1
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid Emergence and Evolution of SARS-CoV-2 Variants in Advanced HIV Infection. bioRxiv 2024:2024.01.05.574420. [PMID: 38313289 PMCID: PMC10836083 DOI: 10.1101/2024.01.05.574420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions1-4, but the evolutionary processes underlying these observations are incompletely understood. Here we used high-throughput, single-genome amplification and sequencing (HT-SGS) to obtain up to ~103 SARS-CoV-2 spike gene sequences in each of 184 respiratory samples from 22 people with HIV (PWH) and 25 people without HIV (PWOH). Twelve of 22 PWH had advanced HIV infection, defined by peripheral blood CD4 T cell counts (i.e., CD4 counts) <200 cells/μL. In PWOH and PWH with CD4 counts ≥200 cells/μL, most single-genome spike sequences in each person matched one haplotype that predominated throughout the infection. By contrast, people with advanced HIV showed elevated intra-host spike diversity with a median of 46 haplotypes per person (IQR 14-114). Higher intra-host spike diversity immediately after COVID-19 symptom onset predicted longer SARS-CoV-2 RNA shedding among PWH, and intra-host spike diversity at this timepoint was significantly higher in people with advanced HIV than in PWOH. Composition of spike sequence populations in people with advanced HIV fluctuated rapidly over time, with founder sequences often replaced by groups of new haplotypes. These population-level changes were associated with a high total burden of intra-host mutations and positive selection at functionally important residues. In several cases, delayed emergence of detectable serum binding to spike was associated with positive selection for presumptive antibody-escape mutations. Taken together, our findings show remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern (VOCs).
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD 21218, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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2
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Cobos Jiménez V, Geretz A, Tokarev A, Ehrenberg PK, Deletsu S, Machmach K, Mudvari P, Howard JN, Zelkoski A, Paquin-Proulx D, Del Prete GQ, Subra C, Boritz EA, Bosque A, Thomas R, Bolton DL. AP-1/c-Fos supports SIV and HIV-1 latency in CD4 T cells infected in vivo. iScience 2023; 26:108015. [PMID: 37860759 PMCID: PMC10582365 DOI: 10.1016/j.isci.2023.108015] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 09/18/2023] [Indexed: 10/21/2023] Open
Abstract
Persistent HIV-1 reservoirs of infected CD4 T cells are a major barrier to HIV-1 cure, although the mechanisms by which they are established and maintained in vivo remain poorly characterized. To elucidate host cell gene expression patterns that govern virus gene expression, we analyzed viral RNA+ (vRNA) CD4 T cells of untreated simian immunodeficiency virus (SIV)-infected macaques by single-cell RNA sequencing. A subset of vRNA+ cells distinguished by spliced and high total vRNA (7-10% of reads) expressed diminished FOS, a component of the Activator protein 1 (AP-1) transcription factor, relative to vRNA-low and -negative cells. Conversely, FOS and JUN, another AP-1 component, were upregulated in HIV DNA+ infected cells compared to uninfected cells from people with HIV-1 on suppressive therapy. Inhibiting c-Fos in latently infected primary cells augmented reactivatable HIV-1 infection. These findings implicate AP-1 in latency establishment and maintenance and as a potential therapeutic target to limit HIV-1 reservoirs.
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Affiliation(s)
- Viviana Cobos Jiménez
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Aviva Geretz
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrey Tokarev
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Philip K. Ehrenberg
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | - Kawthar Machmach
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Amanda Zelkoski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Dominic Paquin-Proulx
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory Q. Del Prete
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Caroline Subra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Rasmi Thomas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Diane L. Bolton
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
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3
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Clark IC, Mudvari P, Thaploo S, Smith S, Abu-Laban M, Hamouda M, Theberge M, Shah S, Ko SH, Pérez L, Bunis DG, Lee JS, Kilam D, Zakaria S, Choi S, Darko S, Henry AR, Wheeler MA, Hoh R, Butrus S, Deeks SG, Quintana FJ, Douek DC, Abate AR, Boritz EA. HIV silencing and cell survival signatures in infected T cell reservoirs. Nature 2023; 614:318-325. [PMID: 36599978 PMCID: PMC9908556 DOI: 10.1038/s41586-022-05556-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/11/2022] [Indexed: 01/06/2023]
Abstract
Rare CD4 T cells that contain HIV under antiretroviral therapy represent an important barrier to HIV cure1-3, but the infeasibility of isolating and characterizing these cells in their natural state has led to uncertainty about whether they possess distinctive attributes that HIV cure-directed therapies might exploit. Here we address this challenge using a microfluidic technology that isolates the transcriptomes of HIV-infected cells based solely on the detection of HIV DNA. HIV-DNA+ memory CD4 T cells in the blood from people receiving antiretroviral therapy showed inhibition of six transcriptomic pathways, including death receptor signalling, necroptosis signalling and antiproliferative Gα12/13 signalling. Moreover, two groups of genes identified by network co-expression analysis were significantly associated with HIV-DNA+ cells. These genes (n = 145) accounted for just 0.81% of the measured transcriptome and included negative regulators of HIV transcription that were higher in HIV-DNA+ cells, positive regulators of HIV transcription that were lower in HIV-DNA+ cells, and other genes involved in RNA processing, negative regulation of mRNA translation, and regulation of cell state and fate. These findings reveal that HIV-infected memory CD4 T cells under antiretroviral therapy are a distinctive population with host gene expression patterns that favour HIV silencing, cell survival and cell proliferation, with important implications for the development of HIV cure strategies.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Samuel Smith
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mohammad Abu-Laban
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mehdi Hamouda
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marc Theberge
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sakshi Shah
- Department of Bioengineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Sung Hee Ko
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel G Bunis
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - James S Lee
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Divya Kilam
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Saami Zakaria
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sally Choi
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Salwan Butrus
- Department of Chemical and Biomolecular Engineering, California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, Berkeley, CA, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California, San Francisco, San Francisco, CA, USA.
