Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments
Abstract
In the search for effective immunologic interventions to prevent and treat HIV-1 infection, standardized reference reagents are a cost-effective way to maintain robustness and reproducibility among immunological assays. To support planned and ongoing studies where clade C predominates, here we describe three virus panels, chosen from 200 well-characterized clade C envelope (Env)-pseudotyped viruses from early infection. All 200 Envs were expressed as a single round of replication pseudoviruses and were tested to quantify neutralization titers by 16 broadly neutralizing antibodies (bnAbs) and sera from 30 subjects with chronic clade C infections. We selected large panels of 50 and 100 Envs either to characterize cross-reactive breadth for sera identified as having potent neutralization activity based on initial screening or to evaluate neutralization magnitude-breadth distributions of newly isolated antibodies. We identified these panels by downselection after hierarchical clustering of bnAb neutralization titers. The resulting panels represent the diversity of neutralization profiles throughout the range of virus sensitivities identified in the original panel of 200 viruses. A small 12-Env panel was chosen to screen sera from vaccine trials or natural-infection studies for neutralization responses. We considered panels selected by previously described methods but favored a computationally informed method that enabled selection of virusesmore »
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Univ. of Cape Town and NHLS, Cape Town (South Africa). Division of Medical Virology & Inst. of Infectious Diseases and Molecular Medicine
- Harvard Medical School, Boston, MA (United States). Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center
- Fred Hutchinson Cancer Research Center, Seattle, WA (United States). Vaccine and Infectious Disease Division
- Duke Univ., Durham, NC (United States). Medical Center, Dept. of Surgery
- National Inst. of Health (NIH), Bethesda, MD (United States). Vaccine Research Center, National Inst. of Allergy and Infectious Diseases
- National Inst. for Communicable Diseases, Johannesburg (South Africa)
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States); New Mexico Consortium, Los Alamos, NM (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- Bill & Melinda Gates Foundation; National Institutes of Health (NIH); South African Government Department of Science and Technology
- OSTI Identifier:
- 1392803
- Report Number(s):
- LA-UR-16-25426
Journal ID: ISSN 0022-538X
- Grant/Contract Number:
- AC52-06NA25396; 38619; 1032144; 1146996; AI51794; 67385; D43TW00231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Virology
- Additional Journal Information:
- Journal Volume: 91; Journal Issue: 19; Journal ID: ISSN 0022-538X
- Publisher:
- American Society for Microbiology
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; Biological Science
Citation Formats
Hraber, Peter, Rademeyer, Cecilia, Williamson, Carolyn, Seaman, Michael S., Gottardo, Raphael, Tang, Haili, Greene, Kelli, Gao, Hongmei, LaBranche, Celia, Mascola, John R., Morris, Lynn, Montefiori, David C., and Korber, Bette. Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments. United States: N. p., 2017.
Web. doi:10.1128/JVI.00991-17.
Hraber, Peter, Rademeyer, Cecilia, Williamson, Carolyn, Seaman, Michael S., Gottardo, Raphael, Tang, Haili, Greene, Kelli, Gao, Hongmei, LaBranche, Celia, Mascola, John R., Morris, Lynn, Montefiori, David C., & Korber, Bette. Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments. United States. https://doi.org/10.1128/JVI.00991-17
Hraber, Peter, Rademeyer, Cecilia, Williamson, Carolyn, Seaman, Michael S., Gottardo, Raphael, Tang, Haili, Greene, Kelli, Gao, Hongmei, LaBranche, Celia, Mascola, John R., Morris, Lynn, Montefiori, David C., and Korber, Bette. Wed .
"Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments". United States. https://doi.org/10.1128/JVI.00991-17. https://www.osti.gov/servlets/purl/1392803.
