The dynamics of HIV-1 adaptation in early infection. (Q42593675)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22209906%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

title

The dynamics of HIV-1 adaptation in early infection (English)

1 reference

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19 January 2020

1

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19 January 2020

author name string

Jack da Silva

series ordinal

1

1 reference

3 November 2017

language of work or name

English

0 references

publication date

29 December 2011

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19 January 2020

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19 January 2020

volume

190

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19 January 2020

issue

3

1 reference

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19 January 2020

page(s)

1087-1099

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22209906%20AND%20SRC:MED&resulttype=core&format=json

Timing of the components of the HIV life cycle in productively infected CD4+ T cells in a population of HIV-infected individuals.

19 January 2020

cites work

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Fitness costs and diversity of the cytotoxic T lymphocyte (CTL) response determine the rate of CTL escape during acute and chronic phases of HIV infection

28 May 2018

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Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule

28 May 2018

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Genetic draft and quasi-neutrality in large facultatively sexual populations

28 May 2018

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Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

28 May 2018

1 reference

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Transmission of single and multiple viral variants in primary HIV-1 subtype C infection

28 May 2018

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Classic selective sweeps were rare in recent human evolution

28 May 2018

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28 May 2018

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

28 May 2018

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28 May 2018

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Accurately measuring recombination between closely related HIV-1 genomes

28 May 2018

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Targeting early infection to prevent HIV-1 mucosal transmission.

28 May 2018

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Fitness epistasis and constraints on adaptation in a human immunodeficiency virus type 1 protein region

28 May 2018

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Recombination rate and selection strength in HIV intra-patient evolution

28 May 2018

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The immune response during acute HIV-1 infection: clues for vaccine development

28 May 2018

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Pervasive natural selection in the Drosophila genome?

28 May 2018

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

28 May 2018

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

28 May 2018

1 reference

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Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation

28 May 2018

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Pervasive hitchhiking at coding and regulatory sites in humans

28 May 2018

1 reference

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Selection dramatically reduces effective population size in HIV-1 infection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

The Hill-Robertson effect: evolutionary consequences of weak selection and linkage in finite populations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Interference among deleterious mutations favours sex and recombination in finite populations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Compensatory substitutions restore normal core assembly in simian immunodeficiency virus isolates with Gag epitope cytotoxic T-lymphocyte escape mutations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Sexual transmission of single human immunodeficiency virus type 1 virions encoding highly polymorphic multisite cytotoxic T-lymphocyte escape variants

28 May 2018

1 reference

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Pervasive genomic recombination of HIV-1 in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Influence of random genetic drift on human immunodeficiency virus type 1 env evolution during chronic infection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Dynamics of HIV-1 recombination in its natural target cells

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Identification of Sequential Viral Escape Mutants Associated with Altered T-Cell Responses in a Human Immunodeficiency Virus Type 1-Infected Individual

28 May 2018

1 reference

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Virologic and immunologic determinants of heterosexual transmission of human immunodeficiency virus type 1 in Africa.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Evolution of lamivudine resistance in human immunodeficiency virus type 1-infected individuals: the relative roles of drift and selection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Genetic drift in an infinite population. The pseudohitchhiking model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Viral load and heterosexual transmission of human immunodeficiency virus type 1. Rakai Project Study Group

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Coalescent estimates of HIV-1 generation time in vivo

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Stochastic processes strongly influence HIV-1 evolution during suboptimal protease-inhibitor therapy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Effective size and polymorphism of linked neutral loci in populations under directional selection.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Quantification of latent tissue reservoirs and total body viral load in HIV-1 infection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

HIV-1: gambling on the evolution of drug resistance?

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Viral counts count in HIV infection

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Substitution processes in molecular evolution. I. Uniform and clustered substitutions in a haploid model.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

HIV population dynamics in vivo: implications for genetic variation, pathogenesis, and therapy

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

The evolutionary advantage of recombination

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

The hitch-hiking effect of a favourable gene

28 May 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

28 May 2018

12 December 2020

Lack of polymorphism on the Drosophila fourth chromosome resulting from selection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

On the number of segregating sites in genetical models without recombination

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

A robust measure of HIV-1 population turnover within chronically infected individuals.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Recombination: Multiply infected spleen cells in HIV patients

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

Selection forces and constraints on retroviral sequence variation.

16 August 2018

1 reference

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The fate of competing beneficial mutations in an asexual population.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

A controlled trial of zidovudine in primary human immunodeficiency virus infection

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3296244

The effect of linkage on limits to artificial selection

16 August 2018

1 reference

12 December 2020

Classification of hypotheses on the advantage of amphimixis

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12 December 2020

Effective population size when fertility is inherited

1 reference

12 December 2020

Molecular Evolution Over the Mutational Landscape

1 reference

12 December 2020

The population genetics of adaptation: the adaptation of DNA sequences

1 reference

12 December 2020

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

1 reference

12 December 2020

On the theory of random mating

1 reference

12 December 2020

CLASSIFICATION OF THE FACTORS OF EVOLUTION

1 reference

12 December 2020

10.1534/GENETICS.111.136366

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22209906%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22209906%20AND%20SRC:MED&resulttype=core&format=json

19 January 2020

PubMed publication ID

22209906

1 reference