Engineered Human Adenoviruses of Species B and C Report Early, Intermediate Early, and Late Viral Gene Expression

Activated blood-derived human primary T cells support replication of HAdV C5 and virus transmission to polarized human primary epithelial cells

Human adenoviruses (HAdVs) cause self-limiting disease but are life-threatening to immunocompromised individuals. HAdV-C5 infects epithelial cells of the airways and eyes through aerosols, contaminated hands, or medical instruments, as well as fecal-oral contacts, gives rise to viremia, persisting in lymphoid cells of the gastrointestinal tract. Here, we show that pre-activated human primary blood-derived T cells can be infected with HAdV-C5 in vitro, upon incubation of the virus with a mixture of three distinct homotrimeric adapter proteins that target the virus to T cells. Each of the adapter proteins can bind 1 of the 12 fiber knobs of the virion through a designed ankyrin repeat protein. Two of the adapters contained a single-chain antibody fragment to T cell surface proteins CD3 or CD28, and the third one contained the cytokine interleukin-2. These adapters mediated efficient infection of primary T cells by HAdV-C5 and infectious progeny release, albeit with donor-to-donor variability. Co-culture of well-polarized air-liquid interface human bronchial epithelial cells with infected CD3+ T cells gave rise to progressively increased viral titers from replicating but not from replication-defective E1-deleted HAdV-C5, notably with similar kinetics as cell-free virus infections, suggesting that progeny virus from T cells was further amplified in epithelial cells. This study provides a platform to explore interactions between epithelial and immune cells in acute and persistent HAdV-C5 infection settings.IMPORTANCEMany human adenoviruses (HAdV), including HAdV-C5, infect and propagate to high titers in epithelial cells of the airways. Virus ends up in lymphoid cells of the gastrointestinal and respiratory mucosa, where it can persist subclinically for years, restricted by memory T cells and humoral immune defense. In immunodeficient patients or newborns, however, HAdV can be fatal, coincident with lymphocytopenia and virus proliferation in epithelial cells. Here, we show that activated blood-derived human primary T lymphocytes can be productively infected with HAdV-C5 coated with trimerized adapter proteins targeting CD3, CD28, and the interleukin 2 receptors. A co-culture model of infected T cells and primary human bronchial epithelial cells in the absence of HAdV-specific immune cells showed that progeny virus from T cells was transferred to epithelial cells and led to increased progeny production compared to infected T cells alone, a situation potentially mimicking persistently infected mucosal lymphoid cells in immunosuppressed patients.

Preexisting cell state rather than stochastic noise confers high or low infection susceptibility of human lung epithelial cells to adenovirus

Viruses display large variability across all stages of their life cycle, including entry, gene expression, replication, assembly, and egress. We previously reported that the immediate early adenovirus (AdV) E1A transcripts accumulate in human lung epithelial A549 cancer cells with high variability, mostly independent of the number of incoming viral genomes, but somewhat correlated to the cell cycle state at the time of inoculation. Here, we leveraged the classical Luria-Delbrück fluctuation analysis to address whether infection variability primarily arises from the cell state or stochastic noise. The E1A expression was measured by the expression of green fluorescent protein (GFP) from the endogenous E1A promoter in AdV-C5_E1A-FS2A-GFP and found to be highly correlated with the viral plaque formation, indicating reliability of the reporter virus. As an ensemble, randomly picked clonal A549 cell isolates displayed significantly higher coefficients of variation in the E1A expression than technical noise, indicating a phenotypic variability larger than noise. The underlying cell state determining infection variability was maintained for at least 9 weeks of cell cultivation. Our results indicate that preexisting cell states tune adenovirus infection in favor of the cell or the virus. These findings have implications for antiviral strategies and gene therapy applications.IMPORTANCEViral infections are known for their variability. Underlying mechanisms are still incompletely understood but have been associated with particular cell states, for example, the eukaryotic cell division cycle in DNA virus infections. A cell state is the collective of biochemical, morphological, and contextual features owing to particular conditions or at random. It affects how intrinsic or extrinsic cues trigger a response, such as cell division or anti-viral state. Here, we provide evidence that cell states with a built-in memory confer high or low susceptibility of clonal human epithelial cells to adenovirus infection. Results are reminiscent of the Luria-Delbrück fluctuation test with bacteriophage infections back in 1943, which demonstrated that mutations, in the absence of selective pressure prior to infection, cause infection resistance rather than being a consequence of infection. Our findings of dynamic cell states conferring adenovirus infection susceptibility uncover new challenges for the prediction and treatment of viral infections.

A versatile automated pipeline for quantifying virus infectivity by label-free light microscopy and artificial intelligence

Virus infectivity is traditionally determined by endpoint titration in cell cultures, and requires complex processing steps and human annotation. Here we developed an artificial intelligence (AI)-powered automated framework for ready detection of virus-induced cytopathic effect (DVICE). DVICE uses the convolutional neural network EfficientNet-B0 and transmitted light microscopy images of infected cell cultures, including coronavirus, influenza virus, rhinovirus, herpes simplex virus, vaccinia virus, and adenovirus. DVICE robustly measures virus-induced cytopathic effects (CPE), as shown by class activation mapping. Leave-one-out cross-validation in different cell types demonstrates high accuracy for different viruses, including SARS-CoV-2 in human saliva. Strikingly, DVICE exhibits virus class specificity, as shown with adenovirus, herpesvirus, rhinovirus, vaccinia virus, and SARS-CoV-2. In sum, DVICE provides unbiased infectivity scores of infectious agents causing CPE, and can be adapted to laboratory diagnostics, drug screening, serum neutralization or clinical samples.

Expanding the adenovirus toolbox: reporter viruses for studying the dynamics of human adenovirus replication

To streamline standard virological assays, we developed a suite of nine fluorescent or bioluminescent replication competent human species C5 adenovirus reporter viruses that mimic their parental wild-type counterpart. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. Moreover, they permit real-time non-invasive measures of viral load, replication dynamics, and infection kinetics over the entire course of infection, allowing measurements that were not previously possible. This suite of replication competent reporter viruses increases the ease, speed, and adaptability of standard assays and has the potential to accelerate multiple areas of human adenovirus research.IMPORTANCEIn this work, we developed a versatile toolbox of nine HAdV-C5 reporter viruses and validated their functions in cell culture. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. The utility of these reporter viruses could also be extended for use in 3D cell culture, organoids, live cell imaging, or animal models, and provides a conceptual framework for the development of new reporter viruses representing other clinically relevant HAdV species.