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A Phenome-Wide Association Study of genes associated with COVID-19 severity reveals shared genetics with complex diseases in the Million Veteran Program

  • Anurag Verma ,

    Contributed equally to this work with: Anurag Verma, Noah L. Tsao

    Roles Conceptualization, Data curation, Formal analysis, Methodology, Visualization, Writing – original draft, Writing – review & editing

    anurag.verma@pennmedicine.upenn.edu (AV); kliao@bwh.harvard.edu (KPL)

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Noah L. Tsao ,

    Contributed equally to this work with: Anurag Verma, Noah L. Tsao

    Roles Data curation, Formal analysis, Writing – original draft, Writing – review & editing

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Lauren O. Thomann,

    Roles Project administration, Resources

    Affiliation VA Boston Healthcare System, Boston, Massachusetts, United States of America

  • Yuk-Lam Ho,

    Roles Data curation, Resources

    Affiliation Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America

  • Sudha K. Iyengar,

    Roles Writing – review & editing

    Affiliations Louis Stokes Cleveland VA Medical Center, Cleveland, Ohio, United States of America, Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America

  • Shiuh-Wen Luoh,

    Roles Writing – review & editing

    Affiliations VA Portland Health Care System, Portland, Oregon, United States of America, Division of Hematology and Medical Oncology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon, United States of America

  • Rotonya Carr,

    Roles Writing – review & editing

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, University of Washington, Division of Gastroenterology, Seattle, Washington, United States of America

  • Dana C. Crawford,

    Roles Writing – review & editing

    Affiliations Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America, Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, United States of America, Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, United States of America

  • Jimmy T. Efird,

    Roles Writing – review & editing

    Affiliation Cooperative Studies Program Epidemiology Center, Health Services Research and Development, DVAHCS (Duke University Affiliate), Durham, North Carolina, United States of America

  • Jennifer E. Huffman,

    Roles Data curation, Writing – review & editing

    Affiliation VA Boston Healthcare System, Boston, Massachusetts, United States of America

  • Adriana Hung,

    Roles Writing – review & editing

    Affiliation Tennessee Valley Healthcare System (Nashville VA) & Vanderbilt University, Nashville, Tennessee, United States of America

  • Kerry L. Ivey,

    Roles Writing – review & editing

    Affiliations Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America, South Australian Health and Medical Research Institute, Infection and Immunity Theme, Adelaide, South Australia, Australia, Harvard T.H. Chan School of Public Health, Department of Nutrition, Cambridge, Massachusetts, United States of America

  • Michael G. Levin,

    Roles Writing – review & editing

    Affiliation Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Julie Lynch,

    Roles Writing – review & editing

    Affiliation VA Informatics and Computing Infrastructure, VA Salt Lake City Health Care System, Salt Lake City, Utah, United States of America

  • Pradeep Natarajan,

    Roles Writing – review & editing

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Cardiovascular Research Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America, Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America

  • Saiju Pyarajan,

    Roles Writing – review & editing

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Harvard Medical School, Boston, Massachusetts, United States of America

  • Alexander G. Bick,

    Roles Writing – review & editing

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Department of Medicine, Vanderbilt University, Nashville, Tennessee, United States of America

  • Lauren Costa,

    Roles Project administration

    Affiliation Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America

  • Giulio Genovese,

    Roles Writing – review & editing

    Affiliations Program in Medical and Population Genetics and the Cardiovascular Disease Initiative, Broad Institute of Harvard & MIT, Cambridge, Massachusetts, United States of America, Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America, Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America

  • Richard Hauger,

    Roles Writing – review & editing

    Affiliation Department of Psychiatry, University of California, San Diego, La Jolla, California; Center of Excellence for Stress and Mental Health, VA San Diego Healthcare System, San Diego, California, United States of America

  • Ravi Madduri,

    Roles Writing – review & editing

    Affiliations University of Chicago Consortium for Advanced Science and Engineering, The University of Chicago, Chicago, Illinois, United States of America, Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois, United States of America

  • Gita A. Pathak,

    Roles Writing – review & editing

    Affiliations VA Connecticut Healthcare System, West Haven, Connecticut, United States of America, Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America

  • Renato Polimanti,

    Roles Writing – review & editing

    Affiliations VA Connecticut Healthcare System, West Haven, Connecticut, United States of America, Department of Psychiatry, Yale School of Medicine, New Haven, Connecticut, United States of America

  • Benjamin Voight,

    Roles Writing – review & editing

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Marijana Vujkovic,

    Roles Writing – review & editing

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Seyedeh Maryam Zekavat,

    Roles Writing – review & editing

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Broad Institute of MIT & Harvard, Cambridge, Massachusetts, United States of America, Yale School of Medicine New Haven, New Haven, Connecticut, United States of America

  • Hongyu Zhao,

    Roles Writing – review & editing

    Affiliations VA Connecticut Healthcare System, West Haven, Connecticut, United States of America, Yale School of Medicine New Haven, New Haven, Connecticut, United States of America, Computational Biology and Bioinformatics Program, Yale University, New Haven, Connecticut, United States of America, Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America

  • Marylyn D. Ritchie,

    Roles Writing – review & editing

    Affiliation Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • VA Million Veteran Program COVID-19 Science Initiative,
  • Kyong-Mi Chang,

    Roles Funding acquisition, Writing – review & editing

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  • Kelly Cho,

    Roles Resources, Writing – review & editing

    Affiliation Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America

  • Juan P. Casas,

    Roles Writing – review & editing

    Affiliations Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America

  • Philip S. Tsao,

    Roles Supervision, Writing – review & editing

    Affiliations VA Palo Alto Health Care System, Palo Alto, California, United States of America, Department of Medicine (Cardiovascular Medicine), Stanford University School of Medicine, Stanford, California, United States of America

  • J. Michael Gaziano,

    Roles Supervision, Writing – review & editing

    Affiliations Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC), VA Boston Healthcare System, Boston, Massachusetts, United States of America, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America

  • Christopher O’Donnell,

    Roles Supervision, Writing – review & editing

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Harvard Medical School, Boston, Massachusetts, United States of America, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America

  • Scott M. Damrauer ,

    Roles Conceptualization, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

    ‡ These authors jointly supervised on this work.

