Virus-host Interactions

Virus Host Interactions

General Virus Replication Cycle

There are six phases in a virus replication cycle. The six phases are:

• Attachment
• Penetration / Entry
• Uncoating
• Replication and Expression
• Assembly
• Release

Virus Life Cycle – Growth Curve

In the attachment part, virus attached to the host cell receptor and gain entry into the cell. In the eclipse stage, virus is busy with replication. Virus titre decreases when there are no infectious particles present during replication process. Virus is detected in external medium only when released. In the burst or released part, new progeny virus gathered and is then released.

Attachment and Entry
Virus attachment protein (VAP) attaches to the receptor of the host cell. Receptor on the host cell enable virus to gain entry into the host cell. Virus can enter the host cells through three different routes. The three different routes are:

• Direct penetration
• Fusion (direct penetration)
• Endocytosis

Receptors on Host Cells
The cells surface molecule contains glycoprotein and glycolipid. Glycoprotein will have sugar group attached to the protein, and glycolipid will have fat or lipid group attached to it. There are many receptors for many different viruses. These receptors have different functions. Viruses take immediate advantage to use these receptors for attachment. Host range and tissue tropism are important factors that must be considered before virus attached to the receptor. Viruses cannot anyhow infect; they must have the right attachment protein. For example, hepatitis head cannot find the attachment protein and thus, heading towards the liver tissue. Human cells do not have particular receptors for virus. Therefore, virus makes use of receptors to attach.

Endocytosis
A process by which materials from outside the cell, such as proteins, are absorbed by cells through engulfing of these materials with their cell membrane is known as endocytosis. All cells of the body use endocytosis due to those important substances are large polar molecules which cannot pass through the plasma membrane.

There are three types of endocytosis. They are:

• Phagocytosis
• Receptor-mediated endocytosis
• Pinocytosis

A process by which cells ingest large objects, such as cells which have undergone apoptosis, bacteria or viruses, is known as phagocytosis. The object is surrounded by membrane, and a large vacuole, phagosome, seal the object.

Receptor-mediated endocytosis is a much more detailed active event in which coated pits are formed when the cytoplasm membrane folds inward. These inward budding vesicles bud to form cytoplasmic vesicles.

Pinocytosis is a process which involved the uptake of solutes and single molecules, such as protein.

Clathrin-mediated endocytosis
Clathrin molecule mediates the major route for endocytosis in most cells. Clathrin is a large protein which helps in the formation of a coated pit on the inner surface of the cell’s plasma membrane. A coated vesicle is formed in the cytoplasm of the cell when this pit buds into the cell. By doing so, a small area of the surface of the cell and a small volume of fluid from outside the cell is brought into the cell.

Infection of Plant and Bacteria

Virus can also be attached to the tool, whereby the tool becomes infected. Tools used on other plants would breach cell wall and then infect the plants. Plant cell wall must be breached before it can be infected. Similarly, infection will only occur in bacteria cell wall when the cell wall is breached. Virus DNA is then infected into the cell.

Stages of life cycle of virus

• Initiation of infection
• - Attatchment and entry
• Replication and expression
  - Genome replication
  - mRNA production, processing and translation
• Assembly and exit
• Viral Pathogenesis

Replication and expression
Genome replication and gene expression very closely linked and characteristics of which depends on the nature of the genome.

Classification of virus
Viruses are not usually classified into conventional taxonomic groups but are usually grouped according to such properties as size, the type of nucleic acid they contain, the structure of the capsid and the number of protein subunits in it, host species, and immunological characteristics.

When a new species of known virus family or genus is investigated it can be done in the context of the information that is available for other members of that group. Without classification scheme, each newly discovered virus would be like a black box, everything would have to be discovered and rediscovered. The development of a classification scheme is therefore an important and inevitable consequence. The current classification scheme allows most newly described viruses to be labeled.

We can state with a degree of confidence that most of the major groupings of viruses infecting humans because there are so few virus discoveries now being made which do not fit into the existing classification scheme and domesticated animals have been identified.

The Baltimore Classification
The Baltimore system of virus classification provides a useful guide with regard to the various mechanisms of viral genome replication. The central theme here is that all viruses must generate positive strand mRNAs from their genomes, in order to produce proteins and replicate themselves.

