although limited, further demonstrate species-specific differences in viral replication kinetics and interferon responses [\u003cspan additionalcitationids=\"CR68 CR69 CR70\" citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e71\u003c/span\u003e]. In contrast, widely used cell lines such as Vero E6 permit efficient viral replication but lack functional type I interferon responses, limiting their utility for studying host antiviral immunity [\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e, \u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eOrganoid models have also proven valuable for studying additional viral pathogens. For example, influenza virus infection in human airway organoids reproduces viral replication dynamics together with cytokine responses resembling those observed in severe respiratory infections, including elevated IL-6, IL-8, and IFN-β levels [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e, \u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. Similarly, intestinal organoid systems have demonstrated differential immune responses to EBOV and MARV infection, with MARV eliciting stronger interferon activation than EBOV [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn addition to modeling viral infection, organoid platforms have provided insights into viral immune evasion strategies. Mpox virus, for example, employs multiple mechanisms to suppress innate immune signaling, including inhibition of cytokine pathways, complement activation, and inflammasome signaling [\u003cspan citationid=\"CR78\" class=\"CitationRef\"\u003e78\u003c/span\u003e]. In human lung and neural organoids, Mpox infection produced relatively attenuated interferon responses, which may contribute to its ability to establish persistent infection. Such findings highlight the potential of organoid systems to elucidate mechanisms of viral immune modulation and host susceptibility. Collectively, the evidence synthesized in this review indicates that human organoids provide physiologically relevant experimental platforms that bridge the gap between oversimplified cell culture systems and species-limited animal models. By preserving human tissue architecture and immune signaling networks, organoids offer valuable tools for investigating viral pathogenesis, antiviral immunity, and preclinical therapeutic strategies.\u003c/p\u003e"},{"header":"5. Limitations","content":"\u003cp\u003eSeveral limitations should be considered when interpreting the findings of this review. Although a comprehensive search strategy was applied, some relevant studies may not have been identified, particularly unpublished data or studies reported in non-indexed sources. Additionally, the included studies exhibited methodological heterogeneity, including differences in stem cell sources, differentiation protocols, organoid maturation stages, and infection models. Such variability may influence immune responsiveness and complicate direct comparison across studies. Variations in experimental design were also observed in the measurement and reporting of immune outcomes, including cytokine assays, transcriptomic analyses, and viral replication metrics. The absence of standardized protocols for organoid infection experiments, therefore, limits cross-study comparability. Another potential limitation is publication bias, as studies demonstrating successful infection models or significant immune responses are more likely to be published than studies reporting negative or inconclusive findings. Finally, although organoid models provide valuable human-specific insights, they still lack certain physiological components present \u003cem\u003ein vivo\u003c/em\u003e, including fully developed vascular networks, systemic immune interactions, and long-term tissue remodeling processes. These limitations highlight the need for continued development of immune-integrated and vascularized organoid platforms.\u003c/p\u003e"},{"header":"6. Implications and Future Research","content":"\u003cp\u003eThe results of this review highlight the value of human organoid models for studying emerging viral infections and host immune responses. For research practice, organoid systems offer a more physiologically relevant experimental platform than conventional cell lines, enabling improved investigation of viral tropism, host immune signaling, and antiviral drug responses. In translational and clinical research contexts, organoid models hold considerable promise for patient-specific disease modeling and therapeutic screening, supporting the development of precision medicine approaches for infectious diseases. The integration of standardized organoid methodologies into regulatory and ethical frameworks could enhance reproducibility and reduce dependence on animal models. Collaboration between research institutions and policy agencies is essential to promote data sharing and protocol harmonization.