Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants
Abstract
Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. With well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. As a result, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogensmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Santa Fe Inst. (SFI), Santa Fe, NM (United States)
- Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine
- Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine
- Duke Univ. Medical Center, Durham, NC (United States). Duke Human Vaccine Inst.
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE; National Institute of Allergy and Infectious Disease (NIAID); National Institutes of Health (NIH)
- OSTI Identifier:
- 1263552
- Alternate Identifier(s):
- OSTI ID: 1321761
- Report Number(s):
- LA-UR-15-24067
Journal ID: ISSN 1999-4915; VIRUBR; PII: v7102881
- Grant/Contract Number:
- UM1 AI100645; AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Viruses
- Additional Journal Information:
- Journal Volume: 7; Journal Issue: 10; Journal ID: ISSN 1999-4915
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; human immunodeficiency virus type 1; vaccine; neutralizing antibodies; immunogen design; envelope glycoprotein; coevolution; immune escape; quasispecies; antigenic swarm; selection; biological science
Citation Formats
Hraber, Peter, Korber, Bette, Wagh, Kshitij, Giorgi, Elena, Bhattacharya, Tanmoy, Gnanakaran, S., Lapedes, Alan S., Learn, Gerald H., Kreider, Edward F., Li, Yingying, Shaw, George M., Hahn, Beatrice H., Montefiori, David C., Alam, S. Munir, Bonsignori, Mattia, Moody, M. Anthony, Liao, Hua-Xin, Gao, Feng, and Haynes, Barton. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants. United States: N. p., 2015.
Web. doi:10.3390/v7102881.
Hraber, Peter, Korber, Bette, Wagh, Kshitij, Giorgi, Elena, Bhattacharya, Tanmoy, Gnanakaran, S., Lapedes, Alan S., Learn, Gerald H., Kreider, Edward F., Li, Yingying, Shaw, George M., Hahn, Beatrice H., Montefiori, David C., Alam, S. Munir, Bonsignori, Mattia, Moody, M. Anthony, Liao, Hua-Xin, Gao, Feng, & Haynes, Barton. Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants. United States. https://doi.org/10.3390/v7102881
Hraber, Peter, Korber, Bette, Wagh, Kshitij, Giorgi, Elena, Bhattacharya, Tanmoy, Gnanakaran, S., Lapedes, Alan S., Learn, Gerald H., Kreider, Edward F., Li, Yingying, Shaw, George M., Hahn, Beatrice H., Montefiori, David C., Alam, S. Munir, Bonsignori, Mattia, Moody, M. Anthony, Liao, Hua-Xin, Gao, Feng, and Haynes, Barton. Wed .
"Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants". United States. https://doi.org/10.3390/v7102881. https://www.osti.gov/servlets/purl/1263552.
@article{osti_1263552,
title = {Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) identifies immune-selected HIV variants},
author = {Hraber, Peter and Korber, Bette and Wagh, Kshitij and Giorgi, Elena and Bhattacharya, Tanmoy and Gnanakaran, S. and Lapedes, Alan S. and Learn, Gerald H. and Kreider, Edward F. and Li, Yingying and Shaw, George M. and Hahn, Beatrice H. and Montefiori, David C. and Alam, S. Munir and Bonsignori, Mattia and Moody, M. Anthony and Liao, Hua-Xin and Gao, Feng and Haynes, Barton},
abstractNote = {Within-host genetic sequencing from samples collected over time provides a dynamic view of how viruses evade host immunity. Immune-driven mutations might stimulate neutralization breadth by selecting antibodies adapted to cycles of immune escape that generate within-subject epitope diversity. Comprehensive identification of immune-escape mutations is experimentally and computationally challenging. With current technology, many more viral sequences can readily be obtained than can be tested for binding and neutralization, making down-selection necessary. Typically, this is done manually, by picking variants that represent different time-points and branches on a phylogenetic tree. Such strategies are likely to miss many relevant mutations and combinations of mutations, and to be redundant for other mutations. Longitudinal Antigenic Sequences and Sites from Intrahost Evolution (LASSIE) uses transmitted founder loss to identify virus “hot-spots” under putative immune selection and chooses sequences that represent recurrent mutations in selected sites. LASSIE favors earliest sequences in which mutations arise. With well-characterized longitudinal Env sequences, we confirmed selected sites were concentrated in antibody contacts and selected sequences represented diverse antigenic phenotypes. As a result, practical applications include rapidly identifying immune targets under selective pressure within a subject, selecting minimal sets of reagents for immunological assays that characterize evolving antibody responses, and for immunogens in polyvalent “cocktail” vaccines.},
doi = {10.3390/v7102881},
journal = {Viruses},
number = 10,
volume = 7,
place = {United States},
year = {Wed Oct 21 00:00:00 EDT 2015},
month = {Wed Oct 21 00:00:00 EDT 2015}
}
Web of Science
Works referenced in this record:
Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivo
journal, October 2012
- Moldt, B.; Rakasz, E. G.; Schultz, N.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 46
Vaccines: Correlates of Vaccine‐Induced Immunity
journal, August 2008
- Plotkin, Stanley A.
