Influenza

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Influenza
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Influenza, measles (both linear RNA) hepatitis
delta virus (circular RNA)
V Single-stranded (-)sense RNA
(Orthomyxoviruses, Rhabdoviruses, etc) Must have
a virion particle RNA directed RNA polymerase. a)
Segmented e.g. Orthomyxoviruses. First step in
replication is transcription of the (-) sense RNA
genome by the virion RNA-dependent RNA polymerase
to produce monocistronic mRNAs, which also serve
as the template for genome replication. b)
Non-segmented e.g. Rhabdoviruses. Replication
occurs as above and monocistronic mRNAs are
produced.
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Influenza

• Orthomyxoviridae family
• 3 serotypes A,B,C
• Membrane bound
• RNA genome (negative strand)
• eight segments
• Replicates in cells nucleus
• (steals methylated caps)
• 10 transcripts from 8 segments
• translated (7 structural 3 non-structural)

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• INFLUENZA
• Epidemic
• A rapid increase in the levels of an infection,
  typical of micro-parasitic infections (lasting
  immunity, short generation times)
• An epidemic is usually heralded by an exponential
  rise in the number of cases in time and a
  subsequent decline as susceptible numbers are
  exhausted.
• Epidemics may arise from the introduction of a
  novel pathogen (or strain) to a previously
  unexposed (naive) population, or as a result of
  the re-growth of a susceptible population some
  time after a previous epidemic (due to the same
  infectious agent. Contrast endemic, pandemic).

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Origin and Control of Pandemic Influenza

• Influenza kills 500,000-1,000,000/year worldwide
• 20,000 US
• Worldwide epidemic pandemic
• 1918 Spanish Flue- most severe recorded
  outbreak of acute disease
• When? could occur any time
• Where? probably China
• Why? crowded conditions and rapid transport
• Millions will become ill, many will die

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Influenza infects Ciliated Epithelial cells Many
epithelial surfaces in the body are ciliated -
covered in cells which contain tiny hair-like
structures beating in synchrony to move
secretions or objects around. Examples include
ciliated epithelia in the vesicles of the brain
which circulate the cerebrospinal fluid, and in
the oviduct which move the ova from the ovary to
the uterus. In the respiratory tract, ciliated
epithelial cells sweep clean dust and germs
trapped in mucus secreted by "goblet cells" in
the epithelium. How important are these cells?
Well, they are the primary target of infection
for "common cold viruses" such as coronaviruses,
influenza virus and rhinoviruses. These viruses
may kill the ciliated cells or simply stop the
cilia beating. In either case, mucus builds up
and forms a good site for secondary bacterial
infections, resulting in the mucus we are all
familiar with when we have a cold. This shows how
important healthy cilia are!
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• The Genes of Influenza A (8 RNA molecules)
• The HA gene. It encodes the hemagglutinin. 3
  distinct hemagglutinins, H1, H2, and H3) are
  found in human infections. 9 others have been
  found in animal flu viruses.
• The NA gene. It encodes the neuraminidase. 2
  different neuraminidases (N1 and N2) have been
  found in human viruses 7 others in other
  animals.
• 3. The NP gene encodes the nucleoprotein.
  Influenza A, B, and C viruses have different
  nucleoproteins.
• 4. The M gene encodes the two matrix proteins
  (using different reading frames of the RNA).
• 5. The NS gene encodes two different
  non-structural proteins (also by using different
  reading frames).
• 6. - 8. one RNA molecule (PA, PB1, PB2) for each
  of the 3 RNA polymerases

