IDEAS home Printed from https://ideas.repec.org/a/plo/pgen00/1011192.html
   My bibliography  Save this article

Canadian COVID-19 host genetics cohort replicates known severity associations

Author

Listed:
  • Elika Garg
  • Paola Arguello-Pascualli
  • Olga Vishnyakova
  • Anat R Halevy
  • Samantha Yoo
  • Jennifer D Brooks
  • Shelley B Bull
  • France Gagnon
  • Celia M T Greenwood
  • Rayjean J Hung
  • Jerald F Lawless
  • Jordan Lerner-Ellis
  • Jessica K Dennis
  • Rohan J S Abraham
  • Jean-Michel Garant
  • Bhooma Thiruvahindrapuram
  • Steven J M Jones
  • CGEn HostSeq Initiative
  • Lisa J Strug
  • Andrew D Paterson
  • Lei Sun
  • Lloyd T Elliott

Abstract

The HostSeq initiative recruited 10,059 Canadians infected with SARS-CoV-2 between March 2020 and March 2023, obtained clinical information on their disease experience and whole genome sequenced (WGS) their DNA. We analyzed the WGS data for genetic contributors to severe COVID-19 (considering 3,499 hospitalized cases and 4,975 non-hospitalized after quality control). We investigated the evidence for replication of loci reported by the International Host Genetics Initiative (HGI); analyzed the X chromosome; conducted rare variant gene-based analysis and polygenic risk score testing. Population stratification was adjusted for using meta-analysis across ancestry groups. We replicated two loci identified by the HGI for COVID-19 severity: the LZTFL1/SLC6A20 locus on chromosome 3 and the FOXP4 locus on chromosome 6 (the latter with a variant significant at P

