Viruses~~~ :)

~~**Welcome**~~ :)

.. to our Microbiology B blog on viruses.
This blog will be posts regarding what we've learnt during microbiology B, or more.
We hope to share with you all regarding if what we've learnt, so that everyone knowledge on viruses would increase!

Click:
~1st tab to study more on viruses- introduction
~2nd tab is on what we've learn in lecture
~3rd tab is to watch video

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♥Eileen Ng Hui Qi
♥Tang Xu Yun
♥Koh Jia Huan
♥Canice Tay

NYP SCL MB0804

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● Virus interaction 1 @ Saturday, December 27, 2008 ●

Lecture 12!

Virus Host Interaction I

1) The virus growth phases:
=Attachment
- this is the phase where the virus attaches itself to its host cell and before more viruses are made for infection.

=Eclipse stage
- no infectious virus are present in this stage, therefore resulting in a fall in virus titre
- it is the period where the virus attempts to gain control of it's host synthetic machinery and produce components vital for viral assembly
- no virus would be detected in an external medium until release

=Latent stage
- it is the period following the eclipse phase from the time the infecting virus disappearing to the appearance of infectious virus in the surroundings
- virus exist internally and must be released to be assayed
- animal viruses may not have a classic burst of viruses but rather release virus slowly over a long period of time it is possible to find large internal pools of virus

=Virus burst
- new progeny virus is assembled and released
- virus yield (determined on the number of virus released per cell) increases sharply

Additional note: Productive infection is defined as any infection that resulted in production of more infectious particles at the end than at the start.

2) The general virus replication cycle involves six steps where each step is crucial for successful replication. They are:
= Attachment
= Penetration
= Uncoating
= Replication
= Assembly/Maturation
= Release

Stages of attachment, penetration and uncoating gives rise to the Eclipse period mentioned above.

= ATTACHMENT. This is where the specific viruses' attachment protein (VAP) attaches itself to the corresponding host cell receptor. The receptor on the host cell then mediates viral entry into the host cell.

RECEPTORS on host cell can be any surface molecule of the cell (glycoprotein and glycolipid). There are multiple receptors for different viruses, all with their own functions and which viruses use for attachment. Host range is defined based on receptor ligand recognition.

= PENETRATION (ROUTES OF HOST ENTRY) methods include:
- receptor-mediated endocytosis (the cell absorbs material from outside the cell by engulfing it with its cell membrane) for enveloped viruses
- clarthin for naked viruses
- fusion, which is also known as direct penetration

= UNCOATING of the virus refers to the release of infectious nucleic acid from the protein coat. Penetration and uncoating can occur simultaneously, as the nucleic acid enters the host and the protein capsid remains outside.

= REPLICATION. The genome replication and gene expression are very closely linked. Their characteristics depend on the nature of the genome. This brings us to the Baltimore classification, where viruses are classified by their genome.

= Class 1: Double-stranded DNA (ds DNA)
->Two groups:
- replication is EXCLUSIVELY NUCLEAR; very dependent on host cell factors
- replication in the CYTOPLASM; viral genome contains all factors for genome replication and transcription (poxviridae)

->Viral genes
- immediate genes

Transcription factors / enzymes
Replication factors/enzymes

-> Early genes

Additional factors to regulate transcription, replication and translation
Have some structural proteins

-> Late genes

Mainly structural proteins
Other proteins associated with virion / nucleocapsid

= Class II: Single-stranded DNA (ss DNA)
- replication of genome in nucleus- forms double-stranded DNA to make new single-stranded daughters
- extreme parasitism. (dependence on superinfecting viruses for early regulatory genes or chemical or UV light that induce similar virus-induced changes to the host cell)
- one example: Parvoviridae

= Class III: Double-stranded RNA (ds RNA)
- genome in several fragments
- replication, transcription, translation all regulated separately
- monocistronic mRNA
- activity takes place only in cytoplasm, not nucleus

= Class IV: Single-stranded POSITIVE RNA
- Most of the animal and plant viruses are categorised under Class IV
- Group 1