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Segment Size(nt) Polypeptide(s) Function 1 2341 P
B2 Transcriptase cap binding 2 2341 PB1 Transcrip
tase elongation 3 2233 PA Transcriptase
protease activity (?) 4 1778 HA Haemagglutinin 5 1
565 NP Nucleoprotein RNA binding part of
transcriptase complex nuclear/cytoplasmic
transport of vRNA 6 1413 NA Neuraminidase
release of virus 7 1027 M1 Matrix protein major
component of virion M2 Integral membrane
protein - ion channel 8 890 NS1 Non-structural
nucleus effects on cellular RNA transport,
splicing, translation. Anti-interferon
protein. NS2 Non-structural nucleuscytoplasm,
function unknown The influenza A NS1 protein
represses interferon-b synthesis by preventing
activation of the NF-kappa-B signaling pathway
transcription of interferon genes
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• The Disease
• Influenza virus invades cells of the respiratory
  passages.
• Hemagglutinin molecules bind to carbohydrate on
  the glycoproteins of the epithelial cells of
  the host.
• The virus is engulfed by receptor mediated
  endocytosis.
• Drop in pH in the endosome (endocytic vesicle)
  produces a change in the structure of the viral
  hemagglutinin
• Fusion the viral membrane with the vesicle
  membrane.
• Contents of the virus in the cytosol.
• RNA enters the nucleus of the cell, fresh copies
  are made.
• They return to the cytosol where some serve as
  mRNA molecules - translated into the proteins of
  fresh virus particles.
• Fresh virus buds off from the plasma membrane of
  the cell (aided by the neuraminidase).
• Infection spreads to new cells.

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• Hemeagglutinin/Neuraminidase Ratio
• The flu virus infects cells by using
  hemagglutinin to attach to sugary "hooks" on the
  cell called sialic acid residues.
• Neuraminidase breaks the bond between
  hemagglutinin and sialic acid residues and frees
  the virus
• The balance of HA and NA activity is important
  for efficient virus entry into and exit from
  cells

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Origin and Control of Pandemic Influenza

• Spanish influenza 1918 - 20 million died
• RNA fragments sequenced
• pathology museums (paraffin fixed)
• frozen in Alaska permafrost
• Sequence of 3 crucial genes completed
• hemeagglutinin
• neuramininidase
• nonstructural protein

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• Pandemics and Antigenic Shift
• Two pandemics of influenza have swept the world
  since the "Spanish flu" of 1918.
• The "Asian" flu pandemic of 1957
• The "Hong Kong" flu pandemic of 1968.
• (The pandemic of 1957 probably made more people
  sick that the one of 1918. But the availability
  of antibiotics to treat the secondary infections,
  that are the usual cause of death, resulted in a
  much lower death rate.)
• The hemagglutinin of the 1918 flu virus was H1,
  its neuraminidase was N1, so it is designated as
  an H1N1 "subtype".
• http//www.ultranet.com/jkimball/BiologyPages/V/V
  iruses.html

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Antigenic Shift

• Date Strain Subtype Notes
• 1918 being studied H1N1 pandemic of "Spanish" flu
• 1957 A/Singapore/57 H2N2 pandemic of "Asian" flu
• 1962 A/Japan/62 H2N2 epidemic
• 1964 A/Taiwan/64 H2N2 epidemic
• 1968 A/Aichi/68 H3N2 pandemic of "Hong Kong" flu
• A/New Jersey/76 H1N1 swine flu in recruits
• These data suggest that flu pandemics occur when
  the virus acquires a new hemagglutinin and/or
  neuraminidase

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• Epidemics and Antigenic Drift
• No antigenic shifts occurred between 1957 ("Hong
  Kong") and 1968 ("Asian"). So what accounts for
  the epidemics of 1962 and 1964?
• Missense mutations in the hemagglutinin (H) gene.
  
• Flu infections create a strong antibody response.
  After a pandemic or major epidemic, most people
  will be immune to the virus strain that caused
  it. The flu virus has two options
• wait until a new crop of susceptible young people
  comes along
• change the epitopes on the hemagglutinin molecule
  (and, to a lesser degree, the neuraminidase) so
  that they are no longer recognized by the
  antibodies circulating in the bodies of previous
  victims.
• By 1972, the H3 molecules of the circulating
  strains differed in 18 amino acids from the
  original "Hong Kong" strain
• By 1975, the difference had increased to 29 amino
  acids.
• The gradual accumulation of new epitopes on the H
  (and N) molecules of flu viruses is called
  antigenic drift. Spontaneous mutations in the H
  (or N) gene give their owners a selective
  advantage as the host population becomes
  increasingly immune to the earlier strains.

