Hi, this is Bob Lessick at Johns Hopkins.
This short lecture will cover viruses,
particularly viral genomes.
We'll look at three types of genomes, and
how influenza subtypes are determined.
Our first objective is to examine three
broad categories of genome types.
Some viruses have an RNA genome.
Others have DNA.
Another category used is an RNA genome,
but first uses
reverse transcriptase to make a DNA
intermediate during its replication cycle.
Those are called retroviruses.
We'll take a look at a retroviral genome.
They are small, with only a few genes.
In the context of influenza, we will
examine hemagglutinin and neuraminidase,
two viral proteins.
And those viral proteins help describe the
influenza subtype.
You may have heard of these subtypes.
Finally, we will briefly mention the NCBI
Influenza Resource.
It's a large collection of influenza
sequences and data.
Perhaps the simplest viral genomes are RNA
based.
The RNA is used to be translated into
viral proteins.
And it is also replicated using a
polymerase that takes an RNA
template and makes an RNA strand that is
complimentary to the template.
This has to be done twice, because
the first RNA synthesized is complimentary
RNA, which
then must be used as a template to make a
copy of the original RNA genome.
Other viruses have DNA genomes.
Upon infecting a cell, the DNA genome must
be transcribed, so that viral proteins can
be translated.
That DNA must also be replicated into new
viral genomes.
Retroviruses have viral genomes, but there
is a twist.
The RNA genome can be translated into
viral proteins.
However, its replication cycle involves
the use of reverse transcriptase.
Well, we know that DNA can be transcribed
into RNA.
When a DNA molecule is made, based on
an RNA template, then that is called
reverse transcription.
That DNA intermediate can be transcribed
to synthesize new viral genomes.
We can divide RNA viruses into three broad
classifications.
Some are actually double stranded like
DNA,
RNA can form a double stranded molecule.
Of the single stranded, there are two
types.
Positive or plus strand or sense RNA
viruses are ones
where a viral protein can translated
directly from the viral genome.
There are many, including SARS and polio.
Others have negative strands or anti sense
RNA.
Before translation, an RNA complement to
the genome must
be synthesized, so that translation of
viral proteins can occur.
RNA has a replication cycle that is far
more error prone than a DNA replication
cycle.
That's why DNA is better suited for genome
use in most organisms.
So, if RNA viruses can evolve
quickly, that makes finding vaccines very
challenging.
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As for DNA viruses, a large majority use
double-stranded DNA.
Some use single stranded.
Most of those are bacterial phages, or
viruses that affect bacteria.
Their challenge is to replicate the genome
using cellular machinery
and to transcribe RNA to be translated
into viral proteins.
Here are some examples.
Most DNA viruses evolve slowly.
Retrovirus have what seems to be a
complicated cycle.
There's a DNA intermediate in replication
that adds some stability to the process.
That DNA intermediate finds its way into
the host genome and
can sit passively in what could be called
a wait defense.
The term enveloped virus refers to the
outside of the virus itself.
If it's lipid-based like a cell membrane,
it's an enveloped virus.
Many viruses simply have a protein coat
without lipids.
Some examples include HIV, the Human
Immunodeficiency virus, and hepatitis B.
Many retroviruses have been linked to
cancer risk.
The basic retroviral genome has only three
genes.
Often the protein gene products are
cleaved into smaller proteins.
Gag is the Group Specific Antigen, which
makes proteins
that are needed for the interior of the
virus.
Pol is the polymerase, for retroviruses
that is reverse transcriptase.
The retrovirus carries the gene it needs
for its own replication cycle.
Sometimes the protease activity for
cleaving the translated proteins
into smaller proteins is found in the Pol
gene.
Env stands for envelope.
And those are the proteins that integrate
into the lipid based envelope.
Here are some examples from the simple
Buring leukemia virus at the top.
There are three genes.
With some other retroviruses you can see
the smaller protein products within the
gene.
For instance in HTLV-1, human t-cell
leukemia virus, the
GAG protein is cleaved into p19, p24 and
p15.
The terminology is based on protein size,
p19 is 19 kilojolts, for instance,
but basically they all have some form of
Gag,
Pol, and Env genes and maybe some
additional smaller ones.
Note that RT means reverse transcriptase
and PR means protease.
Maybe you can figure out or look up
some of the other abbreviations if you are
interested.
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Here is a different virus entirely.
Influenza is negative strand, antisense
RNA, but with eight segments.
We'll focus a little more on two of them.
Segment four is HA, or hemagglutinin.
And section six is NA or neuraminidase.
Hemagglutinin is a surface glycoprotein.
So what does that mean?
A glycoprotein is a protein with sugar
molecules attached.
Surface means it's found on the outside of
the virus itself.
It's used to bind sialic acids in cell
membranes that the virus will infect.
Now, there are 18 known types that we can
number from H1 to H18.
Neuraminidase is an enzyme that breaks
down sialic acids.
It protrudes in a mushroom like shape from
the viral
surface, making it a good target for the
immune system.
Neuraminidase inhibitors have been used as
antiviral drugs.
The nine known influenza subtypes can be
numbered N1 through N9.
Now, we can decode a few things.
You've probably heard of H1N1.
That caused a devastating flu in 1918 and
a bit of a panic in 2009.
What exactly is H1N1?
Well, Influenza A subtypes are determined
by the
type of hemagglutinin and the type of
neuraminidase.
H1N1 has the type 1 HA gene and a type 1
NA gene.
Now, if you're working on vaccines, it's
very important to survey
and predict which subtypes might be
prevalent in any given winter.
Weather it's northern or southern
hemisphere.
I'm simply going to show you the address
to the NCBI influenza resource.
And mention that there is a lot of data
there.
That is very useful to influenza
researchers.
One thing you can do is some geographic
and time studies, to show
how viruses from certain places, times and
subtypes are related to each other.
Note that there is sequence variation,
even within sub types.
To wrap up our really short look at
viruses, they have very small genomes.
Even compared to bacteria.
Some mutate quickly, especially RNA
Viruses and Retroviruses.
The Retroviral genome is really simple,
usually three genes.
And in Flu viruses hemagglutinin and
neuraminidase are used
to determine subtypes that is really
important for vaccine purposes.
Take some time to check the web and NCBI
for more on viruses.
Good luck