immunobiology 2017 christiaan h. van dorp rutger g

Introduction Antigenic cartography T-cell Antigenic cartography Evolution of CTL epitopes Relation to epidemiology Summary

CD8+ T-cell epitopes in the influenza A virusImmunobiology 2017

Christiaan H. van Dorp Rutger G. WoolthuisJeffrey H. C. Yu Can Kesmir Rob J. de Boer

Michiel van Boven

Universiteit Utrecht

RIVM

22/06/2017


MAIN QUESTIONS

1. What is antigenic drift and how can we visualize it?2. Are T-cell epitope escapes of influenza under positive selection?3. Does (T-cell) epitope escape lead to more flu infections?


Introduction


INFLUENZA A VIRUS (IAV)

I Orthomyxoviridae (Influenza A, B, C,...)I Hosts: bird, human, horse, swine,...I Respiratory virus: infects epithelial cellsI ssRNA virus, genome consists of 8 segmentsI Surface proteins (naming: H1N1, H3N2, H7N1):

I Haemagglutinin: binding to target cells (bind sialic acid)I Neuraminidase: release from host cell (cleave sialic acid)

I Other proteins (more conserved):I Nucleoprotein (NP): encapsidates RNAI Matrix protein 1 & 2 (M1, M2)I Polymerase, non-structural proteins: transcription,

replication


IAV IMMUNOLOGY

I IgA Abs against HA canprovide neutralizingimmunity

I Abs against NA alsoeffective

I CD8+ T-cell response: nosterilizing immunity, buthelps to clear infection;

I asymptomatic infectionand reducedinfectiousness.


IAV EVADES THE IMMUNE SYSTEM

Antigenic Drift/Shift

Reassortment


IAV SEASONAL EPIDEMICS (DRIFT/SHIFT)

I Data: Influenza-like illness (ILI) reported by generalpractitioners (GPs), collected by NIVEL.


2009 H1N1 PANDEMIC (RE-ASSORTMENT)

I 2009 ‘swine flu’: reassortment of pig, bird and human flu.I 1918 ‘Spanish flu’ (H1N1): 500 mln infections, 50–100 mln

deaths


HISTORY OF IAV

I multiple re-assortment eventsI co-circulation of H1N1 and H3N2

van de Sandt et al., J. Virol. (2016)


Antigenic cartography


ANTIGENIC MAP SHOWS DRIFT

I H3N2 subtypeI Colored eplipses: IAV strainsI Open elipses: Ab-responses

I How does one draw such a map?

Smith et al. Science (2004)


HEMAGGLUTINATION INHIBITION (HI) ASSAYI HA binds sialic acid on red blood cells (RBCs)I Adding Influenza to blood causes clustering of RBCsI Addition of different concentrations of Abs inhibits

clustering.I compute IC50 value.


MULTI-DIMENSIONAL SCALING

I interpret IC50 values form HI assay as ‘distances’I 2-dimensional representation of the strain-spaceI minimize an error functionI (compare with PCA)

Strains represented as points xv on a map (responses by yw).

E(x1, . . . , xN, y1, . . . , yN) =∑v,w

(D(v,w)− ‖xv − yw‖2)2 (1)

Find x1, . . . , xN, y1, . . . , yN such that E is as small as possible.


ANTIGENIC CARTHOGRAPHY


RELATION TO EPIDEMIOLOGY?

I Large distance between strains = Large epidemic?I Only very little evidence!

Bedford et al. eLife (2014)


T-cell Antigeniccartography


CTL ANTIGENIC MAP FOR THE LPF EPITOPE

I Map for one very variable epitope on NPI Map involving all CD8+ T-cell epitopes?

Boon et al., J Immunol (2004)


IAV EPITOPES IN IEDB

I HLA-I restricted epitopes (8, 9, 10, 11-mers)I experimentally confirmed CTL-responses (160)I and ‘non-immunogenic’ HLA-I binders (59)

www.iedb.org


IAV PROTEOMES FROM GISAID

I H1N1, H2N2, H3N2 whole-proteome strains (≈ 6100)I smaller representative set (314)I from the years 1930–2014

platform.gisaid.org


SUMMARY OF THE DATA

I characteristic virus setI epitope loci can have multiple alleles


SUMMARY OF THE DATA

I full virus setI color: frequency of the allele in a year


DEFINING A METRICI What do we want to measure? cross reactive (memory)

responsesI NB: simplification w.r.t. LPF map...I (adjusted/scaled) Jaccard distance.

