Characterization and treatment of SARS-CoV-2 in nasal and bronchial human airway epithelia

Andrés Pizzorno; Blandine Padey; Thomas Julien; Sophie Trouillet-Assant; Aurélien Traversier; Elisabeth Errazuriz-Cerda; Julien Fouret; Julia Dubois; Alexandre Gaymard; François-Xavier Lescure; Victoria Dulière; Pauline Brun; Samuel Constant; Julien Poissy; Bruno Lina; Yazdan Yazdanpanah; Olivier Terrier; Manuel Rosa-Calatrava

tion, except for the nasal HAE at 48 hpi, in which a strong relative increase of nsp14 RNA was observed (Fig. 1F) . Interestingly, viral genome was detected in the basal medium from 48 hpi, with the peak observed at 72 hpi ( Fig. 1H ) coinciding with the highest impact of SARS-CoV-2 infection on epithelium integrity. 110 To further characterize the biology of the SARS-CoV-2, we inoculated both nasal ( Fig. 2A , B) and bronchial (Fig. 2C, D The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.017889 doi: bioRxiv preprint in Fig. 1 and with a recent study reporting high expression levels of the SARS-CoV-2 cell receptor angiotensin-converting enzyme-2 (ACE2) in both ciliated and goblet respiratory cells (14) . As previously observed in structural studies of other coronaviruses, notably SARS-CoV and MERS-CoV (15-18), we distinguished characteristic clusters in the perinuclear region of infected HAE cells. These clusters are mainly composed of numerous viral single-and double-membrane 120 vesicles (DMV) and mitochondria ( Fig. 2A, A1 The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.31.017889 doi: bioRxiv preprint 48, 72 and 96 hpi (Fig. 3A) . This observation was substantiated by unsupervised analysis of the data using the full gene panel. Indeed, the first component of the principal component analysis 140 (PCA) that accounts for 63% of the variance is mainly driven by the time of infection, with a clear discrimination between 24 hpi and the other time-points (Fig. 3B , red triangles/dots). Interestingly, the immune transcriptomic signatures seem at least partially driven by the nature of the HAE beyond 24 hpi (Fig. 3A) . This is in agreement with the second component analysis, gathering 12.6% of total variance, which allowed a clear differentiation between the nasal and bronchial 145 compartments (Fig. 3B , green/purple triangles versus dots). In the nasal HAE, the response after 24 hpi (peak at 72-96 hpi) is driven by a strong upregulation of type I and type III IFNs (IFNB1, IFNL1, IFNL2-3-4) as well as other immunity-related genes. Whereas only a subset of these genes (CXCL10/IP10, CXCL2/MIP2A, IL1A, IL1B, Mx1 and ZBP1) follow the same pattern in the bronchial HAE, though at overall lower expression levels, the initial modulation of IFNB1, IFNL1, 150 CCL2/MCP1 and IL6 in this tissue seems to fade at 96 hpi. Moreover, the relative expression of a subset of genes associated with the NF-kB and TNFα pathways (e.g. IL18, IL18R1, NFKB2, NFKBIA, TNFA, and TNFAIP3) is mostly unchanged all throughout the infection in bronchial HAE but it is highly upregulated in nasal HAE at 48 hpi and onwards ( Fig. 3C and Data S1).