\u003c/p\u003e \u003cp\u003eFuture research should focus on several key priorities. These include the development of immune-competent organoid models incorporating innate and adaptive immune cells, the integration of vascular and stromal components to better mimic tissue physiology, and the establishment of standardized protocols for viral infection assays and immune response measurements. In addition, multicenter collaborations and shared experimental platforms will be essential to improve reproducibility, protocol harmonization, and data comparability across laboratories. Such efforts will strengthen the evidence base supporting organoid technologies and facilitate their translation into preclinical antiviral research and therapeutic development.\u003c/p\u003e"},{"header":"7. Conclusion","content":"\u003cp\u003eOver the past decade, human organoid models have emerged as powerful and physiologically relevant tools for studying viral pathogenesis and innate immunity. Across diverse tissue systems and viral families, organoids consistently replicate human-specific interferon and cytokine signaling, providing critical insights into host\u0026ndash;virus interactions. The evolution from early neural organoids to advanced immune-cocultured constructs reflects the field\u0026rsquo;s transition toward functional complexity and translational relevance. Collectively, these findings position human organoids at the forefront of preclinical virology, bridging experimental and clinical domains in the study of emerging infectious diseases.\u003c/p\u003e"},{"header":"Abbreviations","content":"\u003cdiv class=\"DefinitionList\"\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eASCs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eAdult Stem Cells\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eDCs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eDendritic Cells\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eDENV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eDengue Virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eEBOV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eEbola Virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eEIDs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eEmerging and Re-emerging Infectious Diseases\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ehESCs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eHuman Embryonic Stem Cells\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ehiPSCs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eInduced Pluripotent Stem Cells\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ehPSCs\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eHuman Pluripotent Stem Cells\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eJEV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eJapanese Encephalitis Virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eMARV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eMarburg Virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eOOC\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eOrgan-on-a-Chip\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eSARS\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eSevere Acute Respiratory Syndrome\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eTLR3\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eToll-Like Receptor 3\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eZIKV\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eZika Virus\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003ch2\u003e\u003cstrong\u003eEthics approval and consent to participate:\u003c/strong\u003e\u003c/h2\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication:\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch2\u003eCompeting interests:\u003c/h2\u003e\n\u003cp\u003eThe authors declare that they have no competing interests\u003c/p\u003e\n\u003ch2\u003eFunding:\u003c/h2\u003e\n\u003cp\u003eNil\u003c/p\u003e\n\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\n\u003cp\u003eConceptualization, A.K.; methodology, A.K. and M.B.; software, A.K. and M.B; validation, A.K., S.C., and M.B.; formal analysis, S.C.; investigation, A.K. and S.C.; data curation, AK.; writing original draft preparation, AK. Writing, review, and editing, A.K., S.C., and M.B.; visualization, A.K.; supervision, S.C. and M.B; project administration, A.K. All authors have read and agreed to the published version of the manuscript.