Margaret A. Scull

Enteroviruses are arguably the most numerous group of viruses infecting humans. While most enterovirus infections are benign and self-resolving, their sheer number inevitably increases the chances of multiple complications. The diversity of enteroviruses means that the development of vaccines is only economically feasible against a select few, and no direct-acting or host-targeted anti-virals are approved to treat enteroviral infections, largely due to the rapid development of resistance against all experimental drugs. Here, we explored a universal property of enterovirus infection—a massive upregulation of phospholipid synthesis as a target for anti-viral interventions. The increased phospholipid synthesis consumes endogenously and exogenously derived long-chain fatty acids (LCFA). We demonstrate that polyunsaturated LCFAs can have a broad anti-enteroviral effect, affecting multiple steps of the virus life cycle. The anti-viral activity of LCFAs did not strictly depend on the degree of unsaturation or their capacity to induce lipid peroxidation, but significantly correlated with their conformation. This suggests that their incorporation into the phospholipid molecules makes the replication organelle membranes incapable of properly accommodating viral replication machinery. Accordingly, the inhibition of neutral lipid synthesis promoted LCFAs retargeting to the membranes in infected cells and increased their anti-viral potency. We show that this approach is effective against diverse enteroviruses in different cell types, including differentiated primary cells, and that attempts to establish viruses resistant to such treatment were unsuccessful. IMPORTANCE: Humans are hosts to more than 300 distinct enteroviruses. Enterovirus infections can induce multiple short-term and long-term complications, including such serious conditions as paralysis, myocarditis, aseptic meningitis, and others. Yet, licensed vaccines are available only against poliovirus and enterovirus A71, and no specific anti-enterovirus drugs are approved for clinical practice. These viruses rapidly develop resistance to either virus- or host-acting experimental compounds. We explored a shared feature of enterovirus infection, a strong upregulation of phospholipid synthesis in infected cells, as a tool to control enterovirus replication. By altering the long-chain fatty acids composition available to infected cells, replication of diverse enteroviruses can be similarly suppressed, and the selection of resistant mutants was not successful. Thus, targeting infection-induced changes in cellular lipid metabolism, rather than individual viral or host factors, may offer a promising approach for controlling enterovirus infections.

The ongoing panzootic of clade 2.3.4.4b highly pathogenic avian influenza (HPAI) H5N1 viruses has reached a critical point, marked by unprecedented mammalian spillover and sustained outbreaks in U.S. dairy cattle. While these viruses remain highly lethal in traditional ferret models, human infections—primarily linked to the B3.13 and D1.1 lineages—have been notably mild, typically presenting as conjunctivitis with minimal respiratory involvement. In this study, we address this disconnect by evaluating the infectivity of recent H5N1 isolates using a physiologically relevant air-liquid interface (ALI) culture system that incorporates an aerosol settling chamber. We demonstrate that while direct liquid inoculation leads to efficient replication, aerosolized H5N1 strains exhibit a significant defect in their ability to infect human respiratory epithelium. In contrast, a prototypic H5N1 virus remains highly pathogenic and lethal in ferrets regardless of the inoculation route, showing systemic dissemination to the brain and other organs. Our findings identify two primary viral determinants driving this respiratory restriction: reduced neuraminidase (NA) enzymatic activity and impaired polymerase activity. Collectively, these results suggest that commonly used mammalian models may overstate current human pandemic risk. This work highlights the critical need for alternative risk- assessment platforms to identify the specific genetic shifts required for these viruses to overcome existing barriers to human adaptation. IMPORTANCE: Current pandemic risk assessments rely heavily on animal models, particularly ferrets, to evaluate the threat posed by emerging influenza viruses. However, recent H5N1 viruses that have caused predominantly mild human infections have remained highly virulent in these models, creating uncertainty about how well they predict human disease. Using a physiologically relevant human airway model infected through aerosol exposure, we demonstrate that contemporary H5N1 are markedly restricted in their ability to establish respiratory infection despite retaining high virulence in ferrets. These findings highlight the importance of incorporating human airway aerosol models into pandemic risk assessment frameworks to better evaluate the human adaptation and respiratory infection potential of emerging influenza viruses.

