Human Genome: sequence, structure, diseases

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Human Genome sequence, structure,
diseases Influenza viruses

• Lecture 11
• BINF 7580
• FALL 2005

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Influenza A virus is a negative-stranded RNA
virus that causes significant human mortality and
morbidity worldwide...
A virus is a small particle which can infect
other biological organisms.
Three types of viruses a bacterial virus,
otherwise called a bacteriophage an
animal virus and a retrovirus. Viruses
consist of either DNA or RNA, surrounded by a
protein coat, or capsid.
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virus usually refers to those particles which
infect eukaryotes, whilst the term bacteriophage
or phage is used to describe those infecting
prokaryotes (bacteria and bacteria-like
organisms). Virus classification

DNA virusesdsDNA viruses
(double stranded DNA)ssDNA viruses (single
stranded DNA) RNA viruses retrovirus (HIV-1 and
HIV-2, the agents that cause AIDS) dsRNA viruses
(double stranded RNA)()ssRNA viruses (positive
single stranded RNA)(-)ssRNA viruses (negative
single-stranded RNA) negative-stranded RNA virus
- A virus whose RNA genome is complementary to
its mRNA. mRNA 5' G G U U C C A A 3'

- RNA 3' C C A A G G
U U 5'
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• A typical retrovirus consists of
• an outer envelope which was derived from the
  membrane of its host.
• many copies of an envelope protein embedded in
  the lipid bilayer of its envelope
• a capsid a protein shell containing
• two molecules of RNA and
• molecules of the enzyme reverse transcriptase
  (RNA -gtDNA

Genetic map of typical retrovirus
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• When a retrovirus infects a cell
• Molecules of reverse transcriptase are attached
  to the viral RNA molecules
• the reverse transcriptase synthesizes DNA copies
  of the RNA
• enter the nucleus
  translate by host ribosomes
• the gag gene into molecules of the capsid protein
  the pol gene
  into molecules of reverse transcriptase
  the env gene into
  molecules of the envelope protein
  other RNA molecules become
  incorporated into fresh virus particles

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Key proteins 1. Hemmagglutinin (HA) mediates
fusion of the viral envelope to the host cell
membrane 2. Neuraminidase (NA) Breaks down sialic
acid receptor of host cells
and assists in
budding
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Hemagglutinin and neuraminidase are surface
glycoproteins on human Influenza A...
glycoprotein - a protein linked to a sugar which
are components of receptor molecules on the outer
surface of cells.
...The virus is divided into subtypes based on
major differences in the surface proteins
hemagglutinin (HA) and neuraminidase, which are
the most important targets for the human immune
system...
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The Hemagglutinin Receptor is abundantly
displayed on the surface of the influenza virus.
It responsible for
the virus infecting cells of the host organism.
Monomer structure of the Hemagglutinin
328 a.a.
8-stranded Jelly-roll structure
?
?
20 a.a. residues at the N-terminal end of HA2 is
called the fusion peptide, associated with the
viral activity of penetrating the host cell
membrane to initiate infection
221 a.a
ß-Sheet with 5 antiparallel strands
?
?
47-residue C-terminal fragment of HA2 inserted in
the membrane envelop
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Hemagglutinin monomer 1 HA1 and 1 HA2,
HA1 and HA2 are held together by S-S- bonds. 3
hemagglutinin monomers,each with 1 HA1 and 1 HA2
form Hemagglutinin receptor
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Hemagglutinin is a surface glycoprotein on human
Influenza A. It is composed of three identical
550 amino acid chains. Each chain is divided into
two subunits HA1 and HA2.
The
entire structure is 135 Å long.
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Receptor conservedbinding sites (green)
the trimeric structure of HA Each monomer is
anchored in the viral membrane by a helical
transmembrane peptide of 27 aa
the polypeptide chains HA1 (gray) and HA2 (red)
of a single monomer of HA HA1 and HA2 are linked
by two disulfide bridges.
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Hemagglutinin In viruses, a protein which is
responsible for attaching the virus to cell
receptors and for initiating infection.
Hemagglutinin (HA) acquired its name because
when added to red blood cells they agglutinated
or clumped together. Hemagglutinin is a surface
glycoprotein on human Influenza A 3 main
activities responsible for binding to Sialic
acid on host cell surface receptors to initiate
the virus cell interaction. mediates the
envy of the virus into cytoplasm by a membrane
fusion event is a major surface antigen of the
virus against which neutralizing antibodies are
produced.
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How the immune system targets influenza
Around Variable antibody binding sites.
Y -antibody
MACROPHAGE
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• The process cell infection
• The influenza viral particle enters a lung cell
  
