Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PubWeight™: 0.78‹?›

🔗 View Article (PMC 2630941)

Published in Virol J on November 24, 2008

Authors

Gama P Bandawe1, Darren P Martin, Florette Treurnicht, Koleka Mlisana, Salim S Abdool Karim, Carolyn Williamson, CAPRISA 002 Acute Infection Study Team

Author Affiliations

1: Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory, South Africa. gama.bandawe@uct.ac.za

Articles cited by this

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol (1987) 266.90

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A (2008) 16.54

Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics (2000) 14.84

Rapid evolution of the neutralizing antibody response to HIV type 1 infection. Proc Natl Acad Sci U S A (2003) 12.75

Analyzing the mosaic structure of genes. J Mol Evol (1992) 10.99

HIV evolution: CTL escape mutation and reversion after transmission. Nat Med (2004) 10.21

Statistical methods for detecting molecular adaptation. Trends Ecol Evol (2000) 10.10

Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia. Nature (2000) 9.80

Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature (2004) 9.53

Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science (2002) 9.17

Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62

Envelope-constrained neutralization-sensitive HIV-1 after heterosexual transmission. Science (2004) 8.60

RDP2: recombination detection and analysis from sequence alignments. Bioinformatics (2004) 7.29

RDP: detection of recombination amongst aligned sequences. Bioinformatics (2000) 6.83

Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A (2001) 6.72

Selection for specific sequences in the external envelope protein of human immunodeficiency virus type 1 upon primary infection. J Virol (1993) 6.41

Reversion of CTL escape-variant immunodeficiency viruses in vivo. Nat Med (2004) 6.33

Possible emergence of new geminiviruses by frequent recombination. Virology (1999) 5.74

GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88

The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34

Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences. Bioinformatics (2000) 4.29

Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22

Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization. J Virol (1996) 4.12

Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin. Glycobiology (2004) 3.98

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. J Virol (2007) 3.93

Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89

An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76

Amplified transmission of HIV-1: comparison of HIV-1 concentrations in semen and blood during acute and chronic infection. AIDS (2007) 3.72

Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet (2002) 3.49

Establishing a cohort at high risk of HIV infection in South Africa: challenges and experiences of the CAPRISA 002 acute infection study. PLoS One (2008) 3.40

Progressive reversion of human immunodeficiency virus type 1 resistance mutations in vivo after transmission of a multiply drug-resistant virus. Clin Infect Dis (2003) 2.92

Anti-human immunodeficiency virus type 1 (HIV-1) antibodies 2F5 and 4E10 require surprisingly few crucial residues in the membrane-proximal external region of glycoprotein gp41 to neutralize HIV-1. J Virol (2005) 2.86

Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol (2005) 2.83

Pervasive genomic recombination of HIV-1 in vivo. Genetics (2004) 2.79

Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59

Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48

Robust inference of positive selection from recombining coding sequences. Bioinformatics (2006) 2.43

Amino acid distributions in integral membrane protein structures. Biochim Biophys Acta (2001) 2.43

Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol (2006) 2.36

HIV evolutionary dynamics within and among hosts. AIDS Rev (2006) 2.32

Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol (2003) 2.27

Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J Virol Methods (2006) 1.99

The transmembrane domain in viral fusion: essential role for a conserved glycine residue in vesicular stomatitis virus G protein. Proc Natl Acad Sci U S A (1998) 1.99

Potential impact of recombination on sitewise approaches for detecting positive natural selection. Genet Res (2003) 1.79

The distribution of HIV-1 recombination breakpoints. Infect Genet Evol (2007) 1.65

Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog (2007) 1.62

Comparative study of adaptive molecular evolution in different human immunodeficiency virus groups and subtypes. J Virol (2004) 1.61

Recombination following superinfection by HIV-1. AIDS (2004) 1.57

Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses. Immunol Rev (1997) 1.49

Increased mucosal transmission but not enhanced pathogenicity of the CCR5-tropic, simian AIDS-inducing simian/human immunodeficiency virus SHIV(SF162P3) maps to envelope gp120. J Virol (2003) 1.42

Env length and N-linked glycosylation following transmission of human immunodeficiency virus Type 1 subtype B viruses. Virology (2008) 1.38

Mutational analysis of conserved N-linked glycosylation sites of human immunodeficiency virus type 1 gp41. J Virol (1992) 1.35