    Affiliations Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America, Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America

  •  [ ... ],
  • Katherine P. Liao

    Roles Conceptualization, Funding acquisition, Supervision, Writing – original draft, Writing – review & editing

    anurag.verma@pennmedicine.upenn.edu (AV); kliao@bwh.harvard.edu (KPL)

    ‡ These authors jointly supervised on this work.

    Affiliations VA Boston Healthcare System, Boston, Massachusetts, United States of America, Harvard Medical School, Boston, Massachusetts, United States of America, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America

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Abstract

The study aims to determine the shared genetic architecture between COVID-19 severity with existing medical conditions using electronic health record (EHR) data. We conducted a Phenome-Wide Association Study (PheWAS) of genetic variants associated with critical illness (n = 35) or hospitalization (n = 42) due to severe COVID-19 using genome-wide association summary data from the Host Genetics Initiative. PheWAS analysis was performed using genotype-phenotype data from the Veterans Affairs Million Veteran Program (MVP). Phenotypes were defined by International Classification of Diseases (ICD) codes mapped to clinically relevant groups using published PheWAS methods. Among 658,582 Veterans, variants associated with severe COVID-19 were tested for association across 1,559 phenotypes. Variants at the ABO locus (rs495828, rs505922) associated with the largest number of phenotypes (nrs495828 = 53 and nrs505922 = 59); strongest association with venous embolism, odds ratio (ORrs495828 1.33 (p = 1.32 x 10−199), and thrombosis ORrs505922 1.33, p = 2.2 x10-265. Among 67 respiratory conditions tested, 11 had significant associations including MUC5B locus (rs35705950) with increased risk of idiopathic fibrosing alveolitis OR 2.83, p = 4.12 × 10−191; CRHR1 (rs61667602) associated with reduced risk of pulmonary fibrosis, OR 0.84, p = 2.26× 10−12. The TYK2 locus (rs11085727) associated with reduced risk for autoimmune conditions, e.g., psoriasis OR 0.88, p = 6.48 x10-23, lupus OR 0.84, p = 3.97 x 10−06. PheWAS stratified by ancestry demonstrated differences in genotype-phenotype associations. LMNA (rs581342) associated with neutropenia OR 1.29 p = 4.1 x 10−13 among Veterans of African and Hispanic ancestry but not European. Overall, we observed a shared genetic architecture between COVID-19 severity and conditions related to underlying risk factors for severe and poor COVID-19 outcomes. Differing associations between genotype-phenotype across ancestries may inform heterogenous outcomes observed with COVID-19. Divergent associations between risk for severe COVID-19 with autoimmune inflammatory conditions both respiratory and non-respiratory highlights the shared pathways and fine balance of immune host response and autoimmunity and caution required when considering treatment targets.

Author summary

Large population based genomic studies have discovered genetic variations associated with severe manifestations of Coronarvirus Disease 2019 (COVID-19). In this study, we screened for other human conditions that share associations with these same variants. Understanding shared genetic variants in known conditions, where the pathophysiology is better understood, can further inform the pathways by which SARS-CoV2, the virus that causes COVID-19, impacts multiple organ systems. While genetic variants associated with severe COVID-19 were also associated with known risk factors and poor outcomes related to COVID-19 such as deep venous thrombosis, a large subset of these variants were also associated with reduced risk of conditions largely comprised of immune-mediated diseases, e.g., psoriasis, lupus, rheumatoid arthritis. With regards to the latter, the shared genetic architecture between COVID-19 and immune-mediated conditions suggests that pathways controlling both immune tolerance and immunodeficiency are important for COVID-19 severity, with implications when considering targeting these pathways for treatment.

Introduction

Coronavirus disease 2019 (COVID-19) first identified in December of 2019[1], became a global pandemic by March 2020. As of September 2021, COVID-19, transmitted by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has resulted in the loss of over 5.4 million lives worldwide [2]. Identifying host genetic variants associated with severe clinical manifestations from COVID-19 can identify key pathways important in the pathogenesis of this condition. International efforts such as the COVID-19 Host Genetics Initiative (HGI)[3] have meta-analyzed genome-wide association study (GWAS) summary statistics at regular intervals to identify novel genetic associations with COVID-19 severity. Thus far, ten independent variants associated with COVID-19 severity at genome-wide significance have been identified, most notably at the ABO locus [4]. These GWASs have also identified variations in genes involving inflammatory cytokines and interferon signaling pathways such as IFNAR2, TYK2, and DPP9 [4].

The unprecedented availability of genome-wide data for COVID-19 provides an opportunity to study clinical conditions that share genetic risk factors for COVID-19 severity. Examining known conditions, each with a body of knowledge regarding important pathways and targets, may in turn improve our understanding of pathways relevant for COVID-19 severity and inform the development of novel treatments against this pathogen. The Phenome-Wide Association Study (PheWAS) is an approach for simultaneously testing genetic variants’ association with a wide spectrum of conditions and phenotypes [5]. The Veteran’s Affairs (VA) Million Veteran Program (MVP) has generated genotypic data on over 650,000 participants linked with electronic health record (EHR) data containing rich phenotypic data, enables large-scale PheWAS. Moreover, MVP has the highest racial and ethnic diversity of the major biobanks worldwide affording an opportunity to compare whether associations are similar across ancestries [6].

The objective of this study was to use existing clinical EHR data to identify conditions that share genetic variants with COVID-19 severity using the disease-agnostic PheWAS approach. Since COVID-19 is a new condition, identifying existing conditions which share genetic susceptibility may allow us to leverage existing knowledge from these known conditions to provide context regarding important pathways for COVID-19 severity, as well as how pathways may differ across subpopulations.

Methods

Ethics statement

The Million Veteran Program received ethical and study protocol approval from the VA Central Institutional Review Board (IRB) in accordance with the principles outlined in the Declaration of Helsinki. All individuals in the study provided written informed consent as part of the MVP.

