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Conserved Molecular Signatures in gp120 Are Associated with the Genetic Bottleneck during Simian Immunodeficiency Virus (SIV), SIV-Human Immunodeficiency Virus (SHIV), and HIV Type 1 (HIV-1) Transmission

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Taking Multiple Infections of Cells and Recombination into Account Leads to Small Within-Host Effective-Population-Size Estimates of HIV-1

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Anti-APOBEC3G Activity of HIV-1 Vif Protein Is Attenuated in Elite Controllers

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Initiation of Therapy during Primary HIV Type 1 Infection Results in a Continuous Decay of Proviral DNA and a Highly Restricted Viral Evolution

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HIV Trafficking Between Blood and Semen During Early Untreated HIV Infection

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Dynamics of In Vitro Fitness Recovery of HIV-1

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HIV-1 Env Glycoprotein Phenotype along with Immune Activation Determines CD4 T Cell Loss in HIV Patients

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Higher levels of Zidovudine resistant HIV in the colon compared to blood and other gastrointestinal compartments in HIV infection

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Neutralization activity in a geographically diverse East London cohort of human immunodeficiency virus type 1-infected patients: clade C infection results in a stronger and broader humoral immune response than clade B infection

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Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform

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Detection of Broadly Neutralizing Activity within the First Months of HIV-1 Infection

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Differential Pathogenesis of Primary CCR5-Using Human Immunodeficiency Virus Type 1 Isolates in Ex Vivo Human Lymphoid Tissue

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Virus and Target Cell Evolution in Human Immunodeficiency Virus Type 1 Infection

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Evolution of Human Immunodeficiency Virus Type 1 Coreceptor Usage during Antiretroviral Therapy: a Bayesian Approach

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The CpG dinucleotide content of the HIV-1 envelope gene may predict disease progression

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Viral Diversity and Diversification of Major Non-Structural Genes vif, vpr, vpu, tat exon 1 and rev exon 1 during Primary HIV-1 Subtype C Infection

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Recombination Enhances HIV-1 Envelope Diversity by Facilitating the Survival of Latent Genomic Fragments in the Plasma Virus Population

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Impact of seminal cytomegalovirus replication on HIV‐1 dynamics between blood and semen

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Evolution of the Equine Infectious Anemia Virus Long Terminal Repeat during the Alteration of Cell Tropism

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Primary and Recombinant HIV Type 1 Strains Resistant to Protease Inhibitors Are Pathogenic in Mature Human Lymphoid Tissues

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Subclinical Genital Herpes Shedding in HIV/Herpes Simplex Virus 2-Coinfected Women during Antiretroviral Therapy Is Associated with an Increase in HIV Tissue Reservoirs and Potentially Promotes HIV Evolution

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A simultaneous knockout knockin genome editing strategy in HSPCs potently inhibits CCR5- and CXCR4-tropic HIV-1 infection

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High intrapatient HIV-1 evolutionary rate is associated with CCR5-to-CXCR4 coreceptor switch

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HIV-1 envelope replication and α4β7 utilization among newly infected subjects and their corresponding heterosexual partners

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Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model

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Disentangling the impact of within-host evolution and transmission dynamics on the tempo of HIV-1 evolution

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Genetic Signatures of HIV-1 Envelope-mediated Bystander Apoptosis

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Longitudinal Assessment of de Novo T Cell Production in Relation to HIV-Associated T Cell Homeostasis Failure

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Human Immunodeficiency Virus Type-1 (HIV-1) Continues to Evolve in Presence of Broadly Neutralizing Antibodies More than Ten Years after Infection

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Characterization of HIV-1 envelopes in acutely and chronically infected injection drug users

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Effect of antiretroviral therapy on HIV-1 genetic evolution during acute infection

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Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC

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Next-generation sequencing analyses of the emergence and maintenance of mutations in CTL epitopes in HIV controllers with differential viremia control

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Genetically barcoded SIV reveals the emergence of escape mutations in multiple viral lineages during immune escape

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Log Transformation Improves Dating of Phylogenies

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Selection in ContextSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AF016760, AF016761, AF016762, AF016763, AF016764, AF016765, AF016766, AF016767, AF016768, AF016769, AF016770, AF016771, AF016772, AF016773, AF016774, AF016775, AF016776, AF016777, AF016778, AF016779, AF016780, AF016781, AF016782, AF016783, AF016784, AF016785, AF016786, AF016787, AF016788, AF016789, AF016790, AF016791, AF016792, AF016793, AF016794, AF016795, AF016796, AF016797, AF016798, AF016799, AF016800, AF016801, AF016802, AF016803, AF016804, AF016805, AF016806, AF016807, AF016808, AF016809, AF016810, AF016811, AF016812, AF016813, AF016814, AF016815, AF016816, AF016817, AF016818, AF016819, AF016820, AF016821, AF016822, AF016823, AF016824, AF016825 and AF089109, AF089708.

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