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Krause R, Snyman J, Shi-Hsia H, Muema D, Karim F, Ganga Y, Ngoepe A, Zungu Y, Gazy I, Bernstein M, Khan K, Mazibuko M, Mthabela N, Ramjit D, Limbo O, Jardine J, Sok D, Wilson IA, Hanekom W, Sigal A, Kløverpris H, Ndung'u T, Leslie A. HIV skews the SARS-CoV-2 B cell response toward an extrafollicular maturation pathway. eLife 2022; 11:79924. [PMID: 36300787 PMCID: PMC9643005 DOI: 10.7554/elife.79924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/23/2022] [Indexed: 11/29/2022] Open
Abstract
Background: HIV infection dysregulates the B cell compartment, affecting memory B cell formation and the antibody response to infection and vaccination. Understanding the B cell response to SARS-CoV-2 in people living with HIV (PLWH) may explain the increased morbidity, reduced vaccine efficacy, reduced clearance, and intra-host evolution of SARS-CoV-2 observed in some HIV-1 coinfections. Methods: We compared B cell responses to COVID-19 in PLWH and HIV negative (HIV-ve) patients in a cohort recruited in Durban, South Africa, during the first pandemic wave in July 2020 using detailed flow cytometry phenotyping of longitudinal samples with markers of B cell maturation, homing, and regulatory features. Results: This revealed a coordinated B cell response to COVID-19 that differed significantly between HIV-ve and PLWH. Memory B cells in PLWH displayed evidence of reduced germinal centre (GC) activity, homing capacity, and class-switching responses, with increased PD-L1 expression, and decreased Tfh frequency. This was mirrored by increased extrafollicular (EF) activity, with dynamic changes in activated double negative (DN2) and activated naïve B cells, which correlated with anti-RBD-titres in these individuals. An elevated SARS-CoV-2-specific EF response in PLWH was confirmed using viral spike and RBD bait proteins. Conclusions: Despite similar disease severity, these trends were highest in participants with uncontrolled HIV, implicating HIV in driving these changes. EF B cell responses are rapid but give rise to lower affinity antibodies, less durable long-term memory, and reduced capacity to adapt to new variants. Further work is needed to determine the long-term effects of HIV on SARS-CoV-2 immunity, particularly as new variants emerge. Funding: This work was supported by a grant from the Wellcome Trust to the Africa Health Research Institute (Wellcome Trust Strategic Core Award [grant number 201433/Z/16/Z]). Additional funding was received from the South African Department of Science and Innovation through the National Research Foundation (South African Research Chairs Initiative [grant number 64809]), and the Victor Daitz Foundation.
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Affiliation(s)
| | | | | | | | - Farina Karim
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal
| | | | | | | | - Inbal Gazy
- KwaZulu-Natal Research Innovation and Sequencing Platform, University of KwaZulu-Natal
| | | | | | | | | | | | | | | | - Devin Sok
- International AIDS Vaccine Initiative
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2
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Asowata OE, Singh A, Ngoepe A, Herbert N, Fardoos R, Reddy K, Zungu Y, Nene F, Mthabela N, Ramjit D, Karim F, Govender K, Ndung'u T, Porterfield JZ, Adamson JH, Madela FG, Manzini VT, Anderson F, Leslie A, Kløverpris HN. Irreversible depletion of intestinal CD4+ T cells is associated with T cell activation during chronic HIV infection. JCI Insight 2021; 6:146162. [PMID: 34618690 PMCID: PMC8663780 DOI: 10.1172/jci.insight.146162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 11/17/2020] [Accepted: 10/06/2021] [Indexed: 01/04/2023] Open
Abstract
HIV infection in the human gastrointestinal (GI) tract is thought to be central to HIV progression, but knowledge of this interaction is primarily limited to cohorts within Westernized countries. Here, we present a large cohort recruited from high HIV endemic areas in South Africa and found that people living with HIV (PLWH) presented at a younger age for investigation in the GI clinic. We identified severe CD4+ T cell depletion in the GI tract, which was greater in the small intestine than in the large intestine and not correlated with years on antiretroviral treatment (ART) or plasma viremia. HIV-p24 staining showed persistent viral expression, particularly in the colon, despite full suppression of plasma viremia. Quantification of mucosal antiretroviral (ARV) drugs revealed no differences in drug penetration between the duodenum and colon. Plasma markers of gut barrier breakdown and immune activation were elevated irrespective of HIV, but peripheral T cell activation was inversely correlated with loss of gut CD4+ T cells in PLWH alone. T cell activation is a strong predictor of HIV progression and independent of plasma viral load, implying that the irreversible loss of GI CD4+ T cells is a key event in the HIV pathogenesis of PLWH in South Africa, yet the underlying mechanisms remain unknown.
