All about Viruses

Virus-host Interactions

2009-01-19T07:07:00.000-08:00

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
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Overview of Microbiology B

2009-01-09T23:57:00.003-08:00

History of Viruses

What is poliomyelitis?

Poliomyelitis is a disease caused by infection with the poliovirus. The virus spreads by direct person-to-person contact, by contact with infected mucus or phlegm from the nose or mouth, or by contact with infected faeces.

The virus enters through the mouth and nose, multiplies in the throat and intestinal tract, and then is absorbed and spread through the blood and lymph system. The time from being infected with the virus to developing symptoms of disease (incubation) ranges from 5 - 35 days (average 7 - 14 days).

Risks include:

Lack of immunization against polio and then exposure to polio
Travel to an area that has experienced a polio outbreak

In areas where there is an outbreak, those most likely to get the disease include children, pregnant women, and the elderly. The disease is more common in the summer and fall.

Between 1840 and the 1950s, polio was a worldwide epidemic. Since the development of polio vaccines, the incidence of the disease has been greatly reduced. Polio has been wiped out in a number of countries. There have been very few cases of polio in the Western hemisphere since the late 1970s. Children in the United States are now routinely vaccinated against the disease.

Outbreaks still occur in the developed world, usually in groups of people who have not been vaccinated. Polio often occurs after someone travels to a region where the disease is common. Thanks to a massive global campaign over the past 20 years, polio exists only in a few countries in Africa and Asia.

What is smallpox?

Smallpox is a contagious, disfiguring and often deadly disease caused by the variola virus. Few other illnesses have had such a profound effect on human health and history. In the 20th century alone, an estimated 300 million people died of smallpox.

The initial signs and symptoms of smallpox, which appear about two weeks after infection, resemble those of the flu — fever, fatigue and headache. Later, severe pus-filled blisters appear on the skin that eventually leave deep, pitted scars. Once symptoms develop, there's no effective treatment for smallpox and no known cure.

Naturally occurring smallpox was finally eradicated worldwide by 1980 — the result of an unprecedented immunization campaign. But the virus didn't disappear entirely. Stocks of smallpox virus, set aside for research purposes, are officially stored in two high-security labs — one in the United States and one in Siberia. This has lead to concerns that smallpox someday may be used as a biological warfare agent.

What is rabies?

Rabies infections in people are rare in the United States. However, worldwide about 50,000 people die from rabies each year, mostly in developing countries where programs for vaccinating dogs against rabies don't exist. But the good news is that problems can be prevented if the exposed person receives treatment before symptoms of the infection develop.

Rabies is a virus that in the U.S. is usually transmitted by a bite from a wild infected animal, such as a bat, raccoon, skunk, or fox. If a bite from a rabid animal goes untreated and an infection develops, it is almost always fatal.

If you suspect that your child has been bitten by a rabid animal, go to the emergency department immediately. Any animal bites — even those that don't involve rabies — can lead to infections and other medical problems. As a precaution, call your doctor any time your child has been bitten.

Who was Edward Jenner?

Edward Jenner was an English country doctor who pioneered vaccination. Jenner's discovery in 1796 that inoculation with cowpox gave immunity to smallpox, was an immense medical breakthrough and has saved countless lives.

Edward Jenner was born on May 17 1749 in the small village of Berkeley in Gloucestershire. From an early age Jenner was a keen observer of nature and after nine years as a surgeon's apprentice he went to St George's Hospital, London to study anatomy and surgery under the prominent surgeon John Hunter. After completing his studies, he returned to Berkeley to set up a medical practice where he stayed until his death in 1823.

What he did?
In 1796 he carried out his now famous experiment on eight-year-old James Phipps. Jenner inserted pus taken from a cowpox pustule and inserted it into an incision on the boy's arm. He was testing his theory, drawn from the folklore of the countryside, that milkmaids who suffered the mild disease of cowpox never contracted smallpox, one of the greatest killers of the period, particularly amongst children. Jenner subsequently proved that having been inoculated with cowpox Phipps was immune to smallpox. He submitted a paper to the Royal Society in 1797 describing his experiment but was told that his ideas were too revolutionary and that he needed more proof. Undaunted, Jenner experimented on several other children, including his own 11-month-old son. In 1798 the results were finally published and Jenner coined the word vaccine from the Latin 'vaccia' for cow.

Who was Louis Pastuer?

Louis Pasteur was a world renowned French chemist and biologist. He was born on December 27 1822 in the town of Dole in Eastern France. Pasteur's parents were peasants; his father was a tanner by trade. He spent the early days of his life in the small town of Arbois where he attended school and where it seems that Pasteur did not do very well, preferring instead to go fishing. His headmaster, however, spotted potential in Pasteur and encouraged him to go to Paris to study. So, aged fifteen Pasteur set off for Paris hoping to study for his entrance exams. Unfortunately, the young Pasteur was so homesick that his father had to travel to Paris to bring him home. He then continued to study locally at Besancon, until he decided to try again in Paris. This time he succeeded and went on to study at the Ecole Normale Superieure. Curiously, although the young Pasteur worked hard during his student days he was not considered to be exceptional in any way at chemistry.

In 1847 Pasteur was awarded his doctorate and then took up a post as assistant to one of his teachers. He spent several years teaching and carrying out research at Dijon and Strasbourg and in 1854 moved to the University of Lille where he became professor of chemistry. Here he continued the work on fermentation he had already started at Strasbourg. By 1857 Pasteur had become world famous and took up a post at the Ecole Normale Superieure in Paris. In 1863 he became dean of the new science faculty at Lille University. While there, he started evening classes for workers. In 1867 a laboratory was established for his discovery of the rabies vaccine, using public funds. It became known as the Pasteur Institute and was headed by Pasteur until his death in 1888.

What he did?
Pasteur founded the science of microbiology and proved that most infectious diseases are caused by micro-organisms. This became known as the "germ theory" of disease. He was the inventor of the process of pasteurisation and also developed vaccines for several diseases including rabies. The discovery of the vaccine for rabies led to the founding of the Pasteur Institute in Paris in 1888.

Who is Robert Koch?

Robert Koch was born in 1843. Koch worked on anthrax and tuberculosis (TB) and he further developed the work of Louis Pasteur. Koch’s fame, alongside that of Alexander Fleming, Edward Jenner, Joseph Lister and Pasteur himself, is firmly cemented in medical history.

What did he discover?
Pasteur was convinced that microbes caused diseases in humans but his work on cholera had failed. He was never able to directly link one microbe with a disease. Koch succeeded in doing this.

The first disease that Koch investigated was anthrax. This was a disease that could seriously affect herds of farm animals and farmers were rightly in fear of it. Other scientists had also been working on anthrax. In 1868, a French scientist called Davaine had proved that a healthy animal that did not have anthrax could get the disease if it was injected with blood containing anthrax. Koch developed this work further and for three years he spent all his spare time finding out what he could about the disease, including its life cycle.

Koch found out that the anthrax microbe produced spores that lived for a long time after an animal had died. He also proved that these spores could then develop into the anthrax germ and could infect other animals.

After this, Koch moved onto germs that specifically affected humans. In 1878, he identified the germ that caused blood poisoning and septicaemia. He also developed new techniques for conducting experiments that influenced the way many other scientists carried out their experiments. He knew that infected blood contained the septicaemia germ but he could not see these germs under a microscope, and therefore, other scientists were unlikely to believe what he thought to be true without the evidence.

Koch discovered that methyl violet dye showed up the septicaemia germ under a microscope by staining it. He also photographed the germs so that people outside of his laboratory could see them.

Koch also devised a method of proving which germ caused an infection. His work was rewarded in 1880 when he was appointed to a post at the Imperial Health Office in Berlin. Here, Koch perfected the technique of growing pure cultures of germs using a mix of potatoes and gelatine. This was a solid enough substance to allow for the germs to be studied better. Koch gathered round him a team of researchers in Berlin in 1881 and began to work on one of the worst diseases of the nineteenth century – tuberculosis (TB).

The TB germ was much smaller than the anthrax germ so the search for it was difficult. Using a more specialised version of his dye technique, Koch and his team searched for the TB germ. In May 1882, Koch announced that his team had found the germ. His announcement caused great excitement. It also generated what became known as ‘microbe hunters’ – a new generation of young scientists who were inspired by the work of both Koch and Pasteur. One of those who was inspired by Koch was Paul Ehrlich.

Koch’s Postulates

The organism must be regularly associated with the disease and its characteristic lesions.
The organism must be isolated from the diseased hosts and grown in culture.
The disease must be reproduced when a pure culture of the organism is introduced into a healthy susceptible host.
The same organism must again be re-isolated from the experimentally infected host.

Discovery of Viruses

On 12th February 1892, Dmitri Iwanowski, a Russian botanist, presented a paper to the St. Petersburg Academy of Science which showed that extracts from diseased tobacco plants could transmit disease to other plants after passage through ceramic filters fine enough to retain the smallest known bacteria. This is generally recognised as the beginning of Virology. Unfortunately, Iwanowski did not recognize that he had discovered a new type of infectious agent.

Six years later, in 1898, a Dutch scientist, Martinus Beijerinick confirmed & extended Iwanowski's results on tobacco mosaic virus & was the first to develop the modern idea of the virus, which he referred to as contagium vivum fluidum ('soluble living germ'). He discovered that the infectious agent which passed through the filter could reproduce but would not grow on Petri dishes used to cultivate bacteria. He further realized that these agents required the presence of a host cell to reproduce. He named the agent responsible for tobacco mosaic disease a virus, after the Latin term for poison. He thought that this agent must be much smaller and simpler than bacteria. The subsequent crystallization and electron microscope images obtained by the American scientist, Wendell Stanley, in 1935 confirmed this, and the agent was named tobacco mosaic virus.

Tobacco mosaic virus causes stunted plant growth and mottled, discoloured plant leaves, especially in tobacco and other members of the tomato family (Solanceae).

In 1898, Freidrich Loeffler & Paul Frosch showed that a similar agent was responsible for foot-and-mouth disease in cattle. Thus these new agents caused disease in animals as well as plants. In spite of these findings, there was resistance to the idea that these mysterious agents might have anything to do with human diseases.

References
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Nature of Viruses

Viruses are:

Sub-microscopic, obligate intracellular parasites.
Viruses are not made up of cells. Compared to animal and plant cells, viruses are structurally simple. Viruses are even simpler than bacteria cells. The basic of structure of all viruses is similar. Viruses have a core of nucleic acid surrounded by a protein coat. At their core, all viruses contain either DNA or RNA.
They are so simple that they are technically not even considered "alive." There are six characteristics of all living things:
- Adaptation to the environment
- Cellular makeup
- Metabolic processes that obtain and use energy
- Movement response to the environment
- Growth and development
- Reproduction
A virus is not able to metabolize, grow, or reproduce on its own, but must take over a host cell that provides these functions; therefore a virus is not considered "living." The structure of a virus is extremely simple and is not sufficient for an independent life.
Viruses are structurally simpler than regular cells. Outside of the host cells, viruses are inactive. However, inside living cells, viruses show some of the characteristics of living things.
Virus particles are produced from the assembly of pre-formed components, whereas other agents 'grow' from an increase in the integrated sum of their components & reproduce by division.
Virus particles (virions) themselves do not 'grow' or undergo division.Viruses lack the genetic information which encodes apparatus necessary for the generation of metabolic energy or for protein synthesis (ribosomes).

General Properties of Viruses

Obligate parasites
Sub-cellular size
- Viruses are among the smallest infectious agents, and most of them can only be seen by electron microscopy and not light microscope. Their sizes range from 20 to 300 nm. They are so small that it would take 30,000 to 750,000 of them, side by side, to stretch to one cm.
Structurally simple
1. Nucleic acid - contains 3-400 genes
Deoxyribonucleic Acid (DNA) -unique features
- Single and/or double stranded
- Glycosylated and/or methylated
- Gaps present in double stranded molecule
- Circular or linear
- Bound protein molecules
- Unique purine and/or pyrimidine bases present
- Ribonucleotides present
Ribonucleic Acid (RNA) - Unique features
- Single or double stranded
- Segmented or unsegmented
- Bound protein molecules
- Unique purine and/or pyrimidine bases present
- Folding pattern
2. Capsid - The capsid accounts for most of the virion mass. It is the protein coat of the virus. It is a complex and highly organized entity which gives form to the virus. Subunits called protomeres aggregate to form capsomeres which in turn aggregate to form the capsid.
3. Envelope - this is an amorphous structure composed of lipid, protein and carbohydrate which lies to the outside of the capsid. It contains a mosaic of antigens from the host and the virus. A naked virus is one without an envelope.
4. Spikes- These are glycoprotein projections which have enzymatic and/or adsorption and/or hemagglutinating activity. They arise from the envelope and are highly antigenic.

Wide variety of host

Structure of viruses

Each virus is made up of two elementary components. The first is a strand of genetic material, either deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). Unlike living cells, viruses will have either DNA or RNA, but not both. The genetic material is a blueprint for determining the structure and behavior of a cell. In a virus, a protein coat called a "capsid" surrounds the nucleic acid. This coat serves to protect the nucleic acid and aid in its transmission between host cells. The capsid is made of many small protein particles called "capsomeres," and can be formed in three general shapes – helical, icosahedral (a 20-sided figure with equilateral triangles on each side), and complex. Some of the more advanced viruses have a third structure that surrounds the capsid. This is called the "envelope" and is composed of a bilipid layer, like the membrane on a cell, and glycoproteins, which are protein and carbohydrate compounds. The envelope serves to disguise the virus to look like a 'real' cell, protecting it from appearing as a foreign substance to the immune system of the host. The structure of a virus is closely related to its mode of reproduction.

Reproduction
A virus's sole purpose is to reproduce, but it needs a host cell to do so. Once a suitable host cell has been located, the virus attaches to the surface of the cell or is ingested into the cell by a process called "phagocytosis." It then releases its genetic material into the cell, and essentially shuts down normal cell processes. The cell stops producing the proteins that it usually makes and uses the new blueprint provided by the virus to begin making viral proteins. The virus uses the cell's energy and materials to produce the nucleic acid and capsomeres to make numerous copies of the original virus. Once these 'clones' are assembled, the virus causes the host cell to rupture, releasing the viruses to infect neighbouring cells.

Reference
http://www.microbiologybytes.com/introduction/introduction.html
http://www.kcom.edu/faculty/chamberlain/Website/Lects/PROPERT.HTM
http://www.miamisci.org/youth/unity/Unity1/Lubens/pages/characteristic.html
http://en.wikipedia.org/wiki/Viruses
http://www.roshanpakistan.com/
http://www.pinkmonkey.com/studyguides/subjects/biology-edited/chap14/b1400001.asp

Classification of Viruses

2009-01-09T23:57:00.001-08:00

Taxonomy and Classification of Viruses

Introduction
There are numerous types of virus present and new species are still being discovered today. They are present in almost every type or organism such as animals, plants, bacteria and fungi and thus require a system of classification so as to have a better understanding on the type of viruses present. According to the WHO, FAO and other international agencies, there are approximately 30,000 viruses, strains and subtypes but many still remain unassigned because they are not properly categorized.

