The evolution of HIV‐1 entry phenotypes as a guide to changing target cells

Through a twist of fate the most common form of HIV‐1, as defined by entry phenotype, was not appreciated until recently. The entry phenotype is closely linked to the target cell and thus to virus–host interactions and pathogenesis. The most abundant form of HIV‐1 uses CCR5 as the coreceptor and requires a high density of CD4 for efficient entry, defining its target cell as the CD4+ memory T cell. This is the transmitted form of the virus, the form that is found in the blood, and the form that rebounds from the latent reservoir. When CD4+/CCR5+ T cells become limiting the virus evolves to use alternative target cells to support viral replication. In the CNS, the virus can evolve to use a cell that displays only a low density of CD4, while maintaining the use of CCR5 as the coreceptor. When this evolutionary variant evolves, it must be sustaining its replication in either macrophages or microglial cells, which display only a low density of CD4 relative to that on T cells. In the blood and lymphoid system, the major switch late in disease is from T cells expressing CD4 and CCR5 to T cells expressing CD4 and CXCR4, with a change in coreceptor specificity. Thus the virus responds in two different ways to different environments when its preferred target cell becomes limiting.

[1]  E. Boritz,et al.  Identification of Genetically Intact HIV-1 Proviruses in Specific CD4+ T Cells from Effectively Treated Participants. , 2017, Cell reports.

[2]  J. Mellors,et al.  No evidence of HIV replication in children on antiretroviral therapy. , 2017, The Journal of clinical investigation.

[3]  Alison L. Hill,et al.  Re-evaluating evolution in the HIV reservoir , 2017, Nature.

[4]  R. Ribeiro,et al.  HIV persistence in tissue macrophages of humanized myeloid only mice during antiretroviral therapy , 2017, Nature Medicine.

[5]  S. Hughes,et al.  Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir , 2017, PLoS pathogens.

[6]  Shuntai Zhou,et al.  Diversity and Tropism of HIV-1 Rebound Virus Populations in Plasma Level After Treatment Discontinuation. , 2016, The Journal of infectious diseases.

[7]  Shuntai Zhou,et al.  Deep Sequencing of the HIV-1 env Gene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions , 2016, Journal of Virology.

[8]  S. Hughes,et al.  Clonally expanded CD4+ T cells can produce infectious HIV-1 in vivo , 2016, Proceedings of the National Academy of Sciences.

[9]  Trevor Bedford,et al.  Persistent HIV-1 replication maintains the tissue reservoir during therapy , 2015, Nature.

[10]  William D. Graham,et al.  Phenotypic Correlates of HIV-1 Macrophage Tropism , 2015, Journal of Virology.

[11]  Shuntai Zhou,et al.  R5 Macrophage-Tropic HIV-1 in the Male Genital Tract , 2015, Journal of Virology.

[12]  R. Swanstrom,et al.  Bottlenecks in HIV-1 transmission: insights from the study of founder viruses , 2015, Nature Reviews Microbiology.

[13]  R. Swanstrom,et al.  Compartmentalized Replication of R5 T Cell-Tropic HIV-1 in the Central Nervous System Early in the Course of Infection , 2015, PLoS pathogens.

[14]  A. Haase,et al.  Large number of rebounding/founder HIV variants emerge from multifocal infection in lymphatic tissues after treatment interruption , 2015, Proceedings of the National Academy of Sciences.

[15]  M. Davenport,et al.  CD4 Depletion in SIV-Infected Macaques Results in Macrophage and Microglia Infection with Rapid Turnover of Infected Cells , 2014, PLoS pathogens.

[16]  D. Margolis,et al.  Quantitation of Replication-Competent HIV-1 in Populations of Resting CD4+ T Cells , 2014, Journal of Virology.

[17]  Brendan B. Larsen,et al.  Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection , 2014, Science.

[18]  J. Mellors,et al.  Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy , 2014, PLoS pathogens.

[19]  Alan S Perelson,et al.  Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations in lymphatic tissues , 2014, Proceedings of the National Academy of Sciences.

