Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection

Marchal, Astrid; COVID Clinicians; Bolze, Alexandre

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dc.contributor.author	Marchal, Astrid
dc.contributor.author	COVID Clinicians
dc.contributor.author	Bolze, Alexandre
dc.date.accessioned	2024-07-15T06:47:06Z
dc.date.available	2024-07-15T06:47:06Z
dc.date.issued	2024
dc.identifier.citation	Marchal A, Cirulli ET, Neveux I, Bellos E, Thwaites RS, Schiabor Barrett KM, et al. Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection. HGG Adv. 2024 Apr 26;5(3):100300. DOI: 10.1016/j.xhgg.2024.100300
dc.identifier.issn	2666-2477
dc.identifier.uri	http://hdl.handle.net/10230/60747
dc.description.abstract	Human genetic studies of critical COVID-19 pneumonia have revealed the essential role of type I interferon-dependent innate immunity to SARS-CoV-2 infection. Conversely, an association between the HLA-B∗15:01 allele and asymptomatic SARS-CoV-2 infection in unvaccinated individuals was recently reported, suggesting a contribution of pre-existing T cell-dependent adaptive immunity. We report a lack of association of classical HLA alleles, including HLA-B∗15:01, with pre-omicron asymptomatic SARS-CoV-2 infection in unvaccinated participants in a prospective population-based study in the United States (191 asymptomatic vs. 945 symptomatic COVID-19 cases). Moreover, we found no such association in the international COVID Human Genetic Effort cohort (206 asymptomatic vs. 574 mild or moderate COVID-19 cases and 1,625 severe or critical COVID-19 cases). Finally, in the Human Challenge Characterisation study, the three HLA-B∗15:01 individuals infected with SARS-CoV-2 developed symptoms. As with other acute primary infections studied, no classical HLA alleles favoring an asymptomatic course of SARS-CoV-2 infection were identified.
dc.description.sponsorship	The Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI63029), the National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1 TR001866), the Yale Center for Mendelian Genomics and the GSP Coordinating Center funded by the National Human Genome Research Institute (NHGRI) (UM1HG006504 and U24HG008956), the Yale High Performance Computing Center (S10OD018521), the Fisher Center for Alzheimer's Research Foundation, the JPB Foundation, the Meyer Foundation, the French National Research Agency (ANR) under the “Investments for the Future” program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (Equation 201903007798), the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), and ANR AI2D (ANR-22-CE15-0046) projects, the ANR-RHU program (ANR-21-RHUS-08), the European Union’s Horizon 2020 research and innovation program under grant agreement No. 824110 (EASI-genomics), the HORIZON-HLTH-2021-DISEASE-04 program under grant agreement 101057100 (UNDINE), the Square Foundation, Grandir - Fonds de solidarité pour l’enfance, Fondation du Souffle, the SCOR Corporate Foundation for Science, William E. Ford, General Atlantic’s Chairman and Chief Executive Officer, Gabriel Caillaux, General Atlantic’s Co-President, Managing Director and Head of business in EMEA, and the General Atlantic Foundation, the Battersea & Bowery Advisory Group, The French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), Institut National de la Santé et de la Recherche Médicale (INSERM), REACTing-INSERM and the University of Paris Cité. A.N.S. is supported by European Union’s Horizon Health research and innovation program under grant agreement No. 101057100, project UNDINE. S.G.T. is supported by an Investigator Grant awarded by the National Health and Medical Research Council of Australia, and a University of New South Wales Sydney COVID Rapid Response Initiative grant. The study was supported by the ORCHESTRA project, which has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 10101616. The French COVID Cohort study group was sponsored by Inserm and supported by the REACTing consortium and by a grant from the French Ministry of Health (Grant PHRC 20-0424). The Cov-Contact Cohort was supported by the REACTing consortium, the French Ministry of Health, European Commission (Grant RECOVER WP 6). The COVIDeF study group was supported by the French Ministry of Health and Fondation AP-HP Programme Hospitalier de Recherche Clinique (PHRC COVID-19-20-0048). Y.Z. is supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, NIH. This project has received funding from the Regione Lazio (Research Group Projects 2020) No. A0375-2020-36663, GecoBiomark, the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement no. 948959), the Swiss National Science Foundation (grant # 310030L_197721 to J.F.), and ERN-RITA. The Canarian Sequencing Hub is funded by Instituto de Salud Carlos III (COV20_01333, COV20_01334, and PI20/00876) and Spanish Ministry of Science and Innovation (RTC-2017-6471-1; AEI/FEDER, UE), co-financed by the European Regional Development Funds, “A way of making Europe” from the European Union, Cabildo Insular de Tenerife (CGIEU0000219140 and “Apuestas científicas del ITER para colaborar en la lucha contra la COVID-19”). This work was funded, at least in part, by grants AJF202019 and AJF20259 from Al Jalila Foundation, Dubai, United Arab Emirates. Sample processing at IrsiCaixa was possible thanks to the crowdfunding initiative YoMeCorono. We thank I. Erkizia, E. Grau, M. Massanella, and J. Guitart from the IrsiCaixa and Hospital Germans Trias i Pujol (Badalona, Spain) for sample collection, handling, and processing.
dc.format.mimetype	application/pdf
dc.language.iso	eng
dc.publisher	Elsevier
dc.relation.ispartof	HGG Adv. 2024 Apr 26;5(3):100300
dc.rights	© 2024 The Author(s). This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
dc.rights.uri	http://creativecommons.org/licenses/by/4.0/
dc.title	Lack of association between classical HLA genes and asymptomatic SARS-CoV-2 infection
dc.type	info:eu-repo/semantics/article
dc.identifier.doi	http://dx.doi.org/10.1016/j.xhgg.2024.100300
dc.subject.keyword	COVID-19
dc.subject.keyword	HLA
dc.subject.keyword	Association
dc.subject.keyword	Asymptomatic infection
dc.subject.keyword	Population stratification
dc.relation.projectID	info:eu-repo/grantAgreement/EC/H2020/824110
dc.relation.projectID	info:eu-repo/grantAgreement/EC/HE/101057100
dc.relation.projectID	info:eu-repo/grantAgreement/EC/H2020/948959
dc.rights.accessRights	info:eu-repo/semantics/openAccess
dc.type.version	info:eu-repo/semantics/publishedVersion