Influenza Mortality in US is >36 k death/yr !

Orthomyxoviruses! http://www.cdc.gov/flu/weekly/

ortho = “true”!
myxo = “mucus”! Seasonal Distribution of Influenza

% of all deaths due to pneumonia and influenza

Epidemic peaks each winter
2008 was a bad year

Where does it go in the summer?

The Great Influenza: The Epic Story 1. Influenza transmission is dependent on temperature and humidity (cold and dry)
http://web.uct.ac.za/depts/mmi/stannard/fluvirus.html
of the Deadliest Plague in History!
2. Transmission is dependent on close contacts (crowding indoors)

The reservoir of human influenza is in the tropics (SE Asia)

Vaccines
Dominant strains are seeded into the Northern Hemisphere each season
(I.e. they do not over-season in the Northern Hemisphere) •! Inactivated (standard) and live
What data do you think leads to this interpretation? attenuated (new) vaccines
•! Given in ~Oct.–Nov. each year
•! Typically includes three envelope
variants chosen in spring of the
previous year
–! H1N1, H3N2, B type
•! ~70-90% efficacy; but less with
Schematic of the dominant seeding hierarchy of seasonal influenza A (H3N2) viruses increasing age
C. A. Russell et al., Science 320, 340 -346 (2008)
 1918 Influenza Pandemic

195,000 influenza deaths in the US during October, 1918

~600,000 in the US during the 1918 pandemic
20-40 million influenza deaths world-wide during the 1918/19 pandemic

Orthomyxoviruses
Negative-stranded segmented RNA viruses
Targets of neutralizing
1 Polymerase subunit, cap recognition antibodies
Different serotypes 5 !
2 Polymerase subunit, endonuclease 1 !
6 !
3 Polymerase subunit 2 ! 7 !
3 ! 8 !
4 Surface glycoprotein, binds receptor; fusion protein 4 !

5 RNA binding (equivalent to N)

6 Surface glycoprotein, neurominadase

HA
7 M1: matrix protein
M2: ion channel NA

8 NS1: IFN antagonist

NS2: nuclear export of vRNPs

Segmentation of the genome allows for Reassortments From Mandell, Bennett and Dolin, Principles and Practice of
Infectious Diseases
 Influenza transcription occurs in the nucleus
“cap snatching” from cellular mRNAs generates primers ! Cellular mRNAs bound by PB2 at 5’ Cap Cleavage of cellular mRNA near cap

The influenza
polymerase complex is a
Cellular mRNA
cap-dependent RNA
endonuclease

5’ end of viral RNA held by PB1 Alignment of 3’ and 5’ ends of vRNA

Capped RNA fragments
from cellular mRNAs are
used as primers for Viral mRNA threaded through polymerase Non-templated G added to cleaved RNA
mRNA transcription of the
influenza genes Viral mRNA
5’

The 5’ end of the cellular

mRNA is covalently
attached to the influenza
Cellular mRNA Influenza mRNA 3’
mRNA
5’ end of vRNA held in place Cleaved cellular mRNA displaces
Leads to polyA stutter at end of message vRNA to prime at 3’ end
One consequence is the host mRNAs cannot be translated

influenza virus replicaiton cycle

Switch from mRNA production to replication of vRNA
and template RNA ! 1. binding 2.
3. M2/HA

2. endocytosis 1. HA

3. Acidification/ 4.NP
fusion

4. Nuclear entry
6. NS2
5. transcription 7. PA/PB1/PB1/NP
5. PA/PB1/PB2
Free NP binds to the 5’ end of vRNA causes initiation of 6. Splicing/transport
anti-genome and genome synthesis
7. Genome
replication 9.NA
The polymerase complex changes conformation and
begins cap-independent RNA synthesis (replacement of 8. Assembly/ 8. M1
PB1 with PA in the active site of the complex) budding 10. cellular
protease on HA
9.release
Two differences between mRNA and template RNA = 5’ end and polyA tail
10.maturation
Replication in the nucleus
Samuel. J. Biol. Chem. 2006;281:8305-8307
 Neurominidase is needed for release of virions from
Antigenic Drift versus Antigenic Shift
the infected cell !
Drift Shift

•! Point mutations in HA •! Reassortment of new

and NA in existing HA and/or NA RNA
human variants! segments from avian
strains into humans!
•! Annual epidemics!
•! Global pandemic !
•! Some cross-protection!
•! No cross-protection!
•! Up to 50% of the
human population
becomes infected!
N Engl J Med. 2005 Jan 27;352(4):323-5
This is a target for the only antiviral agent for influenza

Evolution of the M1 gene of influenza A from a variety of hosts

Antigenic Drift: Evolution of human HA (H3) isolates shows a “catcus-like”
phyologenetic tree
selected for maximum time frames and locations of isolation !
Human
The thick line running from the The vertical lines
lower left (* = root) to the upper indicate the range American gull
right (open square) is called the of isolates from the
trunk and represents the American Avian
flu years (October
successful H3N2 lineage. ! 1 to September 30). !
Equine

Eurasian swine
Very short side-branches The average age Eurasian Gull
of side branch is
Eurasian Avian
1.6 years

H5N1 HPAI

How would you interpret this tree?