Baltimore Classification of viruses,
based on the method of viral mRNA synthesis

The precise mechanisms whereby this is achieved varies for each virus family. These various types of virus genomes can be broken down into seven fundamentally different groups, which obviously require different basic strategies for their replication. David Baltimore, who originated the scheme, has given his name to the so-called "Baltimore Classification" of virus genomes. By convention the top strand of coding DNA written in the 5' - 3' direction is + sense. Same goes to mRNA sequence. The replication strategy of the virus depends on the nature of its genome. Viruses can be classified into seven (arbitrary) groups:

I: Double-stranded DNA (Adenoviruses; Herpesviruses; Poxviruses, etc)Some replicate in the nucleus e.g adenoviruses using cellular proteins. Poxviruses replicate in the cytoplasm and make their own enzymes for nucleic acid replication.

II: Single-stranded (+)sense DNA (Parvoviruses)Replication occurs in the nucleus, involving the formation of a (-)sense strand, which serves as a template for (+)strand RNA and DNA synthesis.

III: Double-stranded RNA (Reoviruses; Birnaviruses)These viruses have segmented genomes. Each genome segment is transcribed separately to produce monocistronic mRNAs.

IV: Single-stranded (+)sense RNA (Picornaviruses; Togaviruses, etc)a) Polycistronic mRNA e.g. Picornaviruses; Hepatitis A. Genome RNA = mRNA. Means naked RNA is infectious, no virion particle associated polymerase. Translation results in the formation of a polyprotein product, which is subsequently cleaved to form the mature proteins.b) Complex Transcription e.g. Togaviruses. Two or more rounds of translation are necessary to produce the genomic 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.

VI: Single-stranded (+)sense RNA with DNA intermediate in life-cycle (Retroviruses)Genome is (+)sense but unique among viruses in that it is DIPLOID, and does not serve as mRNA, but as a template for reverse transcription.

VII: Double-stranded DNA with RNA intermediate (Hepadnaviruses)This group of viruses also relies on reverse transcription, but unlike the Retroviruses, this occurs inside the virus particle on maturation. On infection of a new cell, the first event to occur is repair of the gapped genome, followed by transcription.

Replication of Hepititis B virus
hepatitis B virus (HBV) replication by noncytolytic mechanisms that either destabilize pregenomic (pg)RNA-containing capsids or prevent their assembly. Using immortalized murine hepatocyte cell lines stably transfected with a doxycycline (dox)-inducible HBV replication system, we now show that replication-competent pgRNA-containing capsids are not produced when the cells are pretreated with IFN-β before HBV expression is induced with dox. Furthermore, the turnover rate of preformed HBV RNA-containing capsids is not changed in the presence of IFN-β or IFN-γ under conditions in which further pgRNA synthesis is inhibited by dox removal. In summary, these results demonstrate that types 1 and 2 IFN activate hepatocellular mechanism(s) that prevent the formation of replication-competent HBV capsids and, thereby, inhibit HBV replication.

Virus genome of Hepatitis B
It is circular, and partially doubled-stranded DNA with 4 open reading frames, namely the HBsAg (pre-S1, pre-S2 and S), HBcAg (pre-core and core), polymerase (multifunctional), and HBxAg (transactivating factor). It replicates largely in the liver through RNA intermediate and reverse transcription.

The genes of Hepatitis B virus (HBV).

Thick black lines represent two DNA strands, thin lines indicate locations of genes. The DNA of HBV is a rare example that its two strands do not have the same length.

Diagrammatic representation of the HBV genome. The inner circle represents the virion genomic DNA that is packaged within viral particles in the cytoplasm of infected cells, and the dashes indicate the region of the genome which is incompletely synthesized. The thick arrows represent open reading frames corresponding to core, envelope (surface antigen), polymerase (pol), and HBx proteins. The thin lines represent HBV RNAs.

