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

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) David Beauparlant et al.   PLoS Pathogens

Deep Sequencing of the HIV-1envGene Reveals Discrete X4 Lineages and Linkage Disequilibrium between X4 and R5 Viruses in the V1/V2 and V3 Variable Regions

(2016) Shuntai Zhou et al.   JOURNAL OF VIROLOGY

Compartmentalized Replication of R5 T Cell-Tropic HIV-1 in the Central Nervous System Early in the Course of Infection

(2015) Christa Buckheit Sturdevant et al.   PLoS Pathogens

An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

(2013) Marco Ferrarini et al.   BMC GENOMICS

The Global Transmission Network of HIV-1

(2013) Joel O. Wertheim et al.   JOURNAL OF INFECTIOUS DISEASES

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Correction: 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) Martin Mulinge et al.   PLoS One

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) Gabriella Rozera et al.   JOURNAL OF MEDICAL VIROLOGY

Efficiency of Bridging-Sheet Recruitment Explains HIV-1 R5 Envelope Glycoprotein Sensitivity to Soluble CD4 and Macrophage Tropism

(2012) O. O'Connell et al.   JOURNAL OF VIROLOGY

Variation in HIV-1 R5 macrophage-tropism correlates with sensitivity to reagents that block envelope: CD4 interactions but not with sensitivity to other entry inhibitors

(2012) Paul J Peters et al.   Retrovirology

Independent evolution of macrophage-tropism and increased charge between HIV-1 R5 envelopes present in brain and immune tissue

(2012) Maria P Gonzalez-Perez et al.   Retrovirology

HIV-1 Replication in the Central Nervous System Occurs in Two Distinct Cell Types

(2011) Gretja Schnell et al.   PLoS Pathogens

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

(2011) S. Gnanakaran et al.   PLoS Pathogens

Characterization of monocyte maturation/differentiation that facilitates their transmigration across the blood–brain barrier and infection by HIV: Implications for NeuroAIDS

(2010) Clarisa M. Buckner et al.   CELLULAR IMMUNOLOGY

HIV-1 phylogenetic analysis shows HIV-1 transits through the meninges to brain and peripheral tissues

(2010) Susanna L. Lamers et al.   INFECTION GENETICS AND EVOLUTION

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

The Evolutionary Analysis of Emerging Low Frequency HIV-1 CXCR4 Using Variants through Time—An Ultra-Deep Approach

(2010) John Archer et al.   PLoS Computational Biology

Increased Monocyte Turnover from Bone Marrow Correlates with Severity of SIV Encephalitis and CD163 Levels in Plasma

(2010) Tricia H. Burdo et al.   PLoS Pathogens

HIV, Antiretroviral Therapies, and the Brain

(2010) Kevin J. Liner et al.   Current HIV/AIDS Reports

Selection of HIV Variants with Signature Genotypic Characteristics during Heterosexual Transmission

(2009) Manish Sagar et al.   JOURNAL OF INFECTIOUS DISEASES

Determinants Flanking the CD4 Binding Loop Modulate Macrophage Tropism of Human Immunodeficiency Virus Type 1 R5 Envelopes

(2009) M. J. Duenas-Decamp et al.   JOURNAL OF VIROLOGY

Enhanced macrophage tropism of HIV in brain and lymphoid tissues is associated with sensitivity to the broadly neutralizing CD4 binding site antibody b12

(2009) Rebecca L Dunfee et al.   Retrovirology

Bioinformatic Prediction Programs Underestimate the Frequency of CXCR4 Usage by R5X4 HIV Type 1 in Brain and Other Tissues

(2008) Megan E. Mefford et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

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) M. J. Duenas-Decamp et al.   JOURNAL OF VIROLOGY

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses

(2008) Yi Liu et al.   VIROLOGY

Viral characteristics of transmitted HIV

(2008) Cynthia A Derdeyn et al.   Current Opinion in HIV and AIDS