Virus Panels for Assessing
Vaccine-Elicited Neutralizing Antibodies
Michael Seaman, Ph.D.
Center for Virology and Vaccine Research
Beth Israel Deaconess Medical Center
Harvard Medical School
J. Virol. 2005, 79(16): 10103
First Generation Clade B and C Reference Panels
J. Virol. 2005, 79(16): 10108
J. Virol. 2006, 80(23): 11776
Virology 2009, 385: 505
Clade B Panel (n=12)
Clade C Panel (n=12)
Southern Africa
Clade C Panel (n=12)
India
CA-VIMC Standard Virus Panel Consortium:
>600 Functional env Clones for Pseudovirus Production
SVPCCarolyn Williamson
Francine McCutchan
Sodsai Tovanabutra
Eric Sanders-Buell
Jerome Kim
Beatrice Hahn
Ron Swanstrom
Feng Gao
Michael Thomson
Gama Bandawe
Cecilia Rademeyer
Ray Dolin
Lindsey Baden
Subtype Number
A 8
A (T/F) 3
B 12
B (T/F) 9
C 16
C (T/F) 15
BC 8
CRF01_AE 11
CRF01_AE (T/F) 4
CRF02_AG 9
G 7
D 4
D (T/F) 1
CD 5
AC/ACD 6
Total 118
Standard Multiclade Panel for
Assessing bNAb Potency/Breadth
Neutralization Serotype Discovery Project
205 sera, multiclade
219 viruses, multiclade
SGA gp160sequence
Heatmap
Computational Analysis
Peptide arraybinding
gp160 sequences
NAb assay
deCamp et al., 2014. J. Virol. 88(5):2489
Global Panel of Tier 2 HIV-1 Env Reference Strains
• Goal: Identify panel of Env pseudoviruses that are representative of the global epidemic
• Lasso statistical modeling identified 9 isolates that were highly predictive of
neutralizing activity seen with larger panel of 219
• Additional 3 isolates selected for greater genetic and antigenic diversity (B. Korber)
• Performed nearly as well as clade-matched panels for prediction of sub-type specific
responses
Isolate Clade
246_F3_C10_2 AC
Ce1176_A3 C
CNE55 CRF01_AE
X1632_S2_B10 G
Ce703010217_B6 C
BJOX002000.03.2 CRF07_BC
25710-2.43 C
TRO.11 B
CH119.10 CRF07_BC
X2278_C2_B6 B
CNE8 CRF01_AE
398_F1_F6_20 A
deCamp et al., 2014. J. Virol. 88(5):2489
Neutralization Sensitivity of Global Panel
(Prototypic Tier 1A)
(Prototypic Tier 1B)
Global Panel
Global Panel of Tier 2 HIV-1 Env Reference Strains
• Applicable to multiple vaccine platforms and clades of HIV-1 in
different parts of the world
• Facilitate cross-protocol comparisons
• Highly predictive of clade-specific responses
• Complementary to other panels that may be used, e.g., clade-
matched to vaccine and geographic region
• Useful as initial screen to identify and characterize bNAbs
deCamp et al., 2014. J. Virol. 88(5):2489
Greater Neutralization Potency Within Clade
Hraber et al, 2014. J. Virol. 88(21):12623
Seaman et al, 2010. J. Virol. 84(3):1439
Southern Africa Clade C NSDP Project
200 early infection viruses that are more recent in the epidemic (1998-2010):• 130 South Africa (8 provinces)
• 28 Tanzania
• 23 Malawi
• 13 Zambia
• 6 Botswana
Mostly heterosexual transmissions (1 breastfeeding transmission)
Isolated within the first 100 days of infection. 67 seronegative (Fiebig I/II)
29 early seroconversion (Fiebig II/IV)
104 seropositive with seronegative test within the previous 100 days (Fiebig V/IV)
Viruses phenotyped for Tier classification (global sensitivity to neutralization)
Clade C HIV-1 Env Pseudovirus Panel
Expected Distribution of Tier PhenotypesM
ean
lo
g10 ID
50 +
/-S
D
Each virus assessed for neutralization sensitivity to 30 chronic clade C HIV+ plasma
Rademeyer et al., PLoS Path. 2016 (in press)
Tier 1A: n=2 (1.3%)
Tier 1B: n=17 (8.5%)
Tier 2: n=150 (75%)
Tier 3: n=31 (15.5%)
Computational Selection of Optimal Tier 2
Clade C Reference Panel
(Peter Hraber, Bette Korber, manuscript in preparation)
Objective: Select 12 Envs from larger panel of 200 that will be optimal
for detecting vaccine-elicited neutralizing antibodies
Strategy: Select based on mAb IC50s and Env traits (loop length, charge,
PNGs); compare with serum ID50 profiles
Tier 2 Clade C Isolate
Ce703010010_C4
ZM233M.PB6
2759058_F10_B6
Ce704810053_2B7
So431_C1_1
ZM215F.PB8
3728.v2.c6
2969249
B005582-7_G7.8
CAP382.2.00.D7.19
Ce2103_E8
Ko243_H6.3
• Favored more sensitive viruses for detecting low-level
Nab activity
• Captured diversity of known bnAb sensitivities
• Captured diversity of Env properties associated with
neutralization sensitivity
Non-Standardized Approach:
Rational Tier 2 Virus Panel Selection
• Select viruses on more sensitive end of spectrum
(top quartile of geometric mean serological activity)
• Viruses that are as close as possible to sequence of
vaccine immunogen
• Viruses that have good glycosylation and variable
loop properties
• Viruses that are highly sensitive to epitope-specific
bnAbs of interest
gp41 MPER:
10E8**
V2 Glycan:
PGT145, PGDM1400**,
PG9, CAP256-VRC26.08,
CAP256-VRC26.25**
CD4 Binding Site:
VRC01*, VRC07,
VRC07-523, VRC13,
3BNC117*
V3 Glycan:
PGT121**, PGT128
10-1074*, 10-1074V
Sensitivity of 200 C Panel Viruses to bnAbs
gp120/gp41:
Next time
* Phase I/II trials in progress
** Planned phase I trial
bnAb Lineage Vaccine Strategies:
Selection of Isolates with High Sensitivity Profile
Wagh et al, PLoS Path. 2016 12(3):e1005520
Summary of Points for Consideration
Large numbers of Env pseudoviruses with geographic,
genetic, and antigenic diversity have been extensively
characterized and optimized panels have been developed:
• Global Panel for standardized assessments of NAb across multiple
HIV-1 vaccine platforms in different parts of the world
• Optimally selected clade matched panels representative of
circulating strains in regions in which vaccine trials being conducted
• Rational selection of isolates based on properties of vaccine
immunogen(s) to increase the probability of detecting Tier 2
neutralization
• Rational selection of isolates based on bnAb sensitivities for lineage
induction vaccine strategies
Acknowledgements
Duke University
Kelli Greene
Hongmei Gao
David Montefiori
LANL
Kshitij Wagh
Tanmoy Bhattacharya
Alan Lapedes
Peter Hraber
Bette Korber
VISC
Allan deCamp
Raphael Gottardi
Steve Self
Clade C Panel
Carolyn Williamson
Cecilia Rademeyer
Lynn Morris
Jerome Kim
Feng Gao
Beatrice Hahn
Ronald Swanstrom
SVPC
Carolyn Williamson
Francine McCutchan
Sodsai Tovanabutra
Eric Sanders-Buell
Jerome Kim
Beatrice Hahn
Ron Swanstrom
Feng Gao
Michael Thomson
Gama Bandawe
Cecilia Rademeyer
Ray Dolin
Lindsey Baden