(Q30469621)

10 August 2017

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

1 reference

10 August 2017

whole genome sequencing

1 reference

10

Sante Gnerre

0 references

Olivier Gasser

Olivier Gasser

30

0 references

Chanson J Brumme

Chanson J Brumme

35

0 references

Zabrina L Brumme

Zabrina L Brumme

34

0 references

Christian Brander

Christian Brander

31

0 references

Huldrych F Günthard

Huldrych F Günthard

33

0 references

Damien C Tully

Damien Tully

20

0 references

Bruce D. Walker

47

Bruce D Walker

1 reference

10 August 2017

41

Florencia Pereyra

1 reference

10 August 2017

45

Marcus Altfeld

1 reference

10 August 2017

17

Hendrik Streeck

1 reference

10 August 2017

40

Eric Rosenberg

1 reference

10 August 2017

48

Todd M Allen

1 reference

10 August 2017

36

Suzane Bazner

1 reference

10 August 2017

37

Jenna Rychert

1 reference

10 August 2017

5

Karen A Power

1 reference

10 August 2017

Adrianne Gladden-Young

23

Adrianne D Gladden

1 reference

10 August 2017

38

Jake P Tinsley

1 reference

10 August 2017

15

Yaoyu Wang

1 reference

10 August 2017

22

Karen L Axten

1 reference

10 August 2017

3

Patrick Charlebois

1 reference

10 August 2017

8

Christine M Malboeuf

1 reference

10 August 2017

12

Rachel L Erlich

1 reference

10 August 2017

13

Lisa M Green

1 reference

10 August 2017

14

Andrew Berical

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10 August 2017

21

Ruchi Newman

1 reference

10 August 2017

46

Bruce W Birren

1 reference

10 August 2017

Matthew R Henn

1

1 reference

10 August 2017

Christian L Boutwell

2

1 reference

10 August 2017

Niall J Lennon

4

1 reference

10 August 2017

Alexander R Macalalad

6

1 reference

10 August 2017

Aaron M Berlin

7

1 reference

10 August 2017

Elizabeth M Ryan

9

1 reference

10 August 2017

Michael C Zody

11

1 reference

10 August 2017

Monica Casali

16

1 reference

10 August 2017

Allyson K Bloom

18

1 reference

10 August 2017

Tim Dudek

19

1 reference

10 August 2017

Laura Battis

24

1 reference

10 August 2017

Michael Kemper

25

1 reference

10 August 2017

Qiandong Zeng

26

1 reference

10 August 2017

Terrance P Shea

27

1 reference

10 August 2017

Sharvari Gujja

28

1 reference

10 August 2017

Carmen Zedlack

29

1 reference

10 August 2017

Christoph Hess

32

1 reference

10 August 2017

Ken H Mayer

39

1 reference

10 August 2017

Joshua Z Levin

42

1 reference

10 August 2017

Sarah K Young

43

1 reference

10 August 2017

Heiko Jessen

44

1 reference

10 August 2017

language of work or name

1 reference

8 March 2012

1 reference

10 August 2017

1 reference

10 August 2017

8

1 reference

10 August 2017

3

1 reference

10 August 2017

e1002529

1 reference

Creative Commons Attribution 4.0 International

10 August 2017

start time

8 March 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Dynamics of viral evolution and CTL responses in HIV-1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Phylogenetic approach reveals that virus genotype largely determines HIV set-point viral load

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Whole-genome characterization of human and simian immunodeficiency virus intrahost diversity by ultradeep pyrosequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Comparison of standard PCR/cloning to single genome sequencing for analysis of HIV-1 populations

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T-lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Mosaic vaccines elicit CD8+ T lymphocyte responses that confer enhanced immune coverage of diverse HIV strains in monkeys

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

HLA-associated immune escape pathways in HIV-1 subtype B Gag, Pol and Nef proteins

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Human immunodeficiency virus type 1-specific CD8+ T-cell responses during primary infection are major determinants of the viral set point and loss of CD4+ T cells

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Adaptation of HIV-1 to human leukocyte antigen class I

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

HLA-B57/B*5801 human immunodeficiency virus type 1 elite controllers select for rare gag variants associated with reduced viral replication capacity and strong cytotoxic T-lymphocyte [corrected] recognition

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Immune-driven recombination and loss of control after HIV superinfection.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Cross-clade detection of HIV-1-specific cytotoxic T lymphocytes does not reflect cross-clade antiviral activity

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Escape and compensation from early HLA-B57-mediated cytotoxic T-lymphocyte pressure on human immunodeficiency virus type 1 Gag alter capsid interactions with cyclophilin A.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

HLA Alleles Associated with Delayed Progression to AIDS Contribute Strongly to the Initial CD8(+) T Cell Response against HIV-1.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Selection on the human immunodeficiency virus type 1 proteome following primary infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Inefficient cytotoxic T lymphocyte-mediated killing of HIV-1-infected cells in vivo

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Selective escape from CD8+ T-cell responses represents a major driving force of human immunodeficiency virus type 1 (HIV-1) sequence diversity and reveals constraints on HIV-1 evolution

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

De novo generation of escape variant-specific CD8+ T-cell responses following cytotoxic T-lymphocyte escape in chronic human immunodeficiency virus type 1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Genome sequencing in microfabricated high-density picolitre reactors

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

The majority of currently circulating human immunodeficiency virus type 1 clade B viruses fail to prime cytotoxic T-lymphocyte responses against an otherwise immunodominant HLA-A2-restricted epitope: implications for vaccine design

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

CD8 Epitope Escape and Reversion in Acute HCV Infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Consequences of cytotoxic T-lymphocyte escape: common escape mutations in simian immunodeficiency virus are poorly recognized in naive hosts

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Selection, transmission, and reversion of an antigen-processing cytotoxic T-lymphocyte escape mutation in human immunodeficiency virus type 1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

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

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Rapid evolution of the neutralizing antibody response to HIV type 1 infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

An SNP map of the human genome generated by reduced representation shotgun sequencing

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Development of a malaria vaccine

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Positive selection of HIV-1 cytotoxic T lymphocyte escape variants during primary infection

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Antiviral pressure exerted by HIV-1-specific cytotoxic T lymphocytes (CTLs) during primary infection demonstrated by rapid selection of CTL escape virus

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Prognosis in HIV-1 infection predicted by the quantity of virus in plasma

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Homologous recombination promoted by reverse transcriptase during copying of two distinct RNA templates

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Quantifying the uncertainty in forecasts of anthropogenic climate change

20 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Precise identification of a human immunodeficiency virus type 1 antigen processing mutant

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

HIV-1 viral escape in infancy followed by emergence of a variant-specific CTL response.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Polyvalent vaccines for optimal coverage of potential T-cell epitopes in global HIV-1 variants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Hitting HIV where it hurts: an alternative approach to HIV vaccine design.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Reducing chimera formation during PCR amplification to ensure accurate genotyping.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1002529

Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3297584

Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22412369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

HIV-1 Epitope-Specific CD8+ T Cell Responses Strongly Associated with Delayed Disease Progression Cross-Recognize Epitope Variants Efficiently

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22412369

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PPAT.1002529

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

22412369

1 reference