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Tovanabutra S, Sirijatuphat R, Pham PT, Bonar L, Harbolick EA, Bose M, Song H, Chang D, Oropeza C, O'Sullivan AM, Balinang J, Kroon E, Colby DJ, Sacdalan C, Hellmuth J, Chan P, Prueksakaew P, Pinyakorn S, Jagodzinski LL, Sutthichom D, Pattamaswin S, de Souza M, Gramzinski RA, Kim JH, Michael NL, Robb ML, Phanuphak N, Ananworanich J, Valcour V, Kijak GH, Sanders-Buell E, Spudich S. Deep Sequencing Reveals Central Nervous System Compartmentalization in Multiple Transmitted/Founder Virus Acute HIV-1 Infection. Cells 2019; 8:E902. [PMID: 31443253 PMCID: PMC6721674 DOI: 10.3390/cells8080902] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/10/2019] [Accepted: 08/11/2019] [Indexed: 01/31/2023] Open
Abstract
HIV-1 disseminates to a broad range of tissue compartments during acute HIV-1 infection (AHI). The central nervous system (CNS) can serve as an early and persistent site of viral replication, which poses a potential challenge for HIV-1 remission strategies that target the HIV reservoir. CNS compartmentalization is a key feature of HIV-1 neuropathogenesis. Thus far, the timing of how early CNS compartmentalization develops after infection is unknown. We examined whether HIV-1 transmitted/founder (T/F) viruses differ between CNS and blood during AHI using single-genome sequencing of envelope gene and further examined subregions in pol and env using next-generation sequencing in paired plasma and cerebrospinal fluid (CSF) from 18 individuals. Different proportions of mostly minor variants were found in six of the eight multiple T/F-infected individuals, indicating enrichment of some variants in CSF that may lead to significant compartmentalization in the later stages of infection. This study provides evidence for the first time that HIV-1 compartmentalization in the CNS can occur within days of HIV-1 exposure in multiple T/F infections. Further understanding of factors that determine enrichment of T/F variants in the CNS, as well as potential long-term implications of these findings for persistence of HIV-1 reservoirs and neurological impairment in HIV, is needed.
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Affiliation(s)
- Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA.
| | - Rujipas Sirijatuphat
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Phuc T Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Lydia Bonar
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Elizabeth A Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Hongshuo Song
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - David Chang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Celina Oropeza
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Anne Marie O'Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Joyce Balinang
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Eugene Kroon
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Donn J Colby
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Carlo Sacdalan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Joanna Hellmuth
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Phillip Chan
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | | | - Suteeraporn Pinyakorn
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Linda L Jagodzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | | | | | - Mark de Souza
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Robert A Gramzinski
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Jerome H Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- International Vaccine Institute, Seoul 08826, Korea
| | - Nelson L Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Merlin L Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Nittaya Phanuphak
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
| | - Jintanat Ananworanich
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
- SEARCH, Thai Red Cross AIDS Research Centre, Bangkok 10330, Thailand
- Academic Medical Center, Department of Global Health, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
| | - Victor Valcour
- Memory and Aging Center, Department of Neurology, University of California, San Francisco, CA 94158, USA
| | - Gustavo H Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Serena Spudich
- Department of Neurology, Yale University; New Haven, CT 06510, USA
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Gao Y, Tian W, Han X, Gao F. Immunological and virological characteristics of human immunodeficiency virus type 1 superinfection: implications in vaccine design. Front Med 2017; 11:480-489. [PMID: 29170914 DOI: 10.1007/s11684-017-0594-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/30/2017] [Indexed: 02/04/2023]
Abstract
Superinfection is frequently detected among individuals infected by human immunodeficiency virus type I (HIV-1). Superinfection occurs at similar frequencies at acute and chronic infection stages but less frequently than primary infection. This observation indicates that the immune responses elicited by natural HIV-1 infection may play a role in curb of superinfection; however, these responses are not sufficiently strong to completely prevent superinfection. Thus, a successful HIV-1 vaccine likely needs to induce more potent and broader immune responses than those elicited by primary infection. On the other hand, potent and broad neutralization responses are more often detected after superinfection than during monoinfection. This suggests that broadly neutralizing antibodies are more likely induced by sequential immunization of multiple different immunogens than with only one form of envelope glycoprotein immunogens. Understanding why the protection from superinfection by immunity induced by primary infection is insufficient and if superinfection can lead to cross-reactive immune responses will be highly informative for HIV-1 vaccine design.