- Clinical Infectious Diseases, Vol. 47, Issue 3
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
journal, June 2009
- Goonetilleke, Nilu; Liu, Michael K. P.; Salazar-Gonzalez, Jesus F.
- The Journal of Experimental Medicine, Vol. 206, Issue 6
Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing
journal, February 2008
- Salazar-Gonzalez, J. F.; Bailes, E.; Pham, K. T.
- Journal of Virology, Vol. 82, Issue 8
Amphiphilic block copolymers enhance the cellular uptake of DNA molecules through a facilitated plasma membrane transport
journal, October 2010
- Chèvre, Raphaël; Le Bihan, Olivier; Beilvert, Fanny
- Nucleic Acids Research, Vol. 39, Issue 4
Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies
journal, February 2015
- Wang, Shenshen; Mata-Fink, Jordi; Kriegsman, Barry
- Cell, Vol. 160, Issue 4
HIV-Specific Probabilistic Models of Protein Evolution
journal, June 2007
- Nickle, David C.; Heath, Laura; Jensen, Mark A.
- PLoS ONE, Vol. 2, Issue 6
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
journal, March 2010
- Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent
- Systematic Biology, Vol. 59, Issue 3
Increasing the Potency and Breadth of an HIV Antibody by Using Structure-Based Rational Design
journal, October 2011
- Diskin, R.; Scheid, J. F.; Marcovecchio, P. M.
- Science, Vol. 334, Issue 6060
Emergence of stable polymorphisms driven by evolutionary games between mutants
journal, January 2012
- Huang, Weini; Haubold, Bernhard; Hauert, Christoph
- Nature Communications, Vol. 3, Issue 1
Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains
journal, June 2014
- Fera, D.; Schmidt, A. G.; Haynes, B. F.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 28
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
journal, June 2006
- Kosakovsky Pond, Sergei L.; Frost, Simon D. W.; Grossman, Zehava
- PLoS Computational Biology, Vol. 2, Issue 6
Detecting Individual Sites Subject to Episodic Diversifying Selection
journal, July 2012
- Murrell, Ben; Wertheim, Joel O.; Moola, Sasha
- PLoS Genetics, Vol. 8, Issue 7
Structural definition of a conserved neutralization epitope on HIV-1 gp120
journal, February 2007
- Zhou, Tongqing; Xu, Ling; Dey, Barna
- Nature, Vol. 445, Issue 7129
Emergence of Broadly Neutralizing Antibodies and Viral Coevolution in Two Subjects during the Early Stages of Infection with Human Immunodeficiency Virus Type 1
journal, August 2014
- Sather, D. N.; Carbonetti, S.; Malherbe, D. C.
- Journal of Virology, Vol. 88, Issue 22
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
journal, January 2013
- Brodin, Johanna; Krishnamoorthy, Mohan; Athreya, Gayathri
- BMC Bioinformatics, Vol. 14, Issue 1
Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
journal, March 2007
- Poon, Art F. Y.; Kosakovsky Pond, Sergei L.; Bennett, Phil
- PLoS Pathogens, Vol. 3, Issue 3
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
The implications of patterns in HIV diversity for neutralizing antibody induction and susceptibility
journal, January 2009
- Korber, Bette; Gnanakaran, S.
- Current Opinion in HIV and AIDS, Vol. 4, Issue 5
Viral Escape from HIV-1 Neutralizing Antibodies Drives Increased Plasma Neutralization Breadth through Sequential Recognition of Multiple Epitopes and Immunotypes
journal, October 2013
- Wibmer, Constantinos Kurt; Bhiman, Jinal N.; Gray, Elin S.
- PLoS Pathogens, Vol. 9, Issue 10
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection
journal, March 2012
- Henn, Matthew R.; Boutwell, Christian L.; Charlebois, Patrick
- PLoS Pathogens, Vol. 8, Issue 3
A new method for calculating evolutionary substitution rates
journal, February 1984
- Lanave, Cecilia; Preparata, Giuliano; Sacone, Cecilia
- Journal of Molecular Evolution, Vol. 20, Issue 1
Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals
journal, March 2009
- Scheid, Johannes F.; Mouquet, Hugo; Feldhahn, Niklas
- Nature, Vol. 458, Issue 7238
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
journal, June 2009
- Salazar-Gonzalez, Jesus F.; Salazar, Maria G.; Keele, Brandon F.
