Genomewide Association Study of Severe Covid-19 with Respiratory Failure

Abstract

Background: There is considerable variation in disease behavior among patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (Covid-19). Genomewide association analysis may allow for the identification of potential genetic factors involved in the development of Covid-19.

Methods: We conducted a genomewide association study involving 1980 patients with Covid-19 and severe disease (defined as respiratory failure) at seven hospitals in the Italian and Spanish epicenters of the SARS-CoV-2 pandemic in Europe. After quality control and the exclusion of population outliers, 835 patients and 1255 control participants from Italy and 775 patients and 950 control participants from Spain were included in the final analysis. In total, we analyzed 8,582,968 single-nucleotide polymorphisms and conducted a meta-analysis of the two case-control panels.

Results: We detected cross-replicating associations with rs11385942 at locus 3p21.31 and with rs657152 at locus 9q34.2, which were significant at the genomewide level (P<5×10^-8) in the meta-analysis of the two case-control panels (odds ratio, 1.77; 95% confidence interval [CI], 1.48 to 2.11; P = 1.15×10^-10; and odds ratio, 1.32; 95% CI, 1.20 to 1.47; P = 4.95×10^-8, respectively). At locus 3p21.31, the association signal spanned the genes SLC6A20, LZTFL1, CCR9, FYCO1, CXCR6 and XCR1. The association signal at locus 9q34.2 coincided with the ABO blood group locus; in this cohort, a blood-group-specific analysis showed a higher risk in blood group A than in other blood groups (odds ratio, 1.45; 95% CI, 1.20 to 1.75; P = 1.48×10^-4) and a protective effect in blood group O as compared with other blood groups (odds ratio, 0.65; 95% CI, 0.53 to 0.79; P = 1.06×10^-5).

Conclusions: We identified a 3p21.31 gene cluster as a genetic susceptibility locus in patients with Covid-19 with respiratory failure and confirmed a potential involvement of the ABO blood-group system. (Funded by Stein Erik Hagen and others.).

Figure 1. Timeline of Rapid Covid-19 Genomewide Association Study (GWAS).

The main events and milestones of the study are summarized in the plot. Samples from patients in three Italian hospitals (hospital A: Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan; hospital B: Humanitas Clinical and Research Center, IRCCS, Milan; and hospital C: UNIMIB School of Medicine, San Gerardo Hospital, Monza) and four Spanish hospitals (hospital A: Hospital Clínic and IDIBAPS, Barcelona; hospital B: Hospital Universitario Vall d’Hebron, Barcelona; hospital C: Hospital Universitario Ramón y Cajal, Madrid; and hospital D: Donostia University Hospital, San Sebastian) were obtained around the peak of the local epidemics, and ethics applications were quickly obtained by means of fast-track procedures (i.e., every local ethics review board supported studies of coronavirus disease 2019 [Covid-19] studies by providing rapid turn-around times, thus facilitating this fast de novo data generation). All the obtained blood samples were centrally isolated, genotyped, and analyzed within 8 weeks. Control data were obtained from control participants and from historical control data in Italy and Spain. The rapid workflow from patients to target identification shows the usefulness of GWAS, a standardized research tool that often relies on international and interdisciplinary cooperation. One center alone could not have completed this study, not to mention the increase in statistical power that was available because of the contribution of patients from multiple centers. The speed of data production depended heavily on laboratory automation, and the speed of analyses reflects existing analytic pipelines and the support of public so-called imputation servers (here, the Michigan imputation server of the G. Abecasis group). QC denotes quality control.

Figure 2. GWAS Summary (Manhattan) Plot of the Meta-analysis Association Statistics Highlighting Two Susceptibility Loci with Genomewide Significance for Severe Covid-19 with Respiratory Failure.

Shown is a Manhattan plot of the association statistics from the main meta-analysis (controlled for potential population stratification). The red dashed line indicates the genomewide significance threshold of a P value less than 5×10⁻⁸. Figure S6 in Supplementary Appendix 1 shows Manhattan plots that include hits passing a suggestive significance threshold of a P value less than 1×10⁻⁵ (total of 24 additional suggestive genomic loci) (see the Supplementary Methods section and Supplementary Appendix 4).

Figure 3. Regional Association Plots of Susceptibility Loci Associated with Severe Covid-19 with Respiratory Failure.

Bayesian fine-mapping analysis prioritized 22 and 38 variants for loci 3p21.31 (Panel A) and 9q34.2 (Panel B), respectively, with greater than 95% certainty. The linkage disequilibrium values were calculated on the basis of genotypes of the merged Italian and Spanish data sets derived from TOPMed (Trans-Omics for Precision Medicine) imputation. The positions in the genome assembly hg38 are plotted. The recombination rate is shown in centimorgans (cM) per million base pairs (Mb). The plot shows the names and locations of the genes; the transcribed strand is indicated with an arrow. Genes are represented with intronic and exonic regions. The purple diamond in each panel represents the variant most strongly associated with severe Covid-19 and respiratory failure.