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