Polycistronic mRNA
Polyprotein formed and cleaved

- Group 2

Complex transcription process
2 rounds of translation before formation of genomic RNA

= Class V: Single stranded NEGATIVE RNA
- Group 1:

Non-segmented genome
transcription of negative RNA by RNA-dependent RNA polymerase to give monocistronic mRNA, which acts as a template for genome replication
ambisense organisation

- Group 2:

Orthomyxoviruses (segmented genome)
Monocistronic mRNA in nucleus
Virus transcriptase in nucleocapsid

= Class VI: Single-stranded RNA (ssRNA)
- Retroviruses (example: HIV)
- has a DNA intermediate
- Diploid
- Viral RNA is reverse transcripted to dsDNA by viral RT
- dsDNA is integrated into host genome
- mRNA is not used as viral RNA

= Class VII: Double-stranded RNA (dsRNA)
- has a RNA intermediate
- overlapping reading frames
- example: Hepadnaviridae

= REGULATION OF EXPRESSION. Post-translational modification of the virus protein often occurs here. Polycistronic mRNA is spliced in a differential rate in the nucleus in post-transitional control. The post-translational modification of the viral proteins often occurs, this is also known as maturation. mRNA travels from the nucleus to the cytoplasm.

References:

http://www.ucalgary.ca/~ceri/cmmb421prot/Virus%20Life%20Cycle.html

http://en.wikipedia.org/wiki/Virus

Virus

Knowledges

**~~Viruses!!~~**
• Not made of cells.
• Cannot reproduce on their own.
• Do not grow or undergo division
• Do not transform energy.
• Lack machinery for protein synthesis.
• Are so small that they can only be seen with an electron microscope.

What are viruses made of?
• Viruses are composed of nucleic acid, proteins, in some cases, lipids as well. Nucleic acid which can be either DNA or RNA encodes the genetic information that is necessary to make copies of the virus.
• The nucleic acid is surrounded by a protective protein coat called a capsid. Some viruses are also surrounded by an outer membranous called an envelope, made of lipid and protein.

Structure of viruses?

Viruses display a wide diversity of shapes and sizes, called morphologies. Viruses are about 100 times smaller than bacteria. Most viruses which have been studied have a diameter between 10 and 300 nanometres.Most viruses are too small to be seen under a light microscope so scanning and tramission electron microscope are used to visulualise virus particle.

1) Helical structure

Structure of tobacco mosaic virus: the viral RNA is coiled inside the helix formed by repeating protein sub-units

2) Icosahedral structure

Electron micrograph of icosahedral viruses(Adenovirus)

3) Enveloped structure

Viruses are dependent on the envelope for their infectivity.

4) Complex structure

Structure of a typical bacteriophage

Shape of viruses?
There are predominantly two kinds of shapes found amongst viruses: rods, or filaments, and spheres. The rod shape is due to the linear array of the nucleic acid and the protein subunits making up the capsid. The sphere shape is actually a 20-sided polygon.

Genetic Change

How antigenic shift, or reassortment, can result in novel and highly pathogenic strains of human influenza

Viral Replication

DNA Viruses
The genome replication of most DNA viruses takes place in the cell's nucleus. If the cell has the appropriate receptor on its surface, these viruses enter the cell by fusion with the cell membrane or by endocytosis. Most DNA viruses are entirely dependent on the host cell's DNA and RNA synthesising machinery, and RNA processing machinery. The viral genome must cross the cell's nuclear membrane to access this machinery.

RNA Viruses
RNA viruses are unique because their genetic information is encoded in RNA. Replication usually takes place in the cytoplasm. RNA viruses can be classified into about four groups depending on their modes of replication. The polarity (whether or not it can be used directly to make proteins) of the RNA largely determines the replicative mechanism, and whether the genetic material is single-stranded or double-stranded. RNA viruses use their own RNA replicase enzymes to create copies of their genomes.

Reverse transcribing Viruses
Reverse transcribing viruses replicate using reverse transcription, which form DNA from an RNA template. Reverse transcribing viruses containing RNA genomes use a DNA intermediate to replicate, whereas those containing DNA genomes use an RNA intermediate during genome replication.