HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC (Q21559422)

20 August 2022

Guido Ferrari

8

Guido

Ferrari

1 reference

20 August 2022

Tanmoy Bhattacharya

2

Tanmoy

Bhattacharya

1 reference

20 August 2022

Beatrice H Hahn

12

Beatrice H

Hahn

1 reference

20 August 2022

9

Barton F Haynes

Barton F

Haynes

1 reference

20 August 2022

11

George M Shaw

George M

Shaw

1 reference

20 August 2022

3

Brandon F Keele

Brandon F

Keele

1 reference

20 August 2022

Andrew James McMichael

10

Andrew McMichael

Andrew

McMichael

1 reference

20 August 2022

4

Elena

Giorgi

Elena Giorgi

1 reference

20 August 2022

14

Cathal Seoighe

Cathal

Seoighe

1 reference

20 August 2022

6

Brian

Gaschen

Brian Gaschen

1 reference

20 August 2022

Natasha Wood

1

Natasha

Wood

1 reference

20 August 2022

Michael Liu

series ordinal

5

author given names

Michael

author last names

Liu

1 reference

20 August 2022

Marcus Daniels

series ordinal

7

author given names

Marcus

author last names

Daniels

1 reference

Creative Commons CC0 License

20 August 2022

language of work or name

English

0 references

publication date

May 2009

0 references

published in

PLOS Pathogens

0 references

volume

5

0 references

issue

5

0 references

page(s)

e1000414

0 references

copyright license

start time

8 May 2009

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

0 references

cites work

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Conformational changes of gp120 in epitopes near the CCR5 binding site are induced by CD4 and a CD4 miniprotein mimetic

19 March 2017

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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood

19 March 2017

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Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin

19 March 2017

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Timing the ancestor of the HIV-1 pandemic strains

19 March 2017

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Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models

19 March 2017

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The antigenic structure of the HIV gp120 envelope glycoprotein

19 March 2017

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A codon-based model of nucleotide substitution for protein-coding DNA sequences

19 March 2017

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HyPhy: hypothesis testing using phylogenies

19 March 2017

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Bayes empirical bayes inference of amino acid sites under positive selection

24 March 2017

1 reference

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

7 April 2017

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Control of viremia in simian immunodeficiency virus infection by CD8+ lymphocytes

7 April 2017

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The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens

7 April 2017

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Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene

7 April 2017

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Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase

7 April 2017

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Models of coding sequence evolution

7 April 2017

1 reference

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Estimating selection pressures on HIV-1 using phylogenetic likelihood models.

12 September 2017

1 reference

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

12 September 2017

1 reference

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

12 September 2017

1 reference

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Vaccination and timing influence SIV immune escape viral dynamics in vivo

12 September 2017

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An HIV vaccine--evolving concepts

12 September 2017

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Neutralizing antibody responses in acute human immunodeficiency virus type 1 subtype C infection

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

In vivo CD8+ T cell control of immunodeficiency virus infection in humans and macaques

12 September 2017

1 reference

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Rapid reversion of sequence polymorphisms dominates early human immunodeficiency virus type 1 evolution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Restraining the conformation of HIV-1 gp120 by removing a flexible loop

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Human immunodeficiency virus type 1 V1-V2 envelope loop sequences expand and add glycosylation sites over the course of infection, and these modifications affect antibody neutralization sensitivity

12 September 2017

1 reference

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Induction of multifunctional human immunodeficiency virus type 1 (HIV-1)-specific T cells capable of proliferation in healthy subjects by using a prime-boost regimen of DNA- and modified vaccinia virus Ankara-vectored vaccines expressing HIV-1 Gag c

12 September 2017

1 reference

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Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.

12 September 2017

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

12 September 2017

1 reference

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Consistent patterns of change during the divergence of human immunodeficiency virus type 1 envelope from that of the inoculated virus in simian/human immunodeficiency virus-infected macaques

12 September 2017

1 reference

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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

12 September 2017

1 reference

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Mobile genetic elements: the agents of open source evolution

12 September 2017

1 reference

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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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Rapid viral escape at an immunodominant simian-human immunodeficiency virus cytotoxic T-lymphocyte epitope exacts a dramatic fitness cost

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Fitness costs limit viral escape from cytotoxic T lymphocytes at a structurally constrained epitope

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Determinants of human immunodeficiency virus type 1 escape from the primary CD8+ cytotoxic T lymphocyte response

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

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

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Targeting therapeutics to an exposed and conserved binding element of the HIV-1 fusion protein

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

A novel antiviral intervention results in more accurate assessment of human immunodeficiency virus type 1 replication dynamics and T-cell decay in vivo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Cellular immune responses to HIV.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: deletions and deletions with insertions

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

The C-terminal tail of the gp41 transmembrane envelope glycoprotein of HIV-1 clades A, B, C, and D may exist in two conformations: an analysis of sequence, structure, and function

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

HIV gp120: double lock strategy foils host defences

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

In vivo fitness costs of different Gag CD8 T-cell escape mutant simian-human immunodeficiency viruses for macaques

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Automated phylogenetic detection of recombination using a genetic algorithm

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Recco: recombination analysis using cost optimization

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Reversion of CTL escape–variant immunodeficiency viruses in vivo

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

HIV evolution: CTL escape mutation and reversion after transmission

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Widespread adaptive evolution in the human immunodeficiency virus type 1 genome

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671846

Potential impact of recombination on sitewise approaches for detecting positive natural selection

29 November 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

PCR-sequence-specific primer typing of HLA class I and class II alleles

1 reference

12 December 2020

Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites

1 reference

12 December 2020

Quantifying the uncertainty in forecasts of anthropogenic climate change

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PPAT.1000414

7 January 2021

inferred from DOI database lookup

Identifiers

DOI

10.1371/JOURNAL.PPAT.1000414

1 reference

1 reference

1 reference

1 reference