Predicting Pandemic H1N1 Antigenic Evolution in Humans Using Diversifying

Selection Analysis

July 12, 2015

American Society of Virology 2015

Alexandra Lee M.S

Richard Scheuermann Ph.D

J. Craig Venter Institute

Background

Challenge

Which are the relevant B-cell/Ab epitopes?

HA

HA

Flu virus

Effector B-cell

B-cell/Ab epitope Antibodies (Ab)

Antigenic Drift

HA

NA

Approach

Goal:

Use a data mining approach to identify regions of the influenza HA protein that are the

targets of a protective immune response in humans

Predicting Target B-cell/Ab Epitopes Testing Diversified B-cell/Ab Epitopes

HA

B-cell/Ab epitopes

Pre-pandemic HA

Diversified region

Diversified B-cell/Ab

epitopes

Diversified B-cell/Ab

epitopes

Pandemic HA

Mutation site

Is this mutation site within

the diversified B-cell/Ab

epitope?

1918 1977 2009

Pre-pandemic Post-pandemic

H1 HA B-cell/Ab Epitopes

HA1 HA2

continuous

discontinuous

Diversifying Selection

Fast Unconstrained Bayesian Approximation (FUBAR)

dN : Rate of non-synonymous substitutions CTA (Leu) CCA (Pro)

dS : Rate of synonymous substitutions CTA (Leu) CTG (Leu)

𝑃𝑟𝑜𝑏 𝑑𝑁

𝑑𝑆𝑜𝑏𝑠𝑒𝑟𝑣𝑒𝑑

> 𝑑𝑁

𝑑𝑆𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑

> 0.8

Found 16 sites experiencing diversifying selection

0

0.2

0.4

0.6

0.8

1

1

16

31

46

61

76

91

106

121

136

151

166

181

196

211

226

241

256

271

286

301

316

331

346

361

376

391

406

421

436

451

466

481

496

511

526

541

556

4 52 111

142

158

170

172

177

179

203

204 239 275

278 468

537

Pro

babili

ty

Amino Acid Position

Filter B-cell/Ab Epitopes

HA1 HA2

170

172

177

179

203

204 239 537 52 111 142

Diversified B-cell/Ab

epitopes

4 158

275

278 468

Identify Targeted B-cell/Ab Epitopes

170

172

177

179

203

204 239 537 52 111 142

HA1 HA2

Sa Sb

Ca2

Metadata-driven Comparative Analysis Tool for Sequences (Meta-CATS)

Group 1:

Early pandemic

sequences

Group 2:

Late pandemic

sequences

(12-13, 13-14)

Site with significant sequence variation between

Group 1 vs. Group 2

Early Pandemic Late Pandemic

1. No immunological

memory

2. Population level pre-existing

immunity established

3. Virus mutates to escape

pre-existing immunity

Test Diversified B-cell/Ab Epitopes

180 202

114 220 251 300

391 468 516 273

HA1 HA2

Target B-cell/Ab

epitopes

3D Protein Structure

Sa

468

537 516

177

179

172

170 158

142 180

239

203

204

B-cell/Ab epitope

Pre-pdm diversified site

Pre-pdm diversified site in B-cell/Ab epitope

Significant pdm mutation site

Significant pdm mutation site in B-cell/Ab epitope

Pre-pdm diversified site that mutated in pdm evolution

Legend

Hemagglutinin Inhibition Assay

Summary

• Our approach found putative B-cell/Ab epitopes that are

relevant for protective immunity

• We tested the antibody reactivity of strains containing

variants within these candidate B-cell/Ab epitopes using

HI assay

Acknowledgments

JCVI

• Richard Scheuermann

• Lucy Stewart

• Brett Pickett

• Brian Aevermann

• Suman Das

• Wei Wang

RPRC

• David Topham

• Ann Falsey

• Theresa Fitzgerald

• Donna Neu

NIH/NIAID 𝐻𝐻𝑆𝑁272201200005𝐶

• Robin Mason

• Teresa Hauguel

Air Force Research Laboratory

• Shauna Zorich

• James Hanson

Lee AJ, Das SR, Wang W, Fitzgerald T, Pickett BE, Aevermann

BD, Topham, DJ, Falsey AR, Scheuermann RH. J Virol., 2015;

doi: 10.1128/JVI.03636-14. PMID: 25741011