An example of taxonomy of organisms

The first International Congress of Microbiology was held in Paris in 1930 but it was only during the International Congress of Microbiology held in Moscow in 1966, that the first attempt to come up with a system of classification of viruses was made.

The international Committee on Taxonomy of Viruses (ICTV) is a committee that handles the taxonomy of viruses. They have come up with a universal taxonomic scheme that follows the hierarchy taxa: Order - Family – Sub-family – Genus – Species. So far they have approved of 3 orders, 73 families, 9 subfamilies, 287 genera and 5450 viruses from 1950 species.Their first report was submitted in 1971 and the subsequent reports where released in 1976, 1979, 1982, 1991, 1995, 2000 and 2005.

There is also a classification criteria

Nature of genome and sequence relatedness.
Virus structure (symmetry, shape, etc).
Natural host range.
Cell and tissue tropism.
Pathogenicity and cytopathology.
Mode of transmission.
Physiochemical properties of virions.
Antigenic properties of viral proteins.

Despite having the ICTV, there are other people who come up with their own methods of classification for viruses. Two such examples would be Lwoff’s scheme of classification and David Baltimore’s system for classification. Lwoff’s scheme is based on several factors. They are shared properties of viruses instead of host properties, the physical properties of virus, nucleic acid of virus, symmetry of capsid, presence/absence of an envelope and the dimensions of virion and capsid. Baltimore’s system however, is solely based on the viral genome and its relationship to mRNA.

Baltimore’s system of classification separates the several kinds of DNA and RNA into seven classes as different viruses have different types DNA and RNA. Thus under this system of classification, the viruses are grouped according to their type of DNA and RNA. Below is a table of the classes.

dsDNA - double-stranded DNA.

ssDNA - single-stranded DNA

dsRNA - double-stranded RNA

(+) sense - positive(+) sense

(-) sense - negative(-) sense

(+) sense RNA is identical to mRNA while (-) sense RNA is complimentary to mRNA.

RNA reverse transcribing virus is transcribed from RNA to DNA.

DNA reverse transcribing virus is a DNA polymerase enzyme transcribed from ssRNA to DNA.

An example of classification

Reference
http://en.wikipedia.org/wiki/International_Committee_on_Taxonomy_of_Viruses
http://www.iums.org/Congresses/index.html)-17/12/08
http://www.ictvonline.org/virusTaxInfo.asp)-17/12/08
http://biology.about.com/od/evolution/a/aa092304a.htm)-17/12/08
http://en.wikipedia.org/wiki/Baltimore_classification

Enveloped DNA Viruses on Hepdnaviridae and Herpesviridae

2009-01-09T23:56:00.000-08:00

Hepadnaviridae

Features, Structure and Genome
The hepadna virus belongs to Class 1 under the Baltimore’s system for classification where several kinds of DNA and RNA are classified into seven classes. Its circular, partially doublestranded DNA, mainly present in spherical versions and some pleomorphic ones, is enclosed by a lipid envelope and an icosahedral nucleocapsid made of protein. Due to the partial DNA, it is a RNA intermediate. It is also an endogenous DNA which is dependent on DNA polymerase during DNA replication.

The capsid is has surface 1 antigen that connects to the virus antigen on the virus wall.

The hepadna virus family also consists of the Human HBV, Duck HBV, Ground Qquirrel HV, Snow Goose Virus, Woodchuck HV and Wooley Monkey Virus.

Types of hepatitis virus
There are 5 known hepatitis viruses. A, B, C, D and E. However there are also other viruses such as hepatitis F, G and H and not all of them belong to the hepadnaviridae family. They all infect the liver but cures and vaccination have not surfaced for certain types.

There is vaccination for hepatitis E but none for hepatitis C. Hepatitis C and G belong to the flaviviridae family and are thus RNA and not DNA viruses. Hepatitis D is also an RNA virus and can only propagate in the presence of the Hepatitis B virus. The existence of Hepatitis F has not yet been confirmed and is technically nonexistent. Hepatitis G tends to coexist with the other kinds of hepatitis infections although not known to cause any. Hepatitis H may more or less be the name given to the next hepatitis virus to be isolated.

HBV Infection
Infection can result from sexual intercourse, non sterile, improper and illegal blood transfusions and transplants as well as from mother to baby(transplacenta) or from breast milk feeding. It can also occur in occupational exposure to blood. Infection occurs mostly from blood/bodily fluid and sexual contact.The table below shows how some of the other viruses are transmitted.

Zone of infection of Hepatitis A.

Pathogenesis

The hepadna virus causes liver infections in humans and animals and it can be categorised into two catergories: Acute and Chronic liver infection. The type of infection developed depends on the age in which the person is infected.

In acute liver infection, symptoms are displayed and will change from subclinical to fulminant. Symptoms such as loss of appetite, nausea, vomiting, fever, abdominal pain and jaundice will surface. About 90-95% of acutely infected patients will recover without suffering a relapse but the remaining 5-10% will become chronically infected.

Chronic liver infection develops in 90% of neonates(infants) and 50% of children. Symptoms are not outwardly displayed unlike acute liver infection. It is difficult to detect because symptoms and abnormalities do not show up during lab testings. This may develop further to cirrhosis and hepatocellular carcinoma(primary liver cancer) while clinical apparent chronic hepatitis will also develop.

Diagnosis of liver infection

Diagnosis of liver infection is made on the basis of serology which is the identification of antibodies in the blood serum by drawing blood. The presence of Serum Hepatitis B surface antigen(HBsAg) is detected in the blood is often used to determine if there is infection. However, it may not be present in early stages of infection and the detection of IgM antibodies against the hepatitis B core antigen(HBcAg) in the serum is used instead.

Higher rates of viral replication in cells, detection of Hepatitis B e antigen(HBeAg) will surface. HBeAg will then be cleared and anti-HBe will appear shortly due to the reduction in viral replication.

Detection of IgG antigens against the hepatitis surface B antigen(anti-HBs) and core antigen(anti HBc IgG) will indicate that the host has cleared the infection. IgG remains in the memory of the cell and protects it for life.

Control

Donated body parts/blood are tested for HBV before transplants/transfusion.Risky sexual behaviours should be minimized or better still, avoided.Carrying out vaccination of post 1987 babies against HBV.

Reference

http://www.innvista.com/health/microbes/viruses/hepatf.htm

http://www.kcom.edu/faculty/chamberlain/website/LECTS/Viral.htm
http://www.infekt.ch/updown/images/hbv_verlauf.jpg
http://www.microbiologybytes.com/virology/HBV.html

http://www.infekt.ch/updown/images/hbv_verlauf.jpg

Herpesviridae

About herpesviridae

After primary infection and the patient is supposedly cured from the symptoms, the virus remains latent in the body until some factors such as age, stress, long exposure to sunlight and menstrual periods causes its reactivation. During the term in which it is latent, there are no symptoms displayed. When the latent virus reactivates, it is known as secondary infection. Reactivation however, may result in the development of other diseases.

Herpes means ‘to creep upon’ in Greek. It is given that that because the virus ‘hides’ itself in the nerve tissues during the latent period before reactivation. Herpes also causes viral encephalitis (acute inflammation of the brain) or brain damage if passed from mother to child at childbirth.

There is currently no cure or vaccination for herpes and is labeled as one of the toughest virus to control as infection with herpes, especially HSV-1, is universal.

Structure of the Herpes virus genome

The morphology of all herpes viruses are more or less similar and sometimes even identical. The herpes virus has a linear double-stranded (ds) DNA and is thus from class 1 of the Baltimore’s classification. It is a concentric virion meaning that the layers of structure in the virus share the same centre and axis with each other.

Concentric circles

Herpes virus structure

The structure of the virus consist of a protein based icosahedral capsid that encloses its linear ds DNA. This capsid is surrounded by a layer of amorphous proteins called the tegument. The protein atoms here are not arranged in orderly repeating pattern as in crystalline solids where long-range order is required. Then both are enclosed by a lipid bilayer membrane termed the envelope where the outer layer is dotted with glycoprotein like villi.

It has three origins of replication (ORI) meaning that there are three areas in the DNA where the DNA is recognized by replication initiator proteins and separated into two strands to start a replication fork where DNA synthesis happens.

Replication

The DNA of the herpes virus only transcribes and replicates in the nucleus of the host cell and are thus nuclear-replicating. Infection begins when the virus comes in contact with a cell at specific receptor on the cell surface membrane. There, the glycoprotein on the virus’s lipid bilayer envelope will bind with the receptors of the to-be-host cell and the virus DNA would enter the nucleus of the host cell.

Pathogenesis

There are 7 distinct viruses in the herpes virus family that causes diseases. 3 of them are:

1. Herpes simplex viruses

(a) HSV1

(b) HSV2

2. Varicella Zoster virus

(a) Varicella

(b) Herpes Zoster

3. Epstein-Barr Virus (EBV)

1.Herpes simplex virus

It consist of herpes simplex virus 1 (HSV-1) and herpes simplex 2 (HSV-2). Symptoms produced for both are asymptomatic and similar to each other although severity may differ. HSV-1 is the main cause for orofacial infections whilst HSV-2 is genital herpes.

HSV-1

Primary and recurrent infection occurs for HSV-1. Primary infection can range from orofacial lesions like cold sores and blisters around the mouth/gum, eyes and face that last for about 2-3 weeks to swollen lymph nodes, fever, muscle aches and headaches.

Recurrent infection are more common in HSV-1 than HSV-2.

Lesions

Ulceration

HSV-2

Primary infection last for 2-3 weeks. There is formation of inflamed pastules and vesicles that appear a week after sexual infection. Burning and itching sensations at the genital/anal areas will be experienced as well as pain when urinating. Other common symptoms include foul-smelling discharge from vagina(female) and penis(male), swollen lymph nodes, fever, muscle and headaches.

Infected Penis

Infected Vagina

Unlike HSV-2 which is transmitted sexually, HSV-1 is not sexually transmitted. Rather, it can be transmitted when the virus comes in contact with abraded skin or oral mucosa.

Control for HSV-1/2

Since there is no cure, early treatment may reduce the number of latent of virus in the body and in doing so, reduce the chances for reactivation.Reduce/avoid risky sexual contact.

2. Varicella Zoster Virus

It is divided into tow clinical entities: Varicella and Herpes zoster.Varicella is associated to the cause of chicken pox where else Herpes zoster is associated with shingles. Chicken pox is the primary infection of the varicella zoster virus while shingles is the secondary infection. People that have been vaccinated against chicken pox when they were children have lower chances of developing shingles.

As stated above, the virus ‘hides’ in the nervous system of the patient after the symptoms have been cured, reactivating only in the later stages of life. Its genome morphology is similar to that of the herpes simplex and is susceptible to disinfectants. Although there is vaccination for the Varicella Zoster virus, the effectiveness of the immunity it provides might dwindle overtime and a second dose maybe required to maintain the immunity levels in the body.

The virus is dangerous in pregnant women because it can be passed to the child or even affect the nervous system of the child, causing development of the Guillain Barre syndrome where the child would suffer extreme pain on the slightest touch.

(a) Clinical features of Varicella

Chicken pox only develops around 2-3 weeks after infection is highly contagious during the first few days after rash appears. Primary infection of chicken pox will give life long immunity against chicken pox but does not prevent shingles from developing. Adults are more likely to suffer from more severe effects of chicken pox than children if they have not been infected during childhood.

Infection is usually indicated by the distinctive itchy rash that eventually forms blisters(lesions) all over the body and become scabs. It is accompanied by fever and general malaise(the feeling of feeling unwell). Scratched lesions may lead to secondary infection. Scarring may develop depending on seriousness.

Child with varicella

It can be spread by direct contact with infected people as well as contact with secretions from the lesions on the skin. It can also be spread via the respiratory track from sneezing or coughing.

(b) Clinical features of Shingles

Shingles show different symptoms as compared to chickenpox.Painful rash and eventually lesions is experienced. This is caused by infection of nerve axons under the skin since the virus ‘hides’ in nerve cells during its latent period.

Headache, fever, malaise, burning pain, itching, numbness, sudden short outburst of pain and in some serious cases, loss of sight and hearing.

Control for Varicella Zoster virus
Stay away from infected people.
Get vaccinated.

3. Epstein-Barr virus
Infection is widespread like HVS with almost 100% of the adult population infected due to kissing and close proximity. The EBV test is tested positive almost universally and most children have already been infected by 18months of age.

Instead of remaining latent in the nerve cells like the HVS and VZV, it ’hides’ in the B lymphocytes of the host. The virus is mostly spread via contact with saliva of infected people and is almost impossible to prevent the spreading as the saliva of healthy people also contain the virus. Transmission via blood or respiratory track is uncommon.

The virus can cause infectious mononucleosis aka glandular fever.

Clinical features of EBV

It has an incubation period of 4-7 weeks and acute infection does not last for more than 4 months, chronic infection last for more than 6 months. Some symptoms would include fever, sore throat, malaise, tiredness, swollen lymph glands and atypical lymphocytosis(increase in the amount of lymphocytes in the blood) in the peripheral blood.

The virus can also cause infectious mononucleosis aka glandular fever. Symptoms such as fever, fatigue, sore throat, weight loss, malaise. Development of jaundice and hepatitis(inflammation of liver cells) may occur.

Control

No vaccines are available.

Reduce or avoid risky behaviour.

Diagnosis

Virus culture.

Use antigen tests such as the Enzyme Link Immuno Assay.

Blood tests such as serology.

Electron microscopy for direct detection.

A positive test would show an increase of certain atypical while blood cells in a person infected with EBV. Detection of IgG and IgM against certain antigens for each of the virus.

References
http://en.wikipedia.org/wiki/Herpesviridae

http://www.wrongdiagnosis.com/medical/herpesviridae.htm

http://www.docstoc.com/docs/476432/Herpersviridae

http://web.uct.ac.za/depts/virology/teaching/notes/herpes.htm

http://en.wikipedia.org/wiki/DNA_replication#Origins_of_replication

http://adam.about.com/reports/Herpes-simplex.htm

http://www.medhelp.org/NIHlib/GF-619.html

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

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

http://www.kcom.edu/faculty/chamberlain/Website/Lects/viral6.jpg

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

http://www.brown.edu/Courses/Bio_160/Projects2000/Herpes/EBV/EBVen.jpg

Picornaviridae and Orthomyxoviridae

2009-01-09T23:55:00.004-08:00

Picornaviridae

Introduction to Picornaviridae
‘Pico’ is very small and it is also known as Pico PNA viruses.

