Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection

• Published in: Nature communications Vol. 11; no. 1; p. 6319
• Main Authors: Desai, Niyati, Neyaz, Azfar, Szabolcs, Annamaria, Shih, Angela R., Chen, Jonathan H., Thapar, Vishal, Nieman, Linda T., Solovyov, Alexander, Mehta, Arnav, Lieb, David J., Kulkarni, Anupriya S., Jaicks, Christopher, Xu, Katherine H., Raabe, Michael J., Pinto, Christopher J., Juric, Dejan, Chebib, Ivan, Colvin, Robert B., Kim, Arthur Y., Monroe, Robert, Warren, Sarah E., Danaher, Patrick, Reeves, Jason W., Gong, Jingjing, Rueckert, Erroll H., Greenbaum, Benjamin D., Hacohen, Nir, Lagana, Stephen M., Rivera, Miguel N., Sholl, Lynette M., Stone, James R., Ting, David T., Deshpande, Vikram
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 09.12.2020; Nature Publishing Group; Nature Portfolio
• Subjects: 13/51; 13/56; 38/77; 38/88; 38/90; 38/91; 692/308/575; 692/699/255/2514; Adult; Aged; Aged, 80 and over; Aspartic Acid Endopeptidases - metabolism; Autopsies; Autopsy; Cadavers; COVID-19; COVID-19 - immunology; COVID-19 - metabolism; Damage; Epithelial cells; Epithelial Cells - metabolism; Epithelial Cells - pathology; Epithelial Cells - virology; Female; Fibrosis; Gene expression; Genes; Heterogeneity; Host Microbial Interactions; Humanities and Social Sciences; Humans; Immunity; Immunohistochemistry; In Situ Hybridization; Infections; Inflammation; Interferon; Interferons - genetics; Interferons - metabolism; Lung - pathology; Lung - virology; Lungs; Macrophages; Macrophages - immunology; Male; Middle Aged; Mucin; Mucins - genetics; Mucins - metabolism; multidisciplinary; Patients; Ribonucleic acid; RNA; Science; Science (multidisciplinary); Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spatial heterogeneity; Surface-Active Agents - metabolism; Transcription activation; Transcriptome; Viral diseases; Viral Load; Viruses
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20139-7

The relationship of SARS-CoV-2 pulmonary infection and severity of disease is not fully understood. Here we show analysis of autopsy specimens from 24 patients who succumbed to SARS-CoV-2 infection using a combination of different RNA and protein analytical platforms to characterize inter-patient and intra-patient heterogeneity of pulmonary virus infection. There is a spectrum of high and low virus cases associated with duration of disease. High viral cases have high activation of interferon pathway genes and a predominant M1-like macrophage infiltrate. Low viral cases are more heterogeneous likely reflecting inherent patient differences in the evolution of host response, but there is consistent indication of pulmonary epithelial cell recovery based on napsin A immunohistochemistry and RNA expression of surfactant and mucin genes. Using a digital spatial profiling platform, we find the virus corresponds to distinct spatial expression of interferon response genes demonstrating the intra-pulmonary heterogeneity of SARS-CoV-2 infection. Understanding the pathology in the lungs of patients with COVID-19 might provide clues as to the susceptibility of patients and how the SARS-CoV-2 virus can be fatal. Here the authors analyze cadaveric pulmonary tissue and show one group with high viral load, early death, inflammation and inflammatory damage, and another with low viral load, longer duration of disease, and more M2-like polarization and fibrotic lung damage.