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Phetsouphanh C, Jacka B, Ballouz S, Jackson KJL, Wilson DB, Manandhar B, Klemm V, Tan HX, Wheatley A, Aggarwal A, Akerman A, Milogiannakis V, Starr M, Cunningham P, Turville SG, Kent SJ, Byrne A, Brew BJ, Darley DR, Dore GJ, Kelleher AD, Matthews GV. Improvement of immune dysregulation in individuals with long COVID at 24-months following SARS-CoV-2 infection. Nat Commun 2024; 15:3315. [PMID: 38632311 PMCID: PMC11024141 DOI: 10.1038/s41467-024-47720-8] [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: 10/09/2023] [Accepted: 04/11/2024] [Indexed: 04/19/2024] Open
Abstract
This study investigates the humoral and cellular immune responses and health-related quality of life measures in individuals with mild to moderate long COVID (LC) compared to age and gender matched recovered COVID-19 controls (MC) over 24 months. LC participants show elevated nucleocapsid IgG levels at 3 months, and higher neutralizing capacity up to 8 months post-infection. Increased spike-specific and nucleocapsid-specific CD4+ T cells, PD-1, and TIM-3 expression on CD4+ and CD8+ T cells were observed at 3 and 8 months, but these differences do not persist at 24 months. Some LC participants had detectable IFN-γ and IFN-β, that was attributed to reinfection and antigen re-exposure. Single-cell RNA sequencing at the 24 month timepoint shows similar immune cell proportions and reconstitution of naïve T and B cell subsets in LC and MC. No significant differences in exhaustion scores or antigen-specific T cell clones are observed. These findings suggest resolution of immune activation in LC and return to comparable immune responses between LC and MC over time. Improvement in self-reported health-related quality of life at 24 months was also evident in the majority of LC (62%). PTX3, CRP levels and platelet count are associated with improvements in health-related quality of life.
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Affiliation(s)
| | - Brendan Jacka
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Sara Ballouz
- Garvan Institute for Medical research, Sydney, NSW, Australia
- School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales, Sydney, NSW, Australia
| | | | - Daniel B Wilson
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Bikash Manandhar
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Vera Klemm
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Hyon-Xhi Tan
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Adam Wheatley
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Anupriya Aggarwal
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Anouschka Akerman
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | | | - Mitchell Starr
- NSW State Reference Laboratory for HIV, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Phillip Cunningham
- NSW State Reference Laboratory for HIV, St. Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Stuart G Turville
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Stephen J Kent
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Victoria, VIC, Australia
| | - Anthony Byrne
- Heart Lung Clinic, St. Vincent's Hospital Sydney and Faculty of Medicine and Health (UNSW), Sydney, NSW, Australia
| | - Bruce J Brew
- Peter Duncan Neurosciences Unit- St Vincent's Centre for Applied Medical Research, Sydney, NSW, Australia
| | | | - Gregory J Dore
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia
- St. Vincent's Hospital, Darlinghurst, NSW, Australia
| | - Anthony D Kelleher
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
- St. Vincent's Hospital, Darlinghurst, NSW, Australia.
| | - Gail V Matthews
- The Kirby Institute, University of New South Wales, Sydney, NSW, Australia.
- St. Vincent's Hospital, Darlinghurst, NSW, Australia.
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Activation-induced surface proteins in the identification of antigen-responsive CD4 T cells. Immunol Lett 2019; 219:1-7. [PMID: 31881234 DOI: 10.1016/j.imlet.2019.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/09/2019] [Accepted: 12/22/2019] [Indexed: 02/06/2023]
Abstract
Identification of antigen specificity of CD4 T cells is instrumental in understanding adaptive immune responses in health and disease. The high diversity of CD4 T cell repertoire combined with the functional heterogeneity of the compartment poses a challenge to the assessment of CD4 T cell responses. In spite of that, multiple technologies allow direct or indirect interrogation of antigen specificity of CD4 T cells. In the last decade, multiple surface proteins have been established as cytokine-independent surrogates of in vitro CD4 T cell activation, and have found applications in the live identification and isolation of antigen-responsive CD4 T cells. Here we review the current knowledge of the surface proteins that permit identification of viable antigen-responsive CD4 T cells with high specificity, including those capable of identifying specialized CD4 T subsets such as germinal center follicular helper T cells and CD4 regulatory T cells.