[20]  J. Hoxie,et al.  Quantification of Entry Phenotypes of Macrophage-Tropic HIV-1 across a Wide Range of CD4 Densities , 2013, Journal of Virology.

[21]  E. L. Potter,et al.  Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design , 2013, Journal of Virology.

[22]  Cassandra B. Jabara,et al.  Central Nervous System Compartmentalization of HIV-1 Subtype C Variants Early and Late in Infection in Young Children , 2012, PLoS pathogens.

[23]  Lynn Morris,et al.  Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape , 2012, Nature Medicine.

[24]  Craig B Wilen,et al.  HIV: cell binding and entry. , 2012, Cold Spring Harbor perspectives in medicine.

[25]  H. Ding,et al.  Transmitted/Founder and Chronic Subtype C HIV-1 Use CD4 and CCR5 Receptors with Equal Efficiency and Are Not Inhibited by Blocking the Integrin α4β7 , 2012, PLoS pathogens.

[26]  R. Swanstrom,et al.  HIV-1 Replication in the Central Nervous System Occurs in Two Distinct Cell Types , 2011, PLoS pathogens.

[27]  Dennis R Burton,et al.  Envelope glycans of immunodeficiency virions are almost entirely oligomannose antigens , 2010, Proceedings of the National Academy of Sciences.

[28]  R. Swanstrom,et al.  Evolution of the HIV-1 env Gene in the Rag2−/− γC−/− Humanized Mouse Model , 2009, Journal of Virology.

[29]  Holly Janes,et al.  Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies , 2009, Journal of Virology.

[30]  T. Chou,et al.  A Quantitative Affinity-Profiling System That Reveals Distinct CD4/CCR5 Usage Patterns among Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus Strains , 2009, Journal of Virology.

[31]  Geneviève Boucher,et al.  HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation , 2009, Nature Medicine.

[32]  R. Swanstrom,et al.  Compartmentalized Human Immunodeficiency Virus Type 1 Originates from Long-Lived Cells in Some Subjects with HIV-1–Associated Dementia , 2009, PLoS pathogens.

[33]  G. Alkhatib The biology of CCR5 and CXCR4 , 2009, Current opinion in HIV and AIDS.

[34]  D. Burton,et al.  Determinants Flanking the CD4 Binding Loop Modulate Macrophage Tropism of Human Immunodeficiency Virus Type 1 R5 Envelopes , 2009, Journal of Virology.

[35]  Hui Li,et al.  Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection , 2008, Proceedings of the National Academy of Sciences.

[36]  B. Korber,et al.  Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing , 2008, Journal of Virology.

[37]  M. McCarter,et al.  CTL Fail to Accumulate at Sites of HIV-1 Replication in Lymphoid Tissue12 , 2007, The Journal of Immunology.

[38]  Steven Wolinsky,et al.  The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia , 2006, Proceedings of the National Academy of Sciences.

[39]  Michael Watters,et al.  Lowest ever CD4 lymphocyte count (CD4 nadir) as a predictor of current cognitive and neurological status in human immunodeficiency virus type 1 infection—The Hawaii Aging with HIV Cohort , 2006, Journal of NeuroVirology.

[40]  P. Simmonds,et al.  Non-Macrophage-Tropic Human Immunodeficiency Virus Type 1 R5 Envelopes Predominate in Blood, Lymph Nodes, and Semen: Implications for Transmission and Pathogenesis , 2006, Journal of Virology.

[41]  W. Cao,et al.  HIV-1 tropism for the central nervous system: Brain-derived envelope glycoproteins with lower CD4 dependence and reduced sensitivity to a fusion inhibitor. , 2006, Virology.

[42]  P. Harrigan,et al.  Molecular and clinical epidemiology of CXCR4-using HIV-1 in a large population of antiretroviral-naive individuals. , 2005, The Journal of infectious diseases.

