The Avian flu

Un generador de pandemias

• At the end of every summer million of ducks and wild geese mass on Canadian and Siberian lakes for their annual migration.

• Influenza blooms.– In intestinal tract of juveniles– Diverse strains– Shed virus as they migrate south

Influenza in Mammals

• In humans and pigs influenza is very pathogenic.– Infects the respiratory tract.– Spread by aerosol.

• Three genera of Influenza: A, B, and C.– B and C endemic to human

population– Type A is mostly found in birds

• A, is most lethal to humans.

Evolutionary Shape Shifters

• Compared to other pathogens, influenza A is evolving at record breaking speed.

• From year to year its proteins change amino acids to create modified strains requiring new vaccines (antigenic drift).

• About every 20 -30 years influenza A will change drastically enough to jump species (antigenic Shift).

Influenza A• Hemagglutinin (HA)

– Species specificity– Main antigenic determinant

• Pandemic result of new HA

• Neuraminidase• M2 (protein pump)• Lipid envelope• Single stranded RNA

– Eight segments called ribonucleoproteins (RNAPs)

– make up 10 genes

HA binds toSialic acid on Intestinal and respiratory cells

M2 pumps ions into the interior of endosome to uncoat virus and release RNAPs

NA removes sialic acid and allows for escape

Mutation rate of Influenza

• The synthesis of RNA is radically error prone– DNA polymerases proof read and auto corrects their

mistakes. • 1 mutation every billion nucleotides

– RNA polymerases does not proof or correct their copy• Error rate is 1 million times higher than DNA pol.

• Progeny often referred to as a “mutant swarm”.– Lives on the edge of error catastrophe.

Human Immune system

• The acquired or specific immune system is able to create lymphocytes that are specific for any possible antigen.

• Once an immune response has been launched the bodies immunity keeps in memory every antigen that it has ever responded to.

– Secondary infections are quickly and vigorously attacked.

Evolution of Influenza

• To persist from year to year a strain must be able to infect naive hosts who have never been exposed to its type of HA.

• Fitch and colleagues hypothesized that strains Influenza A which developed new antigenic sites would have a selective advantage.

• Fitch looked at flu strain that had infected humans from 1968 – 1987.

– The frozen flu samples constitute a fossil record – one which genes could be sequenced.

Credit: L. Stammard, 1995

Rate of mutations

• The flu strains accumulated nucleotide substitutions in their haemagglutinin genes at a steady rate.

Phylogenetic analysis

• Most of the flu samples represent extinct side branches on the evolutionary tree.

• The flu strains of the 1980’s turned out to be descended from a single strain of the 1960’s.

What allowed the surviving lineage to endure while the other lineages

perished?

*Mutations in Surviving lineages Extinct lineages

Antigenic sites 33 31

Non-antigenic sites

10 35

*Only mutations that resulted in change of amino acid were counted.P = .002

Hemagglutin, an Important Antigenic site

• More than three quarters of the changed amino acids in the “surviving lineages” occurred at antigenic sites on haemagglutinin.

Comparing Influenza’s Antigenic Drift to The Neutral Theory

• To further test the hypothesis that the human immune system was driving the evolution of Influenza A, Fitch and colleagues compared the mutations found in 357 influenza strains isolated between 1985 and 1986 to the Neutral theory.

Neutral theory:– Mutations resulting in amino acid changes are

deleterious and eliminated by selection.

– Mutations to synonymous codons are neutral and may become fixed in the population by genetic drift.

At First Glance

• Of the 331 nucleotide substitutions, 191 (58%) were silent and 140 (42%) were replacement substitutions

• This was consistent with the neutral theory

A Closer look

• When researchers looked at just the haemagglutinin gene they identified 18 codons that had significantly more replacements substitutions than silent substitutions.

• All 18 codons were for amino acids at antigenic sites.– Not consistent with the neutral theory. The immune

system was pushing the evolution of Influenza A.

Vaccines

• Vaccines take months to prepare. Flu season is between October and March.– The flu virus’ antigenic make up must be

predicted well in advance of the flu season in order to stock pile enough for an epidemic.

Predicting the Next Flu.

• Robin Bush and colleagues devised a way to predict which circulating flu strains is most likely to have surviving descendents in the future.– It will be the current circulating strain with the

most mutations in the 18 codons known to be under positive selection.

The Origin of Pandemic Flu Strains

The Red Queen• Influenza A’s extraordinary heterogeneity

allows it to resist the immune system.– A single amino acid substitution can assure a

strains survival to the next season.

• Point mutations don’t totally outwit the immunological memory of the body. – The high level of partial immunity remaining in

the community ensures that antigenic drift will not cause a pandemic.

The Making of a Pandemic

• Influenza can mutate by great leaps.– RNA is packaged in separate segments. a

co-infection of a host by two different subtypes can result in a reassortment of their genes.

• Influenza can trade RNP’s between different strains. This produce new hybrids.

• These new hybrids have never been seen by the human population. A pandemic will ensue.

The Evidence is in the Phylogeny• The influenza stains can be

broken up into distinct clades based on the immunoprotein.

• The phylogenic tree gives species, year and subtype.– H3N8

• Haemagglutinin 3

• Neuraminidase 8

• Each hemaggluinin group constitutes a clade.

Phylogenies cont.

• Compare:– The Human Northern Territory /60-1968

(H3N2) and– Human / Victoria / 1968 (H2N2)

• NA’s are closely related but HA’s are distant.

Phylogenic evidence

• H3 was never seen in the human population until 1968.

• Global pandemic

• Reassortment with pig.

Phylogenic evidence cont

• Pigs are susceptible to both bird flu and pig flu.

• Pig strains sometimes infect humans.

• Flu pandemic begin when humans strains and bird strains simultaneously infect a pig and swap genes, and later move to humans.

1918 Flu

• Researchers have Isolated and sequenced the genes from the 1918 flu.

• The 1918 flu came from birds.

• It killed more people in 2 months than HIV has killed in 20 years.

N1H5

1. Travel will be restricted.Food supply will shut down. People won’t travel between countries.

Drugs come from other countries. We will run short on pharmaceuticals.

Oil is shipments are likely to lag at transportation between countries grinds to a halt. Heat in the winter months may be short supply

N1H5

• Mask will run out.– No one will be allowed to leave their house

without a mask.– Church and schools will all close.– Many businesses will shut down– Quarantines will be enforced.

N1H5

• How do we handle the dead. – 1.5 million dead in this country alone. – We need to start planning for this.