Genetic mechanisms of critical illness in Covid-19
Authors: Pairo-Castineira Erola , Clohisey Sara , Klaric Lucija , Bretherick Andrew , Rawlik Konrad , Parkinson Nick , Pasko Dorota , Walker Susan , Richmond Anne , Fourman Max Head , Russell Clark D , Law Andrew , Furniss James , Gountouna Elvina , Wrobel Nicola , Moutsianas Loukas , Wang Bo , Meynert Alison , Yang Zhijian , Zhai Ranran , Zheng Chenqing , Griffiths Fiona , Oosthuyzen Wilna , Grimes Graeme , Shih Barbara , Keating Sean , Zechner Marie , Haley Chris , Porteous David J. , Hayward Caroline , Knight Julian , Summers Charlotte , Shankar-Hari Manu , Klenerman Paul , Turtle Lance , Ho Antonia , Hinds Charles , Horby Peter , Nichol Alistair , Maslove David , Ling Lowell , McAuley Danny , Montgomery Hugh , Walsh Timothy ,   The GenOMICC Investigators,   The ISARIC-4C Investigators,   The Covid-19 Human Genetics Initiative, Shen Xia , Rowan Kathy , Fawkes Angie , Murphy Lee , Ponting Chris P. , Tenesa Albert , Caulfield Mark , Scott Richard , Openshaw Peter J.M. , Semple Malcolm G. , Vitart Veronique , Wilson James F. , Baillie J. Kenneth 
Published: September 2020

The subset of patients who develop critical illness in Covid-19 have extensive inflammation affecting the lungs1 and are strikingly different from other patients: immunosuppressive therapy benefits critically-ill patients, but may harm some non-critical cases.2 Since susceptibility to life-threatening infections and immune-mediated diseases are both strongly heritable traits, we reasoned that host genetic variation may identify mechanistic targets for therapeutic development in Covid-19.3

GenOMICC (Genetics Of Mortality In Critical Care, genomicc.org) is a global collaborative study to understand the genetic basis of critical illness. Here we report the results of a genome-wide association study (GWAS) in 2244 critically-ill Covid-19 patients from 208 UK intensive care units (ICUs), representing >95% of all ICU beds. Ancestry-matched controls were drawn from the UK Biobank population study and results were confirmed in GWAS comparisons with two other population control groups: the 100,000 genomes project and Generation Scotland.

We identify and replicate three novel genome-wide significant associations, at chr19p13.3 (rs2109069, p = 3.98 × 10−12), within the gene encoding dipeptidyl peptidase 9 (DPP9), at chr12q24.13 (rs10735079, p =1.65 × 10−8) in a gene cluster encoding antiviral restriction enzyme activators (OAS1, OAS2, OAS3), and at chr21q22.1 (rs2236757, p = 4.99 × 10−8) in the interferon receptor gene IFNAR2. Consistent with our focus on extreme disease in younger patients with less comorbidity, we detect a stronger signal at the known 3p21.31 locus than previous studies (rs73064425, p = 4.77 × 10−30).

We identify potential targets for repurposing of licensed medications. Using Mendelian randomisation we found evidence in support of a causal link from low expression of IFNAR2, and high expression of TYK2, to life-threatening disease. Transcriptome-wide association in lung tissue revealed that high expression of the monocyte/macrophage chemotactic receptor CCR2 is associated with severe Covid-19.

Our results identify robust genetic signals relating to key host antiviral defence mechanisms, and mediators of inflammatory organ damage in Covid-19. Both mechanisms may be amenable to targeted treatment with existing drugs. Large-scale randomised clinical trials will be essential before any change to clinical practice.