Data sources

The VA MVP is a national cohort launched in 2011 designed to study the contributions of genetics, lifestyle, and military exposures to health and disease among US Veterans [6].

Blood biospecimens were collected for DNA isolation and genotyping, and the biorepository was linked with the VA EHR, which includes diagnosis codes (International Classification of Diseases ninth revision [ICD-9] and tenth revision [ICD-10]) for all Veterans followed in the healthcare system up to September 2019. The single nucleotide polymorphism (SNP) data in the MVP cohort was generated using a custom Thermo Fisher Axiom genotyping platform called MVP 1.0. The quality control steps and genotyping imputation using 1000 Genomes cosmopolitan reference panel on the MVP cohort has been described previously [7].

Genetic variant selection.

An overview of the analytic workflow is outlined in Fig 1. Variants were derived from the COVID-19 HGI GWAS meta-analysis release v6 [3]. In this study, we analyzed the following HGI GWAS summary statistics: 1) hospitalized and critically ill COVID-19 vs. population controls denoted as “A2” in HGI, and referred to as “critical COVID” in this study, and 2) hospitalized because of COVID-19 vs. population controls, denoted as “B2” in HGI, referred to as “hospitalized COVID” in this study [3]. For each GWAS, variants with a Benjamini-Hochberg false discovery rate (FDR) corrected p-value < 0.01 were selected as candidate lead SNPs (3,502 associated with critical COVID, and 4,336 associated with hospitalized COVID). Variants with r2 <0.1 were clustered within a 250 kb region according to 1000 Genomes phase 3 trans-ancestry reference panel [8]. Then, the variant with the smallest p-value in the region was selected as lead variant, resulting in 45 independent variants associated with critical COVID and 42 variants associated with hospitalized COVID summary statistics. The lead variants from each set of GWAS summary statistics are available in S1 Table. We used the nearest gene approach to prioritize the potential causal genes. A gene with the smallest genomic distance to a lead variant was selected.

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Fig 1. Overview of variant selection and PheWAS analysis design.

https://doi.org/10.1371/journal.pgen.1010113.g001

Classification of race/ethnicity in MVP.

Race and ethnicity was determined using the harmonized ancestry and race/ethnicity (HARE) method for four major groups [9] corresponding to: (1) African ancestry, non-Hispanic Black (AFR), (2) Asian ancestry, non-Hispanic Asian (ASN), (3) European ancestry, non-Hispanic White (EUR), and (4) Hispanic ancestry (HIS). Individuals without a HARE classification were most likely be from ancestries with insufficient numbers to train the HARE algorithm including Native American, Alaska Native, and Pacific Islanders. Briefly, the HARE method was an algorithm developed to assign each subject to one of four groups using both self-reported race/ethnicity as the input to train a machine learning algorithm using ancestry informative genetic markers. This approach provides a classification for each individual leveraging information from genomic markers if self-reported race/ethnicity was missing, enabling analyses that can stratify by the four major groups. When comparing HARE vs self-reported race and ethnicity, the statistical error rate was estimated at 0.05–0.46%.

Outcomes.

Clinical data prior to the onset of the COVID-19 pandemic were used to reduce potential confounding bias from SARS-CoV-2 infection on existing conditions. Phenotypes were defined by phecodes from prior studies [5,10]. Each phecode represents ICD codes grouped into clinically relevant phenotypes for clinical studies. For example, the phecode “deep venous thrombosis” includes “venous embolism of deep vessels of the distal lower extremities,” and “deep venous thrombosis of the proximal lower extremity,” both of which have distinct ICD codes. Using this approach, all ICD codes for all Veterans in MVP were extracted and each assigned a phenotype defined by a phecode. ICD-9 and ICD-10 codes were mapped to 1,876 phecodes, as previously described [5,10].

For each phecode, participants with ≥2 phecode-mapped ICD-9 or ICD-10 codes were defined as cases, whereas those with no instance of a phecode-mapped ICD-9 or ICD-10 code were defined as controls. Based on our previous simulation studies of ICD EHR data, populations where the phecode comprises < 200 cases were more likely to result in spurious results [11], and we thus applied this threshold in four ancestry groups: AFR, ASN, HIS, and EUR. In total, we analyzed 1,617 (EUR), 1304 (AFR), 993 (HIS), 294 (ASN) phecodes from the MVP cohort.

Phenome-wide association studies.

The primary PheWAS analysis used SNPs identified from the HGI GWAS of critical and hospitalized COVID, and tested association of these SNPs with phenotypes extracted from the EHR using data prior to the COVID-19 pandemic. Logistic regression using PLINK2 to examine the SNP association with phecodes and firth regression was applied when logistic regression model failed to converge. Regression models were adjusted for sex, age (at enrollment), age squared, and the first 20 principal components.

Ancestry-specific PheWAS was first performed in these four groups, and summary data were meta-analyzed using an inverse-variance weighted fixed-effects model implemented in the PheWAS R package [10]. We assessed heterogeneity using I2 and excluded any results with excess heterogeneity (I2 > 40%).

To address multiple testing, an association between SNP and phecode with FDR p < 0.01 was considered significant. Thus, the threshold for significance was p < 6.07 × 10−05 for critical COVID lead variants, and p < 4.13 × 10−05 for hospitalized COVID lead variants. In the main manuscript we highlight PheWAS significant associations using FDR < 0.01 and an effect size associated with increased or reduced risk for a condition by 10%, with complete PheWAS results provided in S2 and S3 Tables.

Results

We studied 658,582 MVP participants, with mean age 68 years, 90% male, with 30% participants from non-European ancestry (Table 1). The PheWAS was performed on 35 genetic variants associated with critical COVID-19, and 42 genetic variants (S1 Table) associated with hospitalized COVID, across 1,559 phenotypes.

