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Gutiérrez-Bautista JF, Díaz-Alberola I, Tarriño M, Aguilera M, Cobo F, Reguera JA, Rodríguez-Granger J, Mendoza J, López-Nevot MÁ, Sampedro A. Follow-up of immune response in patients with common variable immunodeficiency following SARS-CoV-2 vaccination. Clin Exp Immunol 2024; 217:253-262. [PMID: 38693777 PMCID: PMC11310691 DOI: 10.1093/cei/uxae039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 05/01/2024] [Indexed: 05/03/2024] Open
Abstract
The COVID-19 pandemic highlighted the importance of effective vaccination strategies in controlling the spread of infectious diseases. SARS-CoV-2 vaccine has demonstrated high efficacy in preventing COVID-19 infection in the general population. However, the efficacy of this vaccine in patients with predominantly antibody deficiencies, such as common variable immunodeficiency (CVID) and X-linked agammaglobulinemia (XLA), should be closely monitored. CVID and XLA are rare genetic disorders that impair the immune system's ability to produce antibodies, which are crucial for fighting infections. Patients with these disorders have a higher risk of severe disease and mortality from COVID-19 due to their compromised immune systems. In this study, we evaluated the humoral and cellular immune responses after four doses of mRNA-1273 and one BNT162b2 bivalent vaccine in a cohort of patients with CVID and XLA. The response in this population was lower than in the control group. However, the administration of the third dose improved the number of patients with seroconversion and the intensity of the humoral response, as well as the number of patients with a positive cellular response. Finally, the administration of the fourth and fifth doses improves the antibody titer and neutralization against wild type variant, but not against the prevalent XBB1.5 variant.
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Affiliation(s)
- Juan Francisco Gutiérrez-Bautista
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Irene Díaz-Alberola
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - María Tarriño
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
| | - María Aguilera
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
| | - Fernando Cobo
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
| | - Juan Antonio Reguera
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
| | - Javier Rodríguez-Granger
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
| | | | - Miguel Ángel López-Nevot
- Departamento de Bioquímica, Biología Molecular e Inmunología III, University of Granada, Granada, Spain
- Servicio de Análisis Clínicos e Inmunología, University Hospital Virgen de las Nieves, Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
| | - Antonio Sampedro
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), Granada, Spain
- Servicio de Microbiología, University Hospital Virgen de las Nieves, Granada, Spain
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Carretero D, Giménez E, Albert E, Colomer E, Torres I, Olea B, Sánchez-Simarro Á, Navarro D. SARS-CoV-2-Spike T-cell response after receiving one or two Wuhan-Hu-1-based mRNA COVID-19 vaccine booster doses in elderly nursing home residents. J Med Virol 2024; 96:e29790. [PMID: 38994662 DOI: 10.1002/jmv.29790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/05/2024] [Accepted: 07/02/2024] [Indexed: 07/13/2024]
Abstract
The effect of COVID-19 booster vaccination on SARS-CoV-2 T-cell mediated immune responses in elderly nursing home residents has not been explored in depth. Thirty-nine elderly nursing home residents (median age, 91 years) were included, all fully vaccinated with mRNA vaccines. The frequency of and the integrated mean fluorescence (iMFI) for peripheral blood SARS-CoV-2-Spike reactive IFN-γ-producing CD4+ or CD8+ T cells before and after the first (Pre-3D and Post-3D) and second (Pre-4D and Post-4D) vaccine booster doses was determined using flow cytometry for an intracellular staining method. 3D increased significantly (p = 0.01) the percentage of participants displaying detectable SARS-CoV-2-T-cell responses compared with pre-3D (97% vs. 74%). The magnitude of the increase was statistically significant for CD8+ T cells (p = 0.007) but not for CD4+ T cells (p = 0.77). A trend towards higher frequencies of peripheral blood SARS-CoV-2-CD8+ T cells was observed post-3D compared with pre-3D (p = 0.06). The percentage of participants with detectable SARS-S-CoV-2 CD4+ T-cell responses decreased post-4D (p = 0.035). Following 4D, a nonsignificant decrease in the frequencies of both T cell subsets was noticed (p = 0.94 for CD8+ T cells and p = 0.06 for CD4+ T cells). iMFI data mirrored that of T-cell frequencies. The kinetics of SARS-CoV-2 CD8+ and CD4+ T cells following receipt of 3D and 4D were comparable across SARS-CoV-2-experienced and -naïve participants and between individuals receiving a homologous or heterologous vaccine booster. 3D increased the percentage of elderly nursing home residents displaying detectable SARS-CoV-2 T-cell responses but had a marginal effect on T-cell frequencies. The impact of 4D on SARS-CoV-2 T-cell responses was negligible; whether this was due to suboptimal priming or rapid waning could not be ascertained.