- The Journal of Experimental Medicine, Vol. 206, Issue 6
B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study
journal, May 2012
- Haynes, Barton F.; Kelsoe, Garnett; Harrison, Stephen C.
- Nature Biotechnology, Vol. 30, Issue 5
Elucidation of Hepatitis C Virus Transmission and Early Diversification by Single Genome Sequencing
journal, August 2012
- Li, Hui; Stoddard, Mark B.; Wang, Shuyi
- PLoS Pathogens, Vol. 8, Issue 8
Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding
journal, July 2011
- Scheid, J. F.; Mouquet, H.; Ueberheide, B.
- Science, Vol. 333, Issue 6049
Vertical T cell immunodominance and epitope entropy determine HIV-1 escape
journal, December 2012
- Liu, Michael K. P.; Hawkins, Natalie; Ritchie, Adam J.
- Journal of Clinical Investigation
Broad neutralization coverage of HIV by multiple highly potent antibodies
journal, September 2011
- Walker, Laura M.; Huber, Michael; Doores, Katie J.
- Nature, Vol. 477, Issue 7365
Variable and conserved neutralization antigens of human immunodeficiency virus
journal, December 1986
- Weiss, Robin A.; Clapham, Paul R.; Weber, Jonathan N.
- Nature, Vol. 324, Issue 6097
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection
journal, May 2008
- Keele, B. F.; Giorgi, E. E.; Salazar-Gonzalez, J. F.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 21
Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues
journal, June 2013
- West, A. P.; Scharf, L.; Horwitz, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 26
Antibody responses to envelope glycoproteins in HIV-1 infection
journal, May 2015
- Burton, Dennis R.; Mascola, John R.
- Nature Immunology, Vol. 16, Issue 6
HIV-1-specific antibody responses during acute and chronic HIV-1 infection
journal, January 2009
- Tomaras, Georgia D.; Haynes, Barton F.
- Current Opinion in HIV and AIDS, Vol. 4, Issue 5
Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01
journal, July 2010
- Zhou, T.; Georgiev, I.; Wu, X.
- Science, Vol. 329, Issue 5993
Retrieval and on-the-fly alignment of sequence fragments from the HIV database
journal, May 2001
- Gaschen, B.; Kuiken, C.; Korber, B.
- Bioinformatics, Vol. 17, Issue 5
Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies
journal, July 2014
- Gao, Feng; Bonsignori, Mattia; Liao, Hua-Xin
- Cell, Vol. 158, Issue 3
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
journal, March 2003
- Richman, D. D.; Wrin, T.; Little, S. J.
- Proceedings of the National Academy of Sciences, Vol. 100, Issue 7
Acceleration of Hepatitis C Virus Envelope Evolution in Humans Is Consistent with Progressive Humoral Immune Selection during the Transition from Acute to Chronic Infection
journal, March 2010
- Liu, Lin; Fisher, Brian E.; Dowd, Kimberly A.
- Journal of Virology, Vol. 84, Issue 10
Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape
journal, May 2012
- Bar, Katharine J.; Tsao, Chun-yen; Iyer, Shilpa S.
- PLoS Pathogens, Vol. 8, Issue 5
Protection of Macaques against Pathogenic Simian/Human Immunodeficiency Virus 89.6PD by Passive Transfer of Neutralizing Antibodies
journal, January 1999
- Mascola, John R.; Lewis, Mark G.; Stiegler, Gabriela
- Journal of Virology, Vol. 73, Issue 5
Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing
journal, August 2010
- Fischer, Will; Ganusov, Vitaly V.; Giorgi, Elena E.
- PLoS ONE, Vol. 5, Issue 8
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
journal, October 2010
- Giorgi, Elena E.; Funkhouser, Bob; Athreya, Gayathri
- BMC Bioinformatics, Vol. 11, Issue 1
Antibody neutralization and escape by HIV-1
journal, March 2003
- Wei, Xiping; Decker, Julie M.; Wang, Shuyi
- Nature, Vol. 422, Issue 6929
Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation
journal, April 2014
- Kepler, Thomas B.; Munshaw, Supriya; Wiehe, Kevin
- Frontiers in Immunology, Vol. 5
Natural Evolution of Broadly Neutralizing Antibodies
journal, April 2015
- Alter, Galit; Barouch, Dan H.
