Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus (scientific article)

Emergence of monoclonal antibody b12-resistant human immunodeficiency virus type 1 variants during natural infection in the absence of humoral or cellular immune pressure

Q44679186

Rapid dissemination of a pathogenic simian/human immunodeficiency virus to systemic organs and active replication in lymphoid tissues following intrarectal infection

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The prolonged culture of human immunodeficiency virus type 1 in primary lymphocytes increases its sensitivity to neutralization by soluble CD4.

Q45662866

HIV-1 dual infection is associated with faster CD4+ T-cell decline in a cohort of men with primary HIV infection

Q45728319

The most highly amphiphilic alpha-helices include two amino acid segments in human immunodeficiency virus glycoprotein 41.

Q45849311

Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants

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A substantial transmission bottleneck among newly and recently HIV-1-infected injection drug users in St Petersburg, Russia

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HIV-1 genomic RNA diversification following sexual and parenteral virus transmission

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Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission

Q47878972

Genotypic and phenotypic characterization of HIV-1 patients with primary infection

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Preexposure chemoprophylaxis for HIV prevention in men who have sex with men

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

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Statistical significance for genomewide studies

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Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

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Bottlenecks in HIV-1 transmission: insights from the study of founder viruses

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Statistical methods for detecting molecular adaptation

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Dual HIV-1 infection associated with rapid disease progression

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Structure of an unliganded simian immunodeficiency virus gp120 core

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

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Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection

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Reconstruction of viral population structure from next-generation sequencing data using multicommodity flows

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Phylogenetic dependency networks: inferring patterns of CTL escape and codon covariation in HIV-1 Gag.

Q33385995

Inflammatory genital infections mitigate a severe genetic bottleneck in heterosexual transmission of subtype A and C HIV-1

Q33402461

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.

Q33582135

Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis

Q33592278

Error correction of next-generation sequencing data and reliable estimation of HIV quasispecies

Q33645217

Evolution of the HIV-1 env gene in the Rag2-/- gammaC-/- humanized mouse model

Q33676640

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing

Q33680395

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model

Q33727328

Donor and recipient envs from heterosexual human immunodeficiency virus subtype C transmission pairs require high receptor levels for entry

Q33769382

Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B.

Q33780595

Roles of substrate availability and infection of resting and activated CD4+ T cells in transmission and acute simian immunodeficiency virus infection

Q37682617

The number and genetic relatedness of transmitted/founder virus impact clinical outcome in vaginal R5 SHIVSF162P3N infection

Q37683788

Benchmarking of viral haplotype reconstruction programmes: an overview of the capacities and limitations of currently available programmes

Q38068990

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

Q33780649

Mutational analysis of conserved domains within the cytoplasmic tail of gp41 from human immunodeficiency virus type 1: effects on glycoprotein incorporation and infectivity

Q33812739

The genotype of early-transmitting HIV gp120s promotes α (4) β(7)-reactivity, revealing α (4) β(7) +/CD4+ T cells as key targets in mucosal transmission

Q33839456

A preponderance of CCR5(+) CXCR4(+) mononuclear cells enhances gastrointestinal mucosal susceptibility to human immunodeficiency virus type 1 infection.

Q33853988

Wide variation in the multiplicity of HIV-1 infection among injection drug users

Q33877419

Rapid dissemination of SIV follows multisite entry after rectal inoculation.

Q33900344

A signature in HIV-1 envelope leader peptide associated with transition from acute to chronic infection impacts envelope processing and infectivity

Q34005516

Asn 362 in gp120 contributes to enhanced fusogenicity by CCR5-restricted HIV-1 envelope glycoprotein variants from patients with AIDS.

Q34008699

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections

Q34042642

Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations

Q34044256

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

Q34076081

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data

Q34205837

Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection

Q34228730

ART: a next-generation sequencing read simulator.

Q34243055

Stabilized HIV-1 envelope glycoprotein trimers lacking the V1V2 domain, obtained by virus evolution

Q34299053

The tale of the long tail: the cytoplasmic domain of HIV-1 gp41.