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Affiliation(s)
- Diego Carretero
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ester Colomer
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ignacio Torres
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Beatriz Olea
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ángela Sánchez-Simarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain
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3
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Qui M, Hariharaputran S, Hang SK, Zhang J, Tan CW, Chong CY, Low J, Wang L, Bertoletti A, Yung CF, Le Bert N. T cell hybrid immunity against SARS-CoV-2 in children: a longitudinal study. EBioMedicine 2024; 105:105203. [PMID: 38896919 PMCID: PMC11237860 DOI: 10.1016/j.ebiom.2024.105203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 05/27/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Hybrid immunity to SARS-CoV-2, resulting from both vaccination and natural infection, remains insufficiently understood in paediatric populations, despite increasing rates of breakthrough infections among vaccinated children. METHODS We conducted a prospective longitudinal study to investigate the magnitude, specificity, and cytokine profile of antigen-specific T cell responses elicited by breakthrough SARS-CoV-2 infection in a cohort of mRNA-vaccinated children (n = 29) aged 5-11. This longitudinal analysis involved six distinct time points spanning a 16-month period post-vaccination, during which we analysed a total of 159 blood samples. All children who were followed for at least 12 months (n = 26) experienced a breakthrough infection. We conducted cytokine release assays using minimal blood samples, and we verified the cellular origin of these responses through intracellular cytokine staining. FINDINGS After breakthrough infection, children who had received mRNA vaccines showed enhanced Th1 responses specific to Spike peptides. Additionally, their Spike-specific T cells exhibited a distinctive enrichment of CD4+ IFN-γ+IL10+ cells, a characteristic akin to adults with hybrid immunity. Importantly, vaccination did not impede the development of multi-specific T cell responses targeting Membrane, Nucleoprotein, and ORF3a/7/8 antigens. INTERPRETATION Children, previously primed with a Spike-based mRNA vaccine and experiencing either symptomatic or asymptomatic breakthrough infection, retained the ability to enhance and diversify Th1/IL-10 antigen-specific T cell responses against multiple SARS-CoV-2 proteins. These findings mirror characteristics associated with hybrid cellular immunity in adults, known to confer resistance against severe COVID-19. FUNDING This study was funded by the National Medical Research Council (NMRC) Singapore (COVID19RF-0019, MOH-000019, MOH-000535, OFLCG19May-0034 and MOH-OFYIRG19nov-0002).
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Affiliation(s)
- Martin Qui
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | | | - Shou Kit Hang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jinyan Zhang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chia Yin Chong
- KK Women's and Children's Hospital, Department of Paediatrics, Infectious Diseases Service, Singapore; Duke-NUS Medical School, Singapore; Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Jenny Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Singapore General Hospital, Department of Infectious Diseases, Singapore
| | - Linfa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Antonio Bertoletti
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Singapore Immunology Network, A∗STAR, Singapore
| | - Chee Fu Yung
- KK Women's and Children's Hospital, Department of Paediatrics, Infectious Diseases Service, Singapore; Duke-NUS Medical School, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Nina Le Bert
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore.
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Carretero D, Giménez E, Albert E, Colomer E, Montomoli M, Hernani R, Piñana JL, Górriz JL, Solano C, Navarro D. Performance of the Roche Elecsys® IGRA SARS-CoV-2 test for the detection and quantification of virus-reactive T cells in COVID-19-vaccinated immunosuppressed patients and healthy subjects. Eur J Clin Microbiol Infect Dis 2024; 43:1427-1436. [PMID: 38777919 PMCID: PMC11271317 DOI: 10.1007/s10096-024-04852-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
PURPOSE Comparing the performance of commercially available SARS-CoV-2 T-cell immunoassay responses may provide useful information for future observational or intervention studies as well as to their potential customers. METHOD Whole blood was collected from a total of 183 subjects fully vaccinated against COVID-19: 55 healthy controls (Group 1), 50 hematological patients (Group 2), 50 chronic kidney disease patients (Group 3), and 28 elderly nursing home residents (Group 4). Samples were tested with the Roche Elecsys® IGRA (Interferon-gamma release assay) SARS-CoV-2 test (Roche Diagnostics, Rotkreuz, Switzerland), the Euroimmun SARS-CoV-2 test (Euroimmun, Lubeck, Germany), the SARS-CoV-2 T Cell Analysis Kit (Miltenyi Biotec, Bergisch Gladbach, Germany), and a flow-cytometry for intracellular cytokine (IFN-γ) staining-based immunoassay (FC-ICS). RESULTS Overall, the Roche Elecsys® assay returned the highest number of positive results (151/179; 84.3%), followed by the Euroimmun test (127/183; 69%), and the FC-ICS (135/179; 75%). The Kappa coefficient of agreement was best between IGRAs (0.64). Most discordant results across assays involved patients from Group 2. Overall, IFN-γ concentrations measured by both IGRAs correlated strongly (rho = 0.78; 95% CI 0.71-0.84; P < 0.001) irrespective of the study group. The frequencies of SARS-CoV-2-reactive IFN-γ T cells and IFN-γ concentrations measured by the IGRAs correlated moderately for CD4+ T cells, however, weakly for CD8+ T cells. SARS-CoV-2-experienced participants displayed stronger responses than SARS-CoV-2-naïve when IGRAs, rather than FC-ICS, were used. CONCLUSION The SARS-CoV-2 immunoassays evaluated in the present study did not return interchangeable qualitative or quantitative results either in seemingly healthy individuals or in immunosuppressed patients.