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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4
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Clark IC, Wheeler MA, Lee HG, Li Z, Sanmarco LM, Thaploo S, Polonio CM, Shin SW, Scalisi G, Henry AR, Rone JM, Giovannoni F, Charabati M, Akl CF, Aleman DM, Zandee SEJ, Prat A, Douek DC, Boritz EA, Quintana FJ, Abate AR. Identification of astrocyte regulators by nucleic acid cytometry. Nature 2023; 614:326-333. [PMID: 36599367 PMCID: PMC9980163 DOI: 10.1038/s41586-022-05613-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 11/30/2022] [Indexed: 01/06/2023]
Abstract
Multiple sclerosis is a chronic inflammatory disease of the central nervous system1. Astrocytes are heterogeneous glial cells that are resident in the central nervous system and participate in the pathogenesis of multiple sclerosis and its model experimental autoimmune encephalomyelitis2,3. However, few unique surface markers are available for the isolation of astrocyte subsets, preventing their analysis and the identification of candidate therapeutic targets; these limitations are further amplified by the rarity of pathogenic astrocytes. Here, to address these challenges, we developed focused interrogation of cells by nucleic acid detection and sequencing (FIND-seq), a high-throughput microfluidic cytometry method that combines encapsulation of cells in droplets, PCR-based detection of target nucleic acids and droplet sorting to enable in-depth transcriptomic analyses of cells of interest at single-cell resolution. We applied FIND-seq to study the regulation of astrocytes characterized by the splicing-driven activation of the transcription factor XBP1, which promotes disease pathology in multiple sclerosis and experimental autoimmune encephalomyelitis4. Using FIND-seq in combination with conditional-knockout mice, in vivo CRISPR-Cas9-driven genetic perturbation studies and bulk and single-cell RNA sequencing analyses of samples from mouse experimental autoimmune encephalomyelitis and humans with multiple sclerosis, we identified a new role for the nuclear receptor NR3C2 and its corepressor NCOR2 in limiting XBP1-driven pathogenic astrocyte responses. In summary, we used FIND-seq to identify a therapeutically targetable mechanism that limits XBP1-driven pathogenic astrocyte responses. FIND-seq enables the investigation of previously inaccessible cells, including rare cell subsets defined by unique gene expression signatures or other nucleic acid markers.
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Affiliation(s)
- Iain C Clark
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shravan Thaploo
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seung Won Shin
- Department of Bioengineering, College of Engineering, California Institute for Quantitative Biosciences, QB3, University of California Berkeley, Berkeley, CA, USA
| | - Giulia Scalisi
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amy R Henry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Marc Charabati
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Dulce M Aleman
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephanie E J Zandee
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Alexandre Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montreal, Quebec, Canada
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Eli A Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, School of Pharmacy, University of California San Francisco, San Francisco, CA, USA.
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5
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Stein SR, Ramelli SC, Grazioli A, Chung JY, Singh M, Yinda CK, Winkler CW, Sun J, Dickey JM, Ylaya K, Ko SH, Platt AP, Burbelo PD, Quezado M, Pittaluga S, Purcell M, Munster VJ, Belinky F, Ramos-Benitez MJ, Boritz EA, Lach IA, Herr DL, Rabin J, Saharia KK, Madathil RJ, Tabatabai A, Soherwardi S, McCurdy MT, Peterson KE, Cohen JI, de Wit E, Vannella KM, Hewitt SM, Kleiner DE, Chertow DS. SARS-CoV-2 infection and persistence in the human body and brain at autopsy. Nature 2022; 612:758-763. [PMID: 36517603 PMCID: PMC9749650 DOI: 10.1038/s41586-022-05542-y] [Citation(s) in RCA: 263] [Impact Index Per Article: 131.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 11/08/2022] [Indexed: 12/15/2022]
Abstract
Coronavirus disease 2019 (COVID-19) is known to cause multi-organ dysfunction1-3 during acute infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with some patients experiencing prolonged symptoms, termed post-acute sequelae of SARS-CoV-2 (refs. 4,5). However, the burden of infection outside the respiratory tract and time to viral clearance are not well characterized, particularly in the brain3,6-14. Here we carried out complete autopsies on 44 patients who died with COVID-19, with extensive sampling of the central nervous system in 11 of these patients, to map and quantify the distribution, replication and cell-type specificity of SARS-CoV-2 across the human body, including the brain, from acute infection to more than seven months following symptom onset. We show that SARS-CoV-2 is widely distributed, predominantly among patients who died with severe COVID-19, and that virus replication is present in multiple respiratory and non-respiratory tissues, including the brain, early in infection. Further, we detected persistent SARS-CoV-2 RNA in multiple anatomic sites, including throughout the brain, as late as 230 days following symptom onset in one case. Despite extensive distribution of SARS-CoV-2 RNA throughout the body, we observed little evidence of inflammation or direct viral cytopathology outside the respiratory tract. Our data indicate that in some patients SARS-CoV-2 can cause systemic infection and persist in the body for months.
