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Hi, this is Bob Lessick at Johns Hopkins.

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This short lecture will cover viruses,
particularly viral genomes.

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We'll look at three types of genomes, and
how influenza subtypes are determined.

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Our first objective is to examine three
broad categories of genome types.

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Some viruses have an RNA genome.

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Others have DNA.

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Another category used is an RNA genome,
but first uses

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reverse transcriptase to make a DNA
intermediate during its replication cycle.

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Those are called retroviruses.

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We'll take a look at a retroviral genome.

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They are small, with only a few genes.

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In the context of influenza, we will

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examine hemagglutinin and neuraminidase,
two viral proteins.

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And those viral proteins help describe the
influenza subtype.

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You may have heard of these subtypes.

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Finally, we will briefly mention the NCBI
Influenza Resource.

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It's a large collection of influenza
sequences and data.

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Perhaps the simplest viral genomes are RNA
based.

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The RNA is used to be translated into
viral proteins.

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And it is also replicated using a
polymerase that takes an RNA

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template and makes an RNA strand that is
complimentary to the template.

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This has to be done twice, because

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the first RNA synthesized is complimentary
RNA, which

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then must be used as a template to make a
copy of the original RNA genome.

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Other viruses have DNA genomes.

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Upon infecting a cell, the DNA genome must

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be transcribed, so that viral proteins can
be translated.

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That DNA must also be replicated into new
viral genomes.

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Retroviruses have viral genomes, but there
is a twist.

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The RNA genome can be translated into
viral proteins.

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However, its replication cycle involves
the use of reverse transcriptase.

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Well, we know that DNA can be transcribed
into RNA.

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When a DNA molecule is made, based on

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an RNA template, then that is called
reverse transcription.

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That DNA intermediate can be transcribed
to synthesize new viral genomes.

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We can divide RNA viruses into three broad
classifications.

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Some are actually double stranded like
DNA,

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RNA can form a double stranded molecule.

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Of the single stranded, there are two
types.

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Positive or plus strand or sense RNA
viruses are ones

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where a viral protein can translated
directly from the viral genome.

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There are many, including SARS and polio.

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Others have negative strands or anti sense
RNA.

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Before translation, an RNA complement to
the genome must

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be synthesized, so that translation of
viral proteins can occur.

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RNA has a replication cycle that is far

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more error prone than a DNA replication
cycle.

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That's why DNA is better suited for genome
use in most organisms.

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So, if RNA viruses can evolve

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quickly, that makes finding vaccines very
challenging.

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[BLANK_AUDIO]

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As for DNA viruses, a large majority use
double-stranded DNA.

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Some use single stranded.

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Most of those are bacterial phages, or
viruses that affect bacteria.

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Their challenge is to replicate the genome
using cellular machinery

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and to transcribe RNA to be translated
into viral proteins.

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Here are some examples.

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Most DNA viruses evolve slowly.

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Retrovirus have what seems to be a
complicated cycle.

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There's a DNA intermediate in replication
that adds some stability to the process.

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That DNA intermediate finds its way into
the host genome and

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can sit passively in what could be called
a wait defense.

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The term enveloped virus refers to the
outside of the virus itself.

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If it's lipid-based like a cell membrane,
it's an enveloped virus.

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Many viruses simply have a protein coat
without lipids.

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Some examples include HIV, the Human
Immunodeficiency virus, and hepatitis B.

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Many retroviruses have been linked to
cancer risk.

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The basic retroviral genome has only three
genes.

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Often the protein gene products are
cleaved into smaller proteins.

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Gag is the Group Specific Antigen, which
makes proteins

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that are needed for the interior of the
virus.

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Pol is the polymerase, for retroviruses
that is reverse transcriptase.

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The retrovirus carries the gene it needs
for its own replication cycle.

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Sometimes the protease activity for
cleaving the translated proteins

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into smaller proteins is found in the Pol
gene.

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Env stands for envelope.

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And those are the proteins that integrate
into the lipid based envelope.

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Here are some examples from the simple
Buring leukemia virus at the top.

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There are three genes.

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With some other retroviruses you can see

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the smaller protein products within the
gene.

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For instance in HTLV-1, human t-cell
leukemia virus, the

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GAG protein is cleaved into p19, p24 and
p15.

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The terminology is based on protein size,
p19 is 19 kilojolts, for instance,

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but basically they all have some form of
Gag,

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Pol, and Env genes and maybe some
additional smaller ones.

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Note that RT means reverse transcriptase
and PR means protease.

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Maybe you can figure out or look up

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some of the other abbreviations if you are
interested.

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[BLANK_AUDIO]

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Here is a different virus entirely.

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Influenza is negative strand, antisense
RNA, but with eight segments.

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We'll focus a little more on two of them.

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Segment four is HA, or hemagglutinin.

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And section six is NA or neuraminidase.

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Hemagglutinin is a surface glycoprotein.

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So what does that mean?

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A glycoprotein is a protein with sugar
molecules attached.

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Surface means it's found on the outside of
the virus itself.

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It's used to bind sialic acids in cell
membranes that the virus will infect.

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Now, there are 18 known types that we can
number from H1 to H18.

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Neuraminidase is an enzyme that breaks
down sialic acids.

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It protrudes in a mushroom like shape from
the viral

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surface, making it a good target for the
immune system.

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Neuraminidase inhibitors have been used as
antiviral drugs.

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The nine known influenza subtypes can be
numbered N1 through N9.

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Now, we can decode a few things.

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You've probably heard of H1N1.

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That caused a devastating flu in 1918 and
a bit of a panic in 2009.

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What exactly is H1N1?

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Well, Influenza A subtypes are determined
by the

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type of hemagglutinin and the type of
neuraminidase.

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H1N1 has the type 1 HA gene and a type 1
NA gene.

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Now, if you're working on vaccines, it's
very important to survey

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and predict which subtypes might be
prevalent in any given winter.

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Weather it's northern or southern
hemisphere.

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I'm simply going to show you the address
to the NCBI influenza resource.

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And mention that there is a lot of data
there.

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That is very useful to influenza
researchers.

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One thing you can do is some geographic
and time studies, to show

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how viruses from certain places, times and
subtypes are related to each other.

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Note that there is sequence variation,
even within sub types.

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To wrap up our really short look at
viruses, they have very small genomes.

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Even compared to bacteria.

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Some mutate quickly, especially RNA
Viruses and Retroviruses.

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The Retroviral genome is really simple,
usually three genes.

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And in Flu viruses hemagglutinin and
neuraminidase are used

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to determine subtypes that is really
important for vaccine purposes.

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Take some time to check the web and NCBI
for more on viruses.

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Good luck