Ultradeep single-molecule real-time sequencing of HIV envelope reveals complete compartmentalization of highly macrophage-tropic R5 proviral variants in brain and CXCR4-using variants in immune and peripheral tissues

[1]  C. Harbison,et al.  Identification of Emerging Macrophage-Tropic HIV-1 R5 Variants in Brain Tissue of AIDS Patients without Severe Neurological Complications , 2017, Journal of Virology.

[2]  M. Salemi,et al.  Single Genome Sequencing of Expressed and Proviral HIV-1 Envelope Glycoprotein 120 (gp120) and nef Genes. , 2017, Bio-protocol.

[3]  A. Trkola,et al.  Delineating CD4 dependency of HIV-1: Adaptation to infect low level CD4 expressing target cells widens cellular tropism but severely impacts on envelope functionality , 2017, PLoS Pathogens.

[4]  Paolo Piazza,et al.  Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis , 2017, F1000Research.

[5]  O. Laeyendecker,et al.  Identifying Transmission Clusters with Cluster Picker and HIV-TRACE. , 2016, AIDS research and human retroviruses.

[6]  D. Clifford,et al.  HIV-associated neurocognitive disorder , 2016, Current opinion in infectious diseases.

[7]  Yan Guo,et al.  Rapid Sequencing of Complete env Genes from Primary HIV-1 Samples. , 2016, Virus evolution.

[8]  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.

[9]  Liang Ma,et al.  Towards Better Precision Medicine: PacBio Single-Molecule Long Reads Resolve the Interpretation of HIV Drug Resistant Mutation Profiles at Explicit Quasispecies (Haplotype) Level , 2015, Journal of data mining in genomics & proteomics.

[10]  S. Wann,et al.  Chemokine co-receptor usage in HIV-1-infected treatment-naïve voluntary counselling and testing clients in Southern Taiwan , 2015, BMJ Open.

[11]  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.

[12]  L. Jones,et al.  HIV-1 Tropism Dynamics and Phylogenetic Analysis from Longitudinal Ultra-Deep Sequencing Data of CCR5- and CXCR4-Using Variants , 2014, PloS one.

[13]  Sergei L. Kosakovsky Pond,et al.  The global transmission network of HIV-1. , 2014, The Journal of infectious diseases.

[14]  T. Thomas,et al.  Deep sequencing of evolving pathogen populations: applications, errors, and bioinformatic solutions , 2014, Microbial Informatics and Experimentation.

[15]  Riccardo Velasco,et al.  An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome , 2013, BMC Genomics.

[16]  D. Struck,et al.  HIV-1 Tropism Determination Using a Phenotypic Env Recombinant Viral Assay Highlights Overestimation of CXCR4-Usage by Genotypic Prediction Algorithms for CRRF01_AE and CRF02_AG , 2013, PloS one.

[17]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[18]  Art F. Y. Poon,et al.  Reconstructing the Dynamics of HIV Evolution within Hosts from Serial Deep Sequence Data , 2012, PLoS Comput. Biol..

[19]  S. Zolla-Pazner,et al.  Efficiency of Bridging-Sheet Recruitment Explains HIV-1 R5 Envelope Glycoprotein Sensitivity to Soluble CD4 and Macrophage Tropism , 2012, Journal of Virology.

[20]  P. Narciso,et al.  Ultra‐deep sequencing reveals hidden HIV‐1 minority lineages and shifts of viral population between the main cellular reservoirs of the infection after therapy interruption , 2012, Journal of medical virology.

[21]  P. Simmonds,et al.  Independent evolution of macrophage-tropism and increased charge between HIV-1 R5 envelopes present in brain and immune tissue , 2012, Retrovirology.

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

[23]  Feng Gao,et al.  Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections , 2011, PLoS pathogens.

[24]  David L. Robertson,et al.  The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach , 2010, PLoS Comput. Biol..

[25]  S. Turner,et al.  A flexible and efficient template format for circular consensus sequencing and SNP detection , 2010, Nucleic acids research.

[26]  J. McArthur,et al.  Human immunodeficiency virus‐associated neurocognitive disorders: Mind the gap , 2010, Annals of neurology.

[27]  M. Kuroda,et al.  Increased Monocyte Turnover from Bone Marrow Correlates with Severity of SIV Encephalitis and CD163 Levels in Plasma , 2010, PLoS pathogens.

[28]  K. Robertson,et al.  HIV, Antiretroviral Therapies, and the Brain , 2010, Current HIV/AIDS reports.

[29]  C. Kankasa,et al.  Restricted Genetic Diversity of HIV-1 Subtype C Envelope Glycoprotein from Perinatally Infected Zambian Infants , 2010, PloS one.

[30]  E. Thomas,et al.  Enhanced macrophage tropism of HIV in brain and lymphoid tissues is associated with sensitivity to the broadly neutralizing CD4 binding site antibody b12 , 2009, Retrovirology.

[31]  Wei Huang,et al.  Selection of HIV variants with signature genotypic characteristics during heterosexual transmission. , 2009, The Journal of infectious diseases.

[32]  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.