\u003c/p\u003e\n\u003ch2\u003eAcknowledgement\u003c/h2\u003e\n\u003cp\u003eWe acknowledge Dr. Deepti Srivastava, Ph.D., Nimble Scholars, India, for providing support in scientific editing and formatting the manuscript.\u003c/p\u003e\n\u003ch2\u003eAvailability of data and materials:\u003c/h2\u003e\n\u003cp\u003eThe datasets used and/or analysed during the current study are available from the corresponding author.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eWorld Health Organization (2016) Regional Office for South-East Asia. A brief guide to emerging infectious diseases and zoonoses. WHO-SEARO, New Delhi, pp 3\u0026ndash;48\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWang S, Li W, Wang Z, Yang W, Li E, Xia X et al (2024) Emerging and reemerging infectious diseases: global trends and new strategies for their prevention and control. Signal Transduct Target Ther 9(1):223\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBanik A, Basu S (2025) Drivers and consequences of viral zoonoses: public health and economic perspectives. Zoonotic Dis 5(4):32\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRistori MV, Guarrasi V, Soda P, Petrosillo N, Gurrieri F, Longo UG et al (2024) Emerging microorganisms and infectious diseases: one health approach for health shared vision. Genes 15(7):908\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAl-Kabani A, Huda B, Haddad J, Yousuf M, Bhurka F, Ajaz F et al (2025) Exploring experimental models of colorectal cancer: a critical appraisal from 2D cell systems to organoids, humanized mouse avatars, organ-on-chip, CRISPR engineering, and AI-driven platforms. Cancers 17(13):2163\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAdesina PA, Ooka M, TeKrony C, Xia M (2025) Emerging advances in intestinal models for in vitro preclinical research. Am J Physiol Gastrointest Liver Physiol. ;329(3)\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePun S, Haney LC, Barrile R (2021) Modelling human physiology on-chip: historical perspectives and future directions. Micromachines (Basel) 12(10):1250\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMittal R, Woo FW, Castro CS et al (2019) Organ-on-chip models: implications in drug discovery and clinical applications. J Cell Physiol 234:8352\u0026ndash;8380\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBassi G, Grimaudo MA, Panseri S, Montesi M (2021) Advanced multi-dimensional cellular models as emerging reality to reproduce in vitro the human body complexity. Int J Mol Sci 22(3):1195\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGouveia Z, \u0026Ouml;zkan A, Giannobile WV, Santerre JP, Wu DT (2025) Oral tissue spheroid, organoid, and organ-on-chip microphysiological modeling strategies towards enhanced emulation of health and disease. Bioeng Transl Med\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang X, Liu H, Cheng H, Cui Y, Wang J, Yao Q et al (2025) In vitro biomimetic models for respiratory diseases: progress in lung organoids and lung-on-a-chip. Stem Cell Res Ther 16(1):415\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMajorova D, Atkins E, Martineau H, Vokral I, Oosterhuis D, Olinga P et al (2021) Use of precision-cut tissue slices as a translational model to study host-pathogen interaction. Front Vet Sci 8:686088\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHammel JH, Cook SR, Belanger MC, Munson JM, Pompano RR (2021) Modeling immunity in vitro: slices, chips, and engineered tissues. Annu Rev Biomed Eng 23:461\u0026ndash;491\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCherne MD, Sidar B, Sebrell TA, Sanchez HS, Heaton K, Kassama FJ et al (2021) A synthetic hydrogel improves immune cell-epithelial interactions in a tissue chip co-culture model of human gastric organoids and dendritic cells. Front Pharmacol 12:707891\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAguilar C, Alves da Silva M, Saraiva M, Neyazi M, Olsson IA, Bartfeld S (2021) Organoids as host models for infection biology: a review of methods. Exp Mol Med 53(10):1471\u0026ndash;1482\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eIakobachvili N, Peters PJ (2017) Humans in a dish: the potential of organoids in modeling immunity and infectious diseases. Front Microbiol 8:2402\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi T, Peng D, Yao M, Li M, Wang Y, Li S et al (2025) Immune organoids: emerging platforms for modeling and analyzing human adaptive immunity. Front Immunol 16:1632117\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi X, Xiao H, Zhou M, Yang C, Yang X, Cheng T et al (2025) Organoids in respiratory virus research: advances and perspectives. Mol Biomed 6(1):100\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRamadan Q, Hazaymeh R, Zourob M (2023) Immunity-on-a-chip: integration of immune components into organ-on-chip systems. Adv Biol 7(12):2200312\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi L, Xu Q, Zhao J, Qu Y, Luo Y, Zhang X (2025) Engineering immune microenvironments for organoid-on-a-chip systems. Med Mat. :10\u0026ndash;97\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAlonso-Roman R, Mosig AS, Figge MT, Papenfort K, Eggeling C, Schacher FH et al (2024) Organ-on-chip models for infectious disease research. Nat Microbiol 9(4):891\u0026ndash;904\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMoher D, Liberati A, Tetzlaff J, Altman DG (2009) Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement. PLoS Med. ;6\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWorld Health Organization (2011) Asia Pacific strategy for emerging diseases. WHO-SEARO, New Delhi\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWorld Health Organization (2023) Emerging zoonotic diseases and the One Health approach: an overview [Internet]. WHO, Geneva. [cited 2026 Jan 15]\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWorld Health Organization. WHO launches global framework for understanding the origins of new or re-emerging pathogens [Internet] (2024) [cited 2026 Jan 15]\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eAromataris E, Fernandez R, Godfrey C, Holly C, Khalil H, Tungpunkom P (2015) Summarizing systematic reviews: methodological development, conduct and reporting of an umbrella review approach. Int J Evid Based Healthc 13(3):132\u0026ndash;140\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGuyatt GH, Oxman AD, Vist GE, Kunz R, Falck-Ytter Y, Alonso-Coello P et al (2008) GRADE: an emerging consensus on rating quality of evidence and strength of recommendations. BMJ 336(7650):924\u0026ndash;926\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDang J, Tiwari SK, Lichinchi G, Qin Y, Patil VS, Eroshkin AM et al (2016) Zika virus depletes neural progenitors in human cerebral organoids through activation of the innate immune receptor TLR3. Cell Stem Cell 19(2):258\u0026ndash;265. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stem.2016.04.014\u003c/span\u003e\u003cspan address=\"10.1016/j.stem.2016.04.014\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHui KPY, Ching RHH, Chan SKH, Nicholls JM, Sachs N, Clevers H et al (2018) Tropism, replication competence, and innate immune responses of influenza virus: an analysis of human airway organoids and ex vivo bronchus cultures. Lancet Respir Med 6(11):846\u0026ndash;854. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/S2213-2600(18)30236-0\u003c/span\u003e\u003cspan address=\"10.1016/S2213-2600(18)30236-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMuffat J, Li Y, Omer A, Durbin A, Bosch I, Bakiasi G et al (2018) Human induced pluripotent stem cell-derived glial cells and neural progenitors display divergent responses to Zika and dengue infections. Proc Natl Acad Sci U S A 115(27):7117\u0026ndash;7122. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1073/pnas.1719266115\u003c/span\u003e\u003cspan address=\"10.1073/pnas.1719266115\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhang B, He Y, Xu Y, Mo F, Mi T, Shen QS et al (2018) Differential antiviral immunity to Japanese encephalitis virus in developing cortical organoids. Cell Death Dis 9(7):719. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41419-018-0763-y\u003c/span\u003e\u003cspan address=\"10.1038/s41419-018-0763-y\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eXu YP, Qiu Y, Zhang B, Chen G, Chen Q, Wang M et al (2019) Zika virus infection induces RNAi-mediated antiviral immunity in human neural progenitors and brain organoids. Cell Res 29(4):265\u0026ndash;273. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41422-019-0152-9\u003c/span\u003e\u003cspan address=\"10.1038/s41422-019-0152-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJacob F, Pather SR, Huang WK, Zhang F, Wong SZH, Zhou H et al (2020) Human pluripotent stem cell-derived neural cells and brain organoids reveal SARS-CoV-2 neurotropism predominates in choroid plexus epithelium. Cell Stem Cell 27(6):937\u0026ndash;50e9. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stem.2020.09.016\u003c/span\u003e\u003cspan address=\"10.1016/j.stem.2020.09.016\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYang L, Han Y, Nilsson-Payant BE, Gupta V, Wang P, Duan X et al (2020) A human pluripotent stem cell-based platform to study SARS-CoV-2 tropism and model virus infection in human cells and organoids. Cell Stem Cell 27(1):125\u0026ndash;36e7. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stem.2020.06.015\u003c/span\u003e\u003cspan address=\"10.1016/j.stem.2020.06.015\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHan Y, Duan X, Yang L, Nilsson-Payant BE, Wang P, Duan F et al (2021) Identification of SARS-CoV-2 inhibitors using lung and colonic organoids. Nature 589(7841):270\u0026ndash;275. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41586-020-2901-9\u003c/span\u003e\u003cspan address=\"10.1038/s41586-020-2901-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePei R, Feng J, Zhang Y, Sun H, Li L, Yang X et al (2021) Host metabolism dysregulation and cell tropism identification in human airway and alveolar organoids upon SARS-CoV-2 infection. Stem Cell Rep 16(3):437\u0026ndash;445. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stemcr.2021.02.005\u003c/span\u003e\u003cspan address=\"10.1016/j.stemcr.2021.02.005\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTiwari SK, Wang S, Smith D, Carlin AF, Rana TM (2021) Revealing tissue-specific SARS-CoV-2 infection and host responses using human stem cell-derived lung and cerebral organoids. Stem Cell Rep 16(3):437\u0026ndash;445. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stemcr.2021.02.005\u003c/span\u003e\u003cspan address=\"10.1016/j.stemcr.2021.02.005\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhao X, Fu Y, Liu J, Shi Y (2021) Human intestinal organoids recapitulate enteric infections of enterovirus and coronavirus. Stem Cell Rep 16(3):493\u0026ndash;504. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stemcr.2021.02.006\u003c/span\u003e\u003cspan address=\"10.1016/j.stemcr.2021.02.006\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKrenn V, Bosone C, Burkard TR, Spanier J, Kalinke U, Calistri A et al (2021) Organoid modeling of Zika and herpes simplex virus 1 infections reveals virus-specific responses leading to microcephaly. Cell Stem Cell 28(8):1362\u0026ndash;79e7. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.stem.2021.03.004\u003c/span\u003e\u003cspan address=\"10.1016/j.stem.2021.03.004\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSchultz EM, Jones TJ, Xu S, Dean DD, Zechmann B, Barr KL (2021) Cerebral organoids derived from a Parkinson\u0026rsquo;s patient exhibit unique pathogenesis from Chikungunya virus infection when compared to a non-Parkinson\u0026rsquo;s patient. Pathogens 10(7):913. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/pathogens10070913\u003c/span\u003e\u003cspan address=\"10.3390/pathogens10070913\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTsang JO, Zhou J, Zhao X, Li C, Zou Z, Yin F et al (2021) Development of three-dimensional human intestinal organoids as a physiologically relevant model for characterizing the viral replication kinetics and antiviral susceptibility of enteroviruses. Biomedicines 9(1):88. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/biomedicines9010088\u003c/span\u003e\u003cspan address=\"10.3390/biomedicines9010088\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSalgueiro L, Kummer S, Sonntag-Buck V, Weiss A, Schneider MA, Kraeusslich HG et al (2022) Generation of human lung organoid cultures from healthy and tumor tissue to study infectious diseases. J Virol 96(7):e00098\u0026ndash;e00022. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1128/jvi.00098-22\u003c/span\u003e\u003cspan address=\"10.1128/jvi.00098-22\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNatarajan V, Simoneau CR, Erickson AL, Meyers NL, Baron JL, Cooper S et al (2022) Modelling T-cell immunity against hepatitis C virus with liver organoids in a microfluidic coculture system. Open Biol 12(3):210320. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1098/rsob.210320\u003c/span\u003e\u003cspan address=\"10.1098/rsob.210320\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFlores EY, Hume AJ, Olejnik J, Mithal A, D\u0026rsquo;Amico A, Yang M et al (2025) Filovirus infection disrupts epithelial barrier function and ion transport in human iPSC-derived gut organoids. PLoS Pathog 21(11):e1013698. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1371/journal.ppat.1013698\u003c/span\u003e\u003cspan address=\"10.1371/journal.ppat.1013698\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eXu G, Zhou J, Liu K, Zhang P, Zhang Y, Wang Y et al (2025) Macrophage-augmented intestinal organoids model virus\u0026ndash;host interactions in enteric viral diseases and facilitate therapeutic development. Nat Commun 16:4475. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41467-025-59639-9\u003c/span\u003e\u003cspan address=\"10.1038/s41467-025-59639-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNakata Y, Uriu K, Hashimoto R, Yamamoto T, Saito A, Sato K et al (2025) Mpox virus replicates in lung organoids without significantly affecting their cellular function. Biochem Biophys Rep 44:102326. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1016/j.bbrep.2025.102326\u003c/span\u003e\u003cspan address=\"10.1016/j.bbrep.2025.102326\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSchultz-Pernice I, Fahmi A, Brito F, Behrens G, Krahling V, Schwemmle M (2025) Monkeypox virus spreads from cell-to-cell and leads to neuronal death in human neural organoids. Nat Commun 16:5376. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1038/s41467-025-61134-0\u003c/span\u003e\u003cspan address=\"10.1038/s41467-025-61134-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChoo YY, Tan TZ, Zhang SL, Chen MS, Chua ML, Tan NH et al (2025) Comparison of human cerebral organoids infected with wild-type Zika versus attenuated DN-2 virus strains uncovers differences in host immune responses. Cell Commun Signal 23(1):5888. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1186/s12964-025-02588-z\u003c/span\u003e\u003cspan address=\"10.1186/s12964-025-02588-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRothan H, Mostafa A, Bayoumi M, Ye C, Barre RS, Allu\u0026eacute;-Guardia A et al (2025) Emerging highly pathogenic H5N1 influenza triggers fibrotic remodeling in human airway organoids. Emerg Microbes Infect 14(1):2532684. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1080/22221751.2025.2532684\u003c/span\u003e\u003cspan address=\"10.1080/22221751.2025.2532684\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChiok KL, Jenik K, Fenton M, Falzarano D, Dhar N, Banerjee A (2025) MERS-CoV and SARS-CoV-2 infection in diverse human lung organoid-derived cultures. J Virol 99(10):e01098\u0026ndash;e01025. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.1128/jvi.01098-25\u003c/span\u003e\u003cspan address=\"10.1128/jvi.01098-25\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSimian M, Bissell MJ (2017) Organoids: a historical perspective of thinking in three dimensions. J Cell Biol 216(1):31\u0026ndash;40\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu X, Zhou Z, Zhang Y, Zhong H, Cai X, Guan R (2025) Recent progress on organoids: techniques, advantages and applications. Biomed Pharmacother 185:117942\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJusop AS, Thanaskody K, Tye GJ, Dass SA, Wan Kamarul Zaman WS, Nordin F (2023) Development of brain organoid technology derived from iPSC for neurodegenerative disease modelling. Front Mol Neurosci 16:1173433\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDoss MX, Sachinidis A (2019) Current challenges of iPSC-based disease modeling and therapeutic implications. Cells 8(5):403\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKim J, Koo BK, Knoblich JA (2020) Human organoids: model systems for human biology and medicine. Nat Rev Mol Cell Biol 21(10):571\u0026ndash;584\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSchutgens F, Clevers H (2020) Human organoids: tools for understanding biology and treating diseases. Annu Rev Pathol 15:211\u0026ndash;234\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eNovelli G, Spitalieri P, Murdocca M, Centanini E, Sangiuolo F (2023) Organoid factory: the recent role of human induced pluripotent stem cells in precision medicine. Front Cell Dev Biol 10:1059579\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTang XY, Wu S, Wang D, Chu C, Hong Y, Tao M et al (2022) Human organoids in basic research and clinical applications. Signal Transduct Target Ther 7(1):168\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhu S, Chen D, Yang X, Yang L, Han Y (2025) Organoid models to study human infectious diseases. Cell Prolif\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFontoura JC, Viezzer C, Dos Santos FG, Ligabue RA, Weinlich R, Puga RD, Antonow D, Severino P, Bonorino C (2020) Comparison of 2D and 3D cell culture models for cell growth, gene expression and drug resistance. Mater Sci Engineering: C 107:110264\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGeerling E, Pinski AN, Stone TE, DiPaolo RJ, Zulu MZ, Maroney KJ, Brien JD, Messaoudi I, Pinto AK Roles of antiviral sensing and type I interferon signaling in the restriction of SARS-CoV-2 replication. Iscience. 