Picornavirus is one of the ‘oldest’ known viruses, dating back to 1400 B.C., when a temple record tells of poliovirus in ancient Egypt. Picornavirus is one of the most diverse viruses with over 200 sereotypes, causing infections such as Polio, Hepatitis A, and the common flu. Foot-and-mouth virus was one of the first viruses to be recognised in 1898 by Loeffler and Frosch, which cause infections in livestock.

Classification of Picornaviridae
Base on physical properties, the particle density and pH-sensitivity, and serological relatedness, more recently based on nucleotide sequence. The most recent revision of virus taxonomy has recognized nine genera within the family:

Picornaviruses are classed under Baltimore's viral classification system as group IV viruses as they contain a single stranded, positive sense RNA genome of between 7.2 and 9.0 kb in length. Like most positive sense RNA genomes, the genetic material alone is infectious; although substantially less virulent than if contained within the viral particle, the RNA can have increased infectivity when transfected into cells. The genome itself is the same sense as mammalian mRNA, being read 5’ to 3’. Unlike mammalian mRNA Picornaviruses do not have a 5’ CAP but a virally encoded protein known as VPg, however like mammalian mRNA the genome does have a poly A tail at the 3’ end. There is an un-translated region (UTR) at both ends of the Picornavirus genome. The 5’ UTR is longer, being around 600-1200 BP in length, compared to that of the 3’ UTR, which is around 50-100bp. It is thought that the 5’ UTR is important in translation and the 3’ in negative strand synthesis; however the 5’ end may also have a role to play in virulence of the virus. The rest of the genome encodes structural proteins at the 5’ end and non-structural proteins at the 3’ end in a single polyprotein.

The whole of replication occurs within the host cell cytoplasm and infection can even happen in cells that do not contain a nucleus (known as enucleated cells) and those treated with actinomycin D (this antibiotic would inhibit viral replication if this occurred in the nucleus.)

Genome structure of Picornaviridae

Picornavirus

The picornavirus genome consists of a single molecule of linear, postitive(+)-sense, single-strand RNA and is non-segmented. The complete genome is nucleotides long. The 5'-terminus of the genome has a long untranslated region 600-1200 bases in length, which is important in translation, virulence, and possibly encapsidation. There is a shorter untranslated region (50-100 bases in length) on the 3'-terminus, which is important in (-) strand-synthesis. The 5'-terminus untranslated region also has a "clover leaf" secondary structure known as the Internal Ribosome Entry Site (IRES), which distinguishes picornaviruses from other RNA viruses; this structure is important in translation and replication. The 5'-terminus is modified by a covalently-attached VPg protein (which takes the place of a cap), while the 3'-terminus is modified by polyadenylation.

Virion structure of a Picornaviridae

Picornavirus virions consist of a non-enveloped, icosahedrally symmetric capsid. The capsid consists of 12 capsomers and has a diameter of 27-30 nm, which makes it one of the smallest of all viruses (thus the name "picornavirus"). The genome is tightly packed into the capsid. The capsid has four unique proteins: VP1, 2, 3, and 4.

Reproduction cycle of Picornaviridae

Replication of picornaviridae

Using different cellular receptors (depending on the picornavirus), a picornavirus virion attaches to a host cell. Uncoating occurs, and the virus' RNA is released into the cytoplasm of the host cell through a membrane channel. Virus replication occurs entirely in the cytoplasm. The host cell's transcription processes are shut off to a degree that varies with different picornaviruses, while the IRES helps to make sure the virus' transcription is left untouched. Replication occurs. RNA is packaged into preformed capsids. Release of the virus occurs when cell lysis occurs (with the exception of Hepatits A, which is non-lytic and thus creates a more persistent infection).

Viral ecology and pathology
The mode of transmission, ecology, and pathology of picornaviruses vary greatly between the different genera. Interestingly, the genetics of virulence phenotypes of picornaviruses is poorly understood.

Picornaviruses do not have virulence genes per se, but the design of the capsid and how it interacts with the virus receptor expressed on the host cell surface, specific sequences within the nontranslated regions of the viral genome, as well as coding sequences that result in different protein sequences may all have a part in determining the virulence phenotype.

Transmission and effects of picornaviridae

Transmission of picornaviridae

Effect of picornavirus on human

Reference
http://www.microbiologybytes.com/virology/Picornaviruses.html
http://microbewiki.kenyon.edu/index.php/Picornaviridae
http://www.stanford.edu/group/virus/picorna/2004flynn/Picornaviridae2.htm

Orthomyxoviridae

Introduction to orthomyxoviridae

‘Ortho’ is the Greek for straight and ‘Myxa’ is the Greek word mucus. It has a common name, Avian influenza, bird flu, fowl plague.

These viruses cause influenza, an acute respiratory disease with prominent systemic symptoms. Pneumonia may develop as a complication and may be fatal, particularly in elderly persons with underlying chronic disease. Type A viruses cause periodic worldwide epidemics (pandemics); both types A and B cause recurring regional and local epidemics. Influenza epidemics have been recorded throughout history. In temperate climates, the epidemics typically occur in the winter and cause considerable morbidity in all age groups. An epidemic with associated mortality has occurred in most of the past 100 years. The worst of these was the 1918 pandemic, which caused about 20 million deaths worldwide and about 500,000 deaths in the United States.

Classification of orthomyxoviridae
The orthomyxoviridae are a family of RNA viruses that includes the 5 generas, Influenzavirus A, Influenzavirus B, Influenzavirus C, Isavirus and Thogotovirus. Influenza A, B and C causes influenza in vertebrates, like for example, birds, humans and other mammals. Isavirus infect salmon while thogotoviruses infect vertebrates and invertebrates such as mosquitoes and sea lice.

Animal influenza virus

Genome structure of orthomyxoviridae

The genome of the orthomyxovirus consists of six to eight segments of linear, negative-sense, single-stranded RNA. The complete genome is 10000-14600 nucleotides long. Segment 1 is fully sequenced and the complete sequence is nucleotides long. Segment 2 only has an estimate of the sequence, although it is sequenced and is almost the same length as segment 1. Segment 3 is also sequenced, but estimated and the complete sequence is around 2200-2300 nucleotides long. Segment 4 has been completely sequenced and it is 1700-1800 nucleotides long. Segment 5 has been sequenced, but only estimated, and is 300-1900 nucleotides long. Segment 6 has been sequenced, but only estimated, and is 1400-1500 nucleotides long. Segment 7 has been sequenced, but estimated and the complete sequence is 800-1100 nucleotides long.

The genome has terminally redundant sequences and they are repeated at both ends. The nucleotide sequences at the 3'-terminus are identical. The 5'-terminal sequence has conserved regions and repeats complementary to the 3'-terminus; terminal repeats at the 5'-end are 11-14 nucleotides long. The 3'-terminus has conserved nucleotide sequences; is 11-13 nucleotides long; in the genera of same family. The sequence has conserved regions in all RNA species or some RNA segments. The multipartite genome is encapsidated with each segment in a separate nucleocapsid, and the nucleocapsids are surrounded by one envelope. Each virion contains defective interfering copies.

Viririon structure of orthomyxoviridae
Virions of an orthomyxovirus consist of an envelope, a matrix protein, a nucleoprotein complex, a nucleocapsid, and a polymerase complex. The virus capsid is enveloped. Lipids are present and located in the envelope. Virions are composed of 18-37% lipids by weight. The composition of viral lipids and host cell membranes are similar. The lipids are modified cellular lipids and are derived from plasma membranes. Proteins of host derived membranes have been modified during post-translational processes. Host-derived membranes contain viral proteins in place of host proteins.

The virions are spherical to pleomorphic and filamentous forms occur. They are 80-120 nm in diameter and 200-300(-3000) nm long. The surface projections are densely dispersed distinctive hemagglitinin-esterase (HEF) spikes, or spaced widely apart hemagglutinin (HA) spikes. Clusters of neuramidase (NA) irregularly inerpose the major glycoprotein in a ratio of HA to NA about 4-5 to 1.

Human influenza viruses
(Envelope contains rigid "spikes" of haemagglutinin and neuraminidase which form a characteristic halo of projections around negatively stained virus particles.)

There are about 500 spikes evenly dispersed or clustered and are covering the surface comprising hemagglutinin, or neuraminidase, or esterase-esterase. The surface projections are composed of one type of protein or different types of proteins and are 10-14 nm long and 4-6 nm in diameter. The nucleocapsid is elongated with helical symmetry and is segmented with loops at one end. The segments have different sized classes with clear predominate lengths with a length of 50-130 nm (in differnent class sizes) and a width of 9-15 nm.

Reproduction cycle of orthomyxoviridae

Orthomyxovirus replication takes about 6 hours to replicate and kills the host cell. The viruses attach to permissive cells via the hemagglutinin subunit, which binds to cell membrane glycolipids or glycoproteins containing N-acetylneuraminic acid, the receptor for virus adsorption. The virus is then engulfed by pinocytosis into endosomes. Acid environment of the endosome causes the virus envelope to fuse with the plasma membrane of the endosome, uncoating the nucleocapsid and releasing it into the cytoplasm.

A transmembrane protein derived from the matrix gene (M2) forms an ion channel for protons to enter the virion and destabilize protein binding allowing the nucleocapsid to be transported to the nucleus, where genome is transcribed by viral enzymes to yield viral mRNA. Unlike replication of other RNA viruses, orthomyxovirus replication is dependent on the presence of active host cell DNA. The virus scavenges cap sequences from the nascent mRNA generated in the nucleus by transcription of the host DNA and attaches them to its own mRNA. These cap sequences allow the viral mRNA to be transported to the cytoplasm, where it is translated by host ribosomes. The nucleocapsid is assembled in the nucleus.

Virions acquire an envelope and undergo maturation as they bud through the host cell membrane. During budding, the viral envelope hemagglutinin is subjected to proteolytic cleavage by host enzymes. This process is necessary for the released particles to be infectious. Newly synthesized virions have surface glycoproteins which contain N acetylneuraminic acid as a part of their carbohydrate structure, and thus are vulnerable to self-agglutination by the hemagglutinin. One major function of the viral neuraminidase is to remove these residues.

Gene Reassortment
The influenza virus genome is segmented, and because of that, genetic reassortment can occur when a host cell is infected simultaneously with viruses of two different parent strains. If a cell is infected with two strains of type A influenza, for example, some of the progeny virions will contain a mixture of genome segments from the two strains. This process of genetic reassortment probably accounts for the periodic appearance of the novel type A strains that cause influenza pandemics

Viral ecology and pathology
Influenza virus is transmitted from person to person primarily in droplets released by sneezing and coughing. Some of the inhaled virus lands in the lower respiratory tract, and the primary site of the disease is the tracheobronchial tree, although the nasopharynx is also involved. The neuraminidase of the viral envelope may act on the N-acetylneuraminic acid residues in mucus to produce liquefaction. This liquified mucus may help spread the virus through the respiratory tract in concert with the mucociliary transport. The superficial mucosa suffers cellular destrcution and desquamation because of the infection of the mucosal cells. Nonproductive cough, sore throat and nasal discharge are some sysmptoms that result from the endema and mononuclear cell infiltration of the involved areas. The cough may be persistent but the most prominent symptoms of influenza are systemic-- fever, muscle aches and general prostration. These systemic symptoms are not caused directly by the virus because viremia is rare. A possible cause is circulating interferon, as administration of theraupetic interferon causes systemic symptoms resembling those of influenza.

The evidence shows that the extent of virus-induced cellular destruction is the prime factor determining the occurence, severity and duration of clinical illness. It is possible to recover virus from respiratory secretions for 3 to 8 days in an uncomplicated case. At times of maximal illness, peak quantities of 104 to 107 infectious units/ml are detected. The titer begis to drop in concert with the progressive abatement of disease after 1 to 4 days of peak shedding

The infection may extensively involve the alveoli, particularly in patients with underlying heart or lung disease. This may result in interstitial pneumonia, sometimes with marked accumulation of lung hemorrhage and endema. Pure viral pneumonia of this type is a severe illness with a high mortality. Virus titers in secretions are high, and viral shedding is prolonged. However, in most cases, bacteria are the causative agent of pneumonia associated with influenza. Examples include pneumococci, staphylococci, and Gram-negative bacteria. The preceding viral infection damages the normal defenses of the lung, setting the stage for the bacteria to invade and cause disease.

Host defences
Immune mechanisms are responsibe for recovery from influenza have not been clearly delineated. Several mechanisms probably act in concert. Interferon appears in respiratory secretions shortly after viral titers reach their peak level, and may play a role in the subsequent reduction in viral shedding. Antibody usually is not detected in serum or secretions until later in recovery or during convalescence; nevertheless, local antibody appears responsible for the final clearing of virus from secretions. T cells and antibody-dependent cell-mediated cytotoxicity also participate in clearing the infection.

Antibody is the primary defense in immunity to reinfection. IgG antibody, which predominates in lower respiratory secretions, appears to be the most important. The IgG in these secretions is derived from the serum, which accounts for the close correlation between serum antibody titer and resistance to influenza. IgA antibody, which predominates in upper respiratory secretions, is less persistent than IgG but also contributes to immunity.

Only antibody directed against the hemagglutinin is able to prevent infection. A sufficient titer of anti-hemagglutinin antibody will prevent infection. Lower titers of anti-hemagglutinin antibody lessen the severity of infection. Anti-hemagglutinin antibody administered after an infection is under way reduces the number of infectious units released from infected cells, presumably because the divalent antibody aggregates many virions into a single infectious unit. Antibody directed against the neuraminidase also reduces the number of infectious units (and thus the intensity of disease), presumably by impairing the action of neuraminidase against N-acetylneuraminic acid residues in the virion envelope and thus promoting virus aggregation. Antibody directed against nucleoprotein has no effect on virus infectivity or on the course of disease.

Immunity to an influenza virus strain lasts for many years. Recurrent cases of influenza are caused primarily by antigenically different strains.

Diagnosis

Electron micrograph of influenza virus particles

Diagnosis of influenza is suggested by the clinical picture of sudden onset of fever, malaise, headache, marked muscle aches, sore throat, nonproductive cough, and coryza. When a syndrome resembling influenza occurs in the winter in an adult (the etiologies of illnesses of this type are more complex in children), an influenza virus is a likely cause. If an epidemic of febrile respiratory disease is known to be under way in the community, the diagnosis is yet more likely. Definitive diagnosis, however, relies on detecting either the virus or a significant rise in antibody titer between acute phase and convalescent-phase sera.

