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Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature 2023; 620:128-136. [PMID: 37468623 PMCID: PMC10396966 DOI: 10.1038/s41586-023-06331-x] [Citation(s) in RCA: 48] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/15/2023] [Indexed: 07/21/2023]
Abstract
Studies have demonstrated that at least 20% of individuals infected with SARS-CoV-2 remain asymptomatic1-4. Although most global efforts have focused on severe illness in COVID-19, examining asymptomatic infection provides a unique opportunity to consider early immunological features that promote rapid viral clearance. Here, postulating that variation in the human leukocyte antigen (HLA) loci may underly processes mediating asymptomatic infection, we enrolled 29,947 individuals, for whom high-resolution HLA genotyping data were available, in a smartphone-based study designed to track COVID-19 symptoms and outcomes. Our discovery cohort (n = 1,428) comprised unvaccinated individuals who reported a positive test result for SARS-CoV-2. We tested for association of five HLA loci with disease course and identified a strong association between HLA-B*15:01 and asymptomatic infection, observed in two independent cohorts. Suggesting that this genetic association is due to pre-existing T cell immunity, we show that T cells from pre-pandemic samples from individuals carrying HLA-B*15:01 were reactive to the immunodominant SARS-CoV-2 S-derived peptide NQKLIANQF. The majority of the reactive T cells displayed a memory phenotype, were highly polyfunctional and were cross-reactive to a peptide derived from seasonal coronaviruses. The crystal structure of HLA-B*15:01-peptide complexes demonstrates that the peptides NQKLIANQF and NQKLIANAF (from OC43-CoV and HKU1-CoV) share a similar ability to be stabilized and presented by HLA-B*15:01. Finally, we show that the structural similarity of the peptides underpins T cell cross-reactivity of high-affinity public T cell receptors, providing the molecular basis for HLA-B*15:01-mediated pre-existing immunity.
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Affiliation(s)
- Danillo G Augusto
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC, USA
- Programa de Pós-Graduação em Genética, Universidade Federal do Paraná, Curitiba, Brazil
| | - Lawton D Murdolo
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Demetra S M Chatzileontiadou
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Joseph J Sabatino
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Tasneem Yusufali
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Noah D Peyser
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Xochitl Butcher
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kerry Kizer
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Karoline Guthrie
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA
| | - Victoria W Murray
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Vivian Pae
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Sannidhi Sarvadhavabhatla
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Fiona Beltran
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gurjot S Gill
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Cassandra Yun
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Colin T Maguire
- Clinical and Translational Science Institute, University of Utah, Salt Lake City, UT, USA
| | - Michael J Peluso
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Rebecca Hoh
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Timothy J Henrich
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Steven G Deeks
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Michelle Davidson
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Scott Lu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Sarah A Goldberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - J Daniel Kelly
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- F.I. Proctor Foundation, University of California, San Francisco, CA, USA
| | - Jeffrey N Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Cynthia A Vierra-Green
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephen R Spellman
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | | | - Michael J Dewar-Oldis
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development Brisbane, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Peter J Barnard
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sulggi Lee
- Division of HIV, Infectious Diseases and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Gregory M Marcus
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Jeffrey E Olgin
- Division of Cardiology, Department of Medicine, University of California, San Francisco, CA, USA
| | - Mark J Pletcher
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
- Division of General Internal Medicine, University of California, San Francisco, CA, USA
| | - Martin Maiers
- CIBMTR (Center for International Blood and Marrow Transplant Research), National Marrow Donor Program/Be The Match, Minneapolis, MN, USA
| | - Stephanie Gras
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Jill A Hollenbach
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, CA, USA.
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
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Swaminathan S, Lineburg KE, Panikkar A, Raju J, Murdolo LD, Szeto C, Crooks P, Le Texier L, Rehan S, Dewar-Oldis MJ, Barnard PJ, Ambalathingal GR, Neller MA, Short KR, Gras S, Khanna R, Smith C. Ablation of CD8 + T cell recognition of an immunodominant epitope in SARS-CoV-2 Omicron variants BA.1, BA.2 and BA.3. Nat Commun 2022; 13:6387. [PMID: 36302758 PMCID: PMC9607807 DOI: 10.1038/s41467-022-34180-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 10/17/2022] [Indexed: 12/25/2022] Open
Abstract
The emergence of the SARS-CoV-2 Omicron variant has raised concerns of escape from vaccine-induced immunity. A number of studies have demonstrated a reduction in antibody-mediated neutralization of the Omicron variant in vaccinated individuals. Preliminary observations have suggested that T cells are less likely to be affected by changes in Omicron. However, the complexity of human leukocyte antigen genetics and its impact upon immunodominant T cell epitope selection suggests that the maintenance of T cell immunity may not be universal. In this study, we describe the impact that changes in Omicron BA.1, BA.2 and BA.3 have on recognition by spike-specific T cells. These T cells constitute the immunodominant CD8+ T cell response in HLA-A*29:02+ COVID-19 convalescent and vaccinated individuals; however, they fail to recognize the Omicron-encoded sequence. These observations demonstrate that in addition to evasion of antibody-mediated immunity, changes in Omicron variants can also lead to evasion of recognition by immunodominant T cell responses.
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Affiliation(s)
- Srividhya Swaminathan
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia ,grid.1003.20000 0000 9320 7537Faculty of Medicine, The University of Queensland, Herston, QLD 4006 Australia
| | - Katie E. Lineburg
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Archana Panikkar
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Jyothy Raju
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Lawton D. Murdolo
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Christopher Szeto
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Pauline Crooks
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Laetitia Le Texier
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Sweera Rehan
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Michael J. Dewar-Oldis
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - Peter J. Barnard
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia
| | - George R. Ambalathingal
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Michelle A. Neller
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia
| | - Kirsty R. Short
- grid.1003.20000 0000 9320 7537School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - Stephanie Gras
- grid.1018.80000 0001 2342 0938Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086 Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800 Australia
| | - Rajiv Khanna
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia ,grid.1003.20000 0000 9320 7537Faculty of Medicine, The University of Queensland, Herston, QLD 4006 Australia
| | - Corey Smith
- grid.1049.c0000 0001 2294 1395QIMR Berghofer Centre for Immunotherapy and Vaccine Development and Translational and Human Immunology Laboratory, Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Herston, QLD 4006 Australia ,grid.1003.20000 0000 9320 7537Faculty of Medicine, The University of Queensland, Herston, QLD 4006 Australia
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