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Monomer of HA Protein Close up shows it bound to
the cell receptor sialic acid. Fusion peptide
mediates fusion between viral and cellular
membranes
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Recombination in the Hemagglutinin Gene of the
1918 Spanish Flu Mark J. Gibbs, John S.
Armstrong, Adrian J. Gibbs When gene sequences
from the influenza virus that caused the 1918
pandemic were first compared with those of
related viruses, they yielded few clues about its
origins and virulence. Our reanalysis indicates
that the hemagglutinin gene,a key virulence
determinant, originated by recombination. The
globular domain of the 1918 hemagglutinin protein
was encoded by a part of a gene derived from a
swine-lineage influenza, whereas the stalk was
encoded by parts derived from a human-lineage
influenza.
Phylogenetic analyses showed that this
recombination, which probably changed the
virulence of the virus, occurred at the start of,
or immediately before, the pandemic and thus may
have triggered it.
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Molecular Basis for High Virulence of Hong Kong
H5N1 Influenza A Viruses Masato Hatta, 1 Peng
Gao, 1 Peter Halfmann, 1Yoshihiro Kawaoka
1,2 In 1997, an H5N1 influenza A virus was
transmitted from birds to humans in Hong Kong,
killing 6 of the 18 people infected. When mice
were infected with the human isolates, two
virulence groups became apparent. Using reverse
genetics, we showed that a mutation at position
627 in the PB2 protein influenced the outcome of
infection in mice. Moreover, high cleavability of
the hemagglutinin glycoprotein was an essential
requirement for lethal infection.
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3 processes by which influenza virus evades the
immune system Re-assortment - antigenic
shift Spontaneous mutation - antigenic
drift Recombination
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Anti-influenza drugs Amantadine and
Rimantadine block the shift in pH that the flu
virion needs in order to get its contents into
the cytosol. (A strains only it doesn't work for
B) Zanamivir (Relenza) and Oseltamivir
(Tamiflu) block neuraminidase and inhibits the
release of fresh virions. Spraying zanamivir into
the nose or inhaling it shortens the duration of
disease symptoms by one to three days.
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Beating the flu. Crystallographic structure of
influenza virus neuraminidase (N9 subtype)
showing the rationally designed anti-flu drug,
Relenza (4-guanidino-Neu5Ac2en), bound to the
active site of the enzyme
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http//www.ultranet.com/jkimball/BiologyPages/I/I
nfluenza.html
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SCIENCE Online Epidemiology Virology Clues
into the molecular basis for the lethality of
some outbreaks of influenza A in this century are
the subject of two reports (see the Editorial by
Layne et al. and the Perspectives by Webster and
by Laver and Garman). The 1918 influenza pandemic
swept through the United States Army and escaped
to slaughter more young adults than did World War
I. A reanalysis of the gene sequences by Gibbs et
al. (p. 1842) indicates that a recombination
event between swine and human lineages in the
hemagglutinin gene of the virus triggered the
pandemic. This event would have meant a change in
antigenicity, and owing to the previous
demography of flu, the immunologically naïve
population was apparently precisely the age group
that showed the highest mortality from severe
lower respiratory tract oedema and hemorrhage. In
1997, a strain of influenza A transmitted from
birds killed 6 of 18 infected persons in Hong
Kong. Hatta et al. (p. 1840) infected mice with
human viral isolates and found that a mutation at
position 627 of polymerase 1 and cleavabililty of
the hemagglutanin glycoprotein had the greatest
effects on pathogenecity.