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Affiliation(s)
- Osaretin E Asowata
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Alveera Singh
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Abigail Ngoepe
- Africa Health Research Institute (AHRI), Durban, South Africa
| | | | - Rabiah Fardoos
- Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Kavidha Reddy
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Yenzekile Zungu
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Faith Nene
- Africa Health Research Institute (AHRI), Durban, South Africa
| | | | - Dirhona Ramjit
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Katya Govender
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Thumbi Ndung'u
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,University College London, Division of Infection and Immunity, London, United Kingdom.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - J Zachary Porterfield
- Africa Health Research Institute (AHRI), Durban, South Africa.,Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky, USA
| | - John H Adamson
- Africa Health Research Institute (AHRI), Durban, South Africa
| | - Fusi G Madela
- Division Upper Gastrointestinal Tract and Colorectal Surgery, Inkosi Albert Luthuli Central Hospital (IALCH), University of KwaZulu-Natal, Durban, South Africa
| | - Vukani T Manzini
- Division Upper Gastrointestinal Tract and Colorectal Surgery, Inkosi Albert Luthuli Central Hospital (IALCH), University of KwaZulu-Natal, Durban, South Africa
| | - Frank Anderson
- Division Upper Gastrointestinal Tract and Colorectal Surgery, Inkosi Albert Luthuli Central Hospital (IALCH), University of KwaZulu-Natal, Durban, South Africa
| | - Alasdair Leslie
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,University College London, Division of Infection and Immunity, London, United Kingdom
| | - Henrik N Kløverpris
- Africa Health Research Institute (AHRI), Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Immunology and Microbiology, University of Copenhagen, Denmark.,University College London, Division of Infection and Immunity, London, United Kingdom
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3
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Karim F, Gazy I, Cele S, Zungu Y, Krause R, Bernstein M, Khan K, Ganga Y, Rodel H, Mthabela N, Mazibuko M, Muema D, Ramjit D, Ndung'u T, Hanekom W, Gosnell B, Lessells RJ, Wong EB, de Oliveira T, Moosa MYS, Lustig G, Leslie A, Kløverpris H, Sigal A. HIV status alters disease severity and immune cell responses in Beta variant SARS-CoV-2 infection wave. eLife 2021; 10:e67397. [PMID: 34608862 PMCID: PMC8676326 DOI: 10.7554/elife.67397] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/07/2021] [Indexed: 01/08/2023] Open
Abstract
There are conflicting reports on the effects of HIV on COVID-19. Here, we analyzed disease severity and immune cell changes during and after SARS-CoV-2 infection in 236 participants from South Africa, of which 39% were people living with HIV (PLWH), during the first and second (Beta dominated) infection waves. The second wave had more PLWH requiring supplemental oxygen relative to HIV-negative participants. Higher disease severity was associated with low CD4 T cell counts and higher neutrophil to lymphocyte ratios (NLR). Yet, CD4 counts recovered and NLR stabilized after SARS-CoV-2 clearance in wave 2 infected PLWH, arguing for an interaction between SARS-CoV-2 and HIV infection leading to low CD4 and high NLR. The first infection wave, where severity in HIV negative and PLWH was similar, still showed some HIV modulation of SARS-CoV-2 immune responses. Therefore, HIV infection can synergize with the SARS-CoV-2 variant to change COVID-19 outcomes.