- Cell, Vol. 161, Issue 3
Sequence logos: a new way to display consensus sequences
journal, January 1990
- Schneider, Thomas D.; Stephens, R. Michael
- Nucleic Acids Research, Vol. 18, Issue 20
Prognosis in HIV-1 Infection Predicted by the Quantity of Virus in Plasma
journal, May 1996
- Mellors, J. W.; Rinaldo, C. R.; Gupta, P.
- Science, Vol. 272, Issue 5265
Selection Pressure From Neutralizing Antibodies Drives Sequence Evolution During Acute Infection With Hepatitis C Virus
journal, June 2009
- Dowd, Kimberly A.; Netski, Dale M.; Wang, Xiao–Hong
- Gastroenterology, Vol. 136, Issue 7
Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors
journal, January 2013
- Kepler, Thomas B.
- F1000Research, Vol. 2
B-cell–lineage immunogen design in vaccine development with HIV-1 as a case study
journal, May 2012
- Haynes, Barton F.; Kelsoe, Garnett; Harrison, Stephen C.
- Nature Biotechnology, Vol. 30, Issue 5
Progress in HIV-1 vaccine development
journal, July 2014
- Haynes, Barton F.; Moody, M. Anthony; Alam, Munir
- Journal of Allergy and Clinical Immunology, Vol. 134, Issue 1
Human Antibodies that Neutralize HIV-1: Identification, Structures, and B Cell Ontogenies
journal, September 2012
- Kwong, Peter D.; Mascola, John R.
- Immunity, Vol. 37, Issue 3
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120
journal, May 2013
- Kong, Leopold; Lee, Jeong Hyun; Doores, Katie J.
- Nature Structural & Molecular Biology, Vol. 20, Issue 7
Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
journal, March 2014
- Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason
- Nature, Vol. 509, Issue 7498
Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses
journal, September 2015
- Moody, M. Anthony; Gao, Feng; Gurley, Thaddeus C.
- Cell Host & Microbe, Vol. 18, Issue 3
Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing
journal, August 2011
- Wu, X.; Zhou, T.; Zhu, J.
- Science, Vol. 333, Issue 6049
Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
journal, March 2007
- Poon, Art F. Y.; Kosakovsky Pond, Sergei L.; Bennett, Phil
- PLoS Pathogens, Vol. 3, Issue 3
The Route of HIV Escape from Immune Response Targeting Multiple Sites Is Determined by the Cost-Benefit Tradeoff of Escape Mutations
journal, October 2014
- Batorsky, Rebecca; Sergeev, Rinat A.; Rouzine, Igor M.
- PLoS Computational Biology, Vol. 10, Issue 10
Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection
journal, June 2009
- Salazar-Gonzalez, Jesus F.; Salazar, Maria G.; Keele, Brandon F.
- The Journal of Experimental Medicine, Vol. 206, Issue 6
Structure and immune recognition of trimeric pre-fusion HIV-1 Env
journal, October 2014
- Pancera, Marie; Zhou, Tongqing; Druz, Aliaksandr
- Nature, Vol. 514, Issue 7523
Highly potent HIV-specific antibody neutralization in vitro translates into effective protection against mucosal SHIV challenge in vivo
journal, October 2012
- Moldt, B.; Rakasz, E. G.; Schultz, N.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 46
Vaccines: Correlates of Vaccine‐Induced Immunity
journal, August 2008
- Plotkin, Stanley A.
- Clinical Infectious Diseases, Vol. 47, Issue 3
Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies
journal, February 2015
- Wang, Shenshen; Mata-Fink, Jordi; Kriegsman, Barry
- Cell, Vol. 160, Issue 4
Detecting Individual Sites Subject to Episodic Diversifying Selection
journal, July 2012
- Murrell, Ben; Wertheim, Joel O.; Moola, Sasha
- PLoS Genetics, Vol. 8, Issue 7
Broad neutralization coverage of HIV by multiple highly potent antibodies
journal, September 2011
- Walker, Laura M.; Huber, Michael; Doores, Katie J.
- Nature, Vol. 477, Issue 7365
Affinity maturation in an HIV broadly neutralizing B-cell lineage through reorientation of variable domains
journal, June 2014
- Fera, D.; Schmidt, A. G.; Haynes, B. F.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 28
Emergence of stable polymorphisms driven by evolutionary games between mutants
journal, January 2012
- Huang, Weini; Haubold, Bernhard; Hauert, Christoph
- Nature Communications, Vol. 3, Issue 1
Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing
journal, August 2011
- Wu, X.; Zhou, T.; Zhu, J.
- Science, Vol. 333, Issue 6049
Envelope Variants Circulating as Initial Neutralization Breadth Developed in Two HIV-Infected Subjects Stimulate Multiclade Neutralizing Antibodies in Rabbits
journal, September 2014
- Malherbe, D. C.; Pissani, F.; Sather, D. N.