Respiratory viruses are a significant cause of morbidity and mortality world-wide and an important trigger of acute exacerbation in chronic lung disease. Secreted airway mucus – a front-line defense system against respiratory virus infection – is largely composed of glycosylated mucins that promote virus trapping via steric and adhesive interactions. Still, the degree to which mucus can trap specific viruses is unclear. Further, mucin expression is altered in chronic lung disease with undefined impacts on host susceptibility to infection. Here, we devised an inverse Transwell assay (ITA) to specifically probe the barrier function of mucus towards infection without the confounding effects of ongoing mucus secretion and transport on viral dynamics. Using the ITA, we assessed the barrier function of human airway epithelial (HAE) culture-derived mucus towards influenza (IAV), rhinovirus (RV), adenovirus, and parainfluenza virus. Results showed differences in mucus penetration efficiency between viruses, with IAV being the most inhibited relative to no mucus controls. Notably, IAV and RV penetration efficiency was similar between normal mucus and mucus sourced from an in-vitro model of asthmatic epithelium. To further explore the role of specific mucins during infection, we employed CRISPR/Cas9-modified HAE cultures lacking either MUC5B or MUC5AC expression. Direct infection in these cultures with IAV yielded higher viral titers compared to control HAE, suggesting both MUC5B and MUC5AC contribute to antiviral defense. Application of mucus harvested from specific mucin-knockout or control HAE in the ITA revealed that while RV penetration was similar across conditions, IAV was more efficient in breaching MUC5AC-depleted gels. Subsequent biophysical analysis of these mucus gels revealed a larger pore structure in the absence of MUC5AC. Together, these data indicate mucus-mediated restriction is virus dependent and highlight the contribution of MUC5AC to mucus structure and antiviral capabilities. Further, they establish the ITA as a tunable platform enabling investigation into mucus penetration by diverse viruses and the effects of altered mucus composition on barrier function. Clinical Relevance: Mucus composition is altered in chronic lung disease states and during inflammation with unknown consequences on its barrier function towards respiratory virus infection. Using an inverse Transwell assay, we describe virus-specific kinetics through mucus representative of health and disease and identify a critical role for MUC5AC in defense towards influenza A virus. This work can inform future strategies to improve infection prevention or mucus targeted therapies, and may help explain differences in susceptibility to viral infections across the population.

The human airway epithelium (HAE) is composed of diverse cell types that coordinate essential functions and host defenses. Among these defenses, interferons (IFNs) are central to antiviral programs. However, the gene regulatory networks (GRNs) governing HAE cellular identities and their IFN responses are incompletely defined. At single-cell resolution, we characterized the transcriptomes and accessible chromatin landscapes of HAE cell types, at steady state and following IFNβ stimulation. The resulting scRNA-seq and snATAC-seq data informed genome-scale GRN construction and inference of transcriptional circuits underlying cell identities. In response to IFN, we identified a shared transcriptional program across HAE cell types, and an expanded set of interferon-responsive genes exhibiting cell type-associated expression patterns. Cell type-associated transcription factors and chromatin accessibility contribute to distinct IFN-responsive gene expression programs. Together, these data provide a blueprint for molecular regulation of complex HAE responses and a foundation for therapeutic strategies to enhance host antiviral defense.

The airway mucus barrier is both the first point of contact between respiratory viruses and the host and a frontline defense system that viruses must overcome prior to infection. Mucin glycoproteins within this barrier protect the underlying epithelium through trapping and clearance mechanisms and influence multiple aspects of viral pathogenesis including inflammation and transmission. Further, changes in mucin expression either associated with preexisting lung disease or induced during infection can affect disease severity. Research over the past century has aided our understanding of secreted and tethered mucin-mediated defenses and revealed insights into specific virus-mucin interactions and the effect of both physical virion attributes and viral glycoprotein function in facilitating mucus penetration. Here we discuss these advancements and highlight efforts to apply current knowledge to the development of mucin-inspired antiviral therapeutics. Still, given the diversity among respiratory viruses and complexity of mucin biology, open questions remain, indicating avenues for continued investigation.