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Affiliation(s)
- Sydney R. Stein
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Sabrina C. Ramelli
- grid.410305.30000 0001 2194 5650Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - Alison Grazioli
- grid.419635.c0000 0001 2203 7304Kidney Disease Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Joon-Yong Chung
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Manmeet Singh
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Claude Kwe Yinda
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Clayton W. Winkler
- grid.94365.3d0000 0001 2297 5165Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Junfeng Sun
- grid.410305.30000 0001 2194 5650Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA
| | - James M. Dickey
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Kris Ylaya
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Sung Hee Ko
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Andrew P. Platt
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Peter D. Burbelo
- grid.419633.a0000 0001 2205 0568National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD USA
| | - Martha Quezado
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Stefania Pittaluga
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Madeleine Purcell
- grid.411024.20000 0001 2175 4264University of Maryland School of Medicine, Baltimore, MD USA
| | - Vincent J. Munster
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Frida Belinky
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Marcos J. Ramos-Benitez
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA ,grid.280785.00000 0004 0533 7286Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD USA
| | - Eli A. Boritz
- grid.419681.30000 0001 2164 9667Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Izabella A. Lach
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Daniel L. Herr
- grid.411024.20000 0001 2175 4264R Adams Cowley Shock Trauma Center, Department of Medicine and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD USA
| | - Joseph Rabin
- grid.411024.20000 0001 2175 4264R Adams Cowley Shock Trauma Center, Department of Surgery and Program in Trauma, University of Maryland School of Medicine, Baltimore, MD USA
| | - Kapil K. Saharia
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Infectious Disease, University of Maryland School of Medicine, Baltimore, MD USA ,grid.411024.20000 0001 2175 4264Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ronson J. Madathil
- grid.411024.20000 0001 2175 4264Department of Surgery, Division of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD USA
| | - Ali Tabatabai
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD USA
| | - Shahabuddin Soherwardi
- grid.417209.90000 0004 0429 3816Hospitalist Department, TidalHealth Peninsula Regional, Salisbury, MD USA
| | - Michael T. McCurdy
- grid.411024.20000 0001 2175 4264Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD USA ,grid.416700.40000 0004 0440 9540Division of Critical Care Medicine, Department of Medicine, University of Maryland St. Joseph Medical Center, Towson, MD USA
| | | | - Karin E. Peterson
- grid.94365.3d0000 0001 2297 5165Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Jeffrey I. Cohen
- grid.419681.30000 0001 2164 9667Medical Virology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Emmie de Wit
- grid.94365.3d0000 0001 2297 5165Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institute of Health, Hamilton, MT USA
| | - Kevin M. Vannella
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
| | - Stephen M. Hewitt
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - David E. Kleiner
- grid.417768.b0000 0004 0483 9129Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD USA
| | - Daniel S. Chertow
- grid.410305.30000 0001 2194 5650Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD USA ,grid.419681.30000 0001 2164 9667Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD USA
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6
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Strongin Z, Hoang TN, Tharp GK, Rahmberg AR, Harper JL, Nguyen K, Franchitti L, Cervasi B, Lee M, Zhang Z, Boritz EA, Silvestri G, Marconi VC, Bosinger SE, Brenchley JM, Kulpa DA, Paiardini M. The role of CD101-expressing CD4 T cells in HIV/SIV pathogenesis and persistence. PLoS Pathog 2022; 18:e1010723. [PMID: 35867722 PMCID: PMC9348691 DOI: 10.1371/journal.ppat.1010723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 08/03/2022] [Accepted: 07/01/2022] [Indexed: 11/18/2022] Open
Abstract
Despite the advent of effective antiretroviral therapy (ART), human immunodeficiency virus (HIV) continues to pose major challenges, with extensive pathogenesis during acute and chronic infection prior to ART initiation and continued persistence in a reservoir of infected CD4 T cells during long-term ART. CD101 has recently been characterized to play an important role in CD4 Treg potency. Using the simian immunodeficiency virus (SIV) model of HIV infection in rhesus macaques, we characterized the role and kinetics of CD101+ CD4 T cells in longitudinal SIV infection. Phenotypic analyses and single-cell RNAseq profiling revealed that CD101 marked CD4 Tregs with high immunosuppressive potential, distinct from CD101- Tregs, and these cells also were ideal target cells for HIV/SIV infection, with higher expression of CCR5 and α4β7 in the gut mucosa. Notably, during acute SIV infection, CD101+ CD4 T cells were preferentially depleted across all CD4 subsets when compared with their CD101- counterpart, with a pronounced reduction within the Treg compartment, as well as significant depletion in mucosal tissue. Depletion of CD101+ CD4 was associated with increased viral burden in plasma and gut and elevated levels of inflammatory cytokines. While restored during long-term ART, the reconstituted CD101+ CD4 T cells display a phenotypic profile with high expression of inhibitory receptors (including PD-1 and CTLA-4), immunsuppressive cytokine production, and high levels of Ki-67, consistent with potential for homeostatic proliferation. Both the depletion of CD101+ cells and phenotypic profile of these cells found in the SIV model were confirmed in people with HIV on ART. Overall, these data suggest an important role for CD101-expressing CD4 T cells at all stages of HIV/SIV infection and a potential rationale for targeting CD101 to limit HIV pathogenesis and persistence, particularly at mucosal sites.
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Affiliation(s)
- Zachary Strongin
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Timothy N. Hoang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Gregory K. Tharp
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Andrew R. Rahmberg
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Justin L. Harper
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Kevin Nguyen
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Lavinia Franchitti
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Barbara Cervasi
- Flow Cytometry Core, Emory Vaccine Center, Emory University; Atlanta, Georgia, United States of America
| | - Max Lee
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Zhan Zhang
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
| | - Eli A. Boritz
- Vaccine Research Center, National Institutes of Health; Bethesda, Maryland, United States of America
| | - Guido Silvestri
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Vincent C. Marconi
- Division of Infectious Diseases, Emory University School of Medicine; Atlanta, Georgia, United States of America
- Division of Infectious Diseases Research, Atlanta Veterans Affairs Medical Center; Atlanta, Georgia, United States of America
- Rollins School of Public Health, Emory University; Atlanta, Georgia, United States of America
- Emory Vaccine Center, Atlanta, Georgia, United States of America
| | - Steven E. Bosinger
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Jason M. Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, NIAID, NIH; Bethesda, Maryland, United States of America
| | - Deanna A. Kulpa
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
| | - Mirko Paiardini
- Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University; Atlanta, Georgia, United States of America
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine; Atlanta, Georgia, United States of America
- * E-mail:
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7
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DeGrace MM, Ghedin E, Frieman MB, Krammer F, Grifoni A, Alisoltani A, Alter G, Amara RR, Baric RS, Barouch DH, Bloom JD, Bloyet LM, Bonenfant G, Boon ACM, Boritz EA, Bratt DL, Bricker TL, Brown L, Buchser WJ, Carreño JM, Cohen-Lavi L, Darling TL, Davis-Gardner ME, Dearlove BL, Di H, Dittmann M, Doria-Rose NA, Douek DC, Drosten C, Edara VV, Ellebedy A, Fabrizio TP, Ferrari G, Fischer WM, Florence WC, Fouchier RAM, Franks J, García-Sastre A, Godzik A, Gonzalez-Reiche AS, Gordon A, Haagmans BL, Halfmann PJ, Ho DD, Holbrook MR, Huang Y, James SL, Jaroszewski L, Jeevan T, Johnson RM, Jones TC, Joshi A, Kawaoka Y, Kercher L, Koopmans MPG, Korber B, Koren E, Koup RA, LeGresley EB, Lemieux JE, Liebeskind MJ, Liu Z, Livingston B, Logue JP, Luo Y, McDermott AB, McElrath MJ, Meliopoulos VA, Menachery VD, Montefiori DC, Mühlemann B, Munster VJ, Munt JE, Nair MS, Netzl A, Niewiadomska AM, O'Dell S, Pekosz A, Perlman S, Pontelli MC, Rockx B, Rolland M, Rothlauf PW, Sacharen S, Scheuermann RH, Schmidt SD, Schotsaert M, Schultz-Cherry S, Seder RA, Sedova M, Sette A, Shabman RS, Shen X, Shi PY, Shukla M, Simon V, Stumpf S, Sullivan NJ, Thackray LB, Theiler J, Thomas PG, Trifkovic S, Türeli S, Turner SA, Vakaki MA, van Bakel H, VanBlargan LA, Vincent LR, Wallace ZS, Wang L, Wang M, Wang P, Wang W, Weaver SC, Webby RJ, Weiss CD, Wentworth DE, Weston SM, Whelan SPJ, Whitener BM, Wilks SH, Xie X, Ying B, Yoon H, Zhou B, Hertz T, Smith DJ, Diamond MS, Post DJ, Suthar MS. Defining the risk of SARS-CoV-2 variants on immune protection. Nature 2022; 605:640-652. [PMID: 35361968 PMCID: PMC9345323 DOI: 10.1038/s41586-022-04690-5] [Citation(s) in RCA: 93] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/24/2022] [Indexed: 11/09/2022]
Abstract