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Table 1. Patient characteristics of Million Veteran Program participants.

https://doi.org/10.1371/journal.pgen.1010113.t001

From the trans-ancestry meta-analysis, we identified 151 phenotypes significantly associated with critical COVID GWAS-identified variants, and 156 associations with hospitalized COVID GWAS-identified lead variants (FDR, p<0.01). Among these lead variants with significant PheWAS associations, 10 SNPs were associated with reduced risk of critical and hospitalized COVID-19 in HGI. Six variants were common to both critical and hospitalized COVID and had significant PheWAS associations, namely, variations nearest to the genes ABO (rs495828 and rs505922), DPP9 (rs2277732), MUC5B (rs35705950), TYK2 (rs11085727), and CCHCR1 (rs9501257) (S2 and S3 Tables).

Association of ABO loci with known risk factors and outcomes related to COVID-19 severity

In the trans-ancestry meta-analysis, the phenotype with the strongest association with variants near ABO locus (rs495828 and rs505922) was “hypercoagulable state” (ORcritical_PheWAS = 1.48 [1.42–1.54], Pcritical_PheWAS = 1.84 × 10−40; ORhospitalized_PheWAS = 1.51 [1.46–1.56], Phospitalized_PheWAS = 2.11 × 10−55, Fig 2). The ABO loci had the largest number of significant PheWAS association findings, accounting for 35% (53/151) of significant phenotype associations in the critical COVID PheWAS, and 37% (59/156) in the hospitalized COVID PheWAS. The phenotypes with the most significant associations and largest effect size were related to hypercoagulable states and coagulopathies. As expected, conditions not related to coagulopathy associated with the ABO locus, included type 2 diabetes and ischemic heart disease, have been reported as risk factors for or are complications associated with COVID-19 severity and mortality [1,4,12,13] (Fig 2 and S2 and S3 Tables).

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Fig 2. PheWAS results of candidate SNPs from GWAS of critically ill and hospitalized COVID-19.

Significant associations between 48 SNPs from critical ill COVID GWAS (A) and 39 SNPs from hospitalized COVID (C) and EHR derived phenotypes in the Million Veteran Program. The phenotypes are represented on the x-axis and ordered by broader disease categories. The red line denotes the significance threshold using false discovery rate of 1% using the Benjamini-Hochberg procedure. The description of phenotypes is highlighted for the associations with FDR < 0.1 and odds ratio < 0.90 or odds ratio > 1.10. (B) and (D) A heatmap plot of SNPs with at least one significant association (FDR < 0.1). The direction of effect disease risk is represented by odds ratio. A red color indicates increased risk and blue color indicated reduced risk. The results with odds ratio < 0.90 or odds ratio > 1.10 are shown.

https://doi.org/10.1371/journal.pgen.1010113.g002

Associations between variants associated with COVID-19 severity and respiratory conditions and infections

Among 68 respiratory conditions, only 11 diseases had significant associations (FDR < 0.01) shared with genetic variants associated with severe COVID-19. The most significant association was observed between rs35705950 (MUC5B) and idiopathic fibrosing alveolitis (OR = 2.83 [2.76–2.90]; P = 4.12 × 10−191), also known as idiopathic pulmonary fibrosis (IPF). Similarly, rs2277732 near DPP9 was associated with IPF (OR = 1.16 [1.09–1.22]; P = 5.84 × 10−06), both association between MUC5B, DPP9 variants and IPF has been reported in previous studies [14]. However, the association of genetic variants with other respiratory conditions may represent novel findings: the association of intronic variant rs61667602 in CRHR1 with reduced risk of post inflammatory pulmonary fibrosis (OR = 0.84 [0.80–0.89]; P = 2.26× 10−12), “alveolar and parietoalveolar pneumonopathy” (OR = 0.80 [0.72–0.88]; P = 1.58 × 10−08) and IPF (OR = 0.87 [0.82–0.92], P = 7.5 × 10−07). We did not detect associations between any of the variants and other respiratory conditions which are known risk factors for COVID-19 such as chronic obstructive pulmonary disease (COPD, S2 and S3 Tables).

Associations between variants associated with COVID-19 severity and reduced risk for certain phenotypes

The rs11085727-T allele of TYK2, a lead variant from the both critically ill and hospitalized COVID GWAS was associated with a reduced risk for psoriasis (OR = 0.88 [0.86–0.91], P = 6.48 × 10−23), psoriatic arthropathy (OR = 0.82 [0.76–0.87], P = 6.97 × 10−12), and lupus (OR = 0.84 [0.76–0.91], P = 63.97 × 10−06). This TYK2 signal has been previously reported to be associated with reduced risk of psoriasis, psoriatic arthropathy, type 1 diabetes, systemic lupus erythematosus and RA as well as other autoimmune inflammatory conditions (Table 2) [15,16].

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Table 2. Phenotypes sharing association with variants also associated with severe COVID-19 infection, with reduced odds of disease listed in order of p-value*.

https://doi.org/10.1371/journal.pgen.1010113.t002

Ancestry specific PheWAS provide insights into differential disease risks

The PheWAS analyses performed across four major ancestry groups in MVP observed similar findings as the overall meta-analysis with few associations unique to a specific ancestry (Fig 3 and S8 Table). SNP rs581342 (LMNA), associated with severe COVID-19, was a highly prevalent variant among subjects with AFR ancestry (MAF = 0.53) and was associated with neutropenia (ORAFR = 1.29 [1.21–1.39] PAFR = 4.09 × 10−13); this association was also observed in HIS ancestry (ORHIS = 1.65 [1.32–2.06], PHIS = 8.84 × 10−06) but was not in the larger EUR ancestry (S8 Table). To follow-up on this association, we extracted data on laboratory values for white blood cell (WBC) count and neutrophil fraction on all subjects. LMNA was associated with lower WBC in AFR, EUR, and HIS ancestries. However, LMNA was associated with a lower median neutrophil fraction only among Veterans of AFR ancestry (beta = -1.84 [-1.94, -1.75], PAFR = 1 x 10−300) and HIS ancestry (beta = -0.67, PHIS = 7.2 x 10−13) but not among Veterans of EUR ancestry (beta = -0.09, PEUR = 0.005). Among individuals of AFR ancestry, each allele was associated with a 1.84% lower neutrophil fraction, where among individuals of HIS and EUR ancestry, each allele was associated with 0.67% and 0.04% reduction, respectively (S9 Table).