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Affiliation(s)
- Diego Carretero
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Estela Giménez
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Eliseo Albert
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Ester Colomer
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain
| | - Marco Montomoli
- Nephrology Service, Hospital Clínico Universitario de Valencia, INCLIVA Health Research Institute, Valencia, Spain
| | - Rafael Hernani
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, Valencia, Spain
| | - José Luis Piñana
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, Valencia, Spain
| | - José Luis Górriz
- Nephrology Service, Hospital Clínico Universitario de Valencia, INCLIVA Health Research Institute, Valencia, Spain
- Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - Carlos Solano
- Hematology Service, Hospital Clínico Universitario, INCLIVA Health Research Institute, Valencia, Spain
- Department of Medicine, School of Medicine, University of Valencia, Valencia, Spain
| | - David Navarro
- Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain.
- Department of Microbiology, School of Medicine, University of Valencia, Valencia, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
- Microbiology Service, Hospital Clínico Universitario, Instituto de Investigación INCLIVA, Av. Blasco Ibáñez 17, 46010, Valencia, Spain.
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5
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Tarke A, Ramezani-Rad P, Alves Pereira Neto T, Lee Y, Silva-Moraes V, Goodwin B, Bloom N, Siddiqui L, Avalos L, Frazier A, Zhang Z, da Silva Antunes R, Dan J, Crotty S, Grifoni A, Sette A. SARS-CoV-2 breakthrough infections enhance T cell response magnitude, breadth, and epitope repertoire. Cell Rep Med 2024; 5:101583. [PMID: 38781962 PMCID: PMC11228552 DOI: 10.1016/j.xcrm.2024.101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/22/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Little is known about the effect of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or SARS2) vaccine breakthrough infections (BTIs) on the magnitude and breadth of the T cell repertoire after exposure to different variants. We studied samples from individuals who experienced symptomatic BTIs during Delta or Omicron waves. In the pre-BTI samples, 30% of the donors exhibited substantial immune memory against non-S (spike) SARS2 antigens, consistent with previous undiagnosed asymptomatic SARS2 infections. Following symptomatic BTI, we observed (1) enhanced S-specific CD4 and CD8 T cell responses in donors without previous asymptomatic infection, (2) expansion of CD4 and CD8 T cell responses to non-S targets (M, N, and nsps) independent of SARS2 variant, and (3) generation of novel epitopes recognizing variant-specific mutations. These variant-specific T cell responses accounted for 9%-15% of the total epitope repertoire. Overall, BTIs boost vaccine-induced immune responses by increasing the magnitude and by broadening the repertoire of T cell antigens and epitopes recognized.
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Affiliation(s)
- Alison Tarke
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Parham Ramezani-Rad
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | | | - Yeji Lee
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Vanessa Silva-Moraes
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL 34987, USA
| | - Benjamin Goodwin
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Nathaniel Bloom
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Leila Siddiqui
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Liliana Avalos
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - April Frazier
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | - Zeli Zhang
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA
| | | | - Jennifer Dan
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Shane Crotty
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
| | - Alba Grifoni
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA.
| | - Alessandro Sette
- Center for Vaccine Innovation, La Jolla Institute for Immunology (LJI), La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92037, USA.