The global emergence of many severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants jeopardizes the protective antiviral immunity induced after infection or vaccination. To address the public health threat caused by the increasing SARS-CoV-2 genomic diversity, the National Institute of Allergy and Infectious Diseases within the National Institutes of Health established the SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme. This effort was designed to provide a real-time risk assessment of SARS-CoV-2 variants that could potentially affect the transmission, virulence, and resistance to infection- and vaccine-induced immunity. The SAVE programme is a critical data-generating component of the US Government SARS-CoV-2 Interagency Group to assess implications of SARS-CoV-2 variants on diagnostics, vaccines and therapeutics, and for communicating public health risk. Here we describe the coordinated approach used to identify and curate data about emerging variants, their impact on immunity and effects on vaccine protection using animal models. We report the development of reagents, methodologies, models and notable findings facilitated by this collaborative approach and identify future challenges. This programme is a template for the response to rapidly evolving pathogens with pandemic potential by monitoring viral evolution in the human population to identify variants that could reduce the effectiveness of countermeasures.
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Affiliation(s)
- Marciela M DeGrace
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Elodie Ghedin
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Systems Genomics Section, Laboratory of Parasitic Diseases, National Institutes of Health, Rockville, MD, USA
| | - Matthew B Frieman
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Galit Alter
- Ragon Institute of MGH, MIT, and Harvard, Boston, MA, USA
| | - Rama R Amara
- Department of Microbiology and Immunology, Emory Vaccine Center, Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dan H Barouch
- Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jesse D Bloom
- Fred Hutch Cancer Center, Howard Hughes Medical Institute, Seattle, WA, USA
| | - Louis-Marie Bloyet
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Gaston Bonenfant
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Adrianus C M Boon
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Eli A Boritz
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Debbie L Bratt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- CAMRIS, Contractor for NIAID, Bethesda, MD, USA
| | - Traci L Bricker
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Liliana Brown
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - William J Buchser
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Juan Manuel Carreño
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Liel Cohen-Lavi
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Tamarand L Darling
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Meredith E Davis-Gardner
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Bethany L Dearlove
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Han Di
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meike Dittmann
- Microbiology Department, New York University Grossman School of Medicine, New York, NY, USA
| | - Nicole A Doria-Rose
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Daniel C Douek
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
| | - Venkata-Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA
| | - Ali Ellebedy
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Thomas P Fabrizio
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Guido Ferrari
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Will M Fischer
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - William C Florence
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | | | - John Franks
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adam Godzik
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Ana Silvia Gonzalez-Reiche
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Aubree Gordon
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Peter J Halfmann
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Michael R Holbrook
- National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, MD, USA
| | - Yaoxing Huang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Sarah L James
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Lukasz Jaroszewski
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Trushar Jeevan
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert M Johnson
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Terry C Jones
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Astha Joshi
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Yoshihiro Kawaoka
- Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI, USA
- Division of Virology, Department of Microbiology and Immunology, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan
| | - Lisa Kercher
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Bette Korber
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Eilay Koren
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | - Richard A Koup
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Eric B LeGresley
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Mariel J Liebeskind
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Zhuoming Liu
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Brandi Livingston
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - James P Logue
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yang Luo
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Adrian B McDermott
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | | | - Victoria A Meliopoulos
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Vineet D Menachery
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | | | - Barbara Mühlemann
- Institute of Virology, Charité-Universitätsmedizin and German Center for Infection Research (DZIF), Berlin, Germany
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Vincent J Munster
- Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, USA
| | - Jenny E Munt
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Manoj S Nair
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Antonia Netzl
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | | | - Sijy O'Dell
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Andrew Pekosz
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Marjorie C Pontelli
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Barry Rockx
- Department Viroscience, Erasmus MC, Rotterdam, The Netherlands
| | - Morgane Rolland
- US Military HIV Research Program, Henry M. Jackson Foundation for the Advancement of Military Medicine, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Paul W Rothlauf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Sinai Sacharen
- National Institute for Biotechnology in the Negev, Department of Industrial Engineering and Management, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
- The Shraga Segal Department of Microbiology and Immunology, Ben-Gurion University of the Negev, Be'er Sheva, Israel
| | | | - Stephen D Schmidt
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Michael Schotsaert
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stacey Schultz-Cherry
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Robert A Seder
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Mayya Sedova
- University of California Riverside School of Medicine, Riverside, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Reed S Shabman
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Xiaoying Shen
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Maulik Shukla
- University of Chicago Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL, USA
- Data Science and Learning Division, Argonne National Laboratory, Argonne, IL, USA
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Spencer Stumpf
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Nancy J Sullivan
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Vaccine Research Center, Bethesda, MD, USA
| | - Larissa B Thackray
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - James Theiler
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Paul G Thomas
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sanja Trifkovic
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sina Türeli
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Samuel A Turner
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Maria A Vakaki
- High Throughput Screening Center, Washington University School of Medicine, St Louis, MO, USA
| | - Harm van Bakel
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Laura A VanBlargan
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Leah R Vincent
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Zachary S Wallace
- Department of Informatics, J. Craig Venter Institute, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, CA, USA
| | - Li Wang
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maple Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Pengfei Wang
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Wei Wang
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, Institute for Human Infection and Immunity, World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
| | - Richard J Webby
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Carol D Weiss
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - David E Wentworth
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Stuart M Weston
- Center for Pathogen Research, Department of Microbiology and Immunology, The University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sean P J Whelan
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Bradley M Whitener
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Samuel H Wilks
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Baoling Ying
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA
| | - Hyejin Yoon
- Los Alamos National Laboratory, New Mexico Consortium, Los Alamos, NM, USA
| | - Bin Zhou
- CDC COVID-19 Emergency Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tomer Hertz
- Department of Microbiology, Immunology and Genetics Faculty of Health Sciences Ben-Gurion University of the Negev, Be'er Sheva, Israel.
| | - Derek J Smith
- Center for Pathogen Evolution, Department of Zoology, University of Cambridge, Cambridge, UK.
| | - Michael S Diamond
- Department of Medicine, Washington University in St Louis, St Louis, MO, USA.