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Fig 3. PheWAS results of candidate SNPs from GWAS of Hospitalized COVID-19 in individuals of AFR ancestry.

The plot highlights the association between rs581342 SNP and neutropenia, which was only observed in the AFR ancestry. The phenotypes are represented on the x-axis and ordered by broader disease categories. The red line denotes the significance threshold using false discovery rate of 1% using the Benjamini-Hochberg procedure. The table on the top right of the plot shows the association results between rs581342 and neutropenia in other ancestries. The association was not tested among participants of ASN ancestry due to low case numbers.

https://doi.org/10.1371/journal.pgen.1010113.g003

Similarly, associations between rs9268576 (HL-DRA) and thyrotoxicosis was only observed in individuals of AFR ancestry. The EUR ancestry specific PheWAS identified 39 significant associations which were not observed in other ancestry groups. One such association was between MUC5B variant and phecode for “dependence on respirator [ventilator] or supplemental oxygen” (OREUR = 1.16 [1.11–1.12], PEUR = 1.72× 10−10) among individuals of EUR ancestry was not significant in other ancestry groups (S8 Table). It is important to note that the conditions with significant association among individuals of EUR ancestry had similar prevalence among other ancestries. However, since there were overall fewer subjects in non-EUR ancestry groups, this likely resulted in lower statistical power to detect associations. All ancestry specific PheWAS results are available in supplementary tables (S4, S5, S6, and S7 Tables, and S1 and S2 Figs).

Association with variation at sex chromosome

In the hospitalized COVID-19 GWAS, we identified rs4830964 as the only lead variant on chromosome X. The SNP is located near ACE2 and was associated with “non-healing surgical wound” (OR = 0.92 [0.89–0.96], P = 2.23× 10−05). Notably, the SNP had nominal association (p<0.05) with type 2 diabetes and diabetes related complications that are previously reported association with variation in ACE2 (S3 Table). We did not observe any association with this variant in the ancestry specific PheWAS analysis.

Discussion

In this large-scale PheWAS, we identified the shared genetic architecture between variants associated with severe COVID-19 and other complex conditions using data from MVP, one of the largest and most diverse biobanks in the world. Broadly, these risk alleles identified conditions associated with risk factors for severe COVID-19 manifestations such as type 2 diabetes and ischemic heart disease across all ancestries examined here. Notably, the strongest associations with the highest effect size were related to coagulopathies, specifically, hypercoagulable state including deep venous thrombosis and other thrombotic complications, also shared variants associated with severe COVID-19. In contrast, among respiratory conditions, only idiopathic pulmonary fibrosis and chronic alveolar lung disease shared genetic risk factors, with the notable absence of an association with COPD and other respiratory infections. When comparing findings across ancestry groups in MVP, we observed that a risk allele associated with severe COVID-19, LMNA, also shared an association with neutropenia among Veterans of AFR and HIS ancestry. Finally, we observed that variants associated with severe COVID-19 had an opposite association, or reduced odds with autoimmune inflammatory conditions, such as psoriasis, psoriatic arthritis, RA, and inflammatory lung conditions.

A classic GWAS tests the association between millions of genetic variants with the presence or absence of one phenotype, e.g., GWAS of deep venous thrombosis. In the COVID-19 HGI GWAS, the “phenotype” was patients hospitalized for or critically ill from COVID-19. Clinically, this population includes a mixture of patients with a complex list of medical conditions at high risk for severe COVID complications and those who had actual complications from COVID-19. Thus, we would anticipate that many of the significant phenotypes would be associated with risk factors such as obesity and deep venous thrombosis. Additionally, our findings suggest that the PheWAS approach can be a useful tool to identify clinical factors related to emerging infectious diseases regarding severity or complications when genomic data are available.

The PheWAS results of SNPs in the ABO locus served as a positive control for this study. Genetic variations in ABO are an established risk factor for COVID-19 severity. Patients with blood group A have a higher risk of requiring mechanical ventilation and extended ICU stay compared with patients with blood group O [17]. These same variations at ABO had known associations with a spectrum of blood coagulation disorders identified in studies pre-dating COVID-19 [1820]. The PheWAS of ABO variants identified associations with increased risk of deep vein thrombosis, pulmonary embolism, and other circulatory disorders, in line with prior studies, and recent studies among patients hospitalized with COVID-19 [2125].

Among the respiratory conditions, only idiopathic pulmonary fibrosis (IPF) and chronic alveoli lung disease had shared associations with the variants near genes MUC5B, CRHR1, and NSF. Located in the enhancer region of the MUC5B, rs35705950, is a known risk factor for IPF, and a high mortality rate was observed among the COVID-19 patients with pre-existing IPF [26]. However, the MUC5B variant is associated with a reduced risk of severe COVID-19 (OR = 0.89), suggesting the risk allele’s opposing effect for infection and pulmonary fibrosis. In a separate study of MVP participants tested for COVID-19, we identified a significant mediating effect of the MUC5B variant in reducing risk for pneumonia due to COVID-19 [27].

Several conditions shared genetic variants associated with severe COVID-19, however, the association was for reduced odds for these conditions. All except one, rosacea, have an autoimmune etiology. The existing literature can help explain some of the dual association between reduced risk of autoimmune conditions such as psoriasis and RA and increased risk of severe COVID-19 via TYK2. TYK2, a member of the Janus Kinase (JAK) family of genes, plays a key role in cytokine signal transduction and the inflammatory response [28], specifically in type 1 interferon signaling, part of the innate immune response blocking the spread of a virus from infected to uninfected cells. Partial loss of TYK2 function is associated with reduced risk for several autoimmune disorders such as RA and psoriatic disease, conditions treated with immunosuppressive therapy [15,2932]. Humans with complete TYK2 loss of function have clinically significant immunodeficiency with increased susceptibility to mycobacterial and viral infections [28,33]. Thus, this observation for opposing associations of variants with COVID-19 and autoimmune conditions highlights the fine balance between host immune response and autoimmunity.