Q34306883

Phenotypic properties of transmitted founder HIV-1

Q34336058

Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

Q34353398

Comparison of methods to detect HIV dual infection

Q34447788

AAV-expressed eCD4-Ig provides durable protection from multiple SHIV challenges

Q34464133

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

Q34620235

Limited or no protection by weakly or nonneutralizing antibodies against vaginal SHIV challenge of macaques compared with a strongly neutralizing antibody

Q34630446

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial

Q34648825

Estimating per-act HIV transmission risk: a systematic review

Q34661804

HIV disease progression in seroconvertors from the CAPRISA 004 tenofovir gel pre-exposure prophylaxis trial

Q34674930

Rational site-directed mutations of the LLP-1 and LLP-2 lentivirus lytic peptide domains in the intracytoplasmic tail of human immunodeficiency virus type 1 gp41 indicate common functions in cell-cell fusion but distinct roles in virion envelope inc

Q34741962

HIV transmission. Selection bias at the heterosexual HIV-1 transmission bottleneck

Q34906292

Viral RNA levels and env variants in semen and tissues of mature male rhesus macaques infected with SIV by penile inoculation

Q35022735

The HIV Env variant N283 enhances macrophage tropism and is associated with brain infection and dementia.

Q35062297

RELAX: detecting relaxed selection in a phylogenetic framework

Q35081209

Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes

Q35140263

Visualization of HIV-1 interactions with penile and foreskin epithelia: clues for female-to-male HIV transmission

Q35154781

Phenotypic and immunologic comparison of clade B transmitted/founder and chronic HIV-1 envelope glycoproteins

Q35192915

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

Q35558621

SIVmac251 is inefficiently transmitted to rhesus macaques by penile inoculation with a single SIVenv variant found in ramp-up phase plasma

Q35581949

The role of sexually transmitted diseases in HIV transmission

Q35701598

Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-α Resistance

Q35778333

Impact of V2 mutations on escape from a potent neutralizing anti-V3 monoclonal antibody during in vitro selection of a primary human immunodeficiency virus type 1 isolate

Q35785244

Generation of transmitted/founder HIV-1 infectious molecular clones and characterization of their replication capacity in CD4 T lymphocytes and monocyte-derived macrophages

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Adaptation to persistent growth in the H9 cell line renders a primary isolate of human immunodeficiency virus type 1 sensitive to neutralization by vaccine sera

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Human immunodeficiency virus type 1 mutants that escape neutralization by human monoclonal antibody IgG1b12. off.

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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

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MiniCD4 protein resistance mutations affect binding to the HIV-1 gp120 CD4 binding site and decrease entry efficiency

Q36127736

HIV-1 variation before seroconversion in men who have sex with men: analysis of acute/early HIV infection in the multicenter AIDS cohort study

Q36165696

Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions

Q36305433

Innate immune activation enhances hiv acquisition in women, diminishing the effectiveness of tenofovir microbicide gel.

Q36410030

Selective transmission of CCR5-utilizing HIV-1: the 'gatekeeper' problem resolved?

Q36422860

Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing

Q36540055

Transmitted/founder and chronic HIV-1 envelope proteins are distinguished by differential utilization of CCR5.

Q36607127

Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection

Q36647820

Strain specificity and binding affinity requirements of neutralizing monoclonal antibodies to the C4 domain of gp120 from human immunodeficiency virus type 1.

Q36653818

Immune escape by human immunodeficiency virus type 1 from neutralizing antibodies: evidence for multiple pathways.

Q36655438

Antigenicity and immunogenicity of transmitted/founder, consensus, and chronic envelope glycoproteins of human immunodeficiency virus type 1

Q36760169

Comprehensive assessment of HIV target cells in the distal human gut suggests increasing HIV susceptibility toward the anus

Q36930438

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

Q36978861

Localized changes in the gp120 envelope glycoprotein confer resistance to human immunodeficiency virus entry inhibitors BMS-806 and #155.

Q37010292

Infection with Multiple Human Immunodeficiency Virus Type 1 Variants Is Associated with Faster Disease Progression

Q37059806

Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants

Q37145228

Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men.

Q37253688

Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1.

Q37273086

Relationship of human immunodeficiency virus type 1 sequence heterogeneity to stage of disease

Q37273122

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

Q37273158

Heterosexual transmission of human immunodeficiency virus type 1 subtype C: Macrophage tropism, alternative coreceptor use, and the molecular anatomy of CCR5 utilization.

Q37275049

Selection of HIV variants with signature genotypic characteristics during heterosexual transmission

Q37370674

Modeling sequence evolution in acute HIV-1 infection

Q37384535

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

Q37444204

Relative resistance of HIV-1 founder viruses to control by interferon-alpha

Q37532983

Incidence and prevalence of intrasubtype HIV-1 dual infection in at-risk men in the United States.