A rapid specific diagnosis of influenza may be obtained by demonstrating viral antigens in cells obtained from the nasopharynx in immunostaining tests such as immunofluorescence or in enzyme immunoassays (ELISA) employing respiratory secretions. Influenza virus is usually isolated from respiratory secretions by being grown in tissue cultures or chick embryos. Virus growth in tissue cultures is detected by testing for hemadsorption: red cells are added to the culture and adhere to virus budding from infected cells. If the culture tests positive, serologic tests with specific antisera may be used to identify the virus. In the chick embryo culture method, fluid from the amniotic or allantoic cavity of chick embryos is tested for the presence of newly formed viral hemagglutinin; the virus in positive fluids is then identified by hemagglutination inhibition tests with specific antisera. Finally, a rise in serum antibody titer between acute-phase and convalescent-phase sera can be identified by various tests, of which complement fixation, hemagglutination inhibition, and immunodiffusion (using specific viral antigens) are the most common. None of these techniques will identify all infections.

Prevention and treatment
Inactivated influenza virus vaccines have been used for about 40 years to prevent influenza. The viruses for the vaccine are grown in chick embryos, inactivated by formalin, purified to some extent, and adjusted to a dosage known to elicit an antibody response in most individuals. A given vaccine contains the strains of types A and B viruses that are judged most likely to produce epidemics during the following winter. Vaccine is administered parenterally in the fall; one or two doses are required, depending on the immune experience of the population with related antigens. Protection against illness has varied from 50 to 90 percent in civilian populations and from 70 to 90 percent in military populations. Local and systemic reactions to the vaccine are minor and occur in the first day or two after vaccination. During the national swine flu immunization of 1976 in the United States, an increased risk of developing Guillain-Barre syndrome accompanied vaccination; however, this correlation has not been detected since. Annual use of inactivated influenza virus vaccine is currently recommended in the United States for persons at risk of developing pneumonia from the disease and for their close associates. Live attenuated vaccines are being developed as alternatives to inactivated vaccine.

The synthetic drugs amantadine and rimantadine hydrochloride effectively prevent infection and illness caused by type A, but not by type B, viruses. The drugs interfere with virus uncoating and transport by blocking the transmembrane M2 ion channel (see multiplication). Drugs prevent about 50 percent of infections and about 67 percent of illnesses under natural conditions. When administered for 10 days to household contacts of a person with influenza, drugs protect up to 80 percent of the persons from illness. Side effects are greater for amantadine and limited primarily to the central nervous system.

Amantadine and rimantadine are the only specific antiviral treatments available for influenza. As in the case of prophylaxis, they are effective only against type A virus. When administration is started early in the course of illness, drugs hasten the disappearance of fever and other symptoms. Emergence of viral resistance can occur during treatment.

References
http://www.microbiologybytes.com/virology/Orthomyxoviruses.html
http://www.virology.net/Big_Virology/BVRNAortho.html
http://en.wikipedia.org/wiki/Orthomyxoviridae
http://microbewiki.kenyon.edu/index.php/Orthomyxoviridae
http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/00.046.htm
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mmed.section.3069
http://images.google.com.sg/images?um=1&hl=en&q=Orthomyxoviridae

Retroviridae and Flaviviridae

2009-01-09T23:55:00.003-08:00

Retroviridae

Introduction to Retroviruses
Retroviruses are viruses that are capable of using reverse transcription of viral RNA into DNA during replication. Human Immunodeficiency Virus (HIV) is one of the members of this family. Another member is feline leukemia. In 1908, retroviruses were found by Vilhelm Ellermann and Oluf Bang. Animal infection and disease were the focus of study of retroviruses for the first sixty years. Then, in the 1960s and 1970s, viral replication cycle and pathogenic effects at the cellular level were the focus of study. Today, the diverse pathogenic effects of these viruses at the cellular and modular level are the focuses of the study.

History of Retroviruses
Chicken sarcoma, a disease caused by a virus, was uncovered by Peyton Rous in 1911. In 1966, he won the Nobel Prize. In 1970, Howard Temin and David Baltimore found the reverse transcriptase enzyme separately, and they won the 1975 Nobel Prize. In 1989, Michael Bishop and Harold Varmus won the Nobel Prize for discovering the oncogenes and the role of oncogenic viruses and cancer. In 1980, Robert Gallo and his team found the first human retrovirus that resulted in adult T cell leukemia. In 1984, Luc Montagnier found out the agent that caused AIDS and it was confirmed by Gallo.

The Genera of Retroviruses

Retroviridae (family)
Orthoretrovirinae (sub family)
- Alpharetroviruses
- Betaretroviruses
- Gammaretroviruses
- Deltaretroviruses
- Epsilonretroviruses
- Lentivirus
Spumaretrovirinae (sub family)
- Spumaretrovirus

Genome Structure of a Retroviridae
Retroviridae has a positive sense, single-stranded RNA and is linear. It has 3’ polyadenylated tail and 5’ cap. They have reverse transcriptase and they form long terminal repeats before inserting provirus DNA into the host genome.

Virion Structure of a Retroviridae
An envelope, a nucleocapsid and a nucleoid can be found in the virions of a retroviridae.Retroviruses have spherical enveloped virions to pleomorphic enveloped virions which are measured 80nm to 100nm in diameter. Within the icosahedral capsid, it has a central nucleoid that consists of ribonucleoprotein. The nucleoid is either concentric or truncated cone in lentiviruses. The capsid is enveloped with glycoprotein peplomers.

Reproduction Cycle of a Retroviridae in a Host Cell
The virions of a retroviridae interact between a virally-encoded enveloped protein and a cellular receptor and then enter the host cells. The enzyme reverse transcriptase which is present in the virion transcribed viral RNA into DNA copy. The viral DNA copy merges and becomes a permanent part in the host genome. Provirus is referred to this merged DNA. The viral genes are being expressed using the host cell’s transcriptional and translational machinery. To create new viral RNA, the provirus is being transcribed by the host RNA polymerase II. Other cellular processes then transported this new viral RNA out of the nucleus. Some of the new RNAs are being divided to enable the expression of some genes, and those undivided new RNAs are left as full-lengths RNA. The host cell’s translational machinery combines the viral proteins. The viral proteins then gather and sprout from the host cell. All members of the retroviridae go through this reproduction cycle except for spumaviruses. The reverse transcription is completed by the spumaviruses in the virus-producing cells, instead of the infected target cells. DNA genome is found in the infectious virus.

Human T-lymphotropic virus 1 (HTLV-1)
HTLV-1 is a retrovirus that forms tumour and has infected 10 to 20 million of people worldwide. It is considered the first retrovirus that causes Adult T-cell leukemia (ATL). Perinatal transmission by blood or breast milk, sexual contact, or exposure to contaminated blood products can cause ATL. Acute aggressive leukemia can lead to death in a year, and here is no cure to it yet. HTLV-1 also causes Tropical Spastic Para paresis. Neurons are wasted and back pain occurs, which then leads to paralysis.

Human Immunodeficiency Virus (HIV)
Acquired Immunodeficiency Syndrome (AIDS) is caused by HIV. AIDS can be transmitted via sexual contact and any form of contacts with blood. Mother passes the AIDS disease to the child via placenta, mucosa and breast milk. AIDS is being spread worldwide.

Pathogenesis of HIV
Primary Infection

Primary infection is the acute stage whereby the symptoms of it are flu-like symptoms, fever, skin rash and swollen lymph nodes.

Asymptomatic Stage
At this stage, there is no visible disease, but there is a fall in CD4 T-lymphocytes, a primary target cell.
The possible symptoms for this stage are tiredness, depression, loss of weight and memory disorders.

Symptomatic Stage
This is the stage where there is AIDS –related complex. The diseases are not really considered as ADIS, but may lead to HIV infection. This indicates the defect in cell-mediate immunity. When there is a fall in CD4 T lymphocytes, opportunistic infections occur which will then lead to AIDS.

AIDS Therapy
There are four types of AIDS therapy.
1. Non-specific therapeutic management
2. Specific therapeutic management
3. Immunomodulation
4. Vaccines

Non-specific therapeutic management
This therapy helps to boost the general health through the intake of vitamins, minerals, anti-oxidants and many others.

Specific Therapeutic Management
One of the specific therapeutic management is through antiretroviral therapy. There are three types of inhibitors – the nucleoside reverse transcriptase inhibitors, the non- nucleoside reverse transcriptase inhibitors and the protease inhibitors. Azidothymidine (AZT) and lamivudine (3TC) are examples of nucleoside reverse transcriptase inhibitors. Efavirenz and nevirapine are examples of non-nucleoside reverse transcriptase inhibitors. Indinavir and ritonavir are examples of protease inhibitors. The inefficiency of the reverse transcriptase leads to rapid mutations. Hence, to overcome this resistance, there is a need to combine therapy.

Immunomodulation
This therapy is still under study. However, there is an improvement of immune system via treatment with interleukin-2.

Vaccines
Many people are still undergoing development and trails, but so far, none of it are being proved to be useful.

References
http://microbewiki.kenyon.edu/index.php/Retroviridae
http://diverge.hunter.cuny.edu/~weigang/Images/13-19_retroviridae_1.jpg
http://www.stanford.edu/group/virus/retro/2000/retroheader.jpg
http://microbewiki.kenyon.edu/index.php/Human_T-lymphotropic_virus_1
http://www.tthhivclinic.com/fig_3.gif

Flaviviridae

Introduction to Flaviviridae
Arboviruses (arthropod-borne viruses) are viruses that are transmitted by the bite of an arthropod vector. The viruses tend to multiply in the bodies of an arthropod. Alphaviruses and Flaviviruses are the two common types of Arboviruses. Alphaviruses belong to a family, named Togaviridae, and Flaviviruses belong to a family, named Flavivridae. Flaviviridae is a family name and its name came from a type virus of Flaviviridae, known as the Yellow Fever virus. In Latin, flavus means yellow.

A lot of viruses that cause diseases in humans are found in Flaviviridae. A total of 69 pathogens can be found in Flaviviridae. The genus of the Flavivirus consists of many injurious creatures, and this includes the yellow fever virus, the dengue fever virus and the West Nile virus. Hepacivirus genus has hepatitis C virus and its relatives.

Genome Structure of Flaviviridae
The genome of Flaviviridae consists of a linear, positive-sense, single stranded RNA, and the genome is not segmented. The genome has a 5’-end carries a methylated nucleotide cap or genome-linked protein. It also has a 3’ polyadenylated tail, polyprotein from genomic RNA cleaved, 3 structural protein and some non-structural proteins. The genome undergoes cytoplamsic replication.

Virion Structure of Flaviviridae
The virions of the Flaviviridae are spherical to pleomorphic and the virions are enveloped. The virions are measured 40nm to 50nm in diameter. An envelope and a nucleocapsid are present in the virions of Flaviviridae. The capsid is enveloped with glycoprotein peplomers. The surface projections of the capids are made up of small spikes that are surrounded by a prominent fringe. The capsid has a polyhedral symmetry and it is round. The capsid has an inner core protein. The core is measured 20nm to 30nm in diameter, and it is isometric.

Dengue
Dengue is currently the most important arbovirus, and the chances of getting dengue is higher in Southeast Asia, America, Pacific and Africa. Dengue Fever is not a deadly disease. The deadly dengue viruses are Dengue Haemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS).

Dengue has four different serotypes, and the serotypes are based on neutralisation test. There are DEN-1, DEN-2, DEN-3 and DEN-4. Among the four serotypes, DEN-2 displays the greatest antigenic and genotypic distance. After infection homotypic, it produces a protective immunity.

Dengue fever
An illness that is caused by infection with a virus which is transmitted by the Aedes mosquito is known as Dengue Fever. The virus enters the body’s glands when a mosquito, which carries the virus, bites a person. The virus multiplies in the glands and it enters the bloodstream. Dengue fever is not contagious.

The infections of dengue fever are asymptomatic. Fever, severe headache, retro-orbital pain, nausea and vomiting are the results of an acute infection. Symptoms also include severe muscle and joint pain, lower back pain and flushed face. These symptoms last for two to three days. The patient will then experience heavy sweats when the fever drops. The temperature will rise again after the patient feels better after one day. Rashes and headache will also occur. The symptoms normally last till a maximum of ten days. Patient will feel weak and tired for a maximum of one month afterwards. Dengue Haemorrhagic Fever (DHF) or Dengue Shock Syndrome (DSS) are the severe cases f dengue fever.

Dengue Haemorrhagic Fever / Dengue Shock Syndrome
Dengue Haemorrhagic Fever (DHF) and Dengue Shock Syndrome (DSS) normally occur in individuals that are above the age of 15. The biphasic nature of DHF and DSS are similar to yellow fever. DHF and DSS cause fever, headache and cough. The virus causes the swelling and leaking of blood vessels and petechiae is formed. Petechiae are small purple spots found on the skin. The area, in which the bleeding is worse, is shown by the bruised skin. Severe abdominal pains and vomiting of coffee grounds diathesis are the results of gastrointestinal bleeding. When the blood runs out of clotting factors, haemorrhaging occurs. The damaged blood vessels cannot supply the required blood flow and the oxygen it carries to the body’s tissues, when the damaged blood vessels enlarge. This eventually leads to shock which major organs, such as the heart and the kidneys, can be damaged.

Pathogenesis of DHF and DSS
There are 2 theories – virulent strain theory and antibody enhancement. Based on the virulent strain theory, there are some strains which are more virulent than the others. Among the different strains within the serotypes, there are variations in the sequences. This is shown by the molecular studies. Den-2 has been proven by the early evidence.

The antibody enhancement is the main theory for DHF and DSS. Monocytes or macrophages are the main cell target of DEN. Prior infection can be found in most cases of DHF and DSS, or even infants below the age of one had maternal antibody. Similar enhancement had been proven in monkey experiments.

Overreacting of Immune System and Severe Acute Respiratory Syndrome are the possible causes of DHF and DSS.

Control of Dengue
There is no vaccination for dengue. Hence, dengue can only be minimized and controlled by:

Insecticide
Mosquito screen
Removal of stagnant water

Grading of DHF
Grading of DHF is done by WHO, and there are four grade – Grade I, Grade II, Grade III and Grade IV. Fever that is not specific and with constitutional symptoms and the only haemorrhagic proof being a positive tourniquet test are being classified under Grade I.

Grade II is similar to Grade I, but Grade II has specific haemorrhagic manifestations. Signs of circulatory failure or hypertension are graded under Grade III, and lastly, profound shock with pulse and blood pressure that is undetectable is under Grade IV.

Yellow Fever
Yellow fever is a severe viral infection. Yellow fever is transmitted by mosquito, and it is common is tropical areas. Hepatitis is the classic feature of yellow fever. This is also the reason for the yellowing of skin, known as the jaundice.