- Journal of Virology, Vol. 88, Issue 22
HIV-1 neutralizing antibodies: understanding nature's pathways
journal, June 2013
- Mascola, John R.; Haynes, Barton F.
- Immunological Reviews, Vol. 254, Issue 1
The Role of Antibodies in HIV Vaccines
journal, March 2010
- Mascola, John R.; Montefiori, David C.
- Annual Review of Immunology, Vol. 28, Issue 1
Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape
journal, October 2012
- Moore, Penny L.; Gray, Elin S.; Wibmer, C. Kurt
- Nature Medicine, Vol. 18, Issue 11
HIV-Specific Probabilistic Models of Protein Evolution
journal, June 2007
- Nickle, David C.; Heath, Laura; Jensen, Mark A.
- PLoS ONE, Vol. 2, Issue 6
Sequence and Structural Convergence of Broad and Potent HIV Antibodies That Mimic CD4 Binding
journal, July 2011
- Scheid, J. F.; Mouquet, H.; Ueberheide, B.
- Science, Vol. 333, Issue 6049
Analysis of a Clonal Lineage of HIV-1 Envelope V2/V3 Conformational Epitope-Specific Broadly Neutralizing Antibodies and Their Inferred Unmutated Common Ancestors
journal, July 2011
- Bonsignori, M.; Hwang, K. -K.; Chen, X.
- Journal of Virology, Vol. 85, Issue 19
Amphiphilic block copolymers enhance the cellular uptake of DNA molecules through a facilitated plasma membrane transport
journal, October 2010
- Chèvre, Raphaël; Le Bihan, Olivier; Beilvert, Fanny
- Nucleic Acids Research, Vol. 39, Issue 4
The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences
journal, January 2016
- Maher, Stephen J.; Murray, John M.
- European Journal of Operational Research, Vol. 248, Issue 2
Broad diversity of neutralizing antibodies isolated from memory B cells in HIV-infected individuals
journal, March 2009
- Scheid, Johannes F.; Mouquet, Hugo; Feldhahn, Niklas
- Nature, Vol. 458, Issue 7238
Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
journal, March 2007
- Poon, Art F. Y.; Pond, Sergei I. Kosakovsky; Bennett, Phil
- PLOS Pathology
The first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection
journal, June 2009
- Goonetilleke, Nilu; Liu, Michael K. P.; Salazar-Gonzalez, Jesus F.
- The Journal of Experimental Medicine, Vol. 206, Issue 6
Vaccine Induction of Antibodies against a Structurally Heterogeneous Site of Immune Pressure within HIV-1 Envelope Protein Variable Regions 1 and 2
journal, January 2013
- Liao, Hua-Xin; Bonsignori, Mattia; Alam, S. Munir
- Immunity, Vol. 38, Issue 1
Estimating time since infection in early homogeneous HIV-1 samples using a poisson model
journal, October 2010
- Giorgi, Elena E.; Funkhouser, Bob; Athreya, Gayathri
- BMC Bioinformatics, Vol. 11, Issue 1
Antibody neutralization and escape by HIV-1
journal, March 2003
- Wei, Xiping; Decker, Julie M.; Wang, Shuyi
- Nature, Vol. 422, Issue 6929
Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape
journal, May 2012
- Bar, Katharine J.; Tsao, Chun-yen; Iyer, Shilpa S.
- PLoS Pathogens, Vol. 8, Issue 5
Progress in HIV-1 vaccine development
journal, July 2014
- Haynes, Barton F.; Moody, M. Anthony; Alam, Munir
- Journal of Allergy and Clinical Immunology, Vol. 134, Issue 1
Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection
journal, September 2006
- Edwards, C. T. T.; Holmes, E. C.; Pybus, O. G.
- Genetics, Vol. 174, Issue 3
Reconstructing a B-cell clonal lineage. I. Statistical inference of unobserved ancestors
journal, January 2013
- Kepler, Thomas B.
- F1000Research, Vol. 2
DNA/Amphiphilic Block Copolymer Nanospheres Promote Low-dose DNA Vaccination
journal, August 2009
- McIlroy, Dorian; Barteau, Benoît; Cany, Jeannette
- Molecular Therapy, Vol. 17, Issue 8
Rational Design of Envelope Identifies Broadly Neutralizing Human Monoclonal Antibodies to HIV-1
journal, July 2010
- Wu, X.; Yang, Z. -Y.; Li, Y.
- Science, Vol. 329, Issue 5993
Adaptation to Different Human Populations by HIV-1 Revealed by Codon-Based Analyses
journal, June 2006
- Kosakovsky Pond, Sergei L.; Frost, Simon D. W.; Grossman, Zehava
- PLoS Computational Biology, Vol. 2, Issue 6
Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection
journal, April 2015
- Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.