[43]  Steven L Wesselingh,et al.  Uncoupling coreceptor usage of human immunodeficiency virus type 1 (HIV-1) from macrophage tropism reveals biological properties of CCR5-restricted HIV-1 isolates from patients with acquired immunodeficiency syndrome. , 2005, Virology.

[44]  B. Gazzard,et al.  Epidemiology and predictive factors for chemokine receptor use in HIV-1 infection. , 2005, The Journal of infectious diseases.

[45]  John W. Mellors,et al.  Multiple, Linked Human Immunodeficiency Virus Type 1 Drug Resistance Mutations in Treatment-Experienced Patients Are Missed by Standard Genotype Analysis , 2005, Journal of Clinical Microbiology.

[46]  Mario Roederer,et al.  T-Cell Subsets That Harbor Human Immunodeficiency Virus (HIV) In Vivo: Implications for HIV Pathogenesis , 2004, Journal of Virology.

[47]  Martin A. Nowak,et al.  Antibody neutralization and escape by HIV-1 , 2003, Nature.

[48]  John P. Moore,et al.  Increased CCR5 Affinity and Reduced CCR5/CD4 Dependence of a Neurovirulent Primary Human Immunodeficiency Virus Type 1 Isolate , 2002, Journal of Virology.

[49]  N Bischofberger,et al.  Macrophage are the principal reservoir and sustain high virus loads in rhesus macaques after the depletion of CD4+ T cells by a highly pathogenic simian immunodeficiency virus/HIV type 1 chimera (SHIV): Implications for HIV-1 infections of humans. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Hassan Mohammad Naif,et al.  Persistent CCR5 Utilization and Enhanced Macrophage Tropism by Primary Blood Human Immunodeficiency Virus Type 1 Isolates from Advanced Stages of Disease and Comparison to Tissue-Derived Isolates , 1999, Journal of Virology.

[51]  F. Sallusto,et al.  Two subsets of memory T lymphocytes with distinct homing potentials and effector functions , 1999, Nature.

[52]  D. Weissman,et al.  Quantification of CD4, CCR5, and CXCR4 levels on lymphocyte subsets, dendritic cells, and differentially conditioned monocyte-derived macrophages. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M A Nowak,et al.  Presence of an inducible HIV-1 latent reservoir during highly active antiretroviral therapy. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[54]  R Brookmeyer,et al.  Identification of a reservoir for HIV-1 in patients on highly active antiretroviral therapy. , 1997, Science.

[55]  D. Richman,et al.  Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. , 1997, Science.

[56]  R. Connor,et al.  Change in Coreceptor Use Correlates with Disease Progression in HIV-1–Infected Individuals , 1997, The Journal of experimental medicine.

[57]  Ying Sun,et al.  The β-Chemokine Receptors CCR3 and CCR5 Facilitate Infection by Primary HIV-1 Isolates , 1996, Cell.

[58]  Marc Parmentier,et al.  A Dual-Tropic Primary HIV-1 Isolate That Uses Fusin and the β-Chemokine Receptors CKR-5, CKR-3, and CKR-2b as Fusion Cofactors , 1996, Cell.

[59]  C. Broder,et al.  CC CKR5: A RANTES, MIP-1α, MIP-1ॆ Receptor as a Fusion Cofactor for Macrophage-Tropic HIV-1 , 1996, Science.

[60]  Virginia Litwin,et al.  HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5 , 1996, Nature.

[61]  Stephen C. Peiper,et al.  Identification of a major co-receptor for primary isolates of HIV-1 , 1996, Nature.

[62]  Paul E. Kennedy,et al.  HIV-1 Entry Cofactor: Functional cDNA Cloning of a Seven-Transmembrane, G Protein-Coupled Receptor , 1996, Science.

[63]  M. Reitz,et al.  Growth of macrophage-tropic and primary human immunodeficiency virus type 1 (HIV-1) isolates in a unique CD4+ T-cell clone (PM1): failure to downregulate CD4 and to interfere with cell-line-tropic HIV-1 , 1995, Journal of virology.