@article{osti_1392803,
title = {Panels of HIV-1 Subtype C Env Reference Strains for Standardized Neutralization Assessments},
author = {Hraber, Peter and Rademeyer, Cecilia and Williamson, Carolyn and Seaman, Michael S. and Gottardo, Raphael and Tang, Haili and Greene, Kelli and Gao, Hongmei and LaBranche, Celia and Mascola, John R. and Morris, Lynn and Montefiori, David C. and Korber, Bette},
abstractNote = {In the search for effective immunologic interventions to prevent and treat HIV-1 infection, standardized reference reagents are a cost-effective way to maintain robustness and reproducibility among immunological assays. To support planned and ongoing studies where clade C predominates, here we describe three virus panels, chosen from 200 well-characterized clade C envelope (Env)-pseudotyped viruses from early infection. All 200 Envs were expressed as a single round of replication pseudoviruses and were tested to quantify neutralization titers by 16 broadly neutralizing antibodies (bnAbs) and sera from 30 subjects with chronic clade C infections. We selected large panels of 50 and 100 Envs either to characterize cross-reactive breadth for sera identified as having potent neutralization activity based on initial screening or to evaluate neutralization magnitude-breadth distributions of newly isolated antibodies. We identified these panels by downselection after hierarchical clustering of bnAb neutralization titers. The resulting panels represent the diversity of neutralization profiles throughout the range of virus sensitivities identified in the original panel of 200 viruses. A small 12-Env panel was chosen to screen sera from vaccine trials or natural-infection studies for neutralization responses. We considered panels selected by previously described methods but favored a computationally informed method that enabled selection of viruses representing diverse neutralization sensitivity patterns, given that we do nota prioriknow what the neutralization-response profile of vaccine sera will be relative to that of sera from infected individuals. The resulting 12-Env panel complements existing panels. Use of standardized panels enables direct comparisons of data from different trials and study sites testing HIV-1 clade C-specific products. HIV-1 group M includes nine clades and many recombinants. Clade C is the most common lineage, responsible for roughly half of current HIV-1 infections, and is a focus for vaccine design and testing. Standard reference reagents, particularly virus panels to study neutralization by antibodies, are crucial for developing cost-effective and yet rigorous and reproducible assays against diverse examples of this variable virus. We developed clade C-specific panels for use as standardized reagents to monitor complex polyclonal sera for neutralization activity and to characterize the potency and breadth of cross-reactive neutralization by monoclonal antibodies, whether engineered or isolated from infected individuals. We chose from 200 southern African, clade C envelope-pseudotyped viruses with neutralization titers against 16 broadly neutralizing antibodies and 30 sera from chronic clade C infections. We selected panels to represent the diversity of bnAb neutralization profiles and Env neutralization sensitivities. Finally, use of standard virus panels can facilitate comparison of results across studies and sites.},
doi = {10.1128/JVI.00991-17},
journal = {Journal of Virology},
number = 19,
volume = 91,
place = {United States},
year = {Wed Jul 26 00:00:00 EDT 2017},
month = {Wed Jul 26 00:00:00 EDT 2017}
}
Web of Science
Works referenced in this record:
Global trends in molecular epidemiology of HIV-1 during 2000–2007
journal, January 2011
- Hemelaar, Joris; Gouws, Eleanor; Ghys, Peter D.
- AIDS, Vol. 25, Issue 5
T-Cell Vaccine Strategies for Human Immunodeficiency Virus, the Virus with a Thousand Faces
journal, May 2009
- Korber, B. T.; Letvin, N. L.; Haynes, B. F.
- Journal of Virology, Vol. 83, Issue 17, p. 8300-8314
Subtype C Is Associated with Increased Vaginal Shedding of HIV‐1
journal, August 2005
- John‐Stewart, Grace C.; Nduati, Ruth W.; Rousseau, Christine M.
- The Journal of Infectious Diseases, Vol. 192, Issue 3
Preferential detection of HIV subtype C′ over subtype A in cervical cells from a dually infected woman
journal, January 2005
- Iversen, Astrid KN; Learn, Gerald H.; Skinhøj, Peter
- AIDS, Vol. 19, Issue 9
Functional characteristics of HIV-1 subtype C compatible with increased heterosexual transmissibility
journal, January 2009
- Walter, Brandon L.; Armitage, Andrew E.; Graham, Stephen C.
- AIDS, Vol. 23, Issue 9
High replication fitness and transmission efficiency of HIV-1 subtype C from India: Implications for subtype C predominance
journal, March 2009
- Rodriguez, Milka A.; Ding, Ming; Ratner, Deena
- Virology, Vol. 385, Issue 2
Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization
journal, July 2016
- Rademeyer, Cecilia; Korber, Bette; Seaman, Michael S.
- PLOS Pathogens, Vol. 12, Issue 7
Current views on the potential for development of a HIV vaccine
journal, January 2017
- Cohen, Kristen W.; Frahm, Nicole
- Expert Opinion on Biological Therapy, Vol. 17, Issue 3
Comprehensive Characterization of Reference Standard Lots of HIV-1 Subtype C Gp120 Proteins for Clinical Trials in Southern African Regions
journal, May 2016
- Wang, Zihao; Lorin, Clarisse; Koutsoukos, Marguerite
- Vaccines, Vol. 4, Issue 2
Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies
journal, December 2013
- deCamp, A.; Hraber, P.; Bailer, R. T.
- Journal of Virology, Vol. 88, Issue 5
Magnitude and Breadth of a Nonprotective Neutralizing Antibody Response in an Efficacy Trial of a Candidate HIV‐1 gp120 Vaccine
journal, August 2010
- Gilbert, Peter; Wang, Maggie; Wrin, Terri
- The Journal of Infectious Diseases, Vol. 202, Issue 4
Magnitude and Breadth of the Neutralizing Antibody Response in the RV144 and Vax003 HIV-1 Vaccine Efficacy Trials
journal, May 2012
- Montefiori, D. C.; Karnasuta, C.; Huang, Y.
- Journal of Infectious Diseases, Vol. 206, Issue 3
Hierarchical Grouping to Optimize an Objective Function
journal, March 1963
- Ward, Joe H.
- Journal of the American Statistical Association, Vol. 58, Issue 301
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
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
journal, September 2006
- Li, M.; Salazar-Gonzalez, J. F.; Derdeyn, C. A.
