How does influenza virus jump from animals to humans?

Haixu TangSchool of Informatics and Computing

Indiana University, Bloomington

Swine flu outbreak, 2009

Influenza pandemics in human history

• Spanish flu, 1918– Most deadly natural disaster

• Asian flu, 1957• Hong Kong flu, 1968

• Seasonal flu: every year– Vaccine designed based on the observation of the

flu strains spreading in animals

Influenza is cause by a virusLipid B ilayer

matrix protein

RNA/proteincomplex

Hemagglutinin (H)

Neuraminidase (N)

Orthomyxoviridae; a class of RNA virus using

RNA as genetic material; globular article of a

diameter ~100 nm; Protected by a bilayer and

matrix proteins; ~500 copies of H protein

and ~100 copies of N proteins; used for classification

Classification of influenza viruses• 16 H genes and 9 genes found

• Spanish flu, 1918: H1N1– Most deadly natural disaster

• Asian flu, 1957: H2N2• Hong Kong flu, 1968: H3N2• Swine flu: 2009: H1N1• Current pandemic threat: H5N1• Several hundreds of active flu strains

Infection of flu viruses

Host cell

nucleus

1. Virus attached to the host cell;

Infection of flu viruses

1. Virus attached to the host cell;2. Virus swallowed up by the host

cell;

Infection of flu viruses1. Virus is attached to the host cell;2. Virus is swallowed up by the host

cell;3. Viral RNAs is released and enter the

nucleus, where they are reproduced;

Infection of flu viruses1. Virus is attached to the host cell;2. Virus is swallowed up by the host

cell;3. Viral RNAs is released and enter the

nucleus, where they are reproduced;4. Fresh RNAs enter the cytosol;

Infection of flu viruses1. Virus is attached to the host cell;2. Virus is swallowed up by the host

cell;3. Viral RNAs is released and enter the

nucleus, where they are reproduced;4. Fresh RNAs enter the cytosol;5. Viral RNAs act as mRNA to be

translated into proteins forming new virus particles;

Infection of flu viruses1. Virus is attached to the host cell;2. Virus is swallowed up by the host

cell;3. Viral RNAs is released and enter the

nucleus, where they are reproduced;4. Fresh RNAs enter the cytosol;5. Viral RNAs act as mRNA to be

translated into proteins forming new virus particles;

6. New virus buds off from the membrane of the host cell;

Infection of flu viruses1. Virus is attached to the host cell;2. Virus is swallowed up by the host

cell;3. Viral RNAs is released and enter the

nucleus, where they are reproduced;4. Fresh RNAs enter the cytosol;5. Viral RNAs act as mRNA to be

translated into proteins forming new virus particles;

6. New virus buds off from the membrane of the host cell;

Spread of influenza viruses

http://www.healtyhype.com

Recognition of the virus to the host cell:

hemagglutinin (H protein) vs. glycans • On the surface of animal cells,

there exist a heavy coat of glycans (sugars linked to proteins or lipids);

• Different animals may have glycans of different structures;– Human, pig and birds

• Different influenza virus strains with different hemagglutinin proteins (a class of glycan binding protein) recognize glycans of different structures

Structure of glycans

monosaccharide

linkage

Some basic graph theory

• Graph: modeling pairwise relation (edges) between subjects (nodes or vertices)

• Tree: a graph with no cycle– Each node in a tree has zero (leaves) or more child nodes– Subtree: a subset of nodes/edge

• Labels– Nodes: monosaccharides– Edges: linkage types

Animal glycans

Hemagglutinins recognize sialylated glycans

• Human cells mainly express 2-6 linked sialylated glycans;

• Bird cells mainly express 2-3 linked sialylated glycans;

• Pig cells express both.

Vessel theory

Hemagglutinin-glycan interaction is more complicated

• Several influenza strains were observed to be inconsistent with the theory– AV18 strain has hemagglutinin proteins recognize

specifically 2-3 linked glycans, but are not transmissable in birds;

– NY18 and Tx91 strains recognize both 2-3 and 2-6 linked glycans, but NY18 does not transmit efficiently in human population, whereas Tx91 does;

– Some chimeric H1N1 strains with high binding affinity to 2-6 linked glycans, but do not spread efficiently in human and pig.

