Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of coronavirus disease 19 (COVID-19), which ranges from mild respiratory symptoms to acute respiratory distress syndrome, and death in the most severe cases. Immune dysregulation with altered innate cytokine responses is thought to contribute to disease severity. Here, we characterized in depth host cell responses against SARS-CoV-2 in primary human airway epithelia (HAE) and immortalized cell lines. Our results demonstrate that primary HAE and model cells elicit a robust induction of type I and III interferons (IFNs). Importantly, we show for the first time that melanoma differentiation associated gene (MDA)-5 is the main sensor of SARS-CoV-2 in lung cells. IFN exposure strongly inhibited viral replication and de novo production of infectious virions. However, despite high levels of IFNs produced in response to SARS-CoV-2 infection, the IFN response was unable to control viral replication in lung cells, contrary to what was previously reported in intestinal epithelial cells. Altogether, these results highlight the complex and ambiguous interplay between viral replication and the timing of IFN responses. IMPORTANCE Mammalian cells express sensors able to detect specific features of pathogens and induce the interferon response, which is one of the first line of defenses against viruses and help controlling viral replication. The mechanisms and impact of SARS-CoV-2 sensing in lung epithelial cells remained to be deciphered. In this study, we report that despite a high production of type I and III interferons specifically induced by MDA-5-mediated sensing of SARS-CoV-2, primary and immortalized lung epithelial cells are unable to control viral replication. However, exogenous interferons potently inhibited replication, if provided early upon viral exposure. A better understanding of the ambiguous interplay between the interferon response and SARS-CoV-2 replication is essential to guide future therapeutical interventions.

Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. The structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.

ARS-CoV-2 is the etiologic agent of the coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 is the third highly pathogenic coronavirus to cross the species barrier in the 21st century after SARS-CoV-1 in 2002-2003 (refs. 1-3 ) and MERS-CoV in 2012 (ref. 4 ). Four additional HCoVs (HCoV-229E, HCoV-NL63, HCoV-OC43 and HCoV-HKU1) are known to circulate seasonally in humans, contributing to approximately one-third of common cold infections 5 . Like SARS-CoV-1 and HCoV-NL63, SARS-CoV-2 entry into target cells is mediated by the angiotensin-converting enzyme 2 (ACE2) receptor [6][7][8][9][10] . The cellular serine protease transmembrane protease serine 2 (TMPRSS2) is used by both SARS-CoV-1 and SARS-CoV-2 for Spike protein priming at the plasma membrane 6,11 . Cathepsins are also involved in SARS-CoV spike protein cleavage and fusion peptide exposure upon entry via an endocytic route, in the absence of TMPRSS2 (refs. [12][13][14][15] ).Several whole-genome KO CRISPR screens for the identification of coronavirus regulators have been reported [16][17][18][19][20][21] . These screens used naturally permissive simian Vero E6 cells of kidney origin 20 ; human Huh7 cells (or derivatives) of liver origin (ectopically expressing ACE2 and TMPRSS2, or not) 16,18,19 ; and A549 cells of lung origin, ectopically expressing ACE2 17,21 . Here, we conducted genome-wide, loss-of-function CRISPR KO screens and gain-of-function CRISPRa screens in several cell lines, including physiologically relevant human Calu-3 cells and Caco-2 cells, of lung and colorectal adenocarcinoma origin, respectively, followed by secondary screens in these cell lines and in Huh7.5.1 and A549 cells. Well-known SARS-CoV-2 host-dependency factors were identified among top hits, such as ACE2 and either TMPRSS2 or cathepsin L (depending on the cell type). We characterized the mechanism of action of the top hits and assessed their effect on other coronaviruses and influenza A orthomyxovirus. Altogether, this study provides insights into the coronavirus life cycle by identifying host factors that modulate replication and might lead to pan-coronavirus strategies for host-directed therapies. ResultsMeta-analysis of CRISPR KO screens highlights the importance of multiple models. Vero E6 cells present high levels of cytopathic effects (CPEs) upon SARS-CoV-2 replication, making them ideal to perform whole-genome CRISPR screens for host factor identification. A Chlorocebus sabaeus single-guide RNA (sgRNA) library was previously successfully used to identify host factors regulating SARS-CoV-2 (isolate USA-WA1/2020) replication 20 . Therefore, we initially repeated whole-genome CRISPR KO screens in Vero E6 cells using the SARS-CoV-2 isolate BetaCoV/France/ IDF0372/2020 (Fig. 1a). Importantly, ACE2 was a top hit (Fig. 1b