Influenza Virus: Evolution in real time

Influenza (FLU) 20,000 human deaths annually in USA 1918 Spanish flu killed 50 –100 million people globally (about 20% of world population) Direct economic cost of flu about 4.6 billion USD per year

PANDEMICS Since 1880’s, there have been six flu pandemics 1889, 1918, 1968, 1977, 2009 What causes pandemics?

Influenza Taxonomy Three principle clades of influenza: A, B, C ( analogous to genera) A found widely in animals (highest diversity in birds), but mammals (including humans as well) B found in humans and seals C found in humans and pigs (least pathogenic, most diverged)

INFLUENZA STRUCTURE single stranded RNA protein sheath (caspid) 8 gene segments (A&B) three proteins extrude: hemagglutinin (HA), neuraminidase (NA), and matrix 2. HA and NA bind to cell membrane. hemagglutinin

INFLUENZA glycoproteins HA and NA are the principle target of the immune response Influenza A has 16 types of HA proteins and 9 NA types (most types in birds)

INFLUENZA IMMUNE RESPONSE Influenza A has 16 types of HA proteins and 9 NA types (most types in birds) The HA protein binds to sialic acid receptors on the cell surface. Birds have one type of receptor (SAα2,3 intestinal), humans have SAα2,6 (respiratory system), pigs have both (in all organs). HA types don’t necessarily determine receptor affinity

INFLUENZA IMMUNE RESPONSE Host antibodies recognize specific HA and NA structures, that structure is determined by the amino acid sequence in the protein Novel HA and NA structures go unrecognized, allowing influenza virus to replicate

INFLUENZA: Two types of evolution mutational: change in the RNA sequence of a gene segment. mutation rate: 1 x 10-3 to 8 x 10-3 substitutions per site per year (vertebrate autosomal DNA: 1 x 10-(9-12))

antigenic drift: mutations that change the protein amino acid composition (i.e. non-synonymous substitutions) especially at the antigenic sites. In surviving lineage they identified 33 amino acid replacements in antigenic sites and 10 in non antigenic sites. In extinct lineages found 31 replacements in antigenic sites and 35 in non-antigenic sites. What does this mean?

REASSORTMENT When a host cell is simultaneously infected by two different strains, gene segments can be re-assorted among subsequence viral copies (Note: this is a great example of non- Darwinian evolution)

HOST Switching NP protein usually causes virus to be host specific. But the virus can jump species Usually more virulent

h5n1 influenza endemic in Southeast Asia reservoir in wild and domestic waterfowl in mid-2000s spread via migratory birds to Europe and Middle East (only established in Egypt) highly fatal (60% of human patients die, infected birds typically die too) human receptor in lower respiratory tract probably explains why human to human transmission non-existant

REASSORTMENT AND HOST SWITCHING Working model is that reassortment facilitates host switching

Influenza pathogenicity is a by-product of host switching

REASSORTMENTS cause influenza pandemics Bring completely novel gene segment combinations together

2009 Swine flu First detected in Mexico, then quickly in the US in March 2009 During the subsequent 3-4 weeks, it spread to at least 30 countries WHO Pandemic level 5 of 6

REASSORTMENT in 2009 Swine Flu h1n1

2009 Pandemic H1N1 spread very fast across the world Originated either in Mexico or USA

Reassortment is on-going

Influenza persistence depends on ecology and spillover