Symptoms of Yellow Fever
From infection to developing yellow fever, the incubation period is 3 to 6 days. In acute infection, headache, malaise, nausea, lassitude, muscle ache, flushing of head and neck, conjunctival injection and strawberry tongue are the symptoms. There is a remission after acute yellow fever. In severe cases, fever, vomiting, abdominal pain, dehydration, prostration, haemorrhagic, coffee-ground diathesis, and bleeding from puncture sites of injections and drip needles occur. In addition, jaundice, massive haematemesis, haemoptysis, intra-abdominal bleeding, renal failure, hypertension, and shock also occur. Though virus is not present in the blood, antibody titre is still high,. This implies that the autoimmunity may play an important role.

Severe yellow fever resulted in 20% to 50% death rate. Before full recovery, survivors suffered from extended chronic jaundice. Also, renal failure and hepatic may continue.

Control of Yellow Fever
Yellow fever can be controlled by attenuated vaccine. It can also be controlled and minimized by:

Insecticide
Mosquito screen
Removal of stagnant water

West Nile Fever
West Nile Fever is a virus and it comes from a family, called Flaviviridae. West Nile Fever can be found in the tropical areas, as well as temperate areas. West Nile Fever infects mainly the birds, although it is known to infect humans and animals, such as dogs, cats, horses, domestic rabbits and squirrels. Human is infected through the bite of an infected mosquito. West Nile Fever occurs mainly in individuals who are above the age of 50.

History of West Nile Virus
West Nile Virus originated from Uganda and was found out in 1937. West Nile Virus is common in Africa, West Asia, Europe and Middle East. In 1999, West Nile Virus spread through US, New York, and was epidemic in 2002.

Symptoms of West Nile Fever
West Nile Fever has mild or no symptoms. In mild symptoms, fever, headache, body aches, skin rash and swollen lymph glands are the results of it. In severe symptoms, crossing of blood-brain barrier, encephalitis and meningitis are the results.

Control of West Nile Fever
West Nile Fever can be controlled or minimized by:

Insecticide
Mosquito screen
Removal of stagnant water

References
http://microbewiki.kenyon.edu/index.php/Flaviviridae
http://www.triroc.com/sunnen/images/icosahedral337x446.gif
http://media-files.gather.com/images/d209/d946/d743/d224/d96/f3/full.jpg
http://www.lapublichealth.org/acd/images/WnvCycle.gif
http://images.google.com.sg/imgres?imgurl=http://media-files.gather.com/images/d209/d946/d743/d224/d96/f3/full.jpg&imgrefurl=http://www.gather.com/viewArticle.jsp%3FarticleId%3D281474976828599&usg=__Pquq8Gm5NxduCfmqgS4YmWUOECM=&h=367&w=550&sz=30&hl=en&start=7&um=1&tbnid=vPXPB_pO4_NrTM:&tbnh=89&tbnw=133&prev=/images%3Fq%3Ddengue%2Bfever%26um%3D1%26hl%3Den%26sa%3DN
http://www.netdoctor.co.uk/infections/yellowfever.htm
http://en.wikipedia.org/wiki/West_Nile_virus
http://www.ocvcd.org/images/wnv1_clip_image002.jpg

Poxviridae

2009-01-09T23:55:00.001-08:00

Poxviridae

History of poxviridae
Smallpox has figured in two landmark events in the history of medical science and public health. The first documented modern instance of the use of active immunization to confer immunity against disease occurred in 1796 when the British physician Edward Jenner inoculated a person with cowpox virus (also an Orthopoxvirus) to produce protection against smallpox. The terms vaccine and vaccinate derive from vacca, Latin for “cow.” Nearly two centuries after Jenner's achievement, an international vaccination campaign made smallpox the first major disease to be completely eradicated by human action. Smallpox did not cease to be a potential public health concern, however, since there remained the possibility that smallpox virus taken from undestroyed stocks of the virus could be used by terrorists or a belligerent government as a deadly biological weapon.

How Edward Jenner discovered the vaccination for poxviridae

Edward Jenner was an English country doctor who pioneered vaccination. Jenner's discovery in 1796 that inoculation with cowpox gave immunity to smallpox was an immense medical breakthrough and has saved countless lives.

Jenner worked in a rural community and most of his patients were farmers or worked on farms with cattle. In the 18th century smallpox was a very common disease and was a major cause of death. The main treatment was by a method which had brought success to a Dutch physiologist Jan Ingenhaus and was brought to England in 1721 from Turkey by Lady Mary Wortly Montague. This method involved inoculating healthy people with substances from the pustules of those who had a mild case of the disease, but this often had fatal results.

In 1788 an epidemic of smallpox hit Gloucestershire and during this outbreak Jenner observed that those of his patients who worked with cattle and had come in contact with the much milder disease called cowpox never came down with smallpox. Jenner needed a way of showing that his theory actually worked. He was given the opportunity on the 14 May 1796, when a young milkmaid called Sarah Nelmes came to see him with sores on her hands like blisters. Jenner identified that she had caught cowpox from the cows she handled each day.

Jenner now had the opportunity to obtain the material try out his theories. He carefully extracted some liquid from her sores and then took some liquid from the sores of a patient with mild smallpox. He believed that if he could inject someone with cowpox, the germs from the cowpox would make the body able to defend itself against the dangerous smallpox germs which he would inject later.

He approached a local farmer called Phipps and asked him if he could inoculate his son James against smallpox. He explained to the farmer that if his theory was correct, James would never contract smallpox. Surprisingly, the farmer agreed. He made two small cuts on James's left arm. He then poured the liquid from Sarah's cowpox sores into the open wounds which he bandaged. James went down with cowpox but was not very ill. Six weeks later when James had recovered, Jenner vaccinated him again, this time with the smallpox virus. This was an extremely dangerous experiment. If James lived Jenner would have found a way of preventing smallpox. If James developed smallpox and died he would be a murderer. To Jenner's relief James did not catch smallpox. His experiment had worked.

In 1798 after carrying out further successful tests, he published his findings: An Inquiry into the Causes and Effects of the Variolae Vaccinae, a Disease Known by the Name of Cow Pox. Jenner called his idea " vaccination" from the word vaccinia which is latin for cowpox. Jenner also introduced the term virus.

Classification and Taxonomy

Pox viruses are the largest and most complex of all viruses. In fact, they are large enough, with a virion size of 220-350 x 115-260 nm, to be seen under a light microscope. They infect a wide range of hosts, and are divided into two subfamilies: Chordopoxvirinae and Entomopoxviridae. All human pox viruses are in the Chordopoxovirinae subfamily, and most of them belong to either the Orthopoxvirus (variola, vaccinia, cow pox) or the Parapoxvirus (Orf virus) genus. The chicken pox virus does not belong to this family. It is a herpesvirus.

genome: double-stranded DNA, monopartite, linear, noninfectious; encodes over 100 genes, including DNA dependent RNA transcripase

morphology: "complex", ovoid or brick-shaped nucleocapsid
envelope: orthopox are enveloped, parapox are not
replication: takes place in cytoplasm
host range: host range varies by specific virus; zoonoses is common, but small pox only infects humans
oncogenicity: may cause benign tumors

Replication
Occurs in the cytoplasm - the virus is sufficiently complex to have acquired all the functions necessary for genome replication. There is some contribution from the cell but it is not clear what this is - poxvirus gene expression and genome replication occur in enucleated cells, but maturation is blocked.

Characteristics and Prevention

The virus is commonly picked up by inhaling droplets from the mouth and nose of an infected person. It may also be transmitted through contact with material from the skin lesions that appear on an infected individual.

The incubation period for smallpox is between seven and 17 days following exposure, with the average being 12 days. The following are the most common symptoms of smallpox. However, each individual may experience symptoms differently. Symptoms may include:

initial symptoms:
- high fever
- fatigue
- head and back aches
a distinct rash that presents with the following characteristics, most often, two to three days after exposure:
- a rash starts with flat, red lesions, usually on the face, arms, and legs
- lesions become pus-filled and start to crust over early in the second week
- scabs form which then separate and fall off after three to four weeks

A person with smallpox is infectious from the first appearance of fever until all the scabs fall off. There are two chief forms of the disease, variola major and variola minor, and they result in similar lesions. Variola minor follows a milder course, with a fatality rate under 1 percent. Variola major kills an estimated 30 percent of those infected.

There is no specific treatment for smallpox. Administering smallpox vaccine to people soon after they are exposed to the virus, however, may prevent the disease from developing or at least ameliorate its effects. Researchers are exploring the potential use of antiviral drugs against smallpox.

Eradiction of Poxviridae
In 1967 the WHO launched a worldwide vaccination campaign against smallpox; at the time, some 10 to 15 million cases of the disease occurred each year, with more than 2 million deaths. By mid-1975, when all of India was declared free of smallpox, only a few cases were left in two countries, Bangladesh and Ethiopia. In 1979, after two years without a reported case of naturally occurring smallpox, a commission of scientists certified the disappearance of the disease from the earth. The WHO subsequently recommended that countries stop vaccinating against the disease and that laboratory stocks of the virus be destroyed. Underlining the importance of this last request was the death of an English woman in 1979 from smallpox contracted from a laboratory working with the virus. June 1999 was set as the deadline for the destruction of the two known remaining stocks of smallpox virus, kept in guarded freezers at the Centers for Disease Control and Prevention in Atlanta, Ga., and the Russian State Research Center of Virology and Biotechnology in Koltsovo, near Novosibirsk, Siberia. Some scientists, however, argued that the two official stocks should be preserved for research on the virus and on new vaccines and antiviral agents, a position that gained added force from the possibility that additional samples of the virus might exist elsewhere. The WHO accordingly changed the target date for destruction of the virus to 2002. In May 2002, reflecting heightened concerns over the possible use of bioweapons by political extremists, the WHO again put off the elimination of the official stocks.

Vaccination was almost universally adopted worldwide around 1800, but it took a major commitment from the WHO in 1965 to achieve eradication.Eradication of smallpox was possible for 3 reasons:

There is no other reservoir for VV but man.
VV causes only acute infections, from which the infected person either:
- Dies
- Recovers with life-long immunity.
Vaccinia virus is an effective immunogen.

Smallpox as Biological Weapon
Smallpox was used as a biological weapon by Europeans in the Americas, whose indigenous inhabitants were particularly susceptible to the variola virus, since they lacked a history of exposure to it. In the 16th century the Spanish conquistador Francisco Pizarro reputedly gave smallpox-contaminated clothing to South American natives. In the 18th-century French and Indian War in North America, British commanders gave Native Americans blankets and other goods that had been used by smallpox victims; the ensuing death rates reportedly reached as high as 50 percent.
More recently, the virus has been identified as a particularly promising choice for a biological weapon for a variety of reasons, among them: it can be readily produced in a stable aerosol form, which facilitates distribution; fewer than one hundred virus particles may suffice to cause infection; the disease has a relatively short incubation period and is often fatal; and because smallpox was considered eradicated, huge numbers of people have not been vaccinated against it. Smallpox was among the diseases investigated by the Japanese Army's secret germ-warfare operation called Unit 731 that conducted tests on prisoners in Mongolia and China prior to and during World War II. The Soviet Union reportedly began large-scale production of smallpox virus around 1980, and it is possible that other countries have established secret smallpox stockpiles.

Incidents of mail-transmitted anthrax in late 2001 sharpened concern among public health specialists over the potential use of the smallpox virus as a terrorist weapon. The U.S. government consequently began vaccinating certain members of the armed forces against smallpox, launched a program to offer smallpox vaccinations to health-care providers and other individuals involved in the initial emergency response to an outbreak of the disease, and stockpiled enough vaccine to immunize the entire U.S. population in the event a smallpox emergency occurred.

References
http://www.stanford.edu/group/virus/pox/pox.html#Introduction
http://www.history.com/encyclopedia.do?vendorId=FWNE.fw..sm129900.a#FWNE.fw..sm129900.a
http://www.zephyrus.co.uk/edwardjenner.html
http://www.edward-jenner.com/vaccinations.html
http://freemasonry.bcy.ca/biography/jenner_e/jenner_e.html
http://www.microbiologybytes.com/virology/Poxviruses.html
http://www.umm.edu/bioterrorism/smallpox.htm
http://en.wikipedia.org/wiki/Smallpox

Methods of Study of Viruses

2009-01-09T23:54:00.004-08:00

Methods of Study of Viruses

Study of Viruses
The study of viruses is known as virology. Viruses can be studied in two ways. The first way is through isolation and cultivation, and the second way through detection, identification and diagnosis. For isolation and cultivation, animals, plants, chick embryo and tissue culture are used. For detection, identification and diagnosis, there are several methods. These methods include tissue culture methods, physical methods, serological methods, immunological methods, and others and molecular biology.

Isolation and Cultivation
Animals and Chick Embryo
Animals and chick embryo were the first method that was used to cultivate virus. This method is rarely used as it is not convenient. However, when preparing for bulk virus, (e.g. antigen or vaccine production) the usage of chick embryo is useful.

Inoculation of laboratory animals are used when some viruses can only be isolated using this method. Normally, mice are the laboratory animals that are used. Signs of disease or death in animals are observed after inoculation. By testing for neutralization of their pathogenicity for animals by standard sera, the viruses can be identified.

Plants
Tobacco mosaic virus can be found on plants. Virus numbers can be determined by the virus plaques on leaves.

Tissue Culture
The growth of tissue and/or cells that come apart from the organism is known as the tissue culture. There are three types of cell tissue culture – cells grown in vitro, primary cell culture and continuous cell line.

Continuous cell line is obtained from primary cell lines. Continuous cell line can be polyploidy or multiploid.

Detection, Identification and Diagnosis
Tissue Culture Methods
There are two types of tissue culture methods. They are the cytopathic effect (CPE) and the plaque assay.

Cytopathic Effect (CPE)
The degenerative changes of cells that are linked with the multiplication of certain viruses are known as the cytopathic effect (CPE). When in tissue culture, an overlayer of agar restricts the spread of virus. This causes the formation of plaque caused by the cytopathic effect. The examination of the characteristics of cytopathic effect produced on different cell sheets can be used to identify viral infection. However, this technique is not an efficient one, and not all viruses will grow on cell sheets.

Plaque Assay
In 1952, Renato Dulbecco was the first to discover this method. Originally, plaque assay is a virological assay which was introduced to count and measure the infectivity of bacteriaphages. Plaque assay is used to notice and take note of the death of cell in the infected cell culture. When one cell is infected by one virus, it spreads to the surrounding cells. Plaque assay is more accurate when it is at lower concentration.

Plaque assay is very time-consuming and is an easy technique. Plaque assay is only effective for viruses that infect monolayer cells, and for viruses that break down cells. One plaque is formed from one virus on the monolayer. This is the principle of plaque assay.
Plaque assay is used to count only viruses that are capable of multiplying. The culture conditions must be known for virus that is used to study. Samples with very low virus counts use this method. Incubation of virus requires time.

