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Title	Transcriptomic similarities and differences in host response between SARS-CoV-2 and other viral infections.
Author	Thair, Simone A; He, Yudong D; Hasin-Brumshtein, Yehudit; Sakaram, Suraj; Pandya, Rushika; Toh, Jiaying; Rawling, David; Remmel, Melissa; Coyle, Sabrina; Dalekos, George N; Koutsodimitropoulos, Ioannis; Vlachogianni, Glykeria; Gkeka, Eleni; Karakike, Eleni; Damoraki, Georgia; Antonakos, Nikolaos; Khatri, Purvesh; Giamarellos-Bourboulis, Evangelos J; Sweeney, Timothy E
Journal	iScience	Publication Year/Month	2021-Jan
PMID	33437935	PMCID	PMC7786129
Affiliation + expend	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

Publication