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Affiliation(s)
- Yang Gao
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Wen Tian
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China
| | - Xiaoxu Han
- Key Laboratory of AIDS Immunology of National Health and Family Planning Commission, Department of Laboratory Medicine, The First Affiliated Hospital, China Medical University, Shenyang, 110001, China.
| | - Feng Gao
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China. .,Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.
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Kijak GH, Sanders-Buell E, Chenine AL, Eller MA, Goonetilleke N, Thomas R, Leviyang S, Harbolick EA, Bose M, Pham P, Oropeza C, Poltavee K, O’Sullivan AM, Billings E, Merbah M, Costanzo MC, Warren JA, Slike B, Li H, Peachman KK, Fischer W, Gao F, Cicala C, Arthos J, Eller LA, O’Connell RJ, Sinei S, Maganga L, Kibuuka H, Nitayaphan S, Rao M, Marovich MA, Krebs SJ, Rolland M, Korber BT, Shaw GM, Michael NL, Robb ML, Tovanabutra S, Kim JH. Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection. PLoS Pathog 2017; 13:e1006510. [PMID: 28759651 PMCID: PMC5552316 DOI: 10.1371/journal.ppat.1006510] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 08/10/2017] [Accepted: 07/03/2017] [Indexed: 01/12/2023] Open
Abstract
In order to inform the rational design of HIV-1 preventive and cure interventions it is critical to understand the events occurring during acute HIV-1 infection (AHI). Using viral deep sequencing on six participants from the early capture acute infection RV217 cohort, we have studied HIV-1 evolution in plasma collected twice weekly during the first weeks following the advent of viremia. The analysis of infections established by multiple transmitted/founder (T/F) viruses revealed novel viral profiles that included: a) the low-level persistence of minor T/F variants, b) the rapid replacement of the major T/F by a minor T/F, and c) an initial expansion of the minor T/F followed by a quick collapse of the same minor T/F to low frequency. In most participants, cytotoxic T-lymphocyte (CTL) escape was first detected at the end of peak viremia downslope, proceeded at higher rates than previously measured in HIV-1 infection, and usually occurred through the exploration of multiple mutational pathways within an epitope. The rapid emergence of CTL escape variants suggests a strong and early CTL response. Minor T/F viral strains can contribute to rapid and varied profiles of HIV-1 quasispecies evolution during AHI. Overall, our results demonstrate that early, deep, and frequent sampling is needed to investigate viral/host interaction during AHI, which could help identify prerequisites for prevention and cure of HIV-1 infection.
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Affiliation(s)
- Gustavo H. Kijak
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
- * E-mail:
| | - Eric Sanders-Buell
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Agnes-Laurence Chenine
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Michael A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Nilu Goonetilleke
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Rasmi Thomas
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Sivan Leviyang
- Department of Mathematics and Statistics, Georgetown University, Washington, DC, United States of America
| | - Elizabeth A. Harbolick
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Meera Bose
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Phuc Pham
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Celina Oropeza
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Kultida Poltavee
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Anne Marie O’Sullivan
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Erik Billings
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Melanie Merbah
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Margaret C. Costanzo
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Joanna A. Warren
- School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Bonnie Slike
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Hui Li
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Kristina K. Peachman
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Will Fischer
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Claudia Cicala
- Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - James Arthos
- Laboratory of Immunoregulation National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States of America
| | - Leigh A. Eller
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | | | | | | | - Hannah Kibuuka
- Makerere University-Walter Reed Project, Kampala, Uganda
| | | | - Mangala Rao
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Mary A. Marovich
- Vaccine Research Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States of America
| | - Shelly J. Krebs
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Morgane Rolland
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Bette T. Korber
- Theoretical Biology, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - George M. Shaw
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
| | - Nelson L. Michael
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
| | - Merlin L. Robb
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Sodsai Tovanabutra
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, United States of America
| | - Jerome H. Kim
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, United States of America
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