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
Affiliations
Simone A. Thair
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Yudong D. He
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Yehudit Hasin-Brumshtein
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Suraj Sakaram
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Rushika Pandya
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Jiaying Toh
Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
David Rawling
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Melissa Remmel
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
Sabrina Coyle
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA
George N. Dalekos
Department of Internal Medicine, University of Thessaly, Larissa General Hospital, Greece
Ioannis Koutsodimitropoulos
Intensive Care Unit, Latseion General Hospital of Elefsis, Greece
Glykeria Vlachogianni
Intensive Care Unit, Aghios Dimitrios Thessaloniki General Hospital, Greece
Eleni Gkeka
Intensive Care Unit, AHEPA Thessaloniki General Hospital, Greece
Eleni Karakike
4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
Georgia Damoraki
4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
Nikolaos Antonakos
4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
Purvesh Khatri
Institute for Immunity, Transplantation and Infection, School of Medicine, Stanford University, Palo Alto, CA 94305, USA; Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA 94305, USA
Evangelos J. Giamarellos-Bourboulis
4th Department of Internal Medicine, National and Kapodistrian University of Athens, Medical School, 124 62 Athens, Greece
Timothy E. Sweeney
Inflammatix, Inc., 863 Mitten Road, Suite 104, Burlingame, CA 94010, USA; Corresponding author
Summary: 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 CD56bright 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.