- Journal of Virology, Vol. 80, Issue 23
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
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
CATNAP: a tool to compile, analyze and tally neutralizing antibody panels
journal, June 2015
- Yoon, Hyejin; Macke, Jennifer; West, Anthony P.
- Nucleic Acids Research, Vol. 43, Issue W1
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
journal, March 2011
- Gray, E. S.; Madiga, M. C.; Hermanus, T.
- Journal of Virology, Vol. 85, Issue 10
Impact of Clade, Geography, and Age of the Epidemic on HIV-1 Neutralization by Antibodies
journal, August 2014
- Hraber, P.; Korber, B. T.; Lapedes, A. S.
- Journal of Virology, Vol. 88, Issue 21
Tiered Categorization of a Diverse Panel of HIV-1 Env Pseudoviruses for Assessment of Neutralizing Antibodies
journal, November 2009
- Seaman, M. S.; Janes, H.; Hawkins, N.
- Journal of Virology, Vol. 84, Issue 3
Mapping Polyclonal HIV-1 Antibody Responses via Next-Generation Neutralization Fingerprinting
journal, January 2017
- Doria-Rose, Nicole A.; Altae-Tran, Han R.; Roark, Ryan S.
- PLOS Pathogens, Vol. 13, Issue 1
Evaluating Neutralizing Antibodies Against HIV, SIV, and SHIV in Luciferase Reporter Gene Assays
journal, December 2004
- Montefiori, David C.
- Current Protocols in Immunology, Vol. 64, Issue 1
Optimization and validation of the TZM-bl assay for standardized assessments of neutralizing antibodies against HIV-1
journal, July 2014
- Sarzotti-Kelsoe, Marcella; Bailer, Robert T.; Turk, Ellen
- Journal of Immunological Methods, Vol. 409
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
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
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
Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo
journal, August 2014
- Rudicell, R. S.; Kwon, Y. D.; Ko, S. -Y.
- Journal of Virology, Vol. 88, Issue 21
Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors
journal, June 2015
- Zhou, Tongqing; Lynch, Rebecca M.; Chen, Lei
- Cell, Vol. 161, 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
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
Complex-type N-glycan recognition by potent broadly neutralizing HIV antibodies
journal, October 2012
- Mouquet, H.; Scharf, L.; Euler, Z.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 47
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
New Member of the V1V2-Directed CAP256-VRC26 Lineage That Shows Increased Breadth and Exceptional Potency
journal, October 2015
- Doria-Rose, Nicole A.; Bhiman, Jinal N.; Roark, Ryan S.
- Journal of Virology, Vol. 90, Issue 1
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
Recombinant HIV envelope trimer selects for quaternary-dependent antibodies targeting the trimer apex
journal, November 2014
- Sok, Devin; van Gils, Marit J.; Pauthner, Matthias
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 49
Broad and potent neutralization of HIV-1 by a gp41-specific human antibody
journal, September 2012
- Huang, Jinghe; Ofek, Gilad; Laub, Leo
- Nature, Vol. 491, Issue 7424
Broadly Neutralizing Antibodies Targeted to the Membrane-Proximal External Region of Human Immunodeficiency Virus Type 1 Glycoprotein gp41
journal, November 2001
- Zwick, M. B.; Labrijn, A. F.; Wang, M.
- Journal of Virology, Vol. 75, Issue 22
Singular Value Decomposition and Principal Component Analysis
book, January 2005
- Wall, Michael E.; Rechtsteiner, Andreas; Rocha, Luis M.
- A Practical Approach to Microarray Data Analysis
Machine Learning Methods Enable Predictive Modeling of Antibody Feature:Function Relationships in RV144 Vaccinees
journal, April 2015
- Choi, Ickwon; Chung, Amy W.; Suscovich, Todd J.
- PLOS Computational Biology, Vol. 11, Issue 4
Works referencing / citing this record:
Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations
journal, July 2019
- Han, Qifeng; Jones, Julia A.; Nicely, Nathan I.
- Nature Communications, Vol. 10, Issue 1
Incomplete Downregulation of CD4 Expression Affects HIV-1 Env Conformation and Antibody-Dependent Cellular Cytotoxicity Responses
journal, April 2018
- Prévost, Jérémie; Richard, Jonathan; Medjahed, Halima
- Journal of Virology, Vol. 92, Issue 13
Sensitivity to Broadly Neutralizing Antibodies of Recently Transmitted HIV-1 Clade CRF02_AG Viruses with a Focus on Evolution over Time
journal, November 2018
- Stefic, Karl; Bouvin-Pley, Mélanie; Essat, Asma
- Journal of Virology, Vol. 93, Issue 2
HIV-1 Envelope Glycoproteins from Diverse Clades Differentiate Antibody Responses and Durability among Vaccinees
journal, January 2018
- Yates, Nicole L.; deCamp, Allan C.; Korber, Bette T.
- Journal of Virology, Vol. 92, Issue 8
The expanding array of HIV broadly neutralizing antibodies
journal, October 2018
- McCoy, Laura E.
- Retrovirology, Vol. 15, Issue 1