Physical Methods
There are three types of physical methods:
· X-ray crystallography
· Electron microscopy
· Ultracentrifugation
Under electron microscopy, there are transmission electron microscope, scanning electron microscope and STEM. As for ultracentrifugation, one example is the purification.

X-Ray Crystallography
A method that is used to find out the arrangement of atoms within a crystal is known as X-ray crystallography. A beam of X-rays scatters into many directions when it strikes a crystal. According to the angles and intensities of these scattered beams, a three dimensional picture of the density of electrons within a crystal is produced from a crystallography. The mean positions of the atoms in the crystal, their chemical bonding, their disorder and other information can be determined from the electron density.

X-ray Diffraction Patterns

Electron Microscope
Transmission Electron Microscope
A microscopy method in which a beam of electrons transmit through an ultra thin specimen and interacts with the specimen as they pass through is known as the transmission electron microscopy (TEM). The interaction of the electrons that transmit through the specimen forms an image. The objective lens enlarges and focuses the image onto a fluorescent screen on a layer of photographic film. Fluorescent screen is one of the imaging devices. A sensor can also be used to detect the image. An example of such sensor is the CCD camera.

Principle features of light and electron microscopes

Scanning Electron Microscope
An electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern is known as the scanning electron microscope (SEM). Signals that have information about the sample’s surface topography, composition and other properties such as the ability to conduct electricity are produced when electrons interact with the atoms that make up the sample.

Ultracentrifugation
Ultracentrifugation is a process in which a centrifuge spins a rotor at extremely high speeds. Ultracentrifuge has the ability to produce acceleration up to a maximum of 1,000,000 (9,800 km/s²). Purification is one example of ultracentrifugation.

Serological / Immunological Methods
Immunological techniques are used to diagnose virus diseases. This is done so by demonstrating an antigen-antibody reaction to reveal evidence of virus infection. Virus infection can be shown by:

Serology; where development of antibody to the virus at the time of or just after symptoms of disease.
Virus being present in the blood of the patients or other tissues.

There are several serological and immunological methods and these methods include:

Haemagglutination Assay (HA)
Haemagglutination Inhibition (HI)
Virus neutralisation
Complement fixation
Immunostaining
- Immunofluorescence
- Immuno-Gold Electron Microscope
Immunoprecipitation / Immunoblot
ELISA

Haemagglutination Assay (HA)
A quantitative of viruses by haemagglutination is known as haemagglutination assay (HA). Haemagglutination is a particular form a agglutination which involves the participation of red blood cells (RBC).

A type of lattice will be formed by red blood cells when viral families with surface or enveloped proteins stick to humans’ or animals’ red blood cells and bind to its N-acetylneuraminic acid.

This method is relatively fast and easy and large amounts of samples use such methods. This method is carried out in the presence of antibody. The type of virus will require different conditions. For example, at certain pH values, some viruses bind RBCs while others bind RBCs at certain ionic strengths.

Haemagglutination Inhibition (HI)
The agglutination of red blood cells by the haemagglutinating viruses are blocked by the antiviral antibody.

Virus Neutralisation
In the case of cell cultures and laboratories animals, antibody prevents or lowers the viral infectivity. This technique is difficult and slow as it requires long and hard work. However, this method is sometimes indispensable.

Complement fixation
Complement fixation test is an immunological medical test, and is used to discover if certain specific antigen or antibody is present in the serum of a patient. This method is widely used to distinguish and find out the cause of infections. It is particularly used in microorganisms that are difficult to identify by culture methods. However, this method is no longer in use in clinical diagnosis as it has already been replaced by serological methods such as ELISA and by DNA-based methods of pathogen detection, especially the polymerase chain reaction (PCR).

In the technique, complement is fixed or used up when antigen reacts with antibody. Complement can be found in guinea pig serum. When red blood cells are added with anti-red-cell antibody, the red cells undergo lyses due to the presence of complement. A positive reaction is indicated by the absence of haemolysis.

Immunostaining
Immunofluorescence
Labeling of antibodies or antigens with fluorescent dyes is known as immunofluoresence. Visualization of the subcellular distribution of biomolecules of interest uses this method. Fluorescence microscope is used to study the immunofluorescent-labelled tissue sections or cultures.

Immuno-gold Electron Microscope
Immuno-gold electron microscope has the same principle as immunofluorescence. The gold particles, measured with a nanometer, are bind to the antibodies. To localize specific proteins or antigens, it is viewed under the electron microscope.

Immunoprecipitation
Immunoprecipitation is a method in which a protein antigen that is precipitated out of solution using an antibody that specifically attaches to that specific protein. This method can be applied when isolating and concentrating a specific protein from a sample that contains many thousands of proteins not of the same kind. Antibody must be coupled to a solid substrate at the same point in the procedure in the technique.

Immunoblot
Immunoblot is also known as Western Blot, and is an analytical method. Detection of particular proteins in a given sample of tissue homogenate or extract uses this method. In this technique, denatured or native proteins, by length of the polypeptide or by 3-D structure of the protein, are separated by the means of gel electrophoresis. After the proteins are transferred to a nitrocellulose membrane, the proteins are then detected using antibodies. Each protein is attached to an antibody, and an antibody is used to detect antigen. A sensitive indicator is used to label an antibody, and there will be a colour reaction with streptavidin.

ELISA
ELISA is also known as the Enzyme-Linked ImmunoSorbent Assay. In immunology, this technique is used to detect whether an antibody or an antigen is present in a sample. The antigen is detected by antibody and an indicator, such as horse radish peroxidise, is used to label the antibody. A colour reaction is shown. In this method, one molecule must be binded to a solid surface.

Molecular Virology
Molecular virology is the study of the organisation of genome, expression of viral genome, replication of genome and the progeny virus.

Molecular Biology and Others
PAGE or SDS PAGE, Western blot, protein sequencing and X-ray crystallography are used to analyse viral proteins. Agarose gels, restriction analysis, sequencing, southern blot, northern blot, PCR o RT-PCR are used to analyse viral genome.

SDS PAGE
SDS-PAGE, sodium dodecyl sulfate polyacrylamide gel electrophoresis, is a method that is commonly used in biochemistry, forensics, genetics and molecular biology. This method is used in the separation of proteins, based on their electrophoretic mobility.

Protein Sequencing
In every cell, there are proteins present. Proteins play an important role in all biological processes. Protein structure is very complicated; hence, to find out a protein structure, first protein sequencing is involved. The first protein sequencing determines the sequences of the constituent peptides of the amino acids and also the conformation it adopts and if it is complex with any non-peptide molecules. Mass spectrometry and Edman degradation reaction are the two major direct methods of proteins sequencing.

Agarose Gels
A technique that is used in biochemistry and molecular to separate DNA or RNA molecules by size is known as the Agarose Gel electrophoresis. To achieve the separation, nucleic acid molecules, with a negative charge, are moved through an agarose mixture with an electrophoresis. Longer molecules move slower and migrate less far than the shorter ones.

Restriction Analysis
A restriction enzyme cuts double-stranded DNA or single-stranded DNA at a particular recognition nucleotide sequences. These particular recognition nucleotide sequences are called the restriction sites.

These enzymes are present bacteria and archaea. These enzymes evolved to give a defense mechanism against viruses that invade them. Inside a bacterial host, the restriction enzymes cut up irrelevant DNA in restriction process. A modification enzyme, methylase, methylates a host DNA to protect it against the activity of restriction enzyme. Restriction modification system is formed from these two processes.

Sequencing
In genetics and biochemistry, seqeuncing refers to the finding of the primary structure or sequence of an unbranched biopolymer. The results of sequencing in a symbolic linear depiction are the sequence which briefly summarizes most of the atomic-level structure of the sequenced molecule. DNA sequencing is one example of sequencing.

Southern Blot
A method that is used in molecular biology to check if a DNA sequence is present in a DNA sample is known as the Southern blot. For size separation of DNA with techniques to transfer the size-separated DNA to filter membrane for probe hybridization, southern blotting is being combined with agarose gel electrophoresis.

Northern blot
A method that is used in molecular biology research to investigate and observe the expression of gene is known as the northern blot. The difference between Northern blot and Southern blot is that Northern blot uses RNA while Southern blot uses DNA. In Northern blot, RNA is analyzed. However, both the Northern blot and the Southern blot use electrophoresis and detection with a hybridization probe.

PCR
PCR refers to polymerase chain reaction. It is a method which is commonly used in molecular biology. The generated DNA is used as a template for replication, as PCR progresses. The DNA template is exponentially amplified when a chain reaction sets in. With PCR, a single or few copies of a piece of DNA across several orders of magnitude can be amplified. Millions or more copies of the DNA piece are generated. A wide array of genetic manipulations is performed by PCR as it can be modified extensively.

Procedures of PCR
PCR normally has a series of 20 to 40 repeated temperature changes and it is known as cycles. Each cycle have 2 to 3 discrete temperature steps. At high temperature, more than 90°C, the cycling is often preceded by a single temperature step. Another single temperature step is followed at the end for the extension of final product or brief storage. The temperatures used and the length of time are dependent on a variety of parameters. These involve the enzyme used for DNA synthesis, concentration of divalent ions and dNTPs in the reaction, and the melting temperature of the primers.

There are six steps in PCR. The six steps are the initialization step, denaturation step, annealing step, elongation step, final elongation step and final hold.

Initialization step: This step involves the heating of reaction to a temperature of 94-96°C and is held for 1 to 9 minutes. However, temperature of 98°C is applied when extremely thermostable polymerases are used. This step only applies to DNA polymerases that need heat activation by hot-start PCR.

Denaturation step: This step is the first regular cycling event and involves the heating of reaction to 94-98°C for 20-30 seconds. DNA template and primers melt as the hydrogen bonds between the complementary bases of the DNA strands are disrupted. Single strands of DNA are then yielded.

Annealing step: This step involves the annealing of the primers to single stranded DNA template, at the temperature of 50 to 65°C for 20 to 40 seconds. When the primer sequence very closely matches the template sequence, stable DNA-DNA hydrogen bonds are formed. DNA synthesis starts when the polymerase attaches to the primer-template hybrid.

Elongated step: Temperature involved in this step is dependent on the DNA polymerase. At this step, a new DNA strand complementary to the DNA template strand is synthesized by the DNA polymerase. This is done so by adding dNTPs that is complementary to the DNA direction. The time that is extended is dependent on both the DNA polymerase that is being used and the legth of the DNA fragment that is to be amplified.

Final elongation step: This step is normally operated at a temperature of 70 to74°C for 5 to 15 minutes after the last PCR cycle. This is to make sure that the remaining single-stranded DNA is extended fully.

Final hold step: When at 4 to15°C, this step, for an indefinite time, can be used for a short-term storage of the reaction.

RT-PCR
RT-PCR refers to reverse transcription polymerase chain reaction. It is used in molecular biology and is a laboratory method for amplifying a defined piece of RNA molecule. DNA complement is formed when the RNA strand is first reverse transcribed. Amplification of the resulting DNA is followed, using polymerase chain reaction.

Viruses in Bacteria, Plant and Fungi

2009-01-09T23:54:00.003-08:00

Viruses in Bacteria, Plant and Fungi

Introduction to virus
Viruses are too small to be seen by the naked eye. They can't multiply on their own, so they have to invade a 'host' cell and take over its machinery in order to be able to make more virus particles.

Viruses consist of genetic materials (DNA or RNA) surrounded by a protective coat of protein. They are capable of latching onto cells and getting inside them.

The cells of the mucous membranes, such as those lining the respiratory passages that we breathe through, are particularly open to virus attacks because they are not covered by protective skin.

Viruses in bacteria
It's easy to mix these up since compared to us, both are very small.

Bacteria and viruses causes many of the diseases we're familiar with, people often confuse these two microbes. But viruses are as different from bacteria as they differ greatly in size. The biggest viruses are only as large as the tiniest bacteria. Another difference is their structure. Bacteria are complex compared to viruses.

A bacterium has a rigid cell wall and a thin, rubbery cell membrane surrounding the fluid, or cytoplasm, inside the cell. A bacterium contains all of the genetic information needed to make copies of itself—its DNA—in a structure called a chromosome. In addition, it may have extra loose bits of DNA called plasmids floating in the cytoplasm. Bacteria also have ribosomes, tools necessary for copying DNA so bacteria can reproduce. Some have threadlike structures called flagella that they use to move.

T4 bacteriophage is a virus that looks like an alien landing pod with 6 legs, the bacteria attatches to the surface of the much larger bacteria Escherichia coli (E.coli). once attatched, the bacteriophate injects DNA into the bacterium. DNA then instructs the produce masses of new viruses. And as many are produced, E.coli bursts.

Eschericia coli + coliphage T4

Viruses in plants

Plants are susceptible to viral diseases, just like any living systems. Plant viruses are obligate intracellular parasites that do not have the molecular machinery to replicate without the host. Plant viruses are pathogenic to higher plants. Virus cause many plant diseases and are responsible for huge losses in crop production and quality in all parts of the world.

Classification of plant virus
There are 6 major groups, based on the nature of the genome:

Double-stranded DNA (dsDNA): there are no plant viruses in this group, which is defined to include only those viruses that replicate without an RNA intermediate (see Reverse-transcribing viruses, below). It includes those viruses with the largest known genomes (up to about 400,000 base pairs) and there is only one genome component, which may be linear or circular. Well-known viruses in this group include the herpes and pox viruses.
Single-stranded DNA (ssDNA): there are two families of plant viruses in this group and both of these have small circular genome components, often with two or more segments.
Reverse-transcribing viruses: these have dsDNA or ssRNA genomes and their replication includes the synthesis of DNA from RNA by the enzyme reverse transcriptase; many integrate into their host genomes. The group includes the retroviruses, of which Human immunodeficiency virus (HIV), the cause of AIDS, is a member. There is a single family of plant viruses in this group and this is characterised by a single component of circular dsDNA, the replication of which is via an RNA intermediate.
Double-stranded RNA (dsRNA): some plant viruses and many of the mycoviruses are included in this group.
Negative sense single-stranded RNA (ssRNA-): in this group, some or all of the genes are translated into protein from an RNA strand complementary to that of the genome (as packaged in the virus particle). There are some plant viruses in this group and it also includes the viruses that cause measles, influenza and rabies.
Positive sense single-stranded RNA (ssRNA+): the majority of plant viruses are included in this group. It also includes the SARS coronavirus and many other viruses that cause respiratory diseases (including the "common cold"), and the causal agents of polio and foot-and-mouth disease.

And within each of these groups, there are many different characteristics used to classify virus into families, genera and speces, by the combination of characters used. Some of them are:

Particle morphology: the shape and size of particles as seen under the electron microscope.
Genome properties: this includes the number of genome components and the translation strategy. Where genome sequences have been determined, the relatedness of different sequences is often an important factor in discriminating between species.
Biological properties: this may include the type of host and also the mode of transmission.
Serological properties: the relatedness (or otherwise) of the virion protein(s).