Q37635156

P275

Creative Commons Attribution 4.0 International

copyrighted

issue

language of work or name

English

Q1860

P921

main subject

pathogen transmission

Q525512

HIV transmission

Q49029021

sexually transmitted infection

Q12198

sexual transmission

Q45349134

P304

page(s)

e1005619

P577

publication date

2016-05-01

P1433

published in

PLOS Pathogens

Q283209

P1476

title

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

P478

volume

Reverse relations

cites work (P2860)

Q54237723	A Universal Approach to Optimize the Folding and Stability of Prefusion-Closed HIV-1 Envelope Trimers.
Q57811799	Bottlenecks in the transmission of porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and the quasi-species variation of the virus during infection in vaccinated pigs
Q38644317	Brief Report: Selection of HIV-1 Variants With Higher Transmission Potential by 1% Tenofovir Gel Microbicide
Q92524713	CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection
Q89686438	Characterization of HIV-1 diversity in various compartments at the time of primary infection by ultradeep sequencing
Q40393973	Characterization of founder viruses in very early SIV rectal transmission
Q36205668	Deciphering Multiplicity of HIV-1C Infection: Transmission of Closely Related Multiple Viral Lineages
Q36253793	Effect of the Latent Reservoir on the Evolution of HIV at the Within- and Between-Host Levels
Q56797307	Evolution of HIV-1 within untreated individuals and at the population scale in Uganda
Q102210986	Ex vivo rectal explant model reveals potential opposing roles of Natural Killer cells and Marginal Zone-like B cells in HIV-1 infection
Q45323939	HIV-1 and Hepatitis C virus selection bottleneck in Chinese people who inject drugs
Q52590774	Identification of Unequally Represented Founder Viruses Among Tissues in Very Early SIV Rectal Transmission.
Q92376487	Immunization of BLT Humanized Mice Redirects T Cell Responses to Gag and Reduces Acute HIV-1 Viremia
Q40295797	Interferon-I: The Pièce de Résistance of HIV-1 Transmission?
Q56762706	International Congress of Drug Therapy in HIV Infection 23-26 October 2016, Glasgow, UK
Q30490195	Lessons from acute HIV infection
Q61806694	Link between the numbers of particles and variants founding new HIV-1 infections depends on the timing of transmission
Q92523449	Longitudinal within-host evolution of HIV Nef-mediated CD4, HLA and SERINC5 downregulation activity: a case study
Q64968778	Lower Broadly Neutralizing Antibody Responses in Female Versus Male HIV-1 Infected Injecting Drug Users.
Q58089557	Metagenomic sequencing of HIV-1 in the blood and female genital tract reveals little quasispecies diversity during acute infection
Q89575126	Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand
Q38699481	Mother-to-Child HIV Transmission Bottleneck Selects for Consensus Virus with Lower Gag-Protease-Driven Replication Capacity
Q92239576	Negative and Positive Selection Pressure During Sexual Transmission of Transmitted Founder HIV-1
Q58762598	Phylogenetic approach to recover integration dates of latent HIV sequences within-host
Q38849453	Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection
Q33631993	Recent advances in understanding HIV evolution
Q37612507	Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness
Q59359653	Rhesus Macaques Vaccinated with , , and Manifest Early Control of SIVmac239 Replication
Q64089872	Role of HCV Viremia in Corroborated HCV Transmission Events Within Young Adult Injecting Partnerships
Q64979797	Selective use of primate CD4 receptors by HIV-1.
Q54222581	Seminal Simian Immunodeficiency Virus in Chronically Infected Cynomolgus Macaques Is Dominated by Virus Originating from Multiple Genital Organs.
Q93005324	Sexually transmitted infections and HIV in the era of antiretroviral treatment and prevention: the biologic basis for epidemiologic synergy
Q37707466	The Envelope Gene of Transmitted HIV-1 Resists a Late Interferon Gamma-Induced Block.
Q42314454	The HIV-1 transmission bottleneck
Q30240629	Understanding the complex evolution of rapidly mutating viruses with deep sequencing: Beyond the analysis of viral diversity
Q41933352	Vertical transmission of hepatitis C virus: variable transmission bottleneck and evidence of mid-gestation in utero infection

P356	DOI	10.1371/JOURNAL.PPAT.1005619
P8608	Fatcat ID	release_bqkhgwo575fvzeuoa3jolkfu3y
P3181	OpenCitations bibliographic resource ID	1756967
P932	PMC publication ID	4862634
P698	PubMed publication ID	27163788