Mucus is an important component of airway host defenses that acts by enabling the trapping and clearance of infectious materials such as bacteria and viruses. It can be difficult, however, to design experiments that independently determine the extent to which mucus contributes to innate barrier functions in the lung. Here, we provide detailed protocols to collect mucus from human airway epithelial cultures and evaluate how the properties of mucus impact mucociliary transport and protection from viral infection. We include recommended test parameters depending on the specific research question as it relates to respiratory infectious diseases. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.Basic Protocol 1: Analysis of mucociliary transport and ciliary beat frequency in HAE culturesBasic Protocol 2: Collection of mucus from HAE culturesBasic Protocol 3: Transplantation of mucus to HAE cultures and infection with virus

Rhinovirus C (RV-C) infects airway epithelial cells and is an important cause of acute respiratory disease in humans. To interrogate the mechanisms of RV-C-mediated disease, animal models are essential. Towards this, RV-C infection was recently reported in wild-type (WT) mice, yet, titers were not sustained. Therefore, the requirements for RV-C infection in mice remain unclear. Notably, prior work has implicated human cadherin-related family member 3 (CDHR3) and stimulator of interferon genes (STING) as essential host factors for virus uptake and replication, respectively. Here, we report that even though human (h) and murine (m) CDHR3 orthologs have similar tissue distribution, amino acid sequence homology is limited. Further, while RV-C can replicate in mouse lung epithelial type 1 (LET1) cells and produce infectious virus, we observed a significant increase in the frequency and intensity of dsRNA-positive cells following hSTING expression. Based on these findings, we sought to assess the impact of hCDHR3 and hSTING on RV-C infection in mice in vivo. Thus, we developed hCDHR3 transgenic mice, and utilized adeno-associated virus (AAV) to deliver hSTING to the murine airways. Subsequent challenge of these mice with RV-C15 revealed significantly higher titers 24 h post-infection in mice expressing both hCDHR3 and hSTING—compared to either WT mice, or mice with hCDHR3 or hSTING alone, indicating more efficient infection. Ultimately, this mouse model can be further engineered to establish a robust in vivo model, recapitulating viral dynamics and disease.

Background: SARS-CoV-2, the agent responsible for the COVID-19 pandemic, enters cells through viral spike glycoprotein binding to the cellular receptor, angiotensin-converting enzyme 2 (ACE2). Given the lack of effective antivirals targeting SARS-CoV-2, we previously utilized systematic evolution of ligands by exponential enrichment (SELEX) and selected fluoro-arabino nucleic acid (FANA) aptamer R8-9 that was able to block the interaction between the viral receptor-binding domain and ACE2. Methods: Here, we further assessed FANA-R8-9 as an entry inhibitor in contexts that recapitulate infection in vivo. Results: We demonstrate that FANA-R8-9 inhibits spike-bearing pseudovirus particle uptake in cell lines. Then, using an in-vitro model of human airway epithelium (HAE) and SARS-CoV-2 virus, we show that FANA-R8-9 significantly reduces viral infection when added either at the time of inoculation, or several hours later. These results were specific to the R8-9 sequence, not the xeno-nucleic acid utilized to make the aptamer. Importantly, we also show that FANA-R8-9 is stable in HAE culture secretions and has no overt cytotoxic effects. Conclusions: Together, these results suggest that FANA-R8-9 effectively prevents infection by specific SARS-CoV-2 variants and indicate that aptamer technology could be utilized to target other clinically-relevant viruses in the respiratory mucosa.

Background: SARS-CoV-2, the agent responsible for the COVID-19 pandemic, enters cells through viral spike glycoprotein binding to the cellular receptor, angiotensin-converting enzyme 2 (ACE2). Given the lack of effective antivirals targeting SARS-CoV-2, we previously utilized systematic evolution of ligands by exponential enrichment (SELEX) and selected fluoro-arabino nucleic acid (FANA) aptamer R8-9 that was able to block the interaction between the viral receptor-binding domain and ACE2. Methods: Here, we further assessed FANA-R8-9 as an entry inhibitor in contexts that recapitulate infection in vivo . Results: We demonstrate that FANA-R8-9 inhibits spike-bearing pseudovirus particle uptake in cell lines. Then, using an in-vitro model of human airway epithelium (HAE) and SARS-CoV-2 virus, we show that FANA-R8-9 significantly reduces viral infection when added either at the time of inoculation, or several hours later. These results were specific to the R8-9 sequence, not the xeno-nucleic acid utilized to make the aptamer. Importantly, we also show that FANA-R8-9 is stable in HAE culture secretions and has no overt cytotoxic effects. Conclusions: Together, these results suggest that FANA-R8-9 effectively prevents infection by specific SARS-CoV-2 variants and indicate that aptamer technology could be utilized to target other clinically-relevant viruses in the respiratory mucosa.