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Hey-Nguyen WJ, Bailey M, Xu Y, Suzuki K, Van Bockel D, Finlayson R, Leigh Brown A, Carr A, Cooper DA, Kelleher AD, Koelsch KK, Zaunders JJ. HIV-1 DNA Is Maintained in Antigen-Specific CD4+ T Cell Subsets in Patients on Long-Term Antiretroviral Therapy Regardless of Recurrent Antigen Exposure. AIDS Res Hum Retroviruses 2019; 35:112-120. [PMID: 30511878 DOI: 10.1089/aid.2018.0235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Memory CD4+ T cells (mCD4s) containing integrated HIV DNA are considered the main barrier to a cure for HIV infection. Here, we analyzed HIV DNA reservoirs in antigen-specific subsets of mCDs to delineate the mechanisms by which HIV reservoirs persist during antiretroviral therapy (ART). HIV Gag, cytomegalovirus (CMV), and tetanus toxoid (TT)-specific mCD4s were isolated from peripheral blood samples obtained from 11 individual subjects, 2-11 years after commencing ART. Antigen-specific mCD4s were identified by the sensitive OX40 assay and purified by cell sorting. Total HIV DNA levels were quantified by real-time PCR, and clonal viral sequences generated from mCD4 subsets and pre-ART plasma samples. Quantitative results and sequence analysis were restricted to five and three study participants, respectively, which was likely due to the low frequency of the antigen-specific mCD4s and relatively low HIV DNA proviral loads. Median HIV Gag-, CMV-, and TT-specific mCD4s were 0.61%, 2.46%, and 0.78% of total mCD4s, and they contained a median of 2.50, 2.38, and 2.55 log10 copies of HIV DNA per 106 cells, respectively. HIV DNA sequences were derived from antigen-specific mCD4s clustered with sequences derived from pre-ART plasma samples. There was a trend toward increased viral diversity in clonal viral sequences derived from CMV-specific mCD4s relative to TT-specific mCD4s. Despite limitations, this study provides direct evidence that HIV reservoirs persist in memory CD4+ T cell subsets maintained by homeostatic proliferation (TT) and adds to growing evidence against viral evolution during ART. Similar future studies require techniques that sample diverse HIV reservoirs and with improved sensitivity.
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Affiliation(s)
- William J. Hey-Nguyen
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
| | - Michelle Bailey
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
| | - Yin Xu
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
| | - Kazuo Suzuki
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
- St. Vincent's Hospital Sydney, Sydney, Australia
| | - David Van Bockel
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
- St. Vincent's Hospital Sydney, Sydney, Australia
| | - Robert Finlayson
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Taylor Square Private Clinic, Sydney, Australia
| | - Andrew Leigh Brown
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Carr
- St. Vincent's Hospital Sydney, Sydney, Australia
| | - David A. Cooper
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
| | - Anthony D. Kelleher
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
- St. Vincent's Hospital Sydney, Sydney, Australia
| | - Kersten K. Koelsch
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
- St. Vincent's Hospital Sydney, Sydney, Australia
| | - John J. Zaunders
- The Kirby Institute, UNSW Australia, Sydney, Australia
- Centre for Applied Medical Research, St. Vincent's Hospital Sydney, Sydney, Australia
- St. Vincent's Hospital Sydney, Sydney, Australia
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Increase in HSV shedding at initiation of antiretroviral therapy and decrease in shedding over time on antiretroviral therapy in HIV and HSV-2 infected persons. AIDS 2018; 32:2525-2531. [PMID: 30289810 DOI: 10.1097/qad.0000000000002002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVES HIV-infected persons with chronic herpesvirus infections may experience paradoxical worsening after initiation of antiretroviral therapy (ART), but the impact of longer term ART is unclear. We evaluated the relationships between genital herpes simplex virus (HSV) shedding and ART initiation and time on therapy in HIV and HSV-2-infected persons. DESIGN Prospective observational study. METHODS Rates of HSV shedding in 45 HIV and HSV-2-infected persons on or off ART were prospectively followed over up to three, noncontiguous, 60-day periods, during which participants performed daily genital swabs for HSV detection by real-time HSV DNA PCR and reported symptoms. Initiation or discontinuation of ART was at the discretion of participants' healthcare providers. RESULTS In all, 6425 daily genital swabs were obtained from 45 persons (38 men and seven women) during 105 swabbing sessions. During the three sessions, 67, 74, and 92% of persons were on ART. HSV was detected on 26.5% of days in men and 22.3% of days in women. The overall rates of genital HSV shedding were 19.4% of days in persons not on ART, 30.2% in persons within 90 days of ART initiation, and 23.3% in persons on ART for longer than 90 days. After initiation of ART, HSV shedding decreased by 2% per month, or 23% per year (RR 0.98/month on ART; P = 0.0003 in adjusted analysis). This finding was consistent after including consideration of HIV viral load and CD4 cell count. CONCLUSIONS HSV shedding increased significantly shortly after ART initiation, but decreased with time on prolonged ART.
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