Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections

Simone A Thair; Yudong D He; Yehudit Hasin-Brumshtein; Suraj Sakaram; Rushika Pandya; Jiaying Toh; David Rawling; Melissa Remmel; Sabrina Coyle; George N Dalekos; Ioannis Koutsodimitropoulos; Glykeria Vlachogianni; Eleni Gkeka; Eleni Karakike; Georgia Damoraki; Nikolaos Antonakos; Purvesh Khatri; Evangelos J Giamarellos-Bourboulis; Timothy E Sweeney

doi:10.1016/j.isci.2020.101947

Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections

iScience. 2020 Dec 16;24(1):101947. doi: 10.1016/j.isci.2020.101947. eCollection 2021 Jan 22.

Authors

Simone A Thair¹, Yudong D He¹, Yehudit Hasin-Brumshtein¹, Suraj Sakaram¹, Rushika Pandya¹, Jiaying Toh^{2

3}, David Rawling¹, Melissa Remmel¹, Sabrina Coyle¹, George N Dalekos⁴, Ioannis Koutsodimitropoulos⁵, Glykeria Vlachogianni⁶, Eleni Gkeka⁷, Eleni Karakike⁸, Georgia Damoraki⁸, Nikolaos Antonakos⁸, Purvesh Khatri^{2

3}, Evangelos J Giamarellos-Bourboulis⁸, Timothy E Sweeney¹

Affiliations

¹ Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA.
² Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA 94305, USA.
³ Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
⁴ Department of Internal Medicine, University of Thessaly, Larissa General Hospital, Greece.
⁵ Intensive Care Unit, Latseion General Hospital of Elefsis, Greece.
⁶ Intensive Care Unit, Aghios Dimitrios Thessaloniki General Hospital, Greece.
⁷ Intensive Care Unit, AHEPA Thessaloniki General Hospital, Greece.
⁸ 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece.

Abstract

The pandemic 2019 novel coronavirus disease (COVID-19) shares certain clinical characteristics with other acute viral infections. We studied the whole-blood transcriptomic host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using RNAseq from 24 healthy controls and 62 prospectively enrolled patients with COVID-19. We then compared these data to non-COVID-19 viral infections, curated from 23 independent studies profiling 1,855 blood samples covering six viruses (influenza, respiratory syncytial virus (RSV), human rhinovirus (HRV), severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1), Ebola, dengue). We show gene expression changes in COVID-19 versus non-COVID-19 viral infections are highly correlated (r = 0.74, p < 0.001). However, we also found 416 genes specific to COVID-19. Inspection of top genes revealed dynamic immune evasion and counter host responses specific to COVID-19. Statistical deconvolution of cell proportions maps many cell type proportions concordantly shifting. Discordantly increased in COVID-19 were CD56^bright natural killer cells and M2 macrophages. The concordant and discordant responses mapped out here provide a window to explore the pathophysiology of the host response to SARS-CoV-2.

Keywords: Immunology: Bioinformatics; Molecular Biology; Transcriptomics.