Human, Eurasian Swine, and HPAI lineages display temporal patterns of virus evolution

Most Avian lineages show no host, temporal or spatial evolution

This is “antigenic drift” Fitch, Walter M. et al. (1997) Proc. Natl. Acad. Sci. USA 94, 7712-7718 Olsen, Science 312, pp384-388, 2005
 Phylogenetic analysis of NP in different hosts
The reservoir of Influenza A diversity resides in aquatic birds

•! Waterfowl (ducks, gulls, etc) have Influenza grows in the

16 subtypes of HA (H1-H16) and 9 intestinal tract of aquatic
subtypes of NA (N1-N9). birds and causes little or
no disease.
•! Only H1, H2, H3, N1, and N2 have
become endemic in humans. .
Influenza grows in
How do you interpret this graph? respiratory tract of
•! So far
terrestrial birds and
mammals (humans, pigs,
horses)

How do you interpret this tree?

Transfer of segments from avian influenza strains leads to

1918 HINI “Spanish Influenza”
new pandemic human strains This is “shift”
H1N1 H2N2 H3N? 1957 H2N2 “Asian flu” In the initial years of the
pandemics up to 50% of the
1968 H3N2 “Hong Kong flu” human population becomes
infected
1977 H1N1 “Russian flu”

1918 1957 1968 Influenza A subtypes in the human population

today

H3N2 H3N8?
?

H1?
H1N1 H2N2 H3N2
All avian segments PB1, HA, and NA PB1 and HA from
Spanish flu from avian strain avian strain
Asian flu Hong Kong flu 1889 1900 1918 1940 1960 1980 2000

Russian flu (1977) H1N1 Palese, Nat Med 10:S82

 Avian influenza!
H5N1 aka“Bird flu” aka HPAI!
•! H5N1!
–! 1997, Hong Kong - 6 /18 fatal cases!
•! Dramatic and unpredictable spread among wild –! since 2004 continued outbreaks!
–! 100 million domestic birds killed!
and domestic birds
•! H9N2!
–! 1999 - Hong Kong and southern China!
–! 10 million dead chickens!
•! Exceptionally high mortality in humans •! H7N7!
–! 2003 in Netherlands!
–! 30 million birds killed!
•! Limited human-to-human spread so far.! –! Mostly conjunctivitis but 1 (of 83 cases) was
fatal!
•! H7N3!
–! 2004, British Columbia!
–! 1.9 million birds culled!

H5N1 – avian segments only, no reassortment, VERY virulent in chickens!

Areas reporting occurrence of H5N1 avian influenza

Areas with confirmed human cases of H5N1 avian influenza since 2003
in poultry and wild birds between January and June 2008 (as of June 2008)

Notice high fatality rate. Very little human-human spread

 What adaptations are necessary for human-human transmission of H5N1? Why is H5N1 fatal in humans?!
SA!2,3Gal (used by Higher viral loads
HA-SA!2,6Gal
PB2-627K avian HA) is limited to
Other changes? the lower airways in H5N1 H3/H1 H5N1 fatal H5N1 not fatal
humans, while the
upper airway has Viral load in throat swab
SA!2,6Gal (used by (log10 cDNA copy per ml) 7.0; 4.3-8.2 4.8; 4.2-5.8 7.5; 4.7-8.2 5.9; 4.3-7.0
human HA). median; range

Increased levels of chemokines and cytokines produced

by bronchial epithelial cells and aveolar macrophages

HA-SA!2,3Gal median level (log10/ml)

PB2-627E
H5N1 H3/H1 control
Other changes
IP-10 5.1 3.8 2.7
PB2 from avian species (627E) is chemoattractants of
MIG
blocked in human cells by a macrophages 4.3 3.2 2.6
MCP-1
restriction factor that prevents
incorporation into RNPs 2.0 0.8 0.7
IL-8 chemoattractants of
Cell Host and Microbe, 4, 111-122, August 2008!
neutrophils
Lancet (2008) 371; p1464-75
Nature Medicine 12, 1203-1207 (2006)

The 1918 Influenza was unusual in its high death rate

among 15-45 year olds ! Things you should know about influenza !
Mortality usually highest in the very young and very old
•! Basic replication steps
2500 •! Evolution in humans (drift = selection) versus aquatic birds
Specific death rate per 100,000

(stasis) {why do the phylogenetic trees look that way?}

2000
•! Antigenic shifts and origin of the pandemics
1500
•! What is the bird flu, and what are the concerns?
1000 •! Paper for next time: Reconstruction of the 1918 influenza
–! how did they do it?
500
–! what are the theories about why the 1918 influenza was so
deadly?
<1
1-4
5-14
15-24
25-34
35-44
45-54
55-64
65-74
75-84
>85 –! how did those theories change as a result of the data in this
paper
Age Divisions –! what would you do next?
1892 pandemic
Why is there a W-shaped curve?
1911-1915 averaged interpandemic years
1918 pandemic
Reid et al Microbes and Immunity 3, 81-87, 2001