Experimental determination of binding specificities of hemagglutinins

hemagglutinin

virus

Interaction assay

Glycan array

?

The glycan motif finding problem

The glycan motif finding problem

• Input: a set of (glycan) trees that are found to be recognized by a glycan binding protein (e.g. hemagglutinin)

• Output: a l-treelet that is over-represented in the input set

• l-treelet: a tree of a fixed small size l (e.g. l=4).• Over-representation: number of trees in the input

set containing the treelet is much higher than the expected number in a random set of trees

Exhaustive counting of treelets

4

4

3 6

2

4

6

2

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6

2

4 4

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3 6

4

4 2

4

6

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3 6

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3

2

3 6

2

3 6

23

2

4

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2

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2

6

2

4

Finding over-represented treelets

4

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3 6

2

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2

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4

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3 6

2 2

4

6

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4

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3 6

2

4

6

2

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3 6

2

2

6

2

4

6

4

4

4

6

2

4

3

2

4

3 63 6

2

3 6

2

4

4

3

3

2

4

6

2

4

2

4

2

4

2

4

A S N -X-S e r/ Th r

4

4

3 6

3 62

A S N -X-S e r/ Th r

4

4

3 6

3 62

A S N -X-S e r/ Th r

4

4

3 6

3 62

4

3 o r 6

4

3 o r 63 o r 6

4 4

3 o r 6

H ig h -m a n n o s e C o m p le x h yb rid

N -g lyca n s

co re s tru ctu re Glycans are not random!

Many 4-treelets appear in ALL input glycan trees.

The glycan motif finding problemA different formulation

• Input: a positive set of (glycan) trees that are found to be recognized by a glycan binding protein (e.g. hemagglutinin) and a negative set of glycan trees that are found NOT to be recognized by the same protein

• Output: a l-treelet that is over-represented in the input positive set than the negative set

• Over-representation: number of trees in the positive set containing the treelet is much higher than the number of trees in the negative set

Contingency table

6

2

4

6

4

4

4

6

2

4

3

2

4

3 63 6

2

3 6

2

4

4

3

3

2

4

6

2

4

2

4

2

4

2

4

4

4

3 6

2

4

6

n e g a tiv e

4

4

3 6

4

4

3 6

2

3 6

2

4

6

2

4

6

3 6

2 2

4

4

3 6

2

4

6

2

4

6

2

4

p o s itiv e

4

4

3 6

2 2

4

6

2

4

4

6

2

4

4

4

3 6

2

4

6

2

4

3 6

2

26

2

4

+

+

s a m p le

-

-

3

30

0

+

+

s a m p le

-

-

3

00

34

4

3

Fisher’s exact test: significance test of the over-represented treelets

4

4

3 6

2

4

6

n e g a tiv e

4

4

3 6

4

4

3 6

2

3 6

2

4

6

2

4

6

3 6

2 2

4

4

3 6

2

4

6

2

4

6

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4

p o s itiv e

4

4

3 6

2 2

4

6

2

4

4

6

2

4

4

4

3 6

2

4

6

2

4

3 6

2

2

6

2

4

+

+

s a m p le

-

-

3

30

0

+

+

s a m p le

-

-

3

10

22

4

6

+ -

+ ni+ N-ni

+

- ni- M-N-ni

-

M glycans printed on the arrayN positive, M-N negativeni

+ positives contain the treeletni

- negatives contain the treelet

P=0.05

P=0.15

Glycan patterns found to be recognized by hemagglutinin

• R. Sasisekharan and colleagues show is the pattern recognized by human influenza hemagglutinin, but not recognized by avian influenza hemagglutinin;

• 2-6 linked sialylated glycans with long oligosaccharide branch (with multiple lactosamine repeats) are predominantly expressed in the human upper respratory epithelial cells

• Indeed, the binding specificity of hemagglutinin to 2-6 linked sialylated glycans is not sufficient for the spread of the influenza viruses in human populations.

6

2

4

Chandrasekaran A, et al. Nat Biotechnol , 2008; 26:107–113.

Spread of influenza viruses

http://www.healtyhype.com