While non-white populations are disproportionately affected by COVID-19, the majority of studies still predominantly consist of individuals from EUR ancestry. The COVID-19 GWAS data from the HGI consists of participants from over 25 countries EUR (33% non-EUR samples), enabling identification of variants more prevalent in non-EUR populations. We used these data to perform a PheWAS on the linked genotype-phenotype data from MVP, the most racial and ethnically diverse biobank in the US. From this large-scale study across ancestries, we observed that a variant located in the LMNA gene locus was associated with a diagnosis of neutropenia in AFR ancestry and HIS, but not EUR which would otherwise would have been well powered to detect an association. LMNA was associated with lower WBC counts across all ancestries, but its association with a lower fraction of neutrophils was observed in AFR and HIS only, but not EUR, in line with the overall association with diagnoses codes for neutropenia. ASN ancestry comprised the smallest ancestry group in MVP and was not tested due to low case numbers for neutropenia.

LMNA variants are associated with a broad spectrum of cardiomyopathies such as dilated cardiomyopathies, familial atrial fibrillation. However, the association with neutropenia has not been previously reported. Neutropenia refers to an abnormally low number of neutrophils in the blood, and predisposing to increased risk of infection. Epidemiology studies have shown that lower neutrophil counts are more common in individuals of AFR ancestry [34,35] and are hypothesized to be a result of selection and generally considered benign. To our knowledge benign neutropenia has not been previously reported among individuals of HIS ancestry [36]. Whether low neutrophil levels may clinically impact COVID-19 outcomes remains to be seen and warrants further study.

Limitations

The PheWAS of risk alleles associated with severe COVID-19 did not observe an association between other chronic pulmonary conditions such as COPD, a risk factor for severe COVID manifestations [13,37,38]. This absence of association allows us to discuss a few limitations of the PheWAS approach. The PheWAS was designed to broadly screen for potentially clinically relevant associations between genes and thousands of phenotypes. The phenotypes are based on ICD codes, and the accuracy of these codes can vary across conditions. Misclassification of cases and controls would reduce power to detect associations. The clinical definition of COPD itself is an area of active discussion and thus could impact the already modest accuracy of COPD diagnostic codes, further limiting power to detect an association [39,40]. As well, the PheWAS has limited power to detect associations for uncommon conditions and may explain the absence of associations with another chronic pulmonary condition, CF which has a prevalence of 0.02% in this Veteran population. Alternatively, studies to date have yielded mixed results with regards to risk for severe COVID among patients with CF [41]. To enable a trans-ancestry study, we applied a conservative approach using 20 PCs to adjust all models, used in prior studies. One potential pitfall of this approach is that the models may be overadjusted and thus are more likely to miss few significant associations. Finally, COPD is a condition where cigarette smoking, an environmental risk factor, accounts for the majority of cases [42]. While genetics is an important aspect of COPD, the link between variants and COPD may be weaker compared to other conditions where genetic variants drive the phenotype, ABO blood type as an example. Thus, conditions such as COPD where environmental risk factors or where gene-environment interactions play a major role in risk, may be more difficult to identify in a standard PheWAS. Findings from this study suggest that variants associated with severe COVID-19 are also associated with reduced odds of having an autoimmune inflammatory condition. However, the results cannot provide information on the impact of actual SARS-CoV-2 infection in these individuals after diagnosis of an autoimmune disease.

Conclusions

The PheWAS of genetic variants reported to associate with severe COVID-19 demonstrated shared genetic architecture between COVID-19 severity and known underlying risk factors for both severe COVID-19 and poor COVID-19 outcomes, rather than susceptibility to other viral infections. Overall, the associations observed were generally consistent across genetic ancestries, with the exception of a stronger association with neutropenia among Veterans of AFR and HIS ancestry and not EUR. Notably, only few respiratory conditions had a shared genetic association with severe COVID-19. Among these, variants associated with a reduced risk for severe COVID-19 had an opposite association, with reduced risk for inflammatory and fibrotic pulmonary conditions. Similarly, other divergent associations were observed between severe COVID-19 and autoimmune inflammatory conditions, shedding light on the concept of the fine balance between immune tolerance and immunodeficiency. This balance will be important when considering therapeutic targets for COVID-19 therapies where pathways may control both inflammation and the viral host response.

Supporting information

S1 Table. List of lead variants from critical ill and hospitalized COVID GWAS included in the study.

https://doi.org/10.1371/journal.pgen.1010113.s001

(XLSX)

S2 Table. Meta-analysis summary statistics from PheWAS of 35 lead SNPs identified from critical ill COVID GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s002

(XLSX)

S3 Table. Meta-analysis summary statistics from PheWAS of 42 lead SNPs identified from Hospitalized COVID GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s003

(XLSX)

S4 Table. Summary statistics from EUR ancestry PheWAS of lead SNPs identified from critical ill and hospitalized COVID-19 GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s004

(XLSX)

S5 Table. Summary statistics from AFR ancestry PheWAS of lead SNPs identified from critical ill and hospitalized COVID-19 GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s005

(XLSX)

S6 Table. Summary statistics from HIS ancestry PheWAS of lead SNPs identified from critical ill and hospitalized COVID-19 GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s006

(XLSX)

S7 Table. Summary statistics from ASN ancestry PheWAS of lead SNPs identified from critical ill and hospitalized COVID-19 GWAS.

https://doi.org/10.1371/journal.pgen.1010113.s007

(XLSX)

S8 Table. Ancestry specific comparison of PheWAS results.

https://doi.org/10.1371/journal.pgen.1010113.s008

(XLSX)

S9 Table. Ancestry specific comparison of association between rs581342 and median values of neutrophil fraction and white blood cell counts.

https://doi.org/10.1371/journal.pgen.1010113.s009

(XLSX)

S1 Fig.

The PheWAS results of 48 SNPs from critical ill COVID GWAS by each ancestry a) European ancestry, b) African ancestry, c) Hispanic ancestry, and d) Asian ancestry.

https://doi.org/10.1371/journal.pgen.1010113.s010

(TIF)

S2 Fig.