[33]  Steven Wolinsky,et al.  Bioinformatic prediction programs underestimate the frequency of CXCR4 usage by R5X4 HIV type 1 in brain and other tissues. , 2008, AIDS research and human retroviruses.

[34]  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.

[35]  J. Mullins,et al.  Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. , 2008, Virology.

[36]  D. Burton,et al.  Natural Resistance of Human Immunodeficiency Virus Type 1 to the CD4bs Antibody b12 Conferred by a Glycan and an Arginine Residue Close to the CD4 Binding Loop , 2008, Journal of Virology.

[37]  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.

[38]  D. Burton,et al.  Edinburgh Research Explorer Variation in HIV-I R5 macrophage-tropism correlates with sensitivity to reagents that block envelope: CD4 interactions but not with sensitivity to other entry inhibitors , 2022 .

[39]  E. Hunter,et al.  Viral characteristics of transmitted HIV , 2008, Current opinion in HIV and AIDS.

[40]  J. Becker,et al.  Updated research nosology for HIV-associated neurocognitive disorders , 2007, Neurology.

[41]  Steven Wolinsky,et al.  Loss of the N-linked glycosylation site at position 386 in the HIV envelope V4 region enhances macrophage tropism and is associated with dementia. , 2007, Virology.

[42]  C. Nordborg,et al.  Comparison of HIV‐1 pol and env sequences of blood, CSF, brain and spleen isolates collected ante‐mortem and post‐mortem , 2007, Acta neurologica Scandinavica.

[43]  Hui Li,et al.  Neutralizing Antibody Responses in Acute Human Immunodeficiency Virus Type 1 Subtype C Infection , 2007, Journal of Virology.

[44]  Steven Wolinsky,et al.  Macrophage entry mediated by HIV Envs from brain and lymphoid tissues is determined by the capacity to use low CD4 levels and overall efficiency of fusion. , 2007, Virology.

[45]  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.

[46]  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.

[47]  D. Richman,et al.  Genetic attributes of cerebrospinal fluid-derived HIV-1 env. , 2006, Brain : a journal of neurology.

[48]  Xiping Wei,et al.  Evidence for Potent Autologous Neutralizing Antibody Titers and Compact Envelopes in Early Infection with Subtype C Human Immunodeficiency Virus Type 1 , 2006, Journal of Virology.

[49]  Lynn Morris,et al.  A Reliable Phenotype Predictor for Human Immunodeficiency Virus Type 1 Subtype C Based on Envelope V3 Sequences , 2006, Journal of Virology.

[50]  J. Overbaugh,et al.  Neutralization Escape Variants of Human Immunodeficiency Virus Type 1 Are Transmitted from Mother to Infant , 2006, Journal of Virology.

[51]  P. Simmonds,et al.  An immune control model for viral replication in the CNS during presymptomatic HIV infection. , 2006, Brain : a journal of neurology.

[52]  W. Fitch,et al.  Phylodynamic Analysis of Human Immunodeficiency Virus Type 1 in Distinct Brain Compartments Provides a Model for the Neuropathogenesis of AIDS , 2005, Journal of Virology.

[53]  R. Swanstrom,et al.  Increased Human Immunodeficiency Virus Type 1 (HIV-1) env Compartmentalization in the Presence of HIV-1-Associated Dementia , 2005, Journal of Virology.

[54]  Dorothy M. Lang,et al.  Selection for Human Immunodeficiency Virus Type 1 Envelope Glycosylation Variants with Shorter V1-V2 Loop Sequences Occurs during Transmission of Certain Genetic Subtypes and May Impact Viral RNA Levels , 2005, Journal of Virology.

[55]  C. Petito,et al.  Compartmentalization of HIV-1 in the central nervous system: role of the choroid plexus , 2005, AIDS.

[56]  D. Richman,et al.  Genetic Composition of Human Immunodeficiency Virus Type 1 in Cerebrospinal Fluid and Blood without Treatment and during Failing Antiretroviral Therapy , 2005, Journal of Virology.

[57]  B. Brew,et al.  Independent Evolution of Human Immunodeficiency Virus (HIV) Drug Resistance Mutations in Diverse Areas of the Brain in HIV-Infected Patients, with and without Dementia, on Antiretroviral Treatment , 2004, Journal of Virology.

[58]  C. Pikora Glycosylation of the ENV spike of primate immunodeficiency viruses and antibody neutralization. , 2004, Current HIV Research.

[59]  S. Croul,et al.  Macrophage/microglial accumulation and proliferating cell nuclear antigen expression in the central nervous system in human immunodeficiency virus encephalopathy. , 2004, The American journal of pathology.

[60]  Bette T. Korber,et al.  Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission , 2004, Science.

[61]  B. Korber,et al.  Genetic and Functional Analysis of Full-Length Human Immunodeficiency Virus Type 1 env Genes Derived from Brain and Blood of Patients with AIDS , 2003, Journal of Virology.

[62]  D. Kolson,et al.  An unusual syncytia-inducing human immunodeficiency virus type 1 primary isolate from the central nervous system that is restricted to CXCR4, replicates efficiently in macrophages, and induces neuronal apoptosis , 2003, Journal of NeuroVirology.