Rapid and slow progressors differ by a single MHC class I haplotype in a family of MHC-defined rhesus macaques infected with SIV. Immunol Lett (1999) 1.34

Lipid membrane fusion induced by the human immunodeficiency virus type 1 gp41 N-terminal extremity is determined by its orientation in the lipid bilayer. J Virol (1996) 1.32

The evolutionary value of recombination is constrained by genome modularity. PLoS Genet (2005) 1.26

Evolution of the human immunodeficiency virus envelope gene is dominated by purifying selection. Genetics (2006) 1.20

Interhelical interactions in the gp41 core: implications for activation of HIV-1 membrane fusion. Biochemistry (2002) 1.15

Role of asparagine-linked glycosylation in human immunodeficiency virus type 1 transmembrane envelope function. Virology (1992) 1.14

A dual superinfection and recombination within HIV-1 subtype B 12 years after primoinfection. J Acquir Immune Defic Syndr (2006) 1.13

A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc Biol Sci (2002) 1.12

Thymic pathogenicity of an HIV-1 envelope is associated with increased CXCR4 binding efficiency and V5-gp41-dependent activity, but not V1/V2-associated CD4 binding efficiency and viral entry. Virology (2005) 1.12

Conserved residues in the coiled-coil pocket of human immunodeficiency virus type 1 gp41 are essential for viral replication and interhelical interaction. Virology (2004) 1.11

Evidence for heterogeneous selective pressures in the evolution of the env gene in different human immunodeficiency virus type 1 subtypes. J Virol (2005) 1.09

Constraints to genetic exchange support gene coadaptation in a tripartite RNA virus. PLoS Pathog (2007) 1.07

Genetic evolution of gp41 reveals a highly exclusive relationship between codons 36, 38 and 43 in gp41 under long-term enfuvirtide-containing salvage regimen. AIDS (2006) 1.07

Specific amino acids in the N-terminus of the gp41 ectodomain contribute to the stabilization of a soluble, cleaved gp140 envelope glycoprotein from human immunodeficiency virus type 1. Virology (2006) 1.06

Understanding cytotoxic T-lymphocyte escape during simian immunodeficiency virus infection. Immunol Rev (2001) 1.06

Surface exposure of the HIV-1 env cytoplasmic tail LLP2 domain during the membrane fusion process: interaction with gp41 fusion core. J Biol Chem (2008) 1.01

Role of gp41 glycosylation sites in the biological activity of human immunodeficiency virus type 1 envelope glycoprotein. Virology (1998) 0.95

Membrane interactions of the synthetic N-terminal peptide of HIV-1 gp41 and its structural analogs. Biochim Biophys Acta (1999) 0.94

Impact of natural polymorphism within the gp41 cytoplasmic tail of human immunodeficiency virus type 1 on the intracellular distribution of envelope glycoproteins and viral assembly. J Virol (2006) 0.93

Functional role of the glycan cluster of the human immunodeficiency virus type 1 transmembrane glycoprotein (gp41) ectodomain. J Virol (1993) 0.86

Molecular phylogenetic evidence of cytotoxic T lymphocyte (CTL) selection on human immunodeficiency virus type 1 (HIV-1) Mol Biol Evol (1999) 0.86

Differential functional phenotypes of two primary HIV-1 strains resulting from homologous point mutations in the LLP domains of the envelope gp41 intracytoplasmic domain. Virology (2007) 0.86

Between-host evolution of cytotoxic T-lymphocyte epitopes in human immunodeficiency virus type 1: an approach based on phylogenetically independent comparisons. J Virol (2004) 0.86

The N-terminal 12 residue long peptide of HIV gp41 is the minimal peptide sufficient to induce significant T-cell-like membrane destabilization in vitro. J Mol Biol (2006) 0.84

Annotation of selection strengths in viral genomes. Bioinformatics (2007) 0.83

Characterization of the interaction of two peptides from the N terminus of the NHR domain of HIV-1 gp41 with phospholipid membranes. Biochemistry (2007) 0.82

Articles by these authors

Effectiveness of COL-1492, a nonoxynol-9 vaginal gel, on HIV-1 transmission in female sex workers: a randomised controlled trial. Lancet (2002) 11.02

Genetic and neutralization properties of subtype C human immunodeficiency virus type 1 molecular env clones from acute and early heterosexually acquired infections in Southern Africa. J Virol (2006) 5.25