The particle morphology is one where amongst plant viruses, the most frequently encountered shapes are as follows:

Isometric: apparently spherical and (depending on the species) from about 18nm in diameter upwards. The example here shows Tobacco necrosis virus, genus Necrovirus with particles 26 nm in diameter.

Rod-shaped: about 20-25 nm in diameter and from about 100 to 300 nm long. These appear rigid and often have a clear central canal (depending on the staining method used). Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Tobacco mosaic virus, genus Tobamovirus with particles 300 nm long.

Filamentous: usually about 12 nm in diameter and more flexuous than the rod-shaped particles. They can be up to 1000 nm long, or even longer in some instances. Some viruses have two or more different lengths of particle and these contain different genome components. The example here shows Potato virus Y, genus Potyvirus with particles 740 nm long.

Geminate: twinned isometric particles about 30 x 18 nm. These particles are diagnostic for viruses in the family Geminiviridae which are widespread in many crops especially in tropical regions. The example here shows Maize streak virus, genus Mastrevirus.

Bacilliform: Short round-ended rods. These come in various forms up to about 30 nm wide and 300 nm long. The example here shows Cocoa swollen shoot virus, genus Badnavirus with particles 28 x 130 nm.

Genome properties of plant virus

Nature of the genome: circular, as in all known plant DNA viruses, or linear.
Number of genome components: This varies from a single component, example in the genera Potyvirus and Tobamovirus, to 11, in some members of the genus Nanovirus. Individual components vary in size from about 1kb Nanovirus components to about 20 kb in the genus Closterovirus.
Number of genes: These might vary considerably. Most plant viruses have at least 3 genes: 1, or more, concerned with replication of the nucleic acid, 1, or more, concerned with cell-to-cell movement of the virus and 1, or more, encoding a structural protein that is assembled into the virus particle usually called the "coat" or "capsid" protein. There may also be additional genes that have a regulatory function or which are required for transmission between plants association with a vector.
Translation strategy: A variety of strategies are employed to translate the genes from the genome components either directly or via mRNA intermediates and, in some cases, to permit different amounts of protein to be produced from the different genes. These are summarised for each genus in the genus description pages but 3 examples here serve to illustrate some of the variety:
- Genus Potyvirus: in this very large genus, there is one ssRNA component that encodes one large (c. 350 kDa) polyprotein. This is cleaved by 3 different proteases (all encoded by the virus itself) into 10 different mature proteins. The two proteins at the C-terminus of the polyprotein are respectively an RNA-dependent RNA polymerase (Nib) involved in replication of the virus and the single coat protein (CP). Many of the proteins have multiple functions. The genome organisation of a typical member is shown here, indicating the 10 mature proteins and the nine cleavage sites (arrowed).

- Genus Furovirus: in this genus there are two ssRNA components. The 5'-proximal gene on each RNA is translated directly from the genomic RNA: on RNA1 (the larger RNA component) this gene encodes a replication protein and on RNA2 it is the coat protein. The stop codons of both of these genes are "leaky" and in a small percentage of cases, translation continues to produce a larger ("readthrough") protein. On RNA1, the replication protein is extended to include an RNA-dependent RNA polymerase (RdRp) while the readthrough region of the coat protein is probably required for particle assembly and for transmission by the plasmodiophorid vector. There is a further (3'-proximal) gene on each of the RNAs and these are translated from shorter RNA molecules transcribed from the 3'-end of the genomic RNA ("subgenomic" mRNAs). That from RNA1 is a cell-to-cell movement protein (MP) that enables the virus to move between adjacent plant cells via the plasmodesmata while the function of the product from RNA2 is uncertain but may involve supression of the host plant defence reaction. The genome organisation of a typical member is shown here:

- Genus Fijivirus: in this genus there are 10 components of dsRNA. Most of the components encode a single protein and at least 3 of these are structural proteins assembled into the complex virion.
Genome relatedness: the degree of nucleotide identity (or amino acid identity in the protein sequence) between sequences is often used to examine the relationship between different viruses or isolates. For example, recent studies in the genus Carlavirus show that when different species are compared, they have less than 73% nucleotide identity (or 80% amino acid identity) in their coat proteins.

Biological properties

In some families, the type of host is a useful feature for classification. For example, in the family Reoviridae, there are currently 3 genera with plant-infecting members (Fijivirus, Oryzavirus, Phytoreovirus), 1 genus of mycoviruses (Mycoreovirus), 1 genus containing viruses of fish and cephalopods (Aquareovirus), two genera that are restricted to insects (Cypovirus and Entomoreovirus) and 5 genera of vertebrate viruses that sometimes also infect insects.
The mode of transmission is also a useful characteristic of some groups of plant viruses. For example in the family Potyviridae, members of the largest genus (Potyvirus) are transmitted by aphids, while viruses in the genera Rymovirus and Tritimovirus are transmitted by mites of the genus Abacarus or Aceria respectively, those in the genus Ipomovirus are transmitted by whiteflies and those in the genus Bymovirus by plasmodiphorids (root-infecting parasites once considered to be fungi but probably more closely related to protists).

Serological properties
Many viruses are good antigens (elicit strong antibody production when purified preparations are injected into a mammal) and this property has been widely exploited to produce specific antibodies that can be used for virus detection and for examining relationships between viruses. Earlier studies used agar diffusion plates but in the last 20 years these have been largely superseded by ELISA (enzyme-linked immunosorbent assay) procedures. Although serological properties are still important, their significance in taxonomy has declined to some extent now that nucleotide sequence data are available.

Symptoms of plant virus
There are a range of symptoms depending on the disease but often there is leaf yellowing, either of the whole leaf or in a pattern of stripes or blotches, leaf distortion, example curling, and other growth distortions like for example stunting of the whole plant, abnormalities in flower or fruit formation.

Below are some of the examples of viruses in plants:

Pepper mild mottle virus

Yellow mosaic symptoms on lettuce caused by Lettuce mosaic virus

Yellow vein-banding symptoms on grapevine caused by Grapevine fanleaf virus

Fruit distortion on eggplant fruit caused by Tomato bushy stunt virus.
(A healthy fruit is shown on the left.)

Bark scaling caused by Citrus psorosis virus.

Sometimes the virus is restricted to certain parts of the plant, example the vascular system, the discrete spots on the leaf, but in others it spreads throughout the whole plant causing a systemic infection. Infection does not always result in visible symptoms, as witnessed by names such as Carnation latent virus and Lily symptomless virus, both members of the genus Carlavirus. Occasionally, virus infection can result in symptoms of ornamental value, such as 'breaking' of tulips or variegation of Abutilon.

Causes of plant viruses
Some animal and human viruses are spread through aerosols as they have the ‘machiney’ to enter the animal cells directly by fusing with the cell membrane, like those in the lining or gut.

In contrast, plant cells have a robust cell wall and viruses cannot penetrate them unaided. Most plant viruses are therefore transmitted by a vector organism that feeds on the plant or, in some diseases, are introduced through wounds made, for example, during cultural operations, take pruning for example. A small number of viruses can be transmitted through pollen to the seed (e.g. Barley stripe mosaic virus, genus Hordeivirus) while many that cause systemic infections accumulate in vegetatively-propagated crops. The major vectors of plant viruses are:

Insects, this forms the largest and most significant vector group and particularly includes:
# Aphids: transmit viruses from many different genera, including Potyvirus, Cucumovirus and Luteovirus.The picture shows the green peach aphid Myzus persicae, the vector of many plant viruses, including Potato virus Y.

# Whiteflies: transmit viruses from several genera but particularly those in the genus Begomovirus. The picture shows Bemisia tabaci, the vector of many viruses including Tomato yellow leaf curl virus and Lettuce infectious yellows virus.

# Hoppers: transmit viruses from several genera, including those in the families Rhabdoviridae and Reoviridae. The picture shows Micrutalis malleifera, the treehopper vector of Tomato pseudo-curly top virus.

# Thrips: transmit viruses in the genus Tospovirus. The picture shows Frankinella occidentalis, the western flower thrips that is a major vector of Tomato spotted wilt virus.

# Beetles: transmit viruses from several genera, including Comovirus and Sobemovirus
Virus-vector relationships are of several types:
- The association occurs within the feeding apparatus of the insect, where the virus can be rapidly adsorbed and then released into a different plant cell. The feeding insect looses the virus rapidly when feeding on a non-infected plant. Such a relationship is termed "non-persistent". The best studied examples are of potyvirus transmission by aphids.
- On the other hand, the virus is taken up into the vector, circulates within the vector body and is released through the salivary glands. The vector needs to feed on an infected plant for much longer and there is an interval (perhaps several hours) before it can transmit. Once it becomes viruliferous, the vector will remain so for many days and such a relationship is therefore termed "persistent" or "circulative". The best studied examples are of luteovirus transmission by aphids. In some examples of this type like some hoppers and thrips, the virus multiplies within the vector and this is termed "propagative".
# Nematodes: these are root-feeding parasites, some of which transmit viruses in the genera Nepovirus and Tobravirus. The picture shows an adult female of Paratrichodorus pachydermus, the vector of Tobacco rattle virus.

# Plasmodiophorids: these are root-infecting obligate parasites traditionally regarded as fungi but now known to be more closely related to protists. They transmit viruses in the genera Benyvirus, Bymovirus, Furovirus, Pecluvirus and Pomovirus. The picture shows Polymyxa graminis, the vector of several cereal viruses including Barley yellow mosaic virus, growing within a barley root cell.

# Mites: these transmit viruses in the genera Rymovirus and Tritimovirus. The picture shows Aceria tosichella, the vector of Wheat streak mosaic virus.

Prevention of plant virus
Plants virus cannot only be directly controlled by chemical application, in fact, a major means of control is needed, depending on the disease, and they includes:

Chemical or biological control of the vector (the organism transmitting the disease, often an insect): this can be very effective where the vectors need to feed for some time on a crop before the virus is transmitted but are of much less value where transmission occurs very rapidly and may already have taken place before the vector succumbs to the pesticide.
Growing resistant crop varieties: in some crops and for some viruses there are highly effective sources of resistance that plant breeders have been using for many years. However, no such "natural" resistance has been identified for many others. Transgenic resistance has shown considerable promise for many plant-virus combinations following the discovery that the incorporation of part of the virus genome into the host plant may confer a substantial degree of resistance. For example, the use of this approach in Hawaii to control Papaya ringspot virus has been credited with saving the local papaya industry. However, this technology is controversial, particularly in Europe, and the extent to which it will be used commercially is currently uncertain.
Use of virus-free planting material: in vegetatively propagated crops (e.g. potatoes, many fruit crops) and where viruses are transmitted through seed major efforts are made through breeding, certification schemes etc., to ensure that the planting material is virus-free.
Exclusion: the prevention of disease establishment in areas where it does not yet occur. This is a major objective of plant quarantine procedures throughout the world as well as more local schemes.

Virus in fungi

Introduction to bacteria in fungi
Viruses and other genetic elements are common inhabitants of fungi. As viruses have a small genome, increased virulence resulting from a chance mutation is likely. Some of the principles of this page apply to all microbes associated with the host, and some are specific to viruses.

The viruses that have been detected in fungi are all thought to be double stranded RNA. A protein coat may envelope the virion (nucleic acid). Further, some encapsulated virions are wrapped in a membrane of host origin. The observation of a single structural type, must be viewed in recognition that current searches for viruses in fungi assume a structure consisting of double stranded RNA. Other forms may be ignored. Further, some potential viruses might also be considered as transmissible genetic elements, and given a different name. Care must be taken when reading the literature on fungal viruses.

Viruses are thought to be ubiquitous in fungi. Estimates of their presence suggest that 30% of species may be colonised. Most viruses have not been associated with any form of noticeable pathology, or expression of phenotypic change, and are thought to be benign (see below for some exceptions). All viruses have been found within fungi and their existence outside the fungal host is unknown. The lack of an extracellular phase has implications for transmission.

Transmission
In those few associations where transmission has been studied, the virus is transmitted vertically or horizontally, or both

Vertical transmission refers to the movement of virions into the reproductive units of the fungus, to then be expressed in the next generation. The virions may be carried in the spores. Following germination of the spore, the virus appears in the next generation.

Horizontal transmission is where fusion between compatible hyphae results in the movement of cytoplasm containing the virions to the uninfested mycelium. The importance of vegetative compatibility cannot be overemphasised. Compatibility determines the potential for transmission, and is thus enormously important in the ecology of the virus, especially when infection is associated with disease.

Disease of mushrooms
Cultivated mushrooms have been examined for viruses especially after reductions in productivity. Although several different viruses appear to be pathogens, La France disease has been most widely studied.

The presence of an isometric particle has been consistently associated with the disease. Infected cultures grow more slowly. Basidiocarps of infected tissue appear earlier, they are smaller and commonly deformed. Total spore production is reduced though spores appear sooner. The disease is highly infectious, and rapid spread through a production system, and between adjacent farms, is possible.

The virus can be spread vertically and horizontally. Vertical spread is associated with the early appearance and release of spores from infected mushrooms. These spores anastomose with uncontaminated hyphae and transfer the virus. The virus multiplies rapidly and spreads through the contiguous mycelia.

Horizontal transmission means that only a small amount of contaminated mycelia mixed in with spawn may result in the entire bed becoming infected rapidly. Hyphae grow rapidly and establish anastomoses with compatible hyphae (most likely all the bed).

Transmission between farms is possible if they are using fungi with compatible hyphae. This is the case when farmers are using a single variety. Use of different varieties reduces the chance of transmission. However, even unrelated varieties may have a low level of compatibility, thereby enabling the occasional anastomosis and transmission of the virus. Complete incompatibility is uncommon, so virus transmission remains a potential problem for all mushroom farms.

Killer yeast
Killer Yeasts are strains that are infected with one of a group of viruses that produce a toxic protein that kills closely related but uninfected yeasts. The yeasts belong to a wide diversity of fungi, including the bread-making and alcohol-producing Saccharomyces cereviseae and the maize smut Ustilago maydis. Killer yeasts are tolerant of the toxins they produce, but may be susceptible to toxins of different Killer yeasts. The genes that confer immunity and toxin production appear to be on the virus genome. However, replication and other functional genes of the virus may be on the host nucleus.

The fitness of Killer yeasts in natural habitats is partly attributed to their toxin production. The toxin apparently regulates competition and enables the host cell to proliferate.

