Virus Structure and Application, Origin, Definition, Characters, and Example.

Introduction

It is estimated that there is approximately 10^31 virus on earth, which is over ten million times more than the entire stars in the universe.

All of these viruses are not infectious to humans, most of them are living in oceans and they attack bacteria and other microbes.

What is Virus?

Virus is a microscopic, infectious particle that can reproduce or replicate within the living cell of an organism or host. Viruses can not reproduce without a host cell. They infect almost all living forms such as animals, plants, and bacteria.

In 1898, a Dutch scientist, Martinus Beijerinck discovered the world’s first virus which was the tobacco mosaic virus. He conducted an experiment to show that there is another infectious particle that is smaller than bacteria and responsible for the infection in tobacco plants.

Are viruses alive or dead?

Viruses are neither living nor a dead cell. They can not be dead because dead means the organism stops performing biological functions, but they can replicate within the host cell.

But also they are not alive because, at the outside of host cell they act as a nonliving cell. Most scientists consider viruses are nonliving things because they don’t follow these 7 criteria to become alive.

1. Homeostasis

• The first and important criteria of a living thing are – it must be made of cells.
• The virus particles don’t follow this criteria because they are not made of cells. They are called virions and they contain a set of genes bundle which is protected by a protein shell known as a capsid.
• They don’t contain any nuclei, organelles, or cytoplasm as cells do.

2. Reproduction

• As viruses don’t have any nuclei and organelles they can not conduct their own replication process. Because they lack the replication tools which are required to copy their genes.
• Viruses infect the host cell and use the host’s replicating mechanisms to replicate their genetic information and create new capsids and assemble everything together. 
• At the outside of the host cell, they can’t replicate and function as a dead cell.

3. Growth

• Living things use energy and nutrients for their growth and increase their size and become more complex.
• Viruses do not grow means they don’t increase their size and complexity.

4. Energy

• They use host energy to replicate their genetic materials.

5. Respond to Stimuli.

• Viruses do not respond to stimuli such as touch or sound or light as humans, plants and bacteria do (there has not been enough research done to definitively say that viruses do not respond to anything). 

6. Nucleic Acid

• Viruses contain either RNA or DNA (most of the viruses contain RNA), whereas a cell contains only DNA.

7. Adaptation with Environment or Mutation

• Viruses can adapt with the environmental conditions, such as during replication when the host cell is unable to supply energy, viruses undergo a lysogenic phase and they can re-enter the lytic phase when conditions are right.
• This adaptive ability makes HIV as hard to treat, they can mutate quickly.

Origin of Viruses

There are three hypothesis on origin of virus such as;

1. Regressive hypothesis

• According to this theory, viruses initially parasitize larger cells, and they lose their genes over time when genes are not needed for their parasitism. Regressive hypothesis also known as ‘degeneracy hypothesis’, or ‘reduction hypothesis’.
• For example, like viruses, rickettsia and chlamydia can’t reproduce at the outside of the host cell they can only reproduce within the host body. These two bacteria support the ‘degeneracy hypothesis’, or ‘reduction hypothesis’, as they lose their genes which can allow them to survive outside a cell.

2. Cellular origin hypothesis

• This hypothesis is also known as ‘vagrancy hypothesis’ or the ‘escape hypothesis’.
• According to this hypothesis, Some viruses may be produced from the escaped nucleic acid (DNA or RNA) from a larger organism. 
• These nucleic acids could have come from plasmids or transposons (“jumping genes”).

3. Co-evolution hypothesis

• This hypothesis is also known as  the ‘virus-first hypothesis’.
• According to this hypothesis “viruses may have evolved from complex molecules of protein and nucleic acid at the same time that cells first appeared on Earth and would have been dependent on cellular life for billions of years.”
• For example, Viroids are known as subviral agents, but they have some common features of viruses. They are RNA molecules; lack protein cota; mainly infect plants; they use host machinery for their replication.

Characteristics of Virus

• Viruses are smaller than prokaryotic cells, their size is between 20–300 nanometers (nm), whereas a prokaryotic cell’s size is about 0.5–5.0 micrometers (µm) in length.
• They are acellular and can easily be crystallized.
• Viruses are ultramicroscopic and filterable (They can pass through bacteria proof filters).
• They are obligate intracellular parasites, which infect animals, plants and bacteria.
• Viruses are host specific.
• Virions are made of nucleoproteins.
• Viruses are resistant to chemicals, alcohols and environmental changes.
• Viruses don’t have any cell membranes and cytoplasm.
• They lack mitochondria, ribosomes, and other organelles.
• They can’t reproduce independently, they depend on the host cell’s replication mechanisms for their replication.
• They contain either DNA or RNA.
• They get their energy from the host cell for replication.
• The shape of viruses varies based on their types. Viruses can be helical, icosahedral, envelope, and complex in shape.
• They can’t grow or can’t increase their size as cells do.
• The head region or capsid of the virus contains the genetic material.
• The capsid in viruses is made of proteins.
• Some viruses contain spike projections, these are viral encoded proteins involved in receptor recognition and viral tropism.