[63]  R. Beschorner Human brain parenchymal microglia express CD14 and CD45 and are productively infected by HIV-1 in HIV-1 encephalitis. , 2003, Brain pathology.

[64]  E. De Clercq,et al.  Macrophage Tropism of Human Immunodeficiency Virus Type 1 Isolates from Brain and Lymphoid Tissues Predicts Neurotropism Independent of Coreceptor Specificity , 2001, Journal of Virology.

[65]  A. Lackner,et al.  Perivascular Macrophages Are the Primary Cell Type Productively Infected by Simian Immunodeficiency Virus in the Brains of Macaques , 2001, The Journal of experimental medicine.

[66]  C. Petito,et al.  Comparisons of HIV-1 viral sequences in brain, choroid plexus and spleen: potential role of choroid plexus in the pathogenesis of HIV encephalitis. , 2000, Journal of neurovirology.

[67]  J. McArthur,et al.  Analysis of human immunodeficiency virus type 1 gp160 sequences from a patient with HIV dementia: evidence for monocyte trafficking into brain. , 2000, Journal of neurovirology.

[68]  S. Gartner HIV Infection and Dementia , 2000, Science.

[69]  J. Sodroski,et al.  Species-Specific, Postentry Barriers to Primate Immunodeficiency Virus Infection , 1999, Journal of Virology.

[70]  K. Crandall,et al.  Independent evolution of HIV type 1 in different brain regions. , 1999, AIDS research and human retroviruses.

[71]  Y. Soda,et al.  Establishment of a new system for determination of coreceptor usages of HIV based on the human glioma NP-2 cell line. , 1999, Biochemical and biophysical research communications.

[72]  Hanneke Schuitemaker,et al.  Analysis of the Temporal Relationship between Human Immunodeficiency Virus Type 1 Quasispecies in Sequential Blood Samples and Various Organs Obtained at Autopsy , 1998, Journal of Virology.

[73]  D. Richman,et al.  In vivo compartmentalization of human immunodeficiency virus: evidence from the examination of pol sequences from autopsy tissues , 1997, Journal of virology.

[74]  P. Simmonds,et al.  Edinburgh Research Explorer Investigation of the dynamics of the spread of human immunodeficiency virus to brain and other tissues by evolutionary analysis of sequences from the p17gag and env genes , 2022 .

[75]  J. Glass,et al.  Localization of HIV‐1 in human brain using polymerase chain reaction/in situ hybridization and immunocytochemistry , 1996, Annals of neurology.

[76]  J. Glass,et al.  Immunocytochemical quantitation of human immunodeficiency virus in the brain: Correlations with dementia , 1995, Annals of neurology.

[77]  H. Gendelman,et al.  Unraveling the neuroimmune mechanisms for the HIV-1-associated cognitive/motor complex. , 1995, Immunology today.

[78]  B. Korber,et al.  Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain-derived sequences , 1994, Journal of virology.

[79]  P. Simmonds,et al.  Redistribution of HIV outside the lymphoid system with onset of AIDS , 1994, The Lancet.

[80]  P. Simmonds,et al.  Human immunodeficiency virus and the brain: investigation of virus load and neuropathologic changes in pre-AIDS subjects. , 1993, The Journal of infectious diseases.

[81]  W. Wachsman,et al.  Early viral brain invasion in iatrogenic human immunodeficiency virus infection , 1992, Neurology.

[82]  P. Simmonds,et al.  Human immunodeficiency virus-infected individuals contain provirus in small numbers of peripheral mononuclear cells and at low copy numbers , 1990, Journal of virology.

[83]  Jonas Korlach,et al.  Understanding Accuracy in SMRT ® Sequencing , 2013 .

[84]  S. Croul,et al.  CNS invasion by CD14+/CD16+ peripheral blood-derived monocytes in HIV dementia: perivascular accumulation and reservoir of HIV infection , 2011, Journal of NeuroVirology.

[85]  Marco Salemi,et al.  HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues. , 2011, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[86]  J. Berman,et al.  Characterization of monocyte maturation/differentiation that facilitates their transmigration across the blood-brain barrier and infection by HIV: implications for NeuroAIDS. , 2011, Cellular immunology.

[87]  Francisco González-Scarano,et al.  The neuropathogenesis of AIDS , 2005, Nature Reviews Immunology.

[88]  S. Oka,et al.  Active HIV-1 redistribution and replication in the brain with HIV encephalitis , 1999, Archives of Virology.

[89]  Bin Wang,et al.  Unique HIV type 1 V3 region sequences derived from six different regions of brain: region-specific evolution within host-determined quasispecies. , 1998, AIDS research and human retroviruses.

[90]  V. Sasseville,et al.  Neuroinvasion by simian immunodeficiency virus coincides with increased numbers of perivascular macrophages/microglia and intrathecal immune activation. , 1996, Journal of neurovirology.

[91]  P. Simmonds,et al.  Human immunodeficiency virus and the brain , 1993 .

[92]  S. Haggerty,et al.  Predominance of distinct viral genotypes in brain and lymph node compartments of HIV-1-infected individuals. , 1991, Viral immunology.