The PheWAS results of 39 SNPs from hospitalized COVID GWAS by each ancestry a) European ancestry, b) African ancestry, c) Hispanic ancestry, and d) Asian ancestry.

https://doi.org/10.1371/journal.pgen.1010113.s011

(TIF)

S1 Text. VA Million Veteran Program COVID-19 Science Initiative Membership & Acknowledgements.

https://doi.org/10.1371/journal.pgen.1010113.s012

(DOCX)

Acknowledgments

We are grateful to our Veterans for their contributions to MVP. Full acknowledgements for the VA Million Veteran Program COVID-19 Science Initiative can be found in the S1 Text. We would like to thank the Host Genetic Initiative for making their data publicly available (https://www.covid19hg.org/acknowledgements/). This publication does not represent the views of the Department of Veteran Affairs or the United States Government.

References

  1. 1. CDC. About COVID-19—CDC. Available: https://www.cdc.gov/coronavirus/2019-ncov/cdcresponse/about-COVID-19.html
  2. 2. Dong E, Du H, Gardner L. An interactive web-based dashboard to track COVID-19 in real time. Lancet Infect Dis. 2020;20: 533–534. pmid:32087114
  3. 3. The COVID-19 Host Genetics Initiative, ganna andrea. Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis. Genetic and Genomic Medicine; 2021 Mar.
  4. 4. The GenOMICC Investigators, The ISARIC4C Investigators, The COVID-19 Human Genetics Initiative, 23andMe Investigators, BRACOVID Investigators, Gen-COVID Investigators, et al. Genetic mechanisms of critical illness in COVID-19. Nature. 2021;591: 92–98. pmid:33307546
  5. 5. Denny JC, Ritchie MD, Basford MA, Pulley JM, Bastarache L, Brown-Gentry K, et al. PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations. Bioinformatics. 2010;26: 1205–1210. pmid:20335276
  6. 6. Gaziano JM, Concato J, Brophy M, Fiore L, Pyarajan S, Breeling J, et al. Million Veteran Program: A mega-biobank to study genetic influences on health and disease. J Clin Epidemiol. 2016;70: 214–223. pmid:26441289
  7. 7. Hunter-Zinck H, Shi Y, Li M, Gorman BR, Ji S-G, Sun N, et al. Genotyping Array Design and Data Quality Control in the Million Veteran Program. Am J Hum Genet. 2020;106: 535–548. pmid:32243820
  8. 8. 1000 Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM, et al. A global reference for human genetic variation. Nature. 2015;526: 68–74. pmid:26432245
  9. 9. Fang H, Hui Q, Lynch J, Honerlaw J, Assimes TL, Huang J, et al. Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies. Am J Hum Genet. 2019;105: 763–772. pmid:31564439
  10. 10. Carroll RJ, Bastarache L, Denny JC. R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment. Bioinformatics. 2014;30: 2375–2376. pmid:24733291
  11. 11. Verma A, Bradford Y, Dudek S, Lucas AM, Verma SS, Pendergrass SA, et al. A simulation study investigating power estimates in phenome-wide association studies. BMC Bioinformatics. 2018;19: 120. pmid:29618318
  12. 12. Arentz M, Yim E, Klaff L, Lokhandwala S, Riedo FX, Chong M, et al. Characteristics and Outcomes of 21 Critically Ill Patients With COVID-19 in Washington State. JAMA. 2020. pmid:32191259
  13. 13. Gandhi RT, Lynch JB, del Rio C. Mild or Moderate Covid-19. Solomon CG, editor. N Engl J Med. 2020;383: 1757–1766. pmid:32329974
  14. 14. Allen RJ, Guillen-Guio B, Oldham JM, Ma S-F, Dressen A, Paynton ML, et al. Genome-Wide Association Study of Susceptibility to Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med. 2020;201: 564–574. pmid:31710517
  15. 15. Diogo D, Bastarache L, Liao KP, Graham RR, Fulton RS, Greenberg JD, et al. TYK2 Protein-Coding Variants Protect against Rheumatoid Arthritis and Autoimmunity, with No Evidence of Major Pleiotropic Effects on Non-Autoimmune Complex Traits. Chiorini JA, editor. PLOS ONE. 2015;10: e0122271. pmid:25849893
  16. 16. Dendrou CA, Cortes A, Shipman L, Evans HG, Attfield KE, Jostins L, et al. Resolving TYK2 locus genotype-to-phenotype differences in autoimmunity. Sci Transl Med. 2016;8: 363ra149–363ra149. pmid:27807284
  17. 17. Hoiland RL, Fergusson NA, Mitra AR, Griesdale DEG, Devine DV, Stukas S, et al. The association of ABO blood group with indices of disease severity and multiorgan dysfunction in COVID-19. Blood Adv. 2020;4: 4981–4989. pmid:33057633
  18. 18. Zietz M, Zucker J, Tatonetti NP. Associations between blood type and COVID-19 infection, intubation, and death. Nat Commun. 2020;11: 5761. pmid:33188185
  19. 19. Paranjpe I, Fuster V, Lala A, Russak AJ, Glicksberg BS, Levin MA, et al. Association of Treatment Dose Anticoagulation With In-Hospital Survival Among Hospitalized Patients With COVID-19. J Am Coll Cardiol. 2020;76: 122–124. pmid:32387623
  20. 20. Wu Z, McGoogan JM. Characteristics of and Important Lessons From the Coronavirus Disease 2019 (COVID-19) Outbreak in China: Summary of a Report of 72 314 Cases From the Chinese Center for Disease Control and Prevention. JAMA. 2020 [cited 29 Mar 2020]. pmid:32091533
