One of the greatest threats to humanity is the emergence of a pandemic virus. Among those with the greatest potential for such an event include influenza viruses and coronaviruses. In the last century alone, we have observed four major influenza A virus pandemics as well as the emergence of three highly pathogenic coronaviruses including SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic. As no effective antiviral treatments or vaccines are presently available against SARS-CoV-2, it is important to understand the host response to this virus as this may guide the efforts in development towards novel therapeutics. Here, we offer the first in-depth characterization of the host transcriptional response to SARS-CoV-2 and other respiratory infections through in vitro, ex vivo, and in vivo model systems. Our data demonstrate the each virus elicits both core antiviral components as well as unique transcriptional footprints. Compared to the response to influenza A virus and respiratory syncytial virus, SARS-CoV-2 elicits a muted response that lacks robust induction of a subset of cytokines including the Type I and Type III interferons as well as a numerous chemokines. Taken together, these data suggest that the unique transcriptional signature of this virus may be responsible for the development of COVID-19.

SARS-CoV-2 infects less than 1% of cells in the human body, yet it can cause severe damage in a variety of organs. Thus, deciphering the non-cell autonomous effects of SARS-CoV-2 infection is imperative for understanding the cellular and molecular disruption it elicits. Neurological and cognitive defects are among the least understood symptoms of COVID-19 patients, with olfactory dysfunction being their most common sensory deficit. Here, we show that both in humans and hamsters SARS-CoV-2 infection causes widespread downregulation of olfactory receptors (OR) and of their signaling components. This non-cell autonomous effect is preceded by a dramatic reorganization of the neuronal nuclear architecture, which results in dissipation of genomic compartments harboring OR genes. Our data provide a potential mechanism by which SARS-CoV-2 infection alters the cellular morphology and the transcriptome of cells it cannot infect, offering insight to its systemic effects in olfaction and beyond.

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The host response to SARS-CoV-2, the etiologic agent of the COVID-19 pandemic, demonstrates significant inter-individual variability. In addition to showing more disease in males, the elderly, and individuals with underlying co-morbidities, SARS-CoV-2 can seemingly render healthy individuals with profound clinical complications. We hypothesize that, in addition to viral load and host antibody repertoire, host genetic variants also impact vulnerability to infection. Here we apply human induced pluripotent stem cell (hiPSC)-based models and CRISPR-engineering to explore the host genetics of SARS-CoV-2. We demonstrate that a single nucleotide polymorphism (rs4702), common in the population at large, and located in the 3’UTR of the protease FURIN, impacts alveolar and neuron infection by SARS-CoV-2 in vitro. Thus, we provide a proof-of-principle finding that common genetic variation can impact viral infection, and thus contribute to clinical heterogeneity in SARS-CoV-2. Ongoing genetic studies will help to better identify high-risk individuals, predict clinical complications, and facilitate the discovery of drugs that might treat disease.

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9The capacity to edit genomes using CRISPR-Cas systems holds immense potential for 10 countless genetic-based diseases. However, one significant impediment preventing broad 11 therapeutic utilization is in vivo delivery. While genetic editing at a single cell level in vitro can be 12 achieved with high efficiency, the capacity to utilize these same biologic tools in a desired tissue 13 in vivo remains challenging. Non-integrating RNA virus-based vectors constitute efficient 14 platforms for transgene expression and surpass several barriers to in vivo delivery. However, 15 the broad tissue tropism of viral vectors raises the concern for off-target effects. Moreover, 16 prolonged expression of the Cas proteins, regardless of delivery method, can accumulate 17 aberrant RNAs leading to unwanted immunological responses. In an effort to circumvent these 18 shortcomings, here we describe a versatile RNA virus-based technology that can achieve cell-19 specific activity and self-inactivation by combining host microRNA (miRNA) biology with the 20 CRISPR-Cas12a RNA-guided nuclease. Exploiting the RNase activity of Cas12a, we generated 21 a vector that self-inactivates upon delivery of Cas12a and an accompanying CRISPR RNA 22 (crRNA). Furthermore, we show that maturation of the crRNA can be made dependent on cell-23 specific miRNAs, which confers cell-specificity. We demonstrate that this genetic editing circuit 24delivers diminished yet sufficient levels of Cas12a to achieve effective genome editing whilst 25 inducing a minimal immunological response. It can also function in a cell-specific manner 26 thereby facilitating in vivo editing and mitigating the risk of unwanted, off-target effects. 27