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
- The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St Louis, MO, USA.
| | - Diane J Post
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
- Division of Microbiology and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Mehul S Suthar
- Center for Childhood Infections and Vaccines of Children's Healthcare of Atlanta, Department of Pediatrics, Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.
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8
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Gagne M, Corbett KS, Flynn BJ, Foulds KE, Wagner DA, Andrew SF, Todd JPM, Honeycutt CC, McCormick L, Nurmukhambetova ST, Davis-Gardner ME, Pessaint L, Bock KW, Nagata BM, Minai M, Werner AP, Moliva JI, Tucker C, Lorang CG, Zhao B, McCarthy E, Cook A, Dodson A, Teng IT, Mudvari P, Roberts-Torres J, Laboune F, Wang L, Goode A, Kar S, Boyoglu-Barnum S, Yang ES, Shi W, Ploquin A, Doria-Rose N, Carfi A, Mascola JR, Boritz EA, Edwards DK, Andersen H, Lewis MG, Suthar MS, Graham BS, Roederer M, Moore IN, Nason MC, Sullivan NJ, Douek DC, Seder RA. Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in rhesus macaques coincides with anamnestic antibody response in the lung. Cell 2022; 185:113-130.e15. [PMID: 34921774 PMCID: PMC8639396 DOI: 10.1016/j.cell.2021.12.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [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: 10/28/2021] [Revised: 11/23/2021] [Accepted: 11/30/2021] [Indexed: 01/07/2023]
Abstract
mRNA-1273 vaccine efficacy against SARS-CoV-2 Delta wanes over time; however, there are limited data on the impact of durability of immune responses on protection. Here, we immunized rhesus macaques and assessed immune responses over 1 year in blood and upper and lower airways. Serum neutralizing titers to Delta were 280 and 34 reciprocal ID50 at weeks 6 (peak) and 48 (challenge), respectively. Antibody-binding titers also decreased in bronchoalveolar lavage (BAL). Four days after Delta challenge, the virus was unculturable in BAL, and subgenomic RNA declined by ∼3-log10 compared with control animals. In nasal swabs, sgRNA was reduced by 1-log10, and the virus remained culturable. Anamnestic antibodies (590-fold increased titer) but not T cell responses were detected in BAL by day 4 post-challenge. mRNA-1273-mediated protection in the lungs is durable but delayed and potentially dependent on anamnestic antibody responses. Rapid and sustained protection in upper and lower airways may eventually require a boost.
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Affiliation(s)
- Matthew Gagne
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kizzmekia S. Corbett
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Barbara J. Flynn
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kathryn E. Foulds
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle A. Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shayne F. Andrew
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John-Paul M. Todd
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher Cole Honeycutt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lauren McCormick
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saule T. Nurmukhambetova
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Meredith E. Davis-Gardner
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Kevin W. Bock
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Bianca M. Nagata
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Mahnaz Minai
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Anne P. Werner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Juan I. Moliva
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Courtney Tucker
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cynthia G. Lorang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bingchun Zhao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth McCarthy
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - I-Ting Teng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesmine Roberts-Torres
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Farida Laboune
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lingshu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Seyhan Boyoglu-Barnum
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eun Sung Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wei Shi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aurélie Ploquin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - John R. Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | | | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Barney S. Graham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mario Roederer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian N. Moore
- Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20892, USA
| | - Martha C. Nason
- Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel C. Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
| | - Robert A. Seder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA,Corresponding author
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9
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Wuertz KM, Barkei EK, Chen WH, Martinez EJ, Lakhal-Naouar I, Jagodzinski LL, Paquin-Proulx D, Gromowski GD, Swafford I, Ganesh A, Dong M, Zeng X, Thomas PV, Sankhala RS, Hajduczki A, Peterson CE, Kuklis C, Soman S, Wieczorek L, Zemil M, Anderson A, Darden J, Hernandez H, Grove H, Dussupt V, Hack H, de la Barrera R, Zarling S, Wood JF, Froude JW, Gagne M, Henry AR, Mokhtari EB, Mudvari P, Krebs SJ, Pekosz AS, Currier JR, Kar S, Porto M, Winn A, Radzyminski K, Lewis MG, Vasan S, Suthar M, Polonis VR, Matyas GR, Boritz EA, Douek DC, Seder RA, Daye SP, Rao M, Peel SA, Joyce MG, Bolton DL, Michael NL, Modjarrad K. A SARS-CoV-2 spike ferritin nanoparticle vaccine protects hamsters against Alpha and Beta virus variant challenge. NPJ Vaccines 2021; 6:129. [PMID: 34711815 PMCID: PMC8553838 DOI: 10.1038/s41541-021-00392-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a SARS-CoV-2 spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the Alpha (B.1.1.7), and Beta (B.1.351) VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 μg) or low (0.2 μg) dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose vaccinations. Dose-dependent SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.