• the human immune system detect virus and begins
  to make antibodies to connect with HA and marking
  them for destruction by white blood cell.
• But during this process (step 2) virus has time
  to replicate and while doing so undergone
  mutation.
  It interfere by
  antibody recognition. So it needs new antibodies.
• In the rate between human host and virus mutant
  viral strains favors
• so
• This type of natural selection is called positive
  selection to change

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About positive selection Natural selection is
the process by which variants displaying
favorable traits producing more relative to other
individuals of the same population.
In a study published in the Oct. 20, 2005,
Nature, scientists analyzed 11,624 genes,
comparing how genes vary not only among 39 humans
but also between the humans and a chimpanzee,
whose DNA is 99 percent identical to humans.The
comparisons within and between species suggest
that about 9 percent of genes that show some
variability within humans or differences between
humans and chimpanzees have evolved too rapidly
to be explained simply by chance.
The study
suggests that positive Darwinian natural
selection in which some forms of a gene are
favored because they increase the probability of
survival or reproduction is responsible for the
increased rate of evolution. Since genes are
blueprints for proteins, positive selection
causes changes in the amino acid sequence of the
protein for which the gene codes.
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Influenza A viruses are classified and divided
into subtypes based on their surface glycoprotein
antigens 14 subtypes of hemagglutinin (HA or H)
H1-H14 and 9
types of neuraminidase (NA or N) N1-N9. These
influenza type A viruses are able to infect a
number of different species including humans,
swine, horses birds, and aquatic mammals. A
large number of non-crossreactive influenza
antigens are always circulating in nature.
Antibodies produced against HA and NA antigens
are responsible for protection against
re-infection by the identical virus subtype.
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Why then do people get sick with the flu every
couple of years, when there has been no major
change in the HA or NA antigens?
Between major changes in the HA and NA antigens,
point mutations can occur
on the HA and NA molecules and these mutations
may help the virus to avoid the protective
antibodies and produce an illness. This
phenomenon is known as antigenic drift. The H3N2
virus has been able to successfully drift from
its initial appearance in 1968 and still produce
infections in 1999.
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antigenic drift. Small Changes Drift point
mutations on the HA and NA molecules Antigenic
shift Big Changes Shift Major changes in viral
proteins due to mixing of genome segments from
different viruses.

Occurs when two different viruses infect the same
host.
This can cause dramatic changes in surface
antigens and produce new virulent strains.
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.
Glossary Virulence is a term used to refer for
ability to do damage to the host a strain is a
genetic variant or subtype of a virus.
a "flu strain" is
a certain biological form of the influenza or
"flu" virus. Avian influenza (also known as bird
flu)
It was first identified in Italy in the early
1900s now exist worldwide.
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Changes in the external surface HA and NA
antigens is known as antigenic shift if there
is a new piece of RNA from another organism The
virus subtypes that have been so far been known
to infect humans are H1N1, H2N2, and H3N2. The
H1N1 viruses circulated from the beginning of the
century through the 1950's
In 1957, a new H2N2 virus appeared, known as the
Asian Flu, and rapidly spread around the world.

(This virus had both a
new HA and a new NA). In 1968, another new virus
appeared (H3N2 ), known as the Hong Kong Flu.

This virus is
not as severe as the H2N2 virus, since it only
varied in the HA antigen.