Regulation and expression
The expression of hepatitis B virus (HBV) genes is regulated by a number of transcription factors. One such factor, Sp1, has two binding sites in the core promoter and one in its upstream regulatory element, which is also known as the ENII enhancer. In this study, we have analyzed the effects of these three Sp1 binding sites on the expression of HBV genes. Our results indicate that both Sp1 binding sites in the core promoter are important for the transcription of the core RNA and the precore RNA. Moreover, while the downstream Sp1 site (the Sp1-1 site) in the core promoter did not affect the transcription of the S gene and the X gene, the upstream Sp1 site (the Sp1-2 site) in the core promoter was found to negatively regulate the transcription of the S gene and the X gene, as removal of the latter led to enhancement of transcription of these two genes. The Sp1 binding site in the ENII enhancer (the Sp1-3 site) positively regulates the expression of all of the HBV genes, as its removal by mutation suppressed the expression of all of the HBV genes. However, the suppressive effect of the Sp1-3 site mutation on the expression of the S gene and the X gene was abolished if the two Sp1 sites in the core promoter were also mutated. These results indicate that Sp1 can serve both as a positive regulator and as a negative regulator for the expression of HBV genes. This dual activity may be important for the differential regulation of HBV gene expression.

Translation of protein

Amino acids are the monomers which are polymerized to produce proteins. Amino acid synthesis is the set of biochemical processes (metabolic pathways) which build the amino acids from carbon sources like glucose. Not all amino acids may be synthesised by every organism, for example adult humans have to obtain 8 of the 20 amino acids from their diet.

Assembly and exit

Different types of virus have varying sites of synthesis and replication. For example, synthesis and replication for DNA viruses occur in the cell’s nucleus while it is usually the cytoplasm for RNA viruses. Virus assembly depends on the site of synthesis and such sites are the nucleus, endoplasmic reticulum and the Golgi apparatus aka Golgi body. Aside from this, assembly also occurs in the viroplasm which is an inclusion body in a cell.

When the virus has replicated and multiplied, they would want to leave the infected cell and infect other cells. However, they require an envelope to enclose the DNA as well as to bind with the other healthy cells so that they can infect. The viral envelope is the typical lipid bilayer, derived from the host cell itself and sources usually come from the nuclear membrane, endoplasmic reticulum, Golgi apparatus/body and plasma membrane. It also depends on where the virus ‘bud’ off from the host.

Budding is a method which viruses use to exit the cell.

It is an example of asexual reproduction because the buddings are genetically identical.

Other methods for exit would be cell lysis. This method releases the virus from the infected cell by bursting its membrane and this kills the cell as well. Another method is by accumulation of virus particles in vesicles and released via exocytosis. Exocytosis is the process where vesicles containing the virus is secreted/excreted out of the infected cell.

An example of a virus that spreads by budding is the Sindbis virus.

Viral Pathogenesis

There are a variety of ways that viruses can enter the host.

1. Skin

- Abrasions and cuts.

2. Eyes

- Conjunctiva. The conjunctiva helps in preventing microbes from entering the eye as well as physical harm. So its is highly susceptible to infection.

3. Urogenital tract

- risky sexual behaviours increase the chances for viral entry/infection.

4. Respiratory

- airborne viruses are inhaled.

- different parts of the respiratory system are specific to certain viruses.

5. Alimentary

- infected/contaminated food. E.g. Mad Cow disease.

Virus Spread

Spreading method varies with different viruses. Not only are there different ways of spreading, there are also different types of spreading. There are about 3- 4 types of viral spreads in animals/human hosts and below are 3 types.

1. Systemic infection

- infection of multiple organs or mucosal surfaces.

2. Haematogenous spread

- primary and secondary spread of virus through the bloodstream. In primary spread, the virus infects and replicates in the blood before dissemination to the targeted organs. However, in secondary spread, the virus infects and replicates elsewhere (usually on mucosal membranes) before dissemination via the bloodstream to the targeted organs.

3. Neural spread

- infection of the nervous system which includes the central nervous system(CNS) and the peripheral nervous system(PNS). Infection occurs more specifically in the inner areas of the nerves as seen in the second picture. Different virus also affect the different areas of the nerves. An example of neural infection by viruses are measles – cause inflammation of the brain. Enteroviruses are the leading causes for neural spread.

Virus Transmission/Shedding

This is important in the survival/propagation of the virus. The virus needs to be spread so that it can continue reproducing and ensuring the survival of the virus species. The effectiveness of viral transmission depends on the virus concentration and the route of transmission. The higher the viral concentration, the higher the chances of transmission. Some modes of virus transmission include respiratory secretions and salivary pathways.

There are a few different ways/modes of viral transmission.

1. Blood

There are a few ways that the virus can infect the blood and one way is by arthropods. They transmit arthropod-borne viruses (arbovirus) such as flaviviruses and togoviruses upon biting and the virus enters the blood which may cause viraemia.