21;25(1):103553\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCugola FR, Fernandes IR, Russo FB et al (2016) The Brazilian Zika virus strain causes birth defects in experimental models. Nature 534(7606):267\u0026ndash;271\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLi C, Xu D, Ye Q et al (2016) Zika virus disrupts neural progenitor development. Cell Stem Cell 19(1):120\u0026ndash;126\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQian X, Nguyen HN, Song MM et al (2018) Brain-region-specific organoids using mini-bioreactors for modeling ZIKV exposure. Cell 165(5):1238\u0026ndash;1254\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBlanco-Melo D, Nilsson-Payant BE, Liu WC, Uhl S, Hoagland D, M\u0026oslash;ller R, Jordan TX, Oishi K, Panis M, Sachs D, Wang TT (2020) Imbalanced host response to SARS-CoV-2 drives development of COVID-19. Cell 181(5):1036\u0026ndash;1045\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLiu X, Li C, Wan Z, Chiu MC, Huang J, Yu Y, Zhu L, Cai JP, Rong L, Song YQ, Chu H (2022) Analogous comparison unravels heightened antiviral defense and boosted viral infection upon immunosuppression in bat organoids. Signal Transduct Target therapy 7(1):392\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhou J, Li C, Liu X et al (2020) Infection of bat and human intestinal organoids by SARS-CoV-2. Nat Med 26(7):1077\u0026ndash;1083\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eArdestani A, Maedler K, Commentary (2020) A Human Pluripotent Stem Cell-Based Platform to Study SARS-CoV-2 Tropism and Model Virus Infection in Human Cells and Organoids. Front Endocrinol (Lausanne) 11:585922. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3389/fendo.2020.585922\u003c/span\u003e\u003cspan address=\"10.3389/fendo.2020.585922\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHashimi M, Sebrell TA, Hedges JF, Snyder D, Lyon KN, Byrum SD, Mackintosh SG, Crowley D, Cherne MD, Skwarchuk D, Robison A (2023) Antiviral responses in a Jamaican fruit bat intestinal organoid model of SARS-CoV-2 infection. Nat Commun 14(1):6882\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHan Y, Yang L, Lacko LA, Chen S (2022) Human organoid models to study SARS-CoV-2 infection. Nat Methods 19(4):418\u0026ndash;428\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLamers MM, van der Vaart J, Knoops K et al (2020) Human airway and intestinal organoids as models of SARS-CoV-2 infection. Nat Med 26(7):1077\u0026ndash;1083\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eVicenti I, Boccuto A, Giannini A, Dragoni F, Saladini F, Zazzi M (2018) Comparative analysis of different cell systems for Zika virus (ZIKV) propagation and evaluation of anti-ZIKV compounds in vitro. Virus Res 244:64\u0026ndash;70\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLui VC, Hui KP, Babu RO, Yue H, Chung PH, Tam PK, Chan MC, Wong KK (2022) Human liver organoid derived intra-hepatic bile duct cells support SARS-CoV-2 infection and replication. Sci Rep 12(1):5375\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePunyadarsaniya D, Liang CH, Winter C, Petersen H, Rautenschlein S, Hennig-Pauka I, Schwegmann-Wessels C, Wu CY, Wong CH, Herrler G (2011) Infection of differentiated porcine airway epithelial cells by influenza virus: differential susceptibility to infection by porcine and avian viruses. PLoS ONE 6(12):e28429\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eShokouhi H, Gholizadeh F, Sokhandan H, Sisakht MM, Mehrbod P (2025) From monolayer to spheroid: assessing influenza a virus infection in 2D and 3D cell culture of A549 and HEK293. Virol J 22(1):309\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKuzmin IV, Schwarz TM, Ilinykh PA, Jordan I, Ksiazek TG, Sachidanandam R, Basler CF, Bukreyev A (2017) Innate Immune Responses of Bat and Human Cells to Filoviruses: Commonalities and Distinctions. J Virol 91(8):e02471\u0026ndash;e02416\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWiderspick L, Steffen JF, Tappe D, Mu\u0026ntilde;oz-Fontela C (2023) Animal Model Alternatives in Filovirus and Bornavirus Research. Viruses 15(1):158. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003e10.3390/v15010158.https://doi.org/10.3390/v15010158\u003c/span\u003e\u003cspan address=\"10.3390/v15010158.10.3390/v15010158\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWicherska-Pawłowska K, Wr\u0026oacute;bel T, Rybka J (2021) Toll-Like Receptors (TLRs), NOD-like receptors (NLRs), and RIG-I-like receptors (RLRs) in innate immunity. TLRs, NLRs, and RLRs ligands as immunotherapeutic agents for hematopoietic diseases. Int J Mol Sci 22(24):13397\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEkchariyawat P, Hamel R, Bernard E, Wichit S, Surasombatpattana P, Talignani L, Thomas F, Choumet V, Yssel H, Despr\u0026egrave;s P, Briant L (2015) Inflammasome signaling pathways exert antiviral effect against Chikungunya virus in human dermal fibroblasts. Infect Genet Evol 32:401\u0026ndash;408\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSepulveda-Crespo D, Resino S, Martinez I (2020) Innate immune response against hepatitis C virus: targets for vaccine adjuvants. Vaccines 8(2):313\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Organoids, Innate Immunity, Interferons, Communicable Diseases, Emerging, Virus Diseases","lastPublishedDoi":"10.21203/rs.3.rs-9351966/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-9351966/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eHuman organoid models have emerged as powerful tools for studying viral pathogenesis and host immune responses in physiologically relevant human tissues. These three-dimensional systems provide opportunities to investigate virus\u0026ndash;host interactions that are difficult to replicate in traditional cell culture models. However, a comprehensive synthesis of antiviral immune responses across different organoid systems and viral families remains limited. A systematic review was conducted in accordance with PRISMA guidelines to evaluate studies investigating antiviral immune responses in human organoid models. Literature searches were performed across major scientific databases for studies published between 2010- January 2026. After removal of duplicates and screening of titles, abstracts, and full texts based on predefined inclusion criteria, 23 studies were included in the final qualitative synthesis. Data were extracted on organoid origin, virus type, immune signaling pathways, and reported immune responses. The included studies investigated viruses from seven families, including \u003cem\u003eCoronaviridae\u003c/em\u003e, \u003cem\u003eFlaviviridae\u003c/em\u003e, \u003cem\u003eOrthomyxoviridae\u003c/em\u003e, \u003cem\u003ePicornaviridae\u003c/em\u003e, \u003cem\u003eFiloviridae\u003c/em\u003e, \u003cem\u003ePoxviridae\u003c/em\u003e, and \u003cem\u003eTogaviridae\u003c/em\u003e. Organoid models primarily represented neural, respiratory, intestinal, and hepatic tissues derived from human embryonic stem cells, induced pluripotent stem cells, or adult stem cells. Across studies, viral infection commonly activated innate immune pathways involving pattern-recognition receptors such as Toll-like receptors and RIG-I\u0026ndash;like receptors, leading to downstream activation of NF-κB and interferon regulatory factor signaling. These pathways induced production of type I and type III interferons, interferon-stimulated genes, and pro-inflammatory cytokines including IL-6, TNF-α, CXCL10, and CCL5. While several viruses triggered strong interferon-mediated antiviral responses, others demonstrated attenuated immune activation, suggesting virus-specific mechanisms of immune modulation or evasion. Human organoid models provide physiologically relevant platforms for studying antiviral immune responses across diverse viral infections and tissue types. The evidence highlights conserved innate immune pathways alongside virus- and tissue-specific differences in immune activation. These systems hold significant potential for advancing our understanding of viral pathogenesis, immune regulation, and therapeutic development.\u003c/p\u003e","manuscriptTitle":"Antiviral immune responses in human organoid models of emerging viral infections: A systematic review","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-04-09 03:20:14","doi":"10.21203/rs.3.rs-9351966/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"138a3494-2584-406e-8542-b426d6e4590e","owner":[],"postedDate":"April 9th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-04-25T04:38:54+00:00","versionOfRecord":[],"versionCreatedAt":"2026-04-09 03:20:14","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-9351966","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-9351966","identity":"rs-9351966","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}