Suggested Citation

  • Elika Garg & Paola Arguello-Pascualli & Olga Vishnyakova & Anat R Halevy & Samantha Yoo & Jennifer D Brooks & Shelley B Bull & France Gagnon & Celia M T Greenwood & Rayjean J Hung & Jerald F Lawless &, 2024. "Canadian COVID-19 host genetics cohort replicates known severity associations," PLOS Genetics, Public Library of Science, vol. 20(3), pages 1-25, March.
    • Handle: RePEc:plo:pgen00:1011192
    DOI: 10.1371/journal.pgen.1011192
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1011192
    Download Restriction: no
    File URL: https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.1011192&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pgen.1011192?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Tian Ge & Chia-Yen Chen & Yang Ni & Yen-Chen Anne Feng & Jordan W. Smoller, 2019. "Polygenic prediction via Bayesian regression and continuous shrinkage priors," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. Christiaan A de Leeuw & Joris M Mooij & Tom Heskes & Danielle Posthuma, 2015. "MAGMA: Generalized Gene-Set Analysis of GWAS Data," PLOS Computational Biology, Public Library of Science, vol. 11(4), pages 1-19, April.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Yash Patel & Jean Shin & Eeva Sliz & Ariana Tang & Aniket Mishra & Rui Xia & Edith Hofer & Hema Sekhar Reddy Rajula & Ruiqi Wang & Frauke Beyer & Katrin Horn & Max Riedl & Jing Yu & Henry Völzke & Rob, 2024. "Genetic risk factors underlying white matter hyperintensities and cortical atrophy," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    2. Yunfeng Huang & Dora Bodnar & Chia-Yen Chen & Gabriela Sanchez-Andrade & Mark Sanderson & Jun Shi & Katherine G. Meilleur & Matthew E. Hurles & Sebastian S. Gerety & Ellen A. Tsai & Heiko Runz, 2023. "Rare genetic variants impact muscle strength," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    3. Yuji Yamamoto & Yuya Shirai & Kyuto Sonehara & Shinichi Namba & Takafumi Ojima & Kenichi Yamamoto & Ryuya Edahiro & Ken Suzuki & Akinori Kanai & Yoshiya Oda & Yutaka Suzuki & Takayuki Morisaki & Akira, 2025. "Dissecting cross-population polygenic heterogeneity across respiratory and cardiometabolic diseases," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    4. Chachrit Khunsriraksakul & Qinmengge Li & Havell Markus & Matthew T. Patrick & Renan Sauteraud & Daniel McGuire & Xingyan Wang & Chen Wang & Lida Wang & Siyuan Chen & Ganesh Shenoy & Bingshan Li & Xue, 2023. "Multi-ancestry and multi-trait genome-wide association meta-analyses inform clinical risk prediction for systemic lupus erythematosus," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Priya Gupta & Marco Galimberti & Yue Liu & Sarah Beck & Aliza Wingo & Thomas Wingo & Keyrun Adhikari & Henry R. Kranzler & Murray B. Stein & Joel Gelernter & Daniel F. Levey, 2024. "A genome-wide investigation into the underlying genetic architecture of personality traits and overlap with psychopathology," Nature Human Behaviour, Nature, vol. 8(11), pages 2235-2249, November.
    6. Tzu-Ting Chen & Jaeyoung Kim & Max Lam & Yi-Fang Chuang & Yen-Ling Chiu & Shu-Chin Lin & Sang-Hyuk Jung & Beomsu Kim & Soyeon Kim & Chamlee Cho & Injeong Shim & Sanghyeon Park & Yeeun Ahn & Aysu Okbay, 2024. "Shared genetic architectures of educational attainment in East Asian and European populations," Nature Human Behaviour, Nature, vol. 8(3), pages 562-575, March.
    7. Andras Gezsi & Sandra Auwera & Hannu Mäkinen & Nora Eszlari & Gabor Hullam & Tamas Nagy & Sarah Bonk & Rubèn González-Colom & Xenia Gonda & Linda Garvert & Teemu Paajanen & Zsofia Gal & Kevin Kirchner, 2024. "Unique genetic and risk-factor profiles in clusters of major depressive disorder-related multimorbidity trajectories," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    8. Mingyang Li & Xixi Dang & Yiwei Chen & Zhifan Chen & Xinyi Xu & Zhiyong Zhao & Dan Wu, 2024. "Cognitive processing speed and accuracy are intrinsically different in genetic architecture and brain phenotypes," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    9. Maria Niarchou & Daniel E. Gustavson & J. Fah Sathirapongsasuti & Manuel Anglada-Tort & Else Eising & Eamonn Bell & Evonne McArthur & Peter Straub & J. Devin McAuley & John A. Capra & Fredrik Ullén & , 2022. "Genome-wide association study of musical beat synchronization demonstrates high polygenicity," Nature Human Behaviour, Nature, vol. 6(9), pages 1292-1309, September.
    10. Gökberk Alagöz & Else Eising & Yasmina Mekki & Giacomo Bignardi & Pierre Fontanillas & Michel G. Nivard & Michelle Luciano & Nancy J. Cox & Simon E. Fisher & Reyna L. Gordon, 2025. "The shared genetic architecture and evolution of human language and musical rhythm," Nature Human Behaviour, Nature, vol. 9(2), pages 376-390, February.
    11. Shahram Bahrami & Kaja Nordengen & Jaroslav Rokicki & Alexey A. Shadrin & Zillur Rahman & Olav B. Smeland & Piotr P. Jaholkowski & Nadine Parker & Pravesh Parekh & Kevin S. O’Connell & Torbjørn Elvsås, 2024. "The genetic landscape of basal ganglia and implications for common brain disorders," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Jialiang S. Wang & Tushar Kamath & Courtney M. Mazur & Fatemeh Mirzamohammadi & Daniel Rotter & Hironori Hojo & Christian D. Castro & Nicha Tokavanich & Rushi Patel & Nicolas Govea & Tetsuya Enishi & , 2021. "Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin," Nature Communications, Nature, vol. 12(1), pages 1-20, December.
    13. Elena V. Feofanova & Michael R. Brown & Taryn Alkis & Astrid M. Manuel & Xihao Li & Usman A. Tahir & Zilin Li & Kevin M. Mendez & Rachel S. Kelly & Qibin Qi & Han Chen & Martin G. Larson & Rozenn N. L, 2023. "Whole-Genome Sequencing Analysis of Human Metabolome in Multi-Ethnic Populations," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    14. Ambroise Wonkam & Kevin Esoh & Rachel M. Levine & Valentina Josiane Ngo Bitoungui & Khuthala Mnika & Nikitha Nimmagadda & Erin A. D. Dempsey & Siana Nkya & Raphael Z. Sangeda & Victoria Nembaware & Ja, 2025. "FLT1 and other candidate fetal haemoglobin modifying loci in sickle cell disease in African ancestries," Nature Communications, Nature, vol. 16(1), pages 1-21, December.
    15. Chen Wang & Havell Markus & Avantika R. Diwadkar & Chachrit Khunsriraksakul & Laura Carrel & Bingshan Li & Xue Zhong & Xingyan Wang & Xiaowei Zhan & Galen T. Foulke & Nancy J. Olsen & Dajiang J. Liu &, 2025. "Integrating electronic health records and GWAS summary statistics to predict the progression of autoimmune diseases from preclinical stages," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
    16. Olga A Vsevolozhskaya & Min Shi & Fengjiao Hu & Dmitri V Zaykin, 2020. "DOT: Gene-set analysis by combining decorrelated association statistics," PLOS Computational Biology, Public Library of Science, vol. 16(4), pages 1-25, April.
    17. Ruoyu Tian & Tian Ge & Hyeokmoon Kweon & Daniel B. Rocha & Max Lam & Jimmy Z. Liu & Kritika Singh & Daniel F. Levey & Joel Gelernter & Murray B. Stein & Ellen A. Tsai & Hailiang Huang & Christopher F., 2024. "Whole-exome sequencing in UK Biobank reveals rare genetic architecture for depression," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    18. Tuomo Hartonen & Bradley Jermy & Hanna Sõnajalg & Pekka Vartiainen & Kristi Krebs & Andrius Vabalas & Tuija Leino & Hanna Nohynek & Jonas Sivelä & Reedik Mägi & Mark Daly & Hanna M. Ollila & Lili Mila, 2023. "Nationwide health, socio-economic and genetic predictors of COVID-19 vaccination status in Finland," Nature Human Behaviour, Nature, vol. 7(7), pages 1069-1083, July.
    19. James P. Pirruccello & Paolo Achille & Seung Hoan Choi & Joel T. Rämö & Shaan Khurshid & Mahan Nekoui & Sean J. Jurgens & Victor Nauffal & Shinwan Kany & Kenney Ng & Samuel F. Friedman & Puneet Batra , 2024. "Deep learning of left atrial structure and function provides link to atrial fibrillation risk," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    20. Mattia Cordioli & Andrea Corbetta & Hanna Maria Kariis & Sakari Jukarainen & Pekka Vartiainen & Tuomo Kiiskinen & Matteo Ferro & Markus Perola & Mikko Niemi & Samuli Ripatti & Kelli Lehto & Lili Milan, 2024. "Socio-demographic and genetic risk factors for drug adherence and persistence across 5 common medication classes," Nature Communications, Nature, vol. 15(1), pages 1-13, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pgen00:1011192. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosgenetics (email available below). General contact details of provider: https://journals.plos.org/plosgenetics/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.