  21. 21. Matsunaga H, Ito K, Akiyama M, Takahashi A, Koyama S, Nomura S, et al. Transethnic Meta-Analysis of Genome-Wide Association Studies Identifies Three New Loci and Characterizes Population-Specific Differences for Coronary Artery Disease. Circ Genomic Precis Med. 2020;13: e002670. pmid:32469254
  22. 22. Plagnol V, Howson JMM, Smyth DJ, Walker N, Hafler JP, Wallace C, et al. Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. PLoS Genet. 2011;7: e1002216. pmid:21829393
  23. 23. Reilly MP, Li M, He J, Ferguson JF, Stylianou IM, Mehta NN, et al. Identification of ADAMTS7 as a novel locus for coronary atherosclerosis and association of ABO with myocardial infarction in the presence of coronary atherosclerosis: two genome-wide association studies. Lancet Lond Engl. 2011;377: 383–392. pmid:21239051
  24. 24. Trégouët D-A, Heath S, Saut N, Biron-Andreani C, Schved J-F, Pernod G, et al. Common susceptibility alleles are unlikely to contribute as strongly as the FV and ABO loci to VTE risk: results from a GWAS approach. Blood. 2009;113: 5298–5303. pmid:19278955
  25. 25. Larson NB, Bell EJ, Decker PA, Pike M, Wassel CL, Tsai MY, et al. ABO blood group associations with markers of endothelial dysfunction in the Multi-Ethnic Study of Atherosclerosis. Atherosclerosis. 2016;251: 422–429. pmid:27298014
  26. 26. Gallay L, Uzunhan Y, Borie R, Lazor R, Rigaud P, Marchand-Adam S, et al. Risk Factors for Mortality after COVID-19 in Patients with Preexisting Interstitial Lung Disease. Am J Respir Crit Care Med. 2021;203: 245–249. pmid:33252997
  27. 27. Verma A, Minnier J, Huffman JE, Wan ES, Gao L, Joseph J, et al. A MUC5B gene polymorphism, rs35705950-T, confers protective effects in COVID-19 infection. Infectious Diseases (except HIV/AIDS); 2021 Sep.
  28. 28. Nemoto M, Hattori H, Maeda N, Akita N, Muramatsu H, Moritani S, et al. Compound heterozygous TYK2 mutations underlie primary immunodeficiency with T-cell lymphopenia. Sci Rep. 2018;8: 6956. pmid:29725107
  29. 29. Hellquist A, Järvinen TM, Koskenmies S, Zucchelli M, Orsmark-Pietras C, Berglind L, et al. Evidence for Genetic Association and Interaction Between the TYK2 and IRF5 Genes in Systemic Lupus Erythematosus. J Rheumatol. 2009;36: 1631–1638. pmid:19567624
  30. 30. Sigurdsson S, Nordmark G, Göring HHH, Lindroos K, Wiman A-C, Sturfelt G, et al. Polymorphisms in the Tyrosine Kinase 2 and Interferon Regulatory Factor 5 Genes Are Associated with Systemic Lupus Erythematosus. Am J Hum Genet. 2005;76: 528–537. pmid:15657875
  31. 31. The Wellcome Trust Case–Control Consortium (WTCCC) and Alastair Compston, Ban M, Goris A, Lorentzen ÅR, Baker A, Mihalova T, et al. Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor. Eur J Hum Genet. 2009;17: 1309–1313. pmid:19293837
  32. 32. Cunninghame Graham DS, Morris DL, Bhangale TR, Criswell LA, Syvänen A-C, Rönnblom L, et al. Association of NCF2, IKZF1, IRF8, IFIH1, and TYK2 with Systemic Lupus Erythematosus. McCarthy MI, editor. PLoS Genet. 2011;7: e1002341. pmid:22046141
  33. 33. Watford WT, O’Shea JJ. Human Tyk2 Kinase Deficiency: Another Primary Immunodeficiency Syndrome. Immunity. 2006;25: 695–697. pmid:17098200
  34. 34. Boxer L, Dale DC. Neutropenia: Causes and consequences. Semin Hematol. 2002;39: 75–81. pmid:11957188
  35. 35. Reich D, Nalls MA, Kao WHL, Akylbekova EL, Tandon A, Patterson N, et al. Reduced Neutrophil Count in People of African Descent Is Due To a Regulatory Variant in the Duffy Antigen Receptor for Chemokines Gene. Visscher PM, editor. PLoS Genet. 2009;5: e1000360. pmid:19180233
  36. 36. Hsieh MM, Everhart JE, Byrd-Holt DD, Tisdale JF, Rodgers GP. Prevalence of Neutropenia in the U.S. Population: Age, Sex, Smoking Status, and Ethnic Differences. Ann Intern Med. 2007;146: 486. pmid:17404350
  37. 37. Lee SC, Son KJ, Han CH, Park SC, Jung JY. Impact of COPD on COVID-19 prognosis: A nationwide population-based study in South Korea. Sci Rep. 2021;11: 3735. pmid:33580190
  38. 38. CDC. Coronavirus Disease 2019 (COVID-19) in the U.S. In: Centers for Disease Control and Prevention [Internet]. 3 Jul 2020 [cited 4 Jul 2020]. Available: https://www.cdc.gov/coronavirus/2019-ncov/cases-updates/cases-in-us.html
  39. 39. Lowe KE, Regan EA, Anzueto A, Austin E, Austin JHM, Beaty TH, et al. COPDGene® 2019: Redefining the Diagnosis of Chronic Obstructive Pulmonary Disease. Chronic Obstr Pulm Dis J COPD Found. 2019;6: 384–399. pmid:31710793
  40. 40. Gothe H, Rajsic S, Vukicevic D, Schoenfelder T, Jahn B, Geiger-Gritsch S, et al. Algorithms to identify COPD in health systems with and without access to ICD coding: a systematic review. BMC Health Serv Res. 2019;19: 737. pmid:31640678
  41. 41. Mathew HR, Choi MY, Parkins MD, Fritzler MJ. Systematic review: cystic fibrosis in the SARS-CoV-2/COVID-19 pandemic. BMC Pulm Med. 2021;21: 173. pmid:34016096
  42. 42. Maselli DJ, Bhatt SP, Anzueto A, Bowler RP, DeMeo DL, Diaz AA, et al. Clinical Epidemiology of COPD. Chest. 2019;156: 228–238. pmid:31154041