Let Ev, Ew = epitopes in strain v and w, respectively, definedistance

D(v,w) =

(1− #Ev ∩ Ew

#Ev ∪ Ew

)· E[#Ev ∪ Ew] (2)

D(v,w) = (1− 23 + 2 + 2

) · scale ≈ 3 + 2


T-CELL ANTIGENIC MAP

I Antigenic map thatcontains all subtypes(unlike H3N2 Ab-map)

I Antigenic drift/shiftacross subtypes (H1N1→H2N2→ H3N2).

I compare avian strains withpre-existing immunity


Evolution of CTL epitopes


THE NUMBER OF EPITOPES DECREASES

I trend for H3N2 stronger than for H1N1 (−0.38 vs. −0.11e/y). M1 and NP largest contributers

I Why would the number of epitopes decrease?


THE NUMBER OF NON-IMMUNOGENIC PEPTIDES IS

CONSTANT

I Compare epitopes with non-immunogenic peptides (HLAbinders) from IEDB

I Observational bias unlikely


MORE NON-SYNONYMOUS SUBSTITUTIONS AT

EPITOPE SITES?

Problem: HLA typically binds more conserved peptides (HLAtargeting efficiency)

Machkovech et al. JVI (2015); Hertz et al., PNAS (2013)


COMPARE WITH PARALLEL SWINE FLU LINEAGE

I tree for subtype A / H3N2I red: Human flu; blue: Swine fluI Swine flu not targeted by human T-cells!

Machkovech et al. JVI (2015)


CTL ESCAPE EPITOPES UNDER POSITIVE SELECTION?I amino-acid cites indexed by rI Er number of epitopes that contain rI Sr number of non-synonymous substitutions at site rI

F =

∑r Er × Sr∑

r Sr


Relation to epidemiology


EPITOPE GAIN AND LOSS

I How many epitopes (dis)appear each year?I Is there a relation of T-cell antigenic drift (loss) to the sizes

of influenza epidemics?


ESTIMATE SUSCEPTIBILITY FROM ILI DATA

I SIR model: Susceptible, Infected, RecoveredI infection rate β, recovery rate γI start of epidemic t0

I fraction susceptible at start of epidemic: S0

IdSdt

= −βSI , S(t0) = S0

dIdt

= βSI − γI

dRdt

= γI

I Fit model to data...I Age stratified version: age classes 0-4, 5-10, 10-20, 20-45,

45-65, 65+


DATA AND MODEL FIT

black line: data. red line: fitted model


ESTIMATE SUSCEPTIBILITY FROM ILI DATA


COMPUTE EPITOPE LOSS FOR RELEVANT VIRUSES

I only use viruses that circulated during Dutch epidemics(estimated with SIR model)

I Missing data: month and day unknown...


RELATION TO LOSS OF EPITOPES?

I Correct for susceptibility of very young children (0-4 years)I Only significant correlation for 45-64 year age class with

naive timing


SUMMARY

1. IAV evades the immune system by antigenic drift/shiftand re-assortment.

2. IAV evolves in a 2-dimensional antigenic space.3. T-cell escape epitopes are under positive selection.4. Some evidence for effect of drift on epidemics, but not at

all conclusive


REFERENCES

I D.J. Smith et al., Mapping the Antigenic and Genetic Evolution ofInfluenza Virus, Science (2004)

I H.M. Machkoveck et al., Positive Selection in CD8+ T-Cell Epitopesof Influenza Virus Nucleoprotein Revealed by a Comparative Analysisof Human and Swine Viral Lineages, JVI (2015)

I A.C.M. Boon et al., Recognition of homo- and heterosubtypic variantsof influenza A viruses by human CD8+ T lymphocytes, J. Immunol(2004)

I C.E. van de Sandt et al., Differential Recognition of Influenza AViruses by M158-66 Epitope-Specific CD8+ T Cells Is Determined byExtraepitopic Amino Acid Residues J. Virol. (2016)

I T. Hertz et al., HLA targeting efficiency correlates with human T-cellresponse magnitude and with mortality from influenza A infectionPNAS (2013)

I T. Bedford et al. Integrating influenza antigenic dynamics withmolecular evolution eLife (2014)

immunobiology 2017 christiaan h. van dorp rutger g

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