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6
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Suthar MS. Durability of immune responses to SARS-CoV-2 infection and vaccination. Semin Immunol 2024; 73:101884. [PMID: 38861769 DOI: 10.1016/j.smim.2024.101884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/13/2024]
Abstract
Infection with SARS-CoV-2 in humans has caused a pandemic of unprecedented dimensions. SARS-CoV-2 is primarily transmitted through respiratory droplets and targets ciliated epithelial cells in the nasal cavity, trachea, and lungs by utilizing the cellular receptor angiotensin-converting enzyme 2 (ACE2). The innate immune response, including type I and III interferons, inflammatory cytokines (IL-6, TNF-α, IL-1β), innate immune cells (monocytes, DCs, neutrophils, natural killer cells), antibodies (IgG, sIgA, neutralizing antibodies), and adaptive immune cells (B cells, CD8+ and CD4+ T cells) play pivotal roles in mitigating COVID-19 disease. Broad and durable B-cell- and T-cell immunity elicited by infection and vaccination is essential for protection against severe disease, hospitalization and death. However, the emergence of SARS-CoV-2 variants that evade neutralizing antibodies continue to jeopardize vaccine efficacy. In this review, we highlight our understanding the infection- and vaccine-mediated humoral, B and T cell responses, the durability of the immune responses, and how variants continue to threaten the efficacy of SARS-CoV-2 vaccines.
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Affiliation(s)
- Mehul S Suthar
- Emory Vaccine Center, Emory National Primate Research Center, Emory Vaccine Center, Emory University, Atlanta, GA, USA; Emory Center of Excellence of Influenza Research and Response (CEIRR), Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University, Atlanta, GA, USA; Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
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7
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Sohail MS, Ahmed SF, Quadeer AA, McKay MR. Cross-Reactivity Assessment of Vaccine-Derived SARS-CoV-2 T Cell Responses against BA.2.86 and JN.1. Viruses 2024; 16:473. [PMID: 38543838 PMCID: PMC10975570 DOI: 10.3390/v16030473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 03/15/2024] [Indexed: 05/23/2024] Open
Abstract
The SARS-CoV-2 Omicron sub-variants BA.2.86 and JN.1 contain multiple mutations in the spike protein that were not present in previous variants of concern and Omicron sub-variants. Preliminary research suggests that these variants reduce the neutralizing capability of antibodies induced by vaccines, which is particularly significant for JN.1. This raises concern as many widely deployed COVID-19 vaccines are based on the spike protein of the ancestral Wuhan strain of SARS-CoV-2. While T cell responses have been shown to be robust against previous SARS-CoV-2 variants, less is known about the impact of mutations in BA.2.86 and JN.1 on T cell responses. We evaluate the effect of mutations specific to BA.2.86 and JN.1 on experimentally determined T cell epitopes derived from the spike protein of the ancestral Wuhan strain and the spike protein of the XBB.1.5 strain that has been recommended as a booster vaccine. Our data suggest that BA.2.86 and JN.1 affect numerous T cell epitopes in spike compared to previous variants; however, the widespread loss of T cell recognition against these variants is unlikely.
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Affiliation(s)
- Muhammad Saqib Sohail
- Department of Electronic and Computer Engineering, The Hong Kong University of Science and Technology, Hong Kong SAR, China;
| | - Syed Faraz Ahmed
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia;
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Ahmed Abdul Quadeer
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Matthew R. McKay
- Department of Electrical and Electronic Engineering, University of Melbourne, Parkville, VIC 3010, Australia;
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
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8
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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9
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Antunes DA, Baker BM, Cornberg M, Selin LK. Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods. Front Immunol 2024; 15:1377259. [PMID: 38444853 PMCID: PMC10912571 DOI: 10.3389/fimmu.2024.1377259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Affiliation(s)
- Dinler A. Antunes
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Brian M. Baker
- Department of Chemistry and Biochemistry, and Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, United States
| | - Markus Cornberg
- Department of Gastroenterology, Hepatology, Infectious Diseases and Endocrinology, Hannover Medical School, Hannover, Germany
- Centre for Individualized Infection Medicine (CiiM), c/o CRC Hannover, Hannover, Germany
- German Center for Infection Research (DZIF), Partner-site Hannover-Braunschweig, Hannover, Germany
| | - Liisa K. Selin
- Department of Pathology, University of Massachusetts Medical School, Worcester, MA, United States
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10
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Altmann DM, Boyton RJ. Arming up against Omicron subvariants. Cell Host Microbe 2024; 32:147-148. [PMID: 38359794 DOI: 10.1016/j.chom.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 02/17/2024]
Abstract
The rapid evolution of COVID-19 Omicron variants is driven by evasion of neutralizing antibodies. Breakthrough infections are common, even in highly vaccinated populations, making it vital to understand immune cross-protective repertoires to variants. Two studies in this issue show that the primed T cell repertoire comprises strong cross-recognition of current variants.
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Affiliation(s)
- Daniel M Altmann
- Department of Immunology and Inflammation, Faculty of Medicine, Imperial College, London, UK.
| | - Rosemary J Boyton
- Department of Infectious Disease, Faculty of Medicine, Imperial College, London, UK
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