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Affiliation(s)
- Kathryn McGuckin Wuertz
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Erica K Barkei
- Veterinary Pathology Division, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Elizabeth J Martinez
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Ines Lakhal-Naouar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Linda L Jagodzinski
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Gregory D Gromowski
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Isabella Swafford
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Akshaya Ganesh
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Oak Ridge Institute of Science and Education, Oak Ridge, TN, USA
| | - Ming Dong
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, MD, USA
| | - Paul V Thomas
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Rajeshwer S Sankhala
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caroline E Peterson
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Caitlin Kuklis
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sandrine Soman
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Alexander Anderson
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Oak Ridge Institute of Science and Education, Oak Ridge, TN, USA
| | - Janice Darden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Heather Hernandez
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Hannah Grove
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Holly Hack
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Rafael de la Barrera
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Stasya Zarling
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - James F Wood
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jeffrey W Froude
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Matthew Gagne
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Elham Bayat Mokhtari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shelly J Krebs
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Andrew S Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jeffrey R Currier
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | | | | | | | | | | | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Mehul Suthar
- Emory Vaccine Center, Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Gary R Matyas
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Robert A Seder
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sharon P Daye
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheila A Peel
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - M Gordon Joyce
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Diane L Bolton
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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10
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Gagne M, Corbett KS, Flynn BJ, Foulds KE, Wagner DA, Andrew SF, Todd JPM, Honeycutt CC, McCormick L, Nurmukhambetova ST, Davis-Gardner ME, Pessaint L, Bock KW, Nagata BM, Minai M, Werner AP, Moliva JI, Tucker C, Lorang CG, Zhao B, McCarthy E, Cook A, Dodson A, Mudvari P, Roberts-Torres J, Laboune F, Wang L, Goode A, Kar S, Boyoglu-Barnum S, Yang ES, Shi W, Ploquin A, Doria-Rose N, Carfi A, Mascola JR, Boritz EA, Edwards DK, Andersen H, Lewis MG, Suthar MS, Graham BS, Roederer M, Moore IN, Nason MC, Sullivan NJ, Douek DC, Seder RA. Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway. bioRxiv 2021. [PMID: 34729558 DOI: 10.1101/2021.10.23.465542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
mRNA-1273 vaccine efficacy against SARS-CoV-2 Delta wanes over time; however, there are limited data on the impact of durability of immune responses on protection. We immunized rhesus macaques at weeks 0 and 4 and assessed immune responses over one year in blood, upper and lower airways. Serum neutralizing titers to Delta were 280 and 34 reciprocal ID 50 at weeks 6 (peak) and 48 (challenge), respectively. Antibody binding titers also decreased in bronchoalveolar lavage (BAL). Four days after challenge, virus was unculturable in BAL and subgenomic RNA declined ∼3-log 10 compared to control animals. In nasal swabs, sgRNA declined 1-log 10 and virus remained culturable. Anamnestic antibody responses (590-fold increase) but not T cell responses were detected in BAL by day 4 post-challenge. mRNA-1273-mediated protection in the lungs is durable but delayed and potentially dependent on anamnestic antibody responses. Rapid and sustained protection in upper and lower airways may eventually require a boost.
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11
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Wuertz KM, Barkei EK, Chen WH, Martinez EJ, Lakhal-Naouar I, Jagodzinski LL, Paquin-Proulx D, Gromowski GD, Swafford I, Ganesh A, Dong M, Zeng X, Thomas PV, Sankhala RS, Hajduczki A, Peterson CE, Kuklis C, Soman S, Wieczorek L, Zemil M, Anderson A, Darden J, Hernandez H, Grove H, Dussupt V, Hack H, de la Barrera R, Zarling S, Wood JF, Froude JW, Gagne M, Henry AR, Mokhtari EB, Mudvari P, Krebs SJ, Pekosz AS, Currier JR, Kar S, Porto M, Winn A, Radzyminski K, Lewis MG, Vasan S, Suthar M, Polonis VR, Matyas GR, Boritz EA, Douek DC, Seder RA, Daye SP, Rao M, Peel SA, Joyce MG, Bolton DL, Michael NL, Modjarrad K. A SARS-CoV-2 spike ferritin nanoparticle vaccine protects against heterologous challenge with B.1.1.7 and B.1.351 virus variants in Syrian golden hamsters. bioRxiv 2021:2021.06.16.448525. [PMID: 34159328 PMCID: PMC8219092 DOI: 10.1101/2021.06.16.448525] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The emergence of SARS-CoV-2 variants of concern (VOC) requires adequate coverage of vaccine protection. We evaluated whether a spike ferritin nanoparticle vaccine (SpFN), adjuvanted with the Army Liposomal Formulation QS21 (ALFQ), conferred protection against the B.1.1.7 and B.1.351 VOCs in Syrian golden hamsters. SpFN-ALFQ was administered as either single or double-vaccination (0 and 4 week) regimens, using a high (10 μg) or low (0.2 μg) immunogen dose. Animals were intranasally challenged at week 11. Binding antibody responses were comparable between high- and low-dose groups. Neutralizing antibody titers were equivalent against WA1, B.1.1.7, and B.1.351 variants following two high dose two vaccinations. SpFN-ALFQ vaccination protected against SARS-CoV-2-induced disease and viral replication following intranasal B.1.1.7 or B.1.351 challenge, as evidenced by reduced weight loss, lung pathology, and lung and nasal turbinate viral burden. These data support the development of SpFN-ALFQ as a broadly protective, next-generation SARS-CoV-2 vaccine.