Killer yeasts are commonly found on fruits and flowers. They are commonly found widely on grapes. They are important for fermentation of grapes, because they may slow fermentation and leave undesirable flavours in the wine. Killer yeasts can take over fermentation by killing the inoculated yeasts, even when the concentration of killer cells is low at the beginning of the process. The potential of Killer yeasts is being examined for commercial exploitation. The capacity to add desirable fermentation characters to strains that already reduce competitors in the must is a valuable attribute. Use of killer strains may reduce the need to sterilise must at the beginning of fermentation. The sterilant, sulphur dioxide, induces asthma and allergic sinus conditions in some individuals, and is therefore seen as an undesirable though necessary additive to wine.

Pathogenesis of virus in fungi
Pathogenic viruses are only found in a few situations where the fungal population is held at artificially high levels by human intervention. This has led to the suggestion that most viruses are naturally benign. Viruses have become pathogens because chance mutations in the small genome occur at a much faster rate than in the host, and selection is for pathogens when host populations are held at high densities. In other words, disease is a function of the attempts by humans to manipulate the environment. However, the presence of Killer yeasts indicates that the interaction between virus and fungus may be more complex. Where the virus provides a beneficial function for the host, then the virus may become incorporated into the host genome. Competitors may be almost entirely replaced in a population. Thus viruses are not one functional grouping. They have attributes determined by their genome, and we will no doubt find further variants as fungi are used more extensively and intensively.

The vast majority of viruses of fungi have no noticeable effect on host phenotype. In those that modify host function, some are deleterious and others beneficial. Because viruses can be transmitted following compatible anastomoses, single genotypes remain potentially at risk of rapid spread of disease (in industry). Lack of transmission across incompatible strains limits their use in biological control of problem fungi.

Reference
http://www.microbeworld.org/microbes/virus_bacterium.aspx
http://www.cellsalive.com/phage.htm
http://en.wikipedia.org/wiki/Plant_virus
http://www.ext.colostate.edu/Ptlk/1443.html
http://www.dpvweb.net/intro/index.php
http://bugs.bio.usyd.edu.au/Mycology/UsesOf_Fungi/primaryProduction/fungiDiseases.shtml

Virus-host Interactions

2009-01-09T23:54:00.001-08:00

Emerging Viruses

2009-01-09T23:53:00.002-08:00

Emerging Viruses

Introduction to emerging viruses
A virus is an infectious agent that is incapable to grow or reproduce outside a host cell. It itself can cause severe problems with health and even lead to death in a long term or short term period whereby it reproduces itself inside a human body.
With a slight knowledge on the effects of what virus area capable of, we would like to talk about new viruses or evolution of the viruses, in other words, Emerging virus.
The factor that contribute to emerging viruses are usually mutation of the virus which we would term it Spontaneous evolution of virus.

Many viruses, in particular RNA viruses, have short generation times and relatively high mutation rates.
This elevated mutation rate, when combined with natural selection, allows viruses to quickly adapt to changes in their host environment.

For example, a series of outbreaks of virus within the 6 years are as follows;

Year 1999 ( West Nile Virus)
West Nile virus is an emerging virus that first appeared in North America during the summer of 1999 in New York City. There were seven deaths associated with this event. Surveillance reports indicate that the virus had been spreading south and west and in 2002, had been reported in 42 states and the District of Columbia. As of September 2002, there were 2121 total human cases reported, inducing 104 deaths. The fatality rate for the West Nile virus is very low and the majority of individuals will have no clinical symptoms; however, individuals at most risk for more serious form of the disease are the elderly, the immunocompromised, and young individuals. The virus is spread by certain mosquito species and certain populations of birds serve as the reservoir hosts. Because person-to-person transmission does not occur, humans are therefore considered dead-end hosts. Confirmation of cases West Nile virus infections in humans are determined based on clinical and laboratory findings.

September 1998 – April 1999 (Nipah Virus Outbreak)
Nipah virus is a newly recognized zoonotic virus. The virus was 'discovered' in 1999. It has caused disease in animals and in humans, through contact with infectious animals. The virus is named after the location where it was first detected in Malaysia. Nipah is closely related to another newly recognized zoonotic virus (1994), called Hendra virus, named after the town where it first appeared in Australia. Both Nipah and Hendra are members of the virus family Paramyxoviridae. Although members of this group of viruses have only caused a few focal outbreaks, the biologic property of these viruses to infect a wide range of hosts and to produce a disease causing significant mortality in humans has made this emerging viral infection a public health concern.

Nipah Virus

November 2002 – July 2003 (SARS Outbreak)
Severe acute respiratory syndrome (SARS) is a respiratory disease in humans which is caused by the SARS corona virus. There has been one near pandemic to date, between November 2002 and July 2003, with 8,096 known infected cases and 774 deaths worldwide being listed in the World Health Organization's (WHO) 21 April 2004 concluding report. Within a matter of weeks in early 2003, SARS spread from the Guangdong province of China to rapidly infect individuals in some 37 countries around the world. Mortality by age group as of 8 May 2003 is below 1 percent for people aged 24 or younger, 6 percent for those 25 to 44, 15 percent in those 45 to 64 and more than 50 percent for those over 65. For comparison, the case fatality rate for influenza is usually around 0.6 percent but can rise as high as 33 percent in locally severe epidemics of new strains. The mortality rate of the primary viral pneumonia form is about 70 percent.

SAR Virus

Year 2008 (Avian Influenza virus)
Avian influenza, also known as bird flu, is caused by avian influenza virus, which belongs to the family Orthomyxoviridae, and affects most domestic and wild bird species. The influenza viruses are divided on the axiom of their antigenic nature into types A, B and C. Only type A influenza viruses are of diversion to veterinarians, whereas types B and C are usually found in humans. Avian influenza viruses are further sorted by their surface proteins, haemagglutinin and neuraminidase. There are 15 different haemagglutinin (H1-15) and nine neuraminidase (N1-9) subtypes based on serological testing with the haemagglutinin-inhibition and neuraminidase inhibition tests, respectively. The virulence of the avian influenza viruses varies broadly from very low to very high and signs of disease range from mild respiratory to viscera-tropic, multi-systemic infections with catastrophic consequences. Low pathogencity avian influenza (LPAI) viruses can be any of the 15 haemagglutinin and nine neuraminidase subtypes, whereas highly pathogenic avian influenza (HPAI) viruses have only been of the H5 and H7 haemagglutinin subtypes. Generally, antibodies against one of the haemagglutinins offer little or no protection against a virus with a different haemagglutinin subtype.
The virus remains viable for long periods in tissues and faeces. Various physical and chemical treatments can inactivate the virus, such as temperatures of 56°C for 3 hours or 60°C for 30 min, acidic pH, oxidizing agents, sodium dodecyl sulphate, lipid solvents, ß-propiolactone, as well as formalin and iodine disinfectants.

Reference

http://www.lapublichealth.org/
http://microbiology.mtsinai.on.ca/bug/wnv/bug-images/wnv_cycle.jpg
http://www.ncbi.nlm.nih.gov/
http://bepast.org/docs/photos/nipah%20virus/nipah%20virus.jpg
http://www.wpro.who.int/
www.influenzareport.com/ir/ai.htm
http://en.wikipedia.org/wiki/Virus
http://en.wikipedia.org/wiki/West_Nile_Virus
http://en.wikipedia.org/wiki/SARS
http://en.wikipedia.org/wiki/Nipah_Virus
http://en.wikipedia.org/wiki/Avian_Flu

Prions, Viriods and Virusoids

2009-01-09T23:53:00.001-08:00

Prions, Viriods and Virusoids

Prions

Prions are anomalous infectious pathogens that cause a group of constantly fatal neurodegenerative diseases mediated by an entirely contemporary mechanism. Prion diseases may present as genetic, infectious, or sporadic disarrays, all of which involve variation of the prion protein (PrP), a essential of normal mammalian cells. CJD generally presents as progressive dementia, whereas scrapie of sheep and bovine spongiform encephalopathy (BSE) are generally apparent as ataxic illnesses.

Prions are devoid of nucleic acid and seem to be composed exclusively of a modified isoform of PrP designated PrPSc.‡ The normal, cellular PrP, denoted PrPC, is converted into PrPSc through a process whereby a portion of its α-helical and coil structure is refolded into β-sheet (25). This structural transition is accompanied by profound changes in the physicochemical properties of the PrP. The amino acid sequence of PrPSc corresponds to that encoded by the PrP gene of the mammalian host in which it last replicated. In contrast to pathogens with a nucleic acid genome that encode strain-specific properties in genes, prions encipher these properties in the tertiary structure of PrPSc (26–Transgenetic studies argue that PrPSc acts as a template upon which PrPC is refolded into a nascent PrPSc molecule through a process facilitated by another protein.

More than 20 mutations of the PrP gene are now known to cause the inherited human prion diseases, and significant genetic linkage has been established for five of these mutations (4, 16, 29–The prion concept readily explains how a disease can be manifest as a heritable as well as an infectious illness.

One good example of a disease under Prions is Scrapie, which is a fatal, depraving disease that affects the central nervous system of sheep and goats. The transmission of scrapie is mainly due to the unhygienic way of feeding unhealthy or infected food through unlawful methods to the animals. In such cases, infected animals with scrapie such as those dead sheeps made into products were fed to living cows that are reared by farmers, preparing to slaughter them for meat. Another example of Prions disease is the Mad cow disease, also known as BSE, a type of TSE but slight genetically differences.

Shown in the picture above, small vacuoles
are symptoms of prions active in the brain tissues.

Humans are also susceptible to several prion diseases:

CJD: Creutzfeld-Jacob Disease
GSS: Gerstmann-Straussler-Scheinker syndrome
FFI: Fatal familial Insomnia
Kuru
Alpers Syndrome

These original classifications were based on a clinical evaluation of a patients family history symptoms and are still widely used, however more recent and accurate molecular diagnosis of the disease is gradually taking the place of this classification.
The incidence of sporadic CJD is about 1 per million per year.GSS occurs at about 2% of the rate of CJD.

It is estimated that 1 in 10,000 people are infected with CJD at the time of death.These figures are likely to be underestimates since prion diseases may be misdiagnosed as other neurological disorders.

The diseases are characterised by loss of motor control, dementia, paralysis wasting and eventually death, typically following pneumonia. Fatal Familial Insomnia presents with an untreatable insomnia and dysautonomia. Details of pathogenesis are largely unknown.
Visible end results at post-mortem are non-inflammatory lesions, vacuoles, amyloid protein deposits and astrogliosis.

GSS is distinct from CJD, it occurs typically in the 4th-5th decade, characterised by cerebellar ataxia and concomitant motor problems, dementia less common and disease course lasts several years to death. Originally, it is thought to be familial, but now known to occur sporadically as well.

CJD typically occurs a decade later has cerebral involvement so dementia is more common and patient seldom survives a year, which is originally thought to be sporadic, but now known to be familial as well.

FFI pathology is characterised by severe selective atrophy of the thalamus.

Alpers syndrome is the name given to prion diseases in infants.

Scrapie was the first example of this type of disease to be noticed and has been known about for many hundreds of years. There are two possible methods of transmission in sheep:

Infection of pasture with placental tissue carrying the agent followed by ingestion,or direct sheep-lamb transmission i.e. an acquired infection.
Parry showed considerable foresight by suggesting that it is not normally an infectious disease at all but a genetic disorder. He further suggested that selective breeding would get rid of the disease.

Humans might be infected by prions in 2 ways:

Acquired infection (diet and following medical procedures such as surgery, growth hormone injections, corneal transplants) i.e. infectious agent implicated.
Apparent hereditary mendelian transmission where it is an autosomal and dominant trait. This is not prima facie consistent with an infectious agent.

This is one of the features that single out prion diseases for particular attention. They are both infectious and hereditary diseases. They are also sporadic, in the sense that there are also cases in which there is no known risk factor although it seems likely that infection was acquired in one of the two ways listed above.

Kuru is the condition which first brought prion diseases to prominence in the 1950s. Found in geographically isolated tribes in the Fore highlands of New Guinea. Established that ingesting brain tissue of dead relatives for religious reasons was likely to be the route of transmission. They ground up the brain into a pale grey soup, heated it and ate it. Clinically, the disease resembles CJD. Other tribes in the vicinity with same religious habit did not develop the disease. It is speculated that at some point in the past a tribe member developed CJD, and as brain tissue is highly infectious this allowed the disease to spread. Afflicted tribes were encouraged not to ingest brain tissue and the incidence of disease rapidly declined and is now almost unknown.

Viroids

Viroids are plant pathogens that consist of a short stretch of highly complementary, circular, single-stranded RNA without the protein coat that is typical for viruses. The genome of the smallest known viruses capable of causing an infection by themselves is around 2 kilobases in size. The human pathogen hepatitis D is similar to viroids.

Because of their simplified structures both prions and viroids are sometimes called subviral particles. Viroids mainly cause plant diseases but have recently been reported to cause a human disease.

The only human disease known to be caused by a viroid is hepatitis D. This disease was previously imputed to a defective virus called the delta agent. However, it now is known that the delta agent is a viroid enclosed in a hepatitis B virus capsid. For hepatitis D to occur there must be simultaneous infection of a cell with both the hepatitis B virus and the hepatitis D viroid. There is extensive sequence complementarity between the hepatitis D viroid RNA and human liver cell 7S RNA, a small cytoplasmic RNA that is a component of the signal recognition particle, the structure involved in the translocation of secretory and membrane-associated particles. The hepatitis D viroid causes liver cell death via sequestering this 7S RNA and/or cleaving it.

Transmission
The hepatitis D viroid can only enter a human liver cell if it is enclosed in a capsid that contains a binding protein. It obtains this from the hepatitis B virus. The delta agent then enters the blood stream and can be transmitted via blood or serum transfusions.

Virusoid
Virusoids are circular single-stranded RNAs dependent on plant viruses for replication and encapsidation. The genome of virusoids consists of several hundred nucleotides and only encodes structural proteins.
Virusoids are similar to viroids in size, structure and means of replication

Summary of Prions, Viriods and Virusoids
Viroids, virusoids and prions are unusual infectious agents characterised by having a very small genome and in the case of prions, possibly no genome at all.
Viroids are common plant pathogens which are a serious economic problem. 25 different viroid sequences have been determined and numerous variants identified :

Pospiviroidae are a large group, only 2 members of the Avsunviroidae are currently known. The RNA genomes of viroids are 246-375 nucleotides in length and share many similarities:

They are all single stranded covalent circles
There is extensive intramolecular base pairing
A DNA-directed RNA polymerase makes both plus and minus strands
Replication does not depend on the presence of a helper virus
No proteins are encoded

Reference
http://en.wikipedia.org/wiki/Prions
http://www.microbiologybytes.com/virology/Prions.html
http://www.microbiologybytes.com/virology/Viroids.html
http://en.wikipedia.org/wiki/Viroids
http://en.wikipedia.org/wiki/Virusoid
http://www.rkm.com.au/
http://www.pandasthumb.org/
http://www.ens-newswire.com/ens/jul2006/20060710_prions.gif