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Affiliation(s)
- Farina Karim
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | - Inbal Gazy
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
| | - Sandile Cele
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Robert Krause
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Khadija Khan
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Hylton Rodel
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | | | - Daniel Muema
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
| | | | - Thumbi Ndung'u
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-NatalDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
| | - Willem Hanekom
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Bernadett Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalDurbanSouth Africa
| | - Richard J Lessells
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
| | - Emily B Wong
- Africa Health Research InstituteDurbanSouth Africa
- Division of Infectious Diseases, Department of Medicine, University of Alabama at BirminghamBirminghamUnited States
| | - Tulio de Oliveira
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- KwaZulu-Natal Research Innovation and Sequencing PlatformDurbanSouth Africa
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch UniversityStellenboschSouth Africa
- Department of Global Health, University of WashingtonSeattleUnited States
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-NatalDurbanSouth Africa
| | - Gil Lustig
- Centre for the AIDS Programme of Research in South AfricaDurbanSouth Africa
| | - Alasdair Leslie
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Henrik Kløverpris
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
- Department of Immunology and Microbiology, University of CopenhagenCopenhagenDenmark
| | - Alex Sigal
- Africa Health Research InstituteDurbanSouth Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-NatalDurbanSouth Africa
- Max Planck Institute for Infection BiologyBerlinGermany
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4
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Fardoos R, Asowata OE, Herbert N, Nyquist SK, Zungu Y, Singh A, Ngoepe A, Mbano IM, Mthabela N, Ramjit D, Karim F, Kuhn W, Madela FG, Manzini VT, Anderson F, Berger B, Pers TH, Shalek AK, Leslie A, Kløverpris HN. HIV infection drives interferon signaling within intestinal SARS-CoV-2 target cells. JCI Insight 2021; 6:e148920. [PMID: 34252054 PMCID: PMC8409978 DOI: 10.1172/jci.insight.148920] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 12/17/2022] Open
Abstract
SARS-CoV-2 infects epithelial cells of the human gastrointestinal (GI) tract and causes related symptoms. HIV infection impairs gut homeostasis and is associated with an increased risk of COVID-19 fatality. To investigate the potential link between these observations, we analyzed single-cell transcriptional profiles and SARS-CoV-2 entry receptor expression across lymphoid and mucosal human tissue from chronically HIV-infected individuals and uninfected controls. Absorptive gut enterocytes displayed the highest coexpression of SARS-CoV-2 receptors ACE2, TMPRSS2, and TMPRSS4, of which ACE2 expression was associated with canonical interferon response and antiviral genes. Chronic treated HIV infection was associated with a clear antiviral response in gut enterocytes and, unexpectedly, with a substantial reduction of ACE2 and TMPRSS2 target cells. Gut tissue from SARS-CoV-2–infected individuals, however, showed abundant SARS-CoV-2 nucleocapsid protein in both the large and small intestine, including an HIV-coinfected individual. Thus, upregulation of antiviral response genes and downregulation of ACE2 and TMPRSS2 in the GI tract of HIV-infected individuals does not prevent SARS-CoV-2 infection in this compartment. The impact of these HIV-associated intestinal mucosal changes on SARS-CoV-2 infection dynamics, disease severity, and vaccine responses remains unclear and requires further investigation.
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Affiliation(s)
- Rabiah Fardoos
- Africa Health Research Institute, Durban, South Africa.,Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Osaretin E Asowata
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nicholas Herbert
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sarah K Nyquist
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA.,Program in Computational and Systems Biology, MIT, Cambridge, Massachusetts, USA
| | - Yenzekile Zungu
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Alveera Singh
- Africa Health Research Institute, Durban, South Africa
| | | | - Ian M Mbano
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
| | - Warren Kuhn
- ENT Department, General Justice Gizenga Mpanza Regional Hospital (Stanger Hospital), University of KwaZulu-Natal, Durban, South Africa
| | - Fusi G Madela
- Discipline of General Surgery, Inkosi Albert Luthuli Central Hospital, University of KwaZulu-Natal, Durban, South Africa
| | - Vukani T Manzini
- Discipline of General Surgery, Inkosi Albert Luthuli Central Hospital, University of KwaZulu-Natal, Durban, South Africa
| | - Frank Anderson
- Discipline of General Surgery, Inkosi Albert Luthuli Central Hospital, University of KwaZulu-Natal, Durban, South Africa
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory and Department of Mathematics, MIT, Cambridge, Massachusetts, USA
| | - Tune H Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alex K Shalek
- Institute for Medical Engineering & Science, Department of Chemistry, and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Ragon Institute of MGH, MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alasdair Leslie
- Africa Health Research Institute, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Division of Infection and Immunity, University College London, London, United Kingdom
| | - Henrik N Kløverpris
- Africa Health Research Institute, Durban, South Africa.,Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.,Division of Infection and Immunity, University College London, London, United Kingdom
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