[64]  C. Barbas,et al.  Primary isolates of human immunodeficiency virus type 1 are relatively resistant to neutralization by monoclonal antibodies to gp120, and their neutralization is not predicted by studies with monomeric gp120 , 1995, Journal of virology.

[65]  Kees,et al.  Macrophage-tropic variants initiate human immunodeficiency virus type 1 infection after sexual, parenteral, and vertical transmission. , 1994, The Journal of clinical investigation.

[66]  C. Broder,et al.  The block to HIV-1 envelope glycoprotein-mediated membrane fusion in animal cells expressing human CD4 can be overcome by a human cell component(s). , 1993, Virology.

[67]  P. Charneau,et al.  Complementation of murine cells for human immunodeficiency virus envelope/CD4-mediated fusion in human/murine heterokaryons , 1992, Journal of virology.

[68]  R. Weiss,et al.  Specific cell surface requirements for the infection of CD4-positive cells by human immunodeficiency virus types 1 and 2 and by simian immunodeficiency virus , 1991, Virology.

[69]  H. Schuitemaker,et al.  Monocytotropic human immunodeficiency virus type 1 (HIV-1) variants detectable in all stages of HIV-1 infection lack T-cell line tropism and syncytium-inducing ability in primary T-cell culture , 1991, Journal of virology.

[70]  P Balfe,et al.  Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1 , 1990 .

[71]  Reed J. Harris,et al.  Assignment of intrachain disulfide bonds and characterization of potential glycosylation sites of the type 1 recombinant human immunodeficiency virus envelope glycoprotein (gp120) expressed in Chinese hamster ovary cells. , 1990, The Journal of biological chemistry.

[72]  B. Moss,et al.  Human immunodeficiency virus envelope glycoprotein/CD4-mediated fusion of nonprimate cells with human cells , 1990, Journal of virology.

[73]  Lange,et al.  Evidence for a role of virulent human immunodeficiency virus (HIV) variants in the pathogenesis of acquired immunodeficiency syndrome: studies on sequential HIV isolates , 1989, Journal of virology.

[74]  S. Marsters,et al.  Blocking of HIV-1 infectivity by a soluble, secreted form of the CD4 antigen. , 1987, Science.

[75]  G. Nakamura,et al.  Delineation of a region of the human immunodeficiency virus type 1 gp120 glycoprotein critical for interaction with the CD4 receptor , 1987, Cell.

[76]  J. Albert,et al.  REPLICATIVE CAPACITY OF HUMAN IMMUNODEFICIENCY VIRUS FROM PATIENTS WITH VARYING SEVERITY OF HIV INFECTION , 1986, The Lancet.

[77]  G. Nakamura,et al.  Neutralization of the AIDS retrovirus by antibodies to a recombinant envelope glycoprotein. , 1986, Science.

[78]  J K Nicholson,et al.  Binding of HTLV-III/LAV to T4+ T cells by a complex of the 110K viral protein and the T4 molecule. , 1986, Science.

[79]  F. Walshe The structure of medicine. , 1948, Lancet.

[80]  S. Hughes,et al.  B-108 Specific HIV integration sites are linked to clonal expansion and persistence of infected cells , 2016 .

[81]  F. Bushman,et al.  HIV : from biology to prevention and treatment : a subject collection from Cold Spring Harbor perspectives in medicine , 2012 .

[82]  D. Weiner,et al.  Human genes other than CD4 facilitate HIV-1 infection of murine cells. , 1991, Pathobiology : journal of immunopathology, molecular and cellular biology.

[83]  The prognostic value of cellular and serologic markers in infection with human immunodeficiency virus type 1. , 1990, Disease markers.

[84]  Luc Montagnier,et al.  T-lymphocyte T4 molecule behaves as the receptor for human retrovirus  LAV , 1984, Nature.

[85]  M. Greaves,et al.  The CD4 (T4) antigen is an essential component of the receptor for the AIDS retrovirus , 1984, Nature.