The Structure of Virus and Morphology

A virus particle also called as Virion, which is composed of three components such as;

• Capsid
• Envelop
• Nucleic acid

1. Virus capsids

The nucleic acid is enclosed by a protein shell called the capsid, sometimes they are also called a nucleocapsid. It is composed of different protein subunits called capsomeres.

The capsid is responsible for the variation in shape of virus. Capsid comes in various shape such as (morphological of virus);

• Icosahedral
  • These appear in a spherical shape with icosahedral symmetry.
  • It has a 3D shape with 20 equilateral triangles. 
  • Most of the animal viruses are icosahedral.
  • It is made of protein subunits which are arranged in a regular geometrical pattern, like a soccer ball.
  • A single protein is repeated again and again to form this shape that saves space in the viral genome.
  • In an icosahedral the capsid encloses the genetic material.
  • When the cells are braked down and lyse, they release viruses with the icosahedral shape in the environment.

Example: poliovirus, rhinovirus, and adenovirus.

• Helical 
  • This helical shape is made up of a single protein, which is stacked around a central axis.
  • Helical viruses are 15-19nm wide and length is between 300 to 500nm, these are depending on the genome size. 
  • It looks like a hollow tube because it has a central cavity or hollow center, which is formed due to circular arrangement of proteins and makes a disc-like shape.
  • The nucleic acid is arranged within this central cavity.
  • Most of the filamentous viruses appear in a helical shape.
  • Helical viruses can be short and very rigid, to long, and very flexible.

Example:  tobacco mosaic virus (TMV) 

• Prolate
  • In Prolate icosahedron extended along the fivefold axis and a common arrangement of the heads of bacteriophages. 
  • It is made of a cylinder with a cap at either end.
• Complex or Head-tail 
  • These are the combination of both helical and icosahedral and may contain a complex outer wall or head-tail morphology. 
  • These types of head-tail or complex viruses are known as a bacteriophage, they mainly infect the bacteria.
  • The head portion of this virus appears in an icosahedral shape whereas the tail portion appears as helical shape.
  • They use their tail portion to get attached to the surface of the bacterial cell, then it starts to create a hole in the cell wall and injects its DNA within the cell using the tail as a channel.

Example: bacteriophage.

2. Virus envelopes

• Some viruses contain an extra glycoprotein envelope which is covering the capsid known as an envelope.
• The viral envelope is made of two lipid layers that are interspersed with protein molecules and have some material from the host cell membrane.
• During the viral budding, they collect the lipids from the host cell membrane and replace the proteins of the cell membrane with its own proteins. As a result, it produces a hybrid structure that has cell-derived lipids and virus-derived proteins. 
• Some viruses develop spikes on the envelope which help in the attachment of virus particles on specific cell surfaces.

3. Virus genomes or Nucleic Acid

• The viral genomes consist of either DNA or RNA, but they never carry both DNA and RNA
• DNA containing viruses are known as de-oxy-viruses whereas RNA containing viruses are known as riboviruses. Each of them contain two subtypes such as double stranded and single stranded.
• The viral genome contains genetic information for protein synthesis. Most of the viruses contain single-stranded RNA to maintain their genetic information.
• RNA based viruses are divided into two classes such as positive-strand RNA and negative-strand RNA. In most viruses, the genomic RNA is positive because they function as messenger RNA for the translation of protein.

Subtype of Viruses

• Double Stranded or dsDNA: It is mainly found in T2, T4 bacteriophages, coli-phage Lambda, Cauliflower Mosaic, Pox Virus, Adenovirus, Herpes Virus (linear), Polyoma Virus, Simian Virus-40 (SM40), Hepatitis В (circular).
• Single Stranded or ssDNA: It is also called plus strand, mainly occurs in Coli-phage MS 2, Coli-phage fd (linear), Coli-phage ф x 174 (circular).
• Double Stranded or dsRNA: It mainly occurs in Reovirus and Tumour Virus (both linear).
• Single Stranded or ssRNA: These are generally linear and found in Poliomyelitis Virus, Foot and Mouth disease Virus, Influenza Virus, Tobacco Mosaic Virus (TMV), Tobacco Necrosis Virus Potato Mosaic Virus, Bean Mosaic Virus, Retroviruses.

4. Enzymes

• Enzymes are found occasionally in viruses, the bacteriophages contain lysozyme in the region that comes