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Affiliation(s)
- Kathryn McGuckin Wuertz
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Erica K. Barkei
- Veterinary Pathology Division, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Wei-Hung Chen
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Elizabeth J. Martinez
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Ines Lakhal-Naouar
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Linda L. Jagodzinski
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Dominic Paquin-Proulx
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Gregory D. Gromowski
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Isabella Swafford
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Akshaya Ganesh
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Oak Ridge Institute of Science and Education, Oak Ridge, Tennessee USA
| | - Ming Dong
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Xiankun Zeng
- Pathology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland USA
| | - Paul V. Thomas
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Rajeshwer S. Sankhala
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Agnes Hajduczki
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Caroline E. Peterson
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Caitlin Kuklis
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Sandrine Soman
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Lindsay Wieczorek
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Michelle Zemil
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Alexander Anderson
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Oak Ridge Institute of Science and Education, Oak Ridge, Tennessee USA
| | - Janice Darden
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Heather Hernandez
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Hannah Grove
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Vincent Dussupt
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Holly Hack
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Rafael de la Barrera
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Stasya Zarling
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - James F. Wood
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Jeffrey W. Froude
- Pilot Bioproduction Facility, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Matthew Gagne
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Amy R. Henry
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Elham Bayat Mokhtari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Prakriti Mudvari
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Shelly J. Krebs
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Andrew S. Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland USA
| | - Jeffrey R. Currier
- Virus Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | | | | | | | | | | | - Sandhya Vasan
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
| | - Mehul Suthar
- Emory Vaccine Center, Department of Pediatrics, Emory School of Medicine, Atlanta, Georgia USA
| | - Victoria R. Polonis
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Gary R. Matyas
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Eli A. Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Daniel C. Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Robert A. Seder
- Cellular Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland USA
| | - Sharon P. Daye
- One Health Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Mangala Rao
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - Sheila A. Peel
- Diagnostics Countermeasures Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
| | - M. Gordon Joyce
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- These authors contributed equally
| | - Diane L. Bolton
- U.S. Military HIV Research Program, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland USA
- These authors contributed equally
| | - Nelson L. Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- These authors contributed equally
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, Maryland USA
- These authors contributed equally
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12
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Ko SH, Bayat Mokhtari E, Mudvari P, Stein S, Stringham CD, Wagner D, Ramelli S, Ramos-Benitez MJ, Strich JR, Davey RT, Zhou T, Misasi J, Kwong PD, Chertow DS, Sullivan NJ, Boritz EA. High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19. PLoS Pathog 2021; 17:e1009431. [PMID: 33831133 PMCID: PMC8031304 DOI: 10.1371/journal.ppat.1009431] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/28/2021] [Indexed: 12/23/2022] Open
Abstract
Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH2-terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Elham Bayat Mokhtari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
| | - Marcos J. Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jeffrey R. Strich
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
| | - Richard T. Davey
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, Maryland, United States of America
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
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13
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Ko SH, Mokhtari EB, Mudvari P, Stein S, Stringham CD, Wagner D, Ramelli S, Ramos-Benitez MJ, Strich JR, Davey RT, Zhou T, Misasi J, Kwong PD, Chertow DS, Sullivan NJ, Boritz EA. High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19. bioRxiv 2021:2021.02.21.432184. [PMID: 33655255 PMCID: PMC7924285 DOI: 10.1101/2021.02.21.432184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH 2 -terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting. AUTHOR SUMMARY Mutant sequences of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) arising during any individual case of coronavirus disease 2019 (COVID-19) could theoretically enable the virus to evade immune responses or antiviral therapies that target the predominant infecting virus sequence. However, commonly used sequencing technologies are not optimally designed to detect variant virus sequences within each sample. To address this issue, we developed novel technology for sequencing large numbers of individual SARS-CoV-2 genomic RNA molecules across the region encoding the virus surface proteins. This technology revealed extensive genetic diversity in cultured viruses from a clinical isolate of SARS-CoV-2, but lower diversity in samples from 7 individuals with COVID-19. Importantly, concurrent analysis of paired serum samples in selected individuals revealed relatively low levels of antibody binding to the SARS-CoV-2 spike protein at the time of initial sequencing. With increased serum binding to spike protein, we detected multiple SARS-CoV-2 variants bearing independent mutations in a single epitope, as well as a transient increase in virus burden. These findings suggest that SARS-CoV-2 replication creates sufficient virus genetic diversity to allow immune-mediated selection of variants within the time frame of acute COVID-19. Large-scale studies of SARS-CoV-2 variation and specific immune responses will help define the contributions of intra-individual SARS-CoV-2 evolution to COVID-19 clinical outcomes and antiviral drug susceptibility.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elham Bayat Mokhtari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Prakriti Mudvari
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christopher D. Stringham
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danielle Wagner
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sabrina Ramelli
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Marcos J. Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jeffrey R. Strich
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
| | - Richard T. Davey
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - John Misasi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D. Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel S. Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, National Institutes of Health Clinical Center, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nancy J. Sullivan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eli A. Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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14
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Shen CH, DeKosky BJ, Guo Y, Xu K, Gu Y, Kilam D, Ko SH, Kong R, Liu K, Louder MK, Ou L, Zhang B, Chao CW, Corcoran MM, Feng E, Huang J, Normandin E, O'Dell S, Ransier A, Rawi R, Sastry M, Schmidt SD, Wang S, Wang Y, Chuang GY, Doria-Rose NA, Lin B, Zhou T, Boritz EA, Connors M, Douek DC, Karlsson Hedestam GB, Sheng Z, Shapiro L, Mascola JR, Kwong PD. VRC34-Antibody Lineage Development Reveals How a Required Rare Mutation Shapes the Maturation of a Broad HIV-Neutralizing Lineage. Cell Host Microbe 2020; 27:531-543.e6. [PMID: 32130953 PMCID: PMC7467872 DOI: 10.1016/j.chom.2020.01.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 10/29/2019] [Revised: 12/31/2019] [Accepted: 01/30/2020] [Indexed: 01/07/2023]
Abstract
Rare mutations have been proposed to restrict the development of broadly neutralizing antibodies against HIV-1, but this has not been explicitly demonstrated. We hypothesized that such rare mutations might be identified by comparing broadly neutralizing and non-broadly neutralizing branches of an antibody-developmental tree. Because sequences of antibodies isolated from the fusion peptide (FP)-targeting VRC34-antibody lineage suggested it might be suitable for such rare mutation analysis, we carried out next-generation sequencing (NGS) on B cell transcripts from donor N123, the source of the VRC34 lineage, and functionally and structurally characterized inferred intermediates along broadly neutralizing and poorly neutralizing developmental branches. The broadly neutralizing VRC34.01 branch required the rare heavy-chain mutation Y33P to bind FP, whereas the early bifurcated VRC34.05 branch did not require this rare mutation and evolved less breadth. Our results demonstrate how a required rare mutation can restrict development and shape the maturation of a broad HIV-1-neutralizing antibody lineage.