Another way of blood infection would be via direct blood/bodily fluid contact or exposure infected items or people. Some of such viruses include the Hepatitis strain and well as the Human Immunodeficiency Virus (HIV).

2. Saliva

The most common way for transmission is via kissing. Sharing of utensil may also promote virus transmission as there is saliva involved. Examples of such viruses are the herpes viruses and retroviruses.

3. Respiratory secretions

Air-borne viruses and viruses that can only infect the respiratory tract can also be spread by sneezing, coughing, breathing and singing. Although some viruses can be inactivated by drying, it activates again when it enters the body as there is moisture. Contaminated hands from covering a cough or sneeze may also pass on the virus.

4. Feaces

Infection via this method not very common in developed countries where sanitation is relatively good but rather common in areas or poor sanitation, especially third-world countries. Unlike viruses that spread by respiratory means, these viruses are highly resistant to drying meaning they do not get inactivated so easily. This explains allows them to easily infect. Examples of such viruses are the enteric and hepatic viruses.

Virus-induced injury

The cytopathic effect (CPE) (degeneration of the cell due to viral infection) experienced by the cells is on the cellular level. These injuries may include:

• Detachment from substrate.
• Membrane permeability. (changes in permeability hinders the transport of materials required for the cell)
• Lysis. (cell death by bursting its membrane).
• Shape alteration. (shape of the cell is changed which might affect its functions. E.g. RBC)
• Apoptosis. (cell death caused by a series of morphological changes that bring about the breakdown of the various functions of the cell).Membrane fusion; syncytium. (a structure containing many nuclei)

Looking at the bigger picture, virus induced injuries can cause some serious damage such as the shutdown of cellular functions in the host. For example, the polio virus shuts down the cellular functions of the neurons in the CNS and PNS (peripheral nervous system), resulting in cell death which leads to paralysis or even death.

Another kind of injury would be immunopathological (immune system/response related). Here, the immune system is impaired due to infection of the immunity cells such as the WBC. The body becomes relatively weak because its own WBCs are fighting each other. However, due to the weakening of the body’s immune system, the body itself will try to enhance its immune response by for example, increasing body temperature to try to kill the virus, thus causing haemorrhagic fevers.

Example of virus infection in the CNS

References
http://www.influenzareport.com/ir/images/image26.jpg
http://pathmicro.med.sc.edu/mayer/vir-host2000.htm
http://courses.bio.psu.edu/fall2005/biol110/tutorials/tutorial5_files/figure_8_5.gif
http://en.wikipedia.org/wiki/Endocytosis
http://www.psc.edu/science/2007/bardomain/images/endocytosis.jpg
http://www.ivy-rose.co.uk/Topics/Heart/Phagocytosis.jpg
http://faculty.southwest.tn.edu/rburkett/GB1-os23.jpg
http://www.nature.com/nrm/journal/v7/n6/images/nrm1940-f4.jpg
http://csm.colostate-pueblo.edu/biology/dcaprio/301/Onestepvirus.gif
http://micro.magnet.fsu.edu/cells/plants/images/cellwallfigure1.jpg
http://www.ucalgary.ca/~ceri/cmmb421prot/Virus%20morphol1.html

http://gsbs.utmb.edu/microbook/ch050.htmhttp://www.betterhealth.vic.gov.au/bhcv2/bhcarticles.nsf/pages/Viral_encephalitis?OpenDocument
http://www.medicalook.com/diseases_images/viral-infection1.jpg
http://en.wikipedia.org/wiki/File:Nervous_system_diagram.png
http://en.wikipedia.org/wiki/Alimentary
http://www.infovisual.info/03/065_en.html
http://www.hacompound.com/images/EYEBALL.gif
http://pathmicro.med.sc.edu/mhunt/interferon.htm
http://www.google.com.sg/search?hl=en&q=effect+of+interferon+on+viral+infection&meta
http://pathmicro.med.sc.edu/mayer/vir-host2000.htm
http://www.nlv.ch/Virologytutorials/Classification.htm
http://en.wikipedia.org/wiki/Virus_classification
http://www.fda.gov/ohrms/dockets/ac/02/slides/3885S2_02_Hoofnagle/sld006.htm
http://jvi.asm.org/cgi/content/full/78/23/12725
http://jvi.asm.org/cgi/content/abstract/75/18/8400
http://en.wikipedia.org/wiki/Protein_biosynthesis