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Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
TLDR
A mathematical model of random viral evolution and phylogenetic tree construction is developed and used to analyze 3,449 complete env sequences derived by single genome amplification from 102 subjects with acute HIV-1 (clade B) infection, suggesting a finite window of potential vulnerability of HIV- 1 to vaccine-elicited immune responses, although phenotypic properties of transmitted Envs pose a formidable defense.
Timing the ancestor of the HIV-1 pandemic strains.
TLDR
Using a comprehensive full-length envelope sequence alignment, the date of the last common ancestor of the main group of HIV-1 is estimated to be 1931 (1915-41).
Structure of a V3-Containing HIV-1 gp120 Core
TLDR
The third variable region (V3) of the HIV-1 gp120 envelope glycoprotein is immunodominant and contains features essential for coreceptor binding, which provides a structural rationale for the role of V3 in HIV entry and neutralization.
Comprehensive Cross-Clade Neutralization Analysis of a Panel of Anti-Human Immunodeficiency Virus Type 1 Monoclonal Antibodies
TLDR
Broadly neutralizing monoclonal antibodies are potentially important tools in human immunodeficiency virus type 1 (HIV-1) vaccine design and have implications for passive-immunization studies in countries where clade C viruses are common, given that only MAbs b12 and 4E10 were effective against viruses from this clade.
Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission
TLDR
For eight heterosexual transmission pairs, it is shown that recipient viruses were monophyletic, encoding compact, glycan-restricted envelope glycoproteins, and that these viruses were uniquely sensitive to neutralization by antibody from the transmitting partner.
HIV-1 Nomenclature Proposal
A clear and consistent genetic classification of human immunodeficiency virus-type 1 (HIV-1) strains continues to be of great utility in epidemiological tracking of the AIDS pandemic and in vaccine
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
TLDR
Kinetic analysis and mathematical modeling of virus immune escape showed that the contribution of CD8 T cell–mediated killing of productively infected cells was earlier and much greater than previously recognized and that it contributed to the initial decline of plasma virus in acute infection.
Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA
TLDR
Analysis of class I restricted CD8+ T-cell responses against human immunodeficiency virus (HIV-1) indicates that the principal focus of HIV-specific activity is at the HLA-B locus, consistent with the observation that B alleles evolve more rapidly than A alleles.
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
TLDR
Viral properties associated with mucosal HIV-1 transmission and a limited set of rapidly evolving adaptive mutations driven primarily, but not exclusively, by early cytotoxic T cell responses are revealed.
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing
TLDR
It is shown that HIV-1 env genes, other viral genes, and even full-length viral genomes responsible for productive clinical infection can be identified by SGA analysis of plasma virus sampled at intervals typical in large-scale vaccine trials and that pathways of viral diversification and immune escape can be determined accurately.
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