- Cell, Vol. 161, Issue 3
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
journal, April 2013
- Liao, Hua-Xin; Lynch, Rebecca; Zhou, Tongqing
- Nature, Vol. 496, Issue 7446
Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target
journal, September 2009
- Walker, L. M.; Phogat, S. K.; Chan-Hui, P. -Y.
- Science, Vol. 326, Issue 5950
A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
journal, January 2013
- Brodin, Johanna; Krishnamoorthy, Mohan; Athreya, Gayathri
- BMC Bioinformatics, Vol. 14, Issue 1
Evolution of an HIV glycan–dependent broadly neutralizing antibody epitope through immune escape
text, January 2012
- Tandile, Hermanus,; Abdool, Karim, Quarraisha; E., Lambson, Bronwen
- The University of North Carolina at Chapel Hill University Libraries
WebLogo: A Sequence Logo Generator
journal, May 2004
- Crooks, Gavin E.; Hon, Gary; Chandonia, John-Marc
- Genome Research, Vol. 14, Issue 6, p. 1188-1190
Adaptive Evolution of Human Immunodeficiency Virus-Type 1 During the Natural Course of Infection
journal, April 1996
- Wolinsky, S. M.; Korber, B. T. M.; Neumann, A. U.
- Science, Vol. 272, Issue 5261
Genetic Diversity Underlying the Envelope Glycoproteins of Hepatitis C Virus: Structural and Functional Consequences and the Implications for Vaccine Design
journal, July 2015
- Tarr, Alexander; Khera, Tanvi; Hueging, Kathrin
- Viruses, Vol. 7, Issue 7
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
journal, August 2011
- Ganusov, V. V.; Goonetilleke, N.; Liu, M. K. P.
- Journal of Virology, Vol. 85, Issue 20
Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
journal, January 2014
- Pennings, Pleuni S.; Kryazhimskiy, Sergey; Wakeley, John
- PLoS Genetics, Vol. 10, Issue 1
Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
journal, February 2005
- Kosakovsky Pond, Sergei L.; Frost, Simon D. W.
- Molecular Biology and Evolution, Vol. 22, Issue 5
Functional consequences of allotypic polymorphisms in human immunoglobulin G subclasses
journal, July 2022
- Crowley, Andrew R.; Richardson, Simone I.; Tuyishime, Marina
- Immunogenetics, Vol. 75, Issue 1
Loss and Recovery of Genetic Diversity in Adapting Populations of HIV
journal, January 2014
- Pennings, Pleuni S.; Kryazhimskiy, Sergey; Wakeley, John
- PLoS Genetics, Vol. 10, Issue 1
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
journal, July 2010
- Delport, W.; Poon, A. F. Y.; Frost, S. D. W.
- Bioinformatics, Vol. 26, Issue 19
Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01
journal, July 2010
- Zhou, T.; Georgiev, I.; Wu, X.
- Science, Vol. 329, Issue 5993
Motif-optimized subtype A HIV envelope-based DNA vaccines rapidly elicit neutralizing antibodies when delivered sequentially
journal, August 2012
- Pissani, Franco; Malherbe, Delphine C.; Robins, Harlan
- Vaccine, Vol. 30, Issue 37
Sequential Immunization with a Subtype B HIV-1 Envelope Quasispecies Partially Mimics the In Vivo Development of Neutralizing Antibodies
journal, March 2011
- Malherbe, D. C.; Doria-Rose, N. A.; Misher, L.
- Journal of Virology, Vol. 85, Issue 11
Broad and Potent Neutralizing Antibodies from an African Donor Reveal a New HIV-1 Vaccine Target
journal, September 2009
- Walker, L. M.; Phogat, S. K.; Chan-Hui, P. -Y.
- Science, Vol. 326, Issue 5950
Neutralizing antibody responses drive the evolution of human immunodeficiency virus type 1 envelope during recent HIV infection
journal, December 2005
- Frost, S. D. W.; Wrin, T.; Smith, D. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 51
DNA/Amphiphilic Block Copolymer Nanospheres Promote Low-dose DNA Vaccination
journal, August 2009
- McIlroy, Dorian; Barteau, Benoît; Cany, Jeannette
- Molecular Therapy, Vol. 17, Issue 8
Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
journal, March 2014
- Doria-Rose, Nicole A.; Schramm, Chaim A.; Gorman, Jason
- Nature, Vol. 509, Issue 7498
Motif-optimized subtype A HIV envelope-based DNA vaccines rapidly elicit neutralizing antibodies when delivered sequentially
journal, August 2012
- Pissani, Franco; Malherbe, Delphine C.; Robins, Harlan
- Vaccine, Vol. 30, Issue 37
Prognosis in HIV-1 Infection Predicted by the Quantity of Virus in Plasma
journal, May 1996
- Mellors, J. W.; Rinaldo, C. R.; Gupta, P.