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Affiliation(s)
- Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Brandon J DeKosky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Chemical & Petroleum Engineering and Department of Pharmaceutical Chemistry, The University of Kansas, Lawrence, KS 66045, USA
| | - Yicheng Guo
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Kai Xu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ying Gu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Divya Kilam
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Liu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Li Ou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cara W Chao
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Martin M Corcoran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Eric Feng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jesse Huang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Normandin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amy Ransier
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mallika Sastry
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen D Schmidt
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shuishu Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yiran Wang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole A Doria-Rose
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bob Lin
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eli A Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Connors
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda MD 20892, USA
| | - Daniel C Douek
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Zizhang Sheng
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA; Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
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15
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Pérez L, Anderson J, Chipman J, Thorkelson A, Chun TW, Moir S, Haase AT, Douek DC, Schacker TW, Boritz EA. Conflicting evidence for HIV enrichment in CD32 + CD4 T cells. Nature 2018; 561:E9-E16. [PMID: 30232423 DOI: 10.1038/s41586-018-0493-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 03/20/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Liliana Pérez
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jodi Anderson
- Division of Infectious Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey Chipman
- Department of Surgery, University of Minnesota, Minneapolis, MN, USA
| | - Ann Thorkelson
- Division of Infectious Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Tae-Wook Chun
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Susan Moir
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, USA
| | - Ashley T Haase
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy W Schacker
- Division of Infectious Diseases, University of Minnesota, Minneapolis, MN, USA
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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16
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Hiener B, Horsburgh BA, Eden JS, Barton K, Schlub TE, Lee E, von Stockenstrom S, Odevall L, Milush JM, Liegler T, Sinclair E, Hoh R, Boritz EA, Douek D, Fromentin R, Chomont N, Deeks SG, Hecht FM, Palmer S. Identification of Genetically Intact HIV-1 Proviruses in Specific CD4 + T Cells from Effectively Treated Participants. Cell Rep 2018; 21:813-822. [PMID: 29045846 DOI: 10.1016/j.celrep.2017.09.081] [Citation(s) in RCA: 270] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 09/01/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023] Open
Abstract
Latent replication-competent HIV-1 persists in individuals on long-term antiretroviral therapy (ART). We developed the Full-Length Individual Proviral Sequencing (FLIPS) assay to determine the distribution of latent replication-competent HIV-1 within memory CD4+ T cell subsets in six individuals on long-term ART. FLIPS is an efficient, high-throughput assay that amplifies and sequences near full-length (∼9 kb) HIV-1 proviral genomes and determines potential replication competency through genetic characterization. FLIPS provides a genome-scale perspective that addresses the limitations of other methods that also genetically characterize the latent reservoir. Using FLIPS, we identified 5% of proviruses as intact and potentially replication competent. Intact proviruses were unequally distributed between T cell subsets, with effector memory cells containing the largest proportion of genetically intact HIV-1 proviruses. We identified multiple identical intact proviruses, suggesting a role for cellular proliferation in the maintenance of the latent HIV-1 reservoir.
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Affiliation(s)
- Bonnie Hiener
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia.
| | - Bethany A Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia
| | - John-Sebastian Eden
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Kirston Barton
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia
| | - Timothy E Schlub
- Sydney School of Public Health, Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia
| | - Susanne von Stockenstrom
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 77, Sweden
| | - Lina Odevall
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska University Hospital, Stockholm 171 77, Sweden
| | - Jeffrey M Milush
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Teri Liegler
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Elizabeth Sinclair
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Eli A Boritz
- Virus Persistence and Dynamics Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD 20814, USA
| | - Daniel Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Disease, NIH, Bethesda, MD 20814, USA
| | - Rémi Fromentin
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Nicolas Chomont
- Centre de Recherche du CHUM and Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Frederick M Hecht
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, The University of Sydney, Sydney, NSW 2145, Australia
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17
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Abstract
The uneven anatomic distribution of cell subsets that harbor human immunodeficiency virus (HIV) during antiretroviral therapy (ART) complicates investigation of the barriers to HIV cure. Here we propose that while previous studies done largely in blood cells have led to important investigations into HIV latency, other important mechanisms of HIV persistence during ART may not be readily apparent in the bloodstream. We specifically consider as an example the question of ongoing HIV replication during ART. We discuss how growing understanding of key anatomic sanctuaries for the virus can inform future experiments aimed at further clarifying this issue.
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Affiliation(s)
- Eli A Boritz
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
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18
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Boritz EA, Darko S, Swaszek L, Wolf G, Wells D, Wu X, Henry AR, Laboune F, Hu J, Ambrozak D, Hughes MS, Hoh R, Casazza JP, Vostal A, Bunis D, Nganou-Makamdop K, Lee JS, Migueles SA, Koup RA, Connors M, Moir S, Schacker T, Maldarelli F, Hughes SH, Deeks SG, Douek DC. Multiple Origins of Virus Persistence during Natural Control of HIV Infection. Cell 2016; 166:1004-1015. [PMID: 27453467 DOI: 10.1016/j.cell.2016.06.039] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/09/2016] [Accepted: 06/20/2016] [Indexed: 10/21/2022]
Abstract
Targeted HIV cure strategies require definition of the mechanisms that maintain the virus. Here, we tracked HIV replication and the persistence of infected CD4 T cells in individuals with natural virologic control by sequencing viruses, T cell receptor genes, HIV integration sites, and cellular transcriptomes. Our results revealed three mechanisms of HIV persistence operating within distinct anatomic and functional compartments. In lymph node, we detected viruses with genetic and transcriptional attributes of active replication in both T follicular helper (TFH) cells and non-TFH memory cells. In blood, we detected inducible proviruses of archival origin among highly differentiated, clonally expanded cells. Linking the lymph node and blood was a small population of circulating cells harboring inducible proviruses of recent origin. Thus, HIV replication in lymphoid tissue, clonal expansion of infected cells, and recirculation of recently infected cells act together to maintain the virus in HIV controllers despite effective antiviral immunity.
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Affiliation(s)
- Eli A Boritz
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Samuel Darko
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Luke Swaszek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Gideon Wolf
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - David Wells
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Xiaolin Wu
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Amy R Henry
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Farida Laboune
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Jianfei Hu
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - David Ambrozak
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Marybeth S Hughes
- Thoracic and Gastrointestinal Oncology Branch, NCI, NIH, Bethesda, MD 20892, USA
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Joseph P Casazza
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Alexander Vostal
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Daniel Bunis
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - James S Lee
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Richard A Koup
- Immunology Laboratory, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA
| | - Mark Connors
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Susan Moir
- Laboratory of Immunoregulation, NIAID, NIH, Bethesda, MD 20892, USA
| | - Timothy Schacker
- Program in HIV Medicine, Department of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
| | - Frank Maldarelli
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
| | - Stephen H Hughes
- HIV Dynamics and Replication Program, NCI, NIH, Frederick, MD 21702, USA
| | - Steven G Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94110, USA
| | - Daniel C Douek
- Human Immunology Section, Vaccine Research Center, NIAID, NIH, Bethesda, MD 20892, USA.
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