The H1N1 virus also
reappeared in 1977. Currently, both the H3N2 and
H1N1 viruses are circulating through the human
population.
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Emergence of new viruses in the influenza type A
viruses occur by the mixing or re-assorting of
their genetic material.
How is It happen? The genome of
the influenza viruses is composed of 8 RNA
segments. If two different subtypes of influenza
A virus infect the same cell, their genetic
segments are able to re-assort and produce a new
influenza virus with segments from both infecting
viruses. Example, H3N5 virus and a H2N2 virus
infect the same cell the following
offspring viruses can be produced
.
H3N5, H2N2, H3N2, and H2N5.
This
re-assortment can occur between human and animal
isolates. Therefore, new viruses can be produced
which can replicate in humans, but have new
subtypes of animal HA and NA antigens.
There
are no protective antibodies to these antigens in
the human population, so the new virus can spread
very rapidly around the world.
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Influenza viruses were probably a major cause of
disease. influenza epidemics dated at least 1173.
Pandemic of 1918

infected over one-third of the U.S. population
(died approx.
500,000 people )
and globally
killed between 20 and 40 million people, more
than three times the number that died during
World War I 1957 Asian Flu In February 1957,
the Asian influenza pandemic was first identified
in the Far East. (about 69,800 people in the U.S.
died).
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Why the influenza pandemic of 1918 was so
devastating, particularly in younger people, has
intrigued virologists for decades. I had a little
bird,Its name was Enza,I opened the window,And
in-flu-enza. Children's Rhyme, 1918

• What if 1918 came back
• ? probably 50 of the world got it
• No one left alive has immunity
• Could treat the secondary (bacterial) infections
• If Doctors aren't sick
• If there are enough hospitals
• if there are enough drugs on the shelf
• Third world no better off than in 1918
• Vaccine would probably be too late for most
• Faster transmission around the world

antigenic shift ???
Catastrophic for immunity Immunity fails
completely against antigenic shift
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2001 Philosophical Transactions Biological
Sciences


"Integrating historical,
clinical and molecular genetic data in order to
explain the origin and virulence of the 1918
Spanish influenza virus

2003 the Journal of
General Virology
"The origin
of the 1918 pandemic influenza virus A
continuing enigma."

2004 The online
Journal of Translational Medicine
"The
site of origin of the 1918 influenza pandemic and
its public health implications.

2004 Science

The Structure and Receptor
Binding Properties of the 1918 Influenza
Hemagglutinin
2004
Science

Structure of the Uncleaved Human H1 Hemagglutinin
from the Extinct 1918 Influenza Virus
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Question How do we know which vaccine to make?
Answer We don't We have to make best guess.

• Problems with preparedness
• Need to act very quickly and decisively
• Governments like to be slow
• Cost
• Doctors don't think about prevention as much as
  treatment
• there is no treatment!

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• Summary
• Influenza uses H and N proteins to infect cell.
  (see next slide)
• Body develops immunity after fighting off the
  virus
• Influenza alters its HA and NA proteins
• Memory B cells cant recognize it anymore
• Vaccines trick body into developing immunity
• 
  H gene (DNA)
• 
  Inject into human
• Human cells
  produce H protein
• Immune response to H
  protein

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Scientists describe structure of receptor on
surface of 1918 flu virus Science Express on
February 5, 2004 Research of the virus 1918 was
complicated by the fact that Viruses were not
identified as the cause of influenza until the
1930s, However, biopsies from soldiers who died
from influenza in 1918 were preserved and
maintained in the Armed Forces Institute of
Pathology. These samples yielded a number of
pieces of RNA from the virus. The first result


A few years ago, Taubenberger and his
colleagues at the Armed Forces Institute of
Pathology were able to piece together enough
fragments to reconstruct the sequence of the gene
that coded for the viral protein hemagglutinin.
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The second result. Basler and Palese at Mount
Sinai Institute of Medicine in New York managed
to construct an expression system that allowed
them to make the hemagglutinin protein. The third
result Wilson and Stevens made enough of the
protein to crystallize and solve the structure
using x-ray crystallography and compared it to
hemagglutinin proteins from other human, avian,
and pig viruses.
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Conclusion It looks more like an avian virus--
with some human characteristics Because the
surface proteins of the 1918 virus were different
from those found on other flu viruses, people's
immune systems were unaccustomed to them and
unable to fight off the Spanish Flu. This
suggests why the virus may have been so deadly.