Initial B-cell responses to transmitted human immunodeficiency virus type 1: virion-binding immunoglobulin M (IgM) and IgG antibodies followed by plasma anti-gp41 antibodies with ineffective control of initial viremia. J Virol (2008) 5.24

Who infects whom? HIV-1 concordance and discordance among migrant and non-migrant couples in South Africa. AIDS (2003) 4.87

HIV prevention transformed: the new prevention research agenda. Lancet (2011) 4.23

The neutralization breadth of HIV-1 develops incrementally over four years and is associated with CD4+ T cell decline and high viral load during acute infection. J Virol (2011) 4.18

Safety and efficacy of the HVTN 503/Phambili study of a clade-B-based HIV-1 vaccine in South Africa: a double-blind, randomised, placebo-controlled test-of-concept phase 2b study. Lancet Infect Dis (2011) 3.71

Influenza vaccination of pregnant women and protection of their infants. N Engl J Med (2014) 3.68

Establishing a cohort at high risk of HIV infection in South Africa: challenges and experiences of the CAPRISA 002 acute infection study. PLoS One (2008) 3.40

Research capacity. Enabling the genomic revolution in Africa. Science (2014) 3.05

Limited neutralizing antibody specificities drive neutralization escape in early HIV-1 subtype C infection. PLoS Pathog (2009) 2.70

Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59

Evolution of an HIV glycan-dependent broadly neutralizing antibody epitope through immune escape. Nat Med (2012) 2.48

Robust inference of positive selection from recombining coding sequences. Bioinformatics (2006) 2.43

Symptomatic vaginal discharge is a poor predictor of sexually transmitted infections and genital tract inflammation in high-risk women in South Africa. J Infect Dis (2012) 2.42

Recombination patterns in aphthoviruses mirror those found in other picornaviruses. J Virol (2006) 2.36

CD8 T-cell recognition of multiple epitopes within specific Gag regions is associated with maintenance of a low steady-state viremia in human immunodeficiency virus type 1-seropositive patients. J Virol (2006) 2.32

The c3-v4 region is a major target of autologous neutralizing antibodies in human immunodeficiency virus type 1 subtype C infection. J Virol (2007) 2.29

Incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of HIV-1 subtype C-infected female sex workers. J Infect Dis (2004) 2.29

Potent and broad neutralization of HIV-1 subtype C by plasma antibodies targeting a quaternary epitope including residues in the V2 loop. J Virol (2011) 2.26

Dual HIV-1 infection associated with rapid disease progression. Lancet (2004) 2.17

Uptake of provider-initiated HIV testing and counseling among women attending an urban sexually transmitted disease clinic in South Africa - missed opportunities for early diagnosis of HIV infection. AIDS Care (2010) 2.08

Vertical T cell immunodominance and epitope entropy determine HIV-1 escape. J Clin Invest (2012) 2.05

Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression. AIDS (2013) 2.04

Regional clustering of shared neutralization determinants on primary isolates of clade C human immunodeficiency virus type 1 from South Africa. J Virol (2002) 1.97

Plasma cytokine levels during acute HIV-1 infection predict HIV disease progression. AIDS (2010) 1.94

Enrolling adolescents in research on HIV and other sensitive issues: lessons from South Africa. PLoS Med (2006) 1.90

Broad neutralization of human immunodeficiency virus type 1 mediated by plasma antibodies against the gp41 membrane proximal external region. J Virol (2009) 1.78

A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol (2013) 1.69

Generation of genic diversity among Streptococcus pneumoniae strains via horizontal gene transfer during a chronic polyclonal pediatric infection. PLoS Pathog (2010) 1.66

Viral escape from HIV-1 neutralizing antibodies drives increased plasma neutralization breadth through sequential recognition of multiple epitopes and immunotypes. PLoS Pathog (2013) 1.65

Avoidance of protein fold disruption in natural virus recombinants. PLoS Pathog (2007) 1.62

The spread of tomato yellow leaf curl virus from the Middle East to the world. PLoS Pathog (2010) 1.62

Association of HIV-specific and total CD8+ T memory phenotypes in subtype C HIV-1 infection with viral set point. J Immunol (2009) 1.49

Dragonfly cyclovirus, a novel single-stranded DNA virus discovered in dragonflies (Odonata: Anisoptera). J Gen Virol (2011) 1.46

Molecular mechanisms of recombination restriction in the envelope gene of the human immunodeficiency virus. PLoS Pathog (2009) 1.45

Relationship between levels of inflammatory cytokines in the genital tract and CD4+ cell counts in women with acute HIV-1 infection. J Infect Dis (2008) 1.42

Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. BMC Bioinformatics (2009) 1.42

Alphavirus replicon particles as candidate HIV vaccines. IUBMB Life (2002) 1.41

Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus. Arch Virol (2014) 1.38

Novel myco-like DNA viruses discovered in the faecal matter of various animals. Virus Res (2013) 1.35

Revision of Begomovirus taxonomy based on pairwise sequence comparisons. Arch Virol (2015) 1.34

Genetic characteristics of HIV-1 subtype C envelopes inducing cross-neutralizing antibodies. Virology (2007) 1.31

African AIDS vaccine programme for a coordinated and collaborative vaccine development effort on the continent. PLoS Med (2008) 1.23

Interleukin-10 promoter polymorphisms influence HIV-1 susceptibility and primary HIV-1 pathogenesis. J Infect Dis (2009) 1.21

Human immunodeficiency virus-specific gamma interferon enzyme-linked immunospot assay responses targeting specific regions of the proteome during primary subtype C infection are poor predictors of the course of viremia and set point. J Virol (2008) 1.20

Genital tract inflammation during early HIV-1 infection predicts higher plasma viral load set point in women. J Infect Dis (2012) 1.17

Recruitment of high risk women for HIV prevention trials: baseline HIV prevalence and sexual behavior in the CAPRISA 004 tenofovir gel trial. Trials (2011) 1.15

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. J Virol (2013) 1.15

Molecular characterisation of a novel cassava associated circular ssDNA virus. Virus Res (2012) 1.14

Multiple pathways of escape from HIV broadly cross-neutralizing V2-dependent antibodies. J Virol (2013) 1.13

Contraceptive choices, pregnancy rates, and outcomes in a microbicide trial. Obstet Gynecol (2011) 1.13

Mannose-rich glycosylation patterns on HIV-1 subtype C gp120 and sensitivity to the lectins, Griffithsin, Cyanovirin-N and Scytovirin. Virology (2010) 1.13

The HIV-1 epidemic: low- to middle-income countries. Cold Spring Harb Perspect Med (2012) 1.12

Recombination, decreased host specificity and increased mobility may have driven the emergence of maize streak virus as an agricultural pathogen. J Gen Virol (2008) 1.12

Design and preclinical evaluation of a multigene human immunodeficiency virus type 1 subtype C DNA vaccine for clinical trial. J Gen Virol (2006) 1.10

Systematic phylogenetic analysis of influenza A virus reveals many novel mosaic genome segments. Infect Genet Evol (2013) 1.09

Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. Clin Infect Dis (2011) 1.09

APOBEC3G expression is dysregulated in primary HIV-1 infection and polymorphic variants influence CD4+ T-cell counts and plasma viral load. AIDS (2010) 1.08

Extensive recombination detected among beak and feather disease virus isolates from breeding facilities in Poland. J Gen Virol (2013) 1.07

Utilizing nucleic acid amplification to identify acute HIV infection. AIDS (2007) 1.07

Evidence of unique genotypes of beak and feather disease virus in southern Africa. J Virol (2004) 1.06

Genetic variability among complete human respiratory syncytial virus subgroup A genomes: bridging molecular evolutionary dynamics and epidemiology. PLoS One (2012) 1.06

South West Indian Ocean islands tomato begomovirus populations represent a new major monopartite begomovirus group. J Gen Virol (2005) 1.06

Longitudinal analysis of HIV type 1 subtype C envelope sequences from South Africa. AIDS Res Hum Retroviruses (2007) 1.06

HIV type 1 subtype C gag and nef diversity in Southern Africa. AIDS Res Hum Retroviruses (2007) 1.05

A protocol for the rapid isolation of full geminivirus genomes from dried plant tissue. J Virol Methods (2008) 1.05

Construction, characterization, and immunogenicity of a multigene modified vaccinia Ankara (MVA) vaccine based on HIV type 1 subtype C. AIDS Res Hum Retroviruses (2008) 1.05

Co-enrollment in multiple HIV prevention trials - experiences from the CAPRISA 004 Tenofovir gel trial. Contemp Clin Trials (2011) 1.04

Fluidity of HIV-1-specific T-cell responses during acute and early subtype C HIV-1 infection and associations with early disease progression. J Virol (2010) 1.04