- Science, Vol. 272, Issue 5265
Selection Pressure From Neutralizing Antibodies Drives Sequence Evolution During Acute Infection With Hepatitis C Virus
journal, June 2009
- Dowd, Kimberly A.; Netski, Dale M.; Wang, Xiao–Hong
- Gastroenterology, Vol. 136, Issue 7
Cooperation of B Cell Lineages in Induction of HIV-1-Broadly Neutralizing Antibodies
journal, July 2014
- Gao, Feng; Bonsignori, Mattia; Liao, Hua-Xin
- Cell, Vol. 158, Issue 3
Host Genetic and Viral Determinants of HIV-1 RNA Set Point among HIV-1 Seroconverters from Sub-Saharan Africa
journal, December 2014
- Mackelprang, Romel D.; Carrington, Mary; Thomas, Katherine K.
- Journal of Virology, Vol. 89, Issue 4
Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection
journal, March 2012
- Henn, Matthew R.; Boutwell, Christian L.; Charlebois, Patrick
- PLoS Pathogens, Vol. 8, Issue 3
Reconstructing a B-Cell Clonal Lineage. II. Mutation, Selection, and Affinity Maturation
journal, April 2014
- Kepler, Thomas B.; Munshaw, Supriya; Wiehe, Kevin
- Frontiers in Immunology, Vol. 5
Supersite of immune vulnerability on the glycosylated face of HIV-1 envelope glycoprotein gp120
journal, May 2013
- Kong, Leopold; Lee, Jeong Hyun; Doores, Katie J.
- Nature Structural & Molecular Biology, Vol. 20, Issue 7
Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses
journal, September 2015
- Moody, M. Anthony; Gao, Feng; Gurley, Thaddeus C.
- Cell Host & Microbe, Vol. 18, Issue 3
Sequence logos: a new way to display consensus sequences
journal, January 1990
- Schneider, Thomas D.; Stephens, R. Michael
- Nucleic Acids Research, Vol. 18, Issue 20
APE: Analyses of Phylogenetics and Evolution in R language
journal, January 2004
- Paradis, E.; Claude, J.; Strimmer, K.
- Bioinformatics, Vol. 20, Issue 2
Variable and conserved neutralization antigens of human immunodeficiency virus
journal, December 1986
- Weiss, Robin A.; Clapham, Paul R.; Weber, Jonathan N.
- Nature, Vol. 324, Issue 6097
Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection
journal, January 2014
- Hraber, Peter; Seaman, Michael S.; Bailer, Robert T.
- AIDS, Vol. 28, Issue 2
HIV-1 neutralizing antibodies: understanding nature's pathways
journal, June 2013
- Mascola, John R.; Haynes, Barton F.
- Immunological Reviews, Vol. 254, Issue 1
Genotype 1 Hepatitis C Virus Envelope Features That Determine Antiviral Response Assessed through Optimal Covariance Networks
journal, June 2013
- Murray, John M.; Moenne-Loccoz, Rémy; Velay, Aurélie
- PLoS ONE, Vol. 8, Issue 6
Viral Sequence Evolution in Acute Hepatitis C Virus Infection
journal, August 2007
- Kuntzen, Thomas; Timm, Joerg; Berical, Andrew
- Journal of Virology, Vol. 81, Issue 21
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
journal, October 2003
- Guindon, Stéphane; Gascuel, Olivier
- Systematic Biology, Vol. 52, Issue 5
Retrieval and on-the-fly alignment of sequence fragments from the HIV database
journal, May 2001
- Gaschen, B.; Kuiken, C.; Korber, B.
- Bioinformatics, Vol. 17, Issue 5
Structural definition of a conserved neutralization epitope on HIV-1 gp120
journal, February 2007
- Zhou, Tongqing; Xu, Ling; Dey, Barna
- Nature, Vol. 445, Issue 7129
Progress in HIV-1 vaccine development
journal, January 2013
- Haynes, Barton F.; McElrath, M. Juliana
- Current Opinion in HIV and AIDS
The Role of Antibodies in HIV Vaccines
journal, March 2010
- Mascola, John R.; Montefiori, David C.
- Annual Review of Immunology, Vol. 28, Issue 1
Evolution of the Human Immunodeficiency Virus Envelope Gene Is Dominated by Purifying Selection
journal, September 2006
- Edwards, C. T. T.; Holmes, E. C.; Pybus, O. G.
- Genetics, Vol. 174, Issue 3
Antibody responses to envelope glycoproteins in HIV-1 infection
journal, May 2015
- Burton, Dennis R.; Mascola, John R.
- Nature Immunology, Vol. 16, Issue 6
Likelihood Models for Detecting Positively Selected Amino Acid Sites and Applications to the HIV-1 Envelope Gene
journal, March 1998
- Nielsen, Rasmus; Yang, Ziheng
- Genetics, Vol. 148, Issue 3
Works referencing / citing this record:
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection
journal, June 2020
- Illingworth, Christopher J. R.; Raghwani, Jayna; Serwadda, David
- PLOS Pathogens, Vol. 16, Issue 6
Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies
journal, March 2017
- Bonsignori, Mattia; Kreider, Edward F.; Fera, Daniela
- Science Translational Medicine, Vol. 9, Issue 381
The evolution of a super-swarm of foot-and-mouth disease virus in cattle
journal, April 2019
- Arzt, Jonathan; Fish, Ian; Pauszek, Steven J.
- PLOS ONE, Vol. 14, Issue 4
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection
journal, June 2020
- Illingworth, Christopher J. R.; Raghwani, Jayna; Serwadda, David
- PLOS Pathogens, Vol. 16, Issue 6
The evolution of a super-swarm of foot-and-mouth disease virus in cattle
journal, April 2019
- Arzt, Jonathan; Fish, Ian; Pauszek, Steven J.
- PLOS ONE, Vol. 14, Issue 4
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.
text, January 2020
- Illingworth, Christopher; Raghwani, Jayna; Serwadda, David
- Apollo - University of Cambridge Repository
Staged induction of HIV-1 glycan–dependent broadly neutralizing antibodies
text, January 2017
- Todd, Bradley,; Baptiste, Aussedat,; Amit, Kumar,
- The University of North Carolina at Chapel Hill University Libraries
Completeness of HIV-1 Envelope Glycan Shield at Transmission Determines Neutralization Breadth
journal, October 2018
- Wagh, Kshitij; Kreider, Edward F.; Li, Yingying
- Cell Reports, Vol. 25, Issue 4
HIV-1 therapy with monoclonal antibody 3BNC117 elicits host immune responses against HIV-1
journal, May 2016
- Schoofs, T.; Klein, F.; Braunschweig, M.
- Science, Vol. 352, Issue 6288
Antigenic Variation and Immune Escape in the MTBC
book, January 2017
- Ernst, Joel D.
- Strain Variation in the Mycobacterium tuberculosis Complex: Its Role in Biology, Epidemiology and Control
Long-lasting HIV suppression by combined immunotherapy
journal, December 2018
- Jaworski, Juan P.
- The Lancet HIV, Vol. 5, Issue 12
Analysis of HIV-1 envelope evolution suggests antibody-mediated selection of common epitopes among Chinese former plasma donors from a narrow-source outbreak
journal, April 2018
- Andrews, Sophie M.; Zhang, Yonghong; Dong, Tao
- Scientific Reports, Vol. 8, Issue 1
Antibody-virus co-evolution in HIV infection: paths for HIV vaccine development
journal, January 2017
- Bonsignori, Mattia; Liao, Hua-Xin; Gao, Feng
- Immunological Reviews, Vol. 275, Issue 1
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection
text, January 2020
- Illingworth, Christopher J. R.; Raghwani, Jayna; Serwadda, David
- Apollo - University of Cambridge Repository
Antibody-virus co-evolution in HIV infection: paths for HIV vaccine development
journal, January 2017
- Bonsignori, Mattia; Liao, Hua-Xin; Gao, Feng
- Immunological Reviews, Vol. 275, Issue 1
HIV Resistance Prediction to Reverse Transcriptase Inhibitors: Focus on Open Data
journal, April 2018
- Tarasova, Olga; Poroikov, Vladimir
- Molecules, Vol. 23, Issue 4
Stabilizing HIV-1 envelope glycoprotein trimers to induce neutralizing antibodies
journal, September 2018
- Torrents de la Peña, Alba; Sanders, Rogier W.
- Retrovirology, Vol. 15, Issue 1
Safety and antiviral activity of combination HIV-1 broadly neutralizing antibodies in viremic individuals
journal, September 2018
- Bar-On, Yotam; Gruell, Henning; Schoofs, Till
- Nature Medicine, Vol. 24, Issue 11
Polyvalent vaccine approaches to combat HIV-1 diversity
journal, January 2017
- Korber, Bette; Hraber, Peter; Wagh, Kshitij
- Immunological Reviews, Vol. 275, Issue 1