Whole-genome sequencing reveals host factors underlying critical COVID-19

Kousathanas, Athanasios, Pairo-Castineira, Erola, Rawlik, Konrad, Stuckey, Alex, Odhams, Christopher A, Walker, Susan, Russell, Clark D, Malinauskas, Tomas, Wu, Yang, Millar, Jonathan
et al (show 66 more authors) (2022) Whole-genome sequencing reveals host factors underlying critical COVID-19. NATURE, 607 (7917). 97-+.

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Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care<sup>1</sup> or hospitalization<sup>2-4</sup> after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease.

Item Type: Article
Uncontrolled Keywords: GenOMICC investigators, 23andMe investigators, COVID-19 Human Genetics Initiative, Humans, Critical Illness, Fucosyltransferases, Factor VIII, ATP-Binding Cassette Transporters, Phospholipid Transfer Proteins, Cell Adhesion Molecules, E-Selectin, Lectins, C-Type, Receptors, Cell Surface, Nerve Tissue Proteins, Repressor Proteins, Critical Care, Genome, Human, Interleukin-10 Receptor beta Subunit, Host-Pathogen Interactions, Mucin-1, Genome-Wide Association Study, Whole Genome Sequencing, COVID-19, SARS-CoV-2, Galactoside 2-alpha-L-fucosyltransferase
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 31 Mar 2022 07:37
Last Modified: 28 Dec 2023 19:40
DOI: 10.1038/s41586-022-04576-6
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3151780