Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

Journal Article · · PLoS Pathogens
 [1];  [2];  [3];  [4];  [5];  [6];  [6];  [7];  [7];  [5];  [3];  [3];  [2];  [8]
  1. University of Cape Town (South Africa); Centre for High Performance Computing (CHPR), Cape Town (South Africa); DOE/OSTI
  2. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Santa Fe Institute (SFI), Santa Fe, NM (United States)
  3. University of Alabama, Birmingham, AL (United States)
  4. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); University of Massachusetts, Amherst, MA (United States)
  5. University of Oxford (United Kingdom)
  6. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
  7. Duke University, Durham, NC (United States)
  8. University of Cape Town (South Africa); Centre for High Performance Computing (CHPR), Cape Town (South Africa); National University of Ireland Galway (Ireland)
+ Show Author Affiliations

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual’s HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
Bill & Melinda Gates Foundation; National Institutes of Health (NIH); UAB Center for AIDS Research; USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC52-06NA25396
OSTI ID:
1627892
Journal Information:
PLoS Pathogens, Journal Name: PLoS Pathogens Journal Issue: 5 Vol. 5; ISSN 1553-7374
Publisher:
Public Library of ScienceCopyright Statement
Country of Publication:
United States
Language:
English

References (105)

Estimating selection pressures on HIV-1 using phylogenetic likelihood models journal October 2008
Widespread Adaptive Evolution in the Human Immunodeficiency Virus Type 1 Genome journal August 2003
HIV gp120: double lock strategy foils host defences journal August 1998
Potential impact of recombination on sitewise approaches for detecting positive natural selection journal April 2003
Conformational Changes of gp120 in Epitopes near the CCR5 Binding Site Are Induced by CD4 and a CD4 Miniprotein Mimetic † journal July 1999
Tat-specific cytotoxic T lymphocytes select for SIV escape variants during resolution of primary viraemia journal September 2000
Cellular immune responses to HIV journal April 2001
Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS journal February 1997
HIV evolution: CTL escape mutation and reversion after transmission journal February 2004
Mobile genetic elements: the agents of open source evolution journal September 2005
Restraining the conformation of HIV-1 gp120 by removing a flexible loop journal September 2006
Antibody vs. HIV in a clash of evolutionary titans journal October 2005
Targeting therapeutics to an exposed and conserved binding element of the HIV-1 fusion protein journal April 2003
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood journal October 2003
Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response journal November 2004
Models of coding sequence evolution journal October 2008
HyPhy: hypothesis testing using phylogenies journal October 2004
Recco: recombination analysis using cost optimization journal February 2006
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene journal March 1998
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites journal July 2003
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm journal July 2006
Simulation Study of the Reliability and Robustness of the Statistical Methods for Detecting Positive Selection at Single Amino Acid Sites journal November 2002
Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection journal January 2003
HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry journal January 2007
Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses journal October 1997
Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission journal March 2004
AIDS/HIV: Finding Footprints Among the Trees journal March 2007
The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens journal June 1998
Control of Viremia in Simian Immunodeficiency Virus Infection by CD8+ Lymphocytes journal February 1999
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 journal September 2006
Rapid Reversion of Sequence Polymorphisms Dominates Early Human Immunodeficiency Virus Type 1 Evolution journal October 2006
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. journal January 1995
A Novel Antiviral Intervention Results in More Accurate Assessment of Human Immunodeficiency Virus Type 1 Replication Dynamics and T-Cell Decay In Vivo journal April 2003
Selection, Transmission, and Reversion of an Antigen-Processing Cytotoxic T-Lymphocyte Escape Mutation in Human Immunodeficiency Virus Type 1 Infection journal July 2004
Fitness Costs Limit Viral Escape from Cytotoxic T Lymphocytes at a Structurally Constrained Epitope journal December 2004
Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) Envelope Variation and Neutralizing Antibody Responses during Transmission of HIV-1 Subtype B journal May 2005
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 journal November 2005
Rapid Viral Escape at an Immunodominant Simian-Human Immunodeficiency Virus Cytotoxic T-Lymphocyte Epitope Exacts a Dramatic Fitness Cost journal May 2005
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 Coupled to CD8+ T-Cell Epitopes journal May 2006
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 journal January 2006
Human Immunodeficiency Virus Type 1 env Evolves toward Ancestral States upon Transmission to a New Host journal February 2006
Vaccination and Timing Influence SIV Immune Escape Viral Dynamics In Vivo journal January 2008
Transmission of HIV-1 CTL Escape Variants Provides HLA-Mismatched Recipients with a Survival Advantage journal March 2008
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites journal October 2004
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
  • F., Salazar-Gonzalez, Jesus; P., Busch, Michael; S., Perelson, Alan
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/f6s9-vz03
text January 2008
Estimating selection pressures on HIV-1 using phylogenetic likelihood models journal October 2008
Widespread Adaptive Evolution in the Human Immunodeficiency Virus Type 1 Genome journal August 2003
HIV gp120: double lock strategy foils host defences journal August 1998
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 journal July 2005
Potential impact of recombination on sitewise approaches for detecting positive natural selection journal April 2003
Conformational Changes of gp120 in Epitopes near the CCR5 Binding Site Are Induced by CD4 and a CD4 Miniprotein Mimetic † journal July 1999
The antigenic structure of the HIV gp120 envelope glycoprotein journal June 1998
Quantifying the uncertainty in forecasts of anthropogenic climate change journal October 2000
Cellular immune responses to HIV journal April 2001
Late escape from an immunodominant cytotoxic T-lymphocyte response associated with progression to AIDS journal February 1997
HIV evolution: CTL escape mutation and reversion after transmission journal February 2004
Reversion of CTL escape–variant immunodeficiency viruses in vivo journal February 2004
Mobile genetic elements: the agents of open source evolution journal September 2005
Restraining the conformation of HIV-1 gp120 by removing a flexible loop journal September 2006
An HIV Vaccine — Evolving Concepts journal May 2007
Antibody vs. HIV in a clash of evolutionary titans journal October 2005
In vivo CD8+ T cell control of immunodeficiency virus infection in humans and macaques journal April 2007
Targeting therapeutics to an exposed and conserved binding element of the HIV-1 fusion protein journal April 2003
Statistical significance for genomewide studies journal July 2003
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. journal August 1990
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood journal October 2003
Determinants of Human Immunodeficiency Virus Type 1 Escape from the Primary CD8+ Cytotoxic T Lymphocyte Response journal November 2004
Models of coding sequence evolution journal October 2008
HyPhy: hypothesis testing using phylogenies journal October 2004
Recco: recombination analysis using cost optimization journal February 2006
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene journal March 1998
Effect of Recombination on the Accuracy of the Likelihood Method for Detecting Positive Selection at Amino Acid Sites journal July 2003
Tracking global patterns of N-linked glycosylation site variation in highly variable viral glycoproteins: HIV, SIV, and HCV envelopes and influenza hemagglutinin journal July 2004
Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection journal January 2005
Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm journal July 2006
Simulation Study of the Reliability and Robustness of the Statistical Methods for Detecting Positive Selection at Single Amino Acid Sites journal November 2002
Estimating Synonymous and Nonsynonymous Substitution Rates Under Realistic Evolutionary Models journal January 2000
Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection journal January 2003
HIV-1 subtype A envelope variants from early in infection have variable sensitivity to neutralization and to inhibitors of viral entry journal January 2007
Co-evolution of human immunodeficiency virus and cytotoxic T-lymphocyte responses journal October 1997
Envelope-Constrained Neutralization-Sensitive HIV-1 After Heterosexual Transmission journal March 2004
Founder Effects in the Assessment of HIV Polymorphisms and HLA Allele Associations journal March 2007
The HIV-1 Envelope Glycoproteins: Fusogens, Antigens, and Immunogens journal June 1998
Control of Viremia in Simian Immunodeficiency Virus Infection by CD8+ Lymphocytes journal February 1999
Timing the Ancestor of the HIV-1 Pandemic Strains journal June 2000
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 journal September 2006
Neutralizing Antibody Responses in Acute Human Immunodeficiency Virus Type 1 Subtype C Infection journal April 2007
Rapid Reversion of Sequence Polymorphisms Dominates Early Human Immunodeficiency Virus Type 1 Evolution journal October 2006
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing journal February 2008
In Vivo Fitness Costs of Different Gag CD8 T-Cell Escape Mutant Simian-Human Immunodeficiency Viruses for Macaques journal March 2007
Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. journal January 1995
A Novel Antiviral Intervention Results in More Accurate Assessment of Human Immunodeficiency Virus Type 1 Replication Dynamics and T-Cell Decay In Vivo journal April 2003
Selection, Transmission, and Reversion of an Antigen-Processing Cytotoxic T-Lymphocyte Escape Mutation in Human Immunodeficiency Virus Type 1 Infection journal July 2004
Fitness Costs Limit Viral Escape from Cytotoxic T Lymphocytes at a Structurally Constrained Epitope journal December 2004
Characterization of Human Immunodeficiency Virus Type 1 (HIV-1) Envelope Variation and Neutralizing Antibody Responses during Transmission of HIV-1 Subtype B journal May 2005
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 journal May 2005
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 journal November 2005
Rapid Viral Escape at an Immunodominant Simian-Human Immunodeficiency Virus Cytotoxic T-Lymphocyte Epitope Exacts a Dramatic Fitness Cost journal May 2005
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 Coupled to CD8+ T-Cell Epitopes journal May 2006
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 journal January 2006
Human Immunodeficiency Virus Type 1 env Evolves toward Ancestral States upon Transmission to a New Host journal February 2006
Vaccination and Timing Influence SIV Immune Escape Viral Dynamics In Vivo journal January 2008
Transmission of HIV-1 CTL Escape Variants Provides HLA-Mismatched Recipients with a Survival Advantage journal March 2008
Accuracy and Power of Statistical Methods for Detecting Adaptive Evolution in Protein Coding Sequences and for Identifying Positively Selected Sites journal October 2004
HIV-1 Epitope-Specific CD8 + T Cell Responses Strongly Associated with Delayed Disease Progression Cross-Recognize Epitope Variants Efficiently journal May 2006

Cited By (76)

Random Single Amino Acid Deletion Sampling Unveils Structural Tolerance and the Benefits of Helical Registry Shift on GFP Folding and Structure journal June 2014
Inhibiting APOBEC3 Activity with Single-Stranded DNA Containing 2′-Deoxyzebularine Analogues journal November 2018
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection journal June 2009
Perspective: APOBEC mutagenesis in drug resistance and immune escape in HIV and cancer evolution journal March 2018
Role of the host restriction factor APOBEC3 on papillomavirus evolution journal January 2015
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver journal January 2018
Phylogenetic measures of indel rate variation among the HIV-1 group M subtypes journal January 2018
Defining epitope coverage requirements for T cell-based HIV vaccines: Theoretical considerations and practical applications journal December 2011
Increased APOBEC3G and APOBEC3F expression is associated with low viral load and prolonged survival in simian immunodeficiency virus infected rhesus monkeys journal September 2011
Host restriction factors in retroviral infection: promises in virus-host interaction journal December 2012
Emerging complexities of APOBEC3G action on immunity and viral fitness during HIV infection and treatment journal April 2012
HIV-1 tolerates changes in A-count in a small segment of the pol gene journal September 2017
HIV-1 immunogens and strategies to drive antibody responses towards neutralization breadth journal November 2018
Evolutionary Biology for the 21st Century journal January 2013
APOBEC3G-Induced Hypermutation of Human Immunodeficiency Virus Type-1 Is Typically a Discrete “All or Nothing” Phenomenon journal March 2012
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing journal August 2010
In–Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection journal February 2012
Viral Diversity and Diversification of Major Non-Structural Genes vif, vpr, vpu, tat exon 1 and rev exon 1 during Primary HIV-1 Subtype C Infection journal May 2012
Resistance Mutations and CTL Epitopes in Archived HIV-1 DNA of Patients on Antiviral Treatment: Toward a New Concept of Vaccine journal July 2013
Genetic Imprint of Vaccination on Simian/Human Immunodeficiency Virus Type 1 Transmitted Viral Genomes in Rhesus Macaques journal August 2013
Potential Elucidation of a Novel CTL Epitope in HIV-1 Protease by the Protease Inhibitor Resistance Mutation L90M journal August 2013
Lower HIV Provirus Levels Are Associated with More APOBEC3G Protein in Blood Resting Memory CD4+ T Lymphocytes of Controllers In Vivo journal October 2013
Positioning of APOBEC3G/F Mutational Hotspots in the Human Immunodeficiency Virus Genome Favors Reduced Recognition by CD8+ T Cells journal April 2014
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men journal May 2010
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections journal September 2011
Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape journal May 2012
Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection journal July 2014
Interferon-α Subtypes in an Ex Vivo Model of Acute HIV-1 Infection: Expression, Potency and Effector Mechanisms journal November 2015
Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation journal May 2016
Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality journal August 2016
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection journal July 2017
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation text January 2016
APOBEC3G Regulation of the Evolutionary Race Between Adaptive Immunity and Viral Immune Escape Is Deeply Imprinted in the HIV Genome journal January 2019
AID and APOBECs span the gap between innate and adaptive immunity journal October 2014
Retroviral Vectors for Analysis of Viral Mutagenesis and Recombination journal September 2014
Calculating site-specific evolutionary rates at the amino-acid or codon level yields similar rate estimates journal January 2017
Quasispecies characters of hepatitis B virus in immunoprophylaxis failure infants journal April 2018
Interactions of host APOBEC3 restriction factors with HIV-1 in vivo: implications for therapeutics journal January 2010
HIV-1 and interferons: who's interfering with whom? journal April 2015
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection journal June 2009
Genetic Diversity as a Marker for Timing Infection in HIV-Infected Patients: Evaluation of a 6-Month Window and Comparison With BED journal September 2012
Previously Transmitted HIV-1 Strains Are Preferentially Selected During Subsequent Sexual Transmissions journal November 2012
Role of the host restriction factor APOBEC3 on papillomavirus evolution journal January 2015
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver journal January 2018
Estimating the mutational fitness effects distribution during early HIV infection journal July 2018
Estimating the Mutational Fitness Effects Distribution during early HIV infection posted_content September 2017
Impact of suboptimal APOBEC3G neutralization on the emergence of HIV drug resistance in humanized mice journal January 2019
Biological pathways to adaptability - interactions between genome, epigenome, nervous system and environment for adaptive behavior journal December 2011
Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice journal February 2020
Characterization of the Plasmacytoid Dendritic Cell Response to Transmitted/Founder and Nontransmitted Variants of HIV-1 journal October 2018
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation journal July 2016
Suppression of HIV-1 Infection by APOBEC3 Proteins in Primary Human CD4 + T Cells Is Associated with Inhibition of Processive Reverse Transcription as Well as Excessive Cytidine Deamination journal November 2012
Natural Single-Nucleotide Variations in the HIV-1 Genomic SA1prox Region Can Alter Viral Replication Ability by Regulating Vif Expression Levels journal May 2016
Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages journal December 2011
Interplay between HIV-1 and Host Genetic Variation: A Snapshot into Its Impact on AIDS and Therapy Response journal January 2012
Recent developments in the effort to cure HIV infection: going beyond N = 1 journal February 2016
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model journal October 2010
Host restriction factors in retroviral infection: promises in virus-host interaction journal December 2012
HIV-1 immunogens and strategies to drive antibody responses towards neutralization breadth journal November 2018
Natural Polymorphisms in Human APOBEC3H and HIV-1 Vif Combine in Primary T Lymphocytes to Affect Viral G-to-A Mutation Levels and Infectivity journal November 2014
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing journal August 2010
Lower HIV Provirus Levels Are Associated with More APOBEC3G Protein in Blood Resting Memory CD4+ T Lymphocytes of Controllers In Vivo journal October 2013
Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections journal September 2011
Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape journal May 2012
Minimal Contribution of APOBEC3-Induced G-to-A Hypermutation to HIV-1 Recombination and Genetic Variation journal May 2016
Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality journal August 2016
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection journal July 2017
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
  • S., Perelson, Alan; Christina, Ochsenbauer-Jambor,; C., Kappas, John
  • The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/1n1a-3d64
text January 2009
Rare HIV-1 transmitted/founder lineages identified by deep viral sequencing contribute to rapid shifts in dominant quasispecies during acute and early infection text January 2017
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection text January 2009
HIV-1 Protease, Reverse Transcriptase, and Integrase Variation text January 2016
AID and APOBECs span the gap between innate and adaptive immunity journal October 2014
Evolution of Foamy Viruses: The Most Ancient of All Retroviruses journal September 2013
Estimating the mutational fitness effects distribution during early HIV infection text January 2018
The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence journal July 2016
Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver text January 2018

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
HIV-1
evolutionary immunology
immune response
microbial mutation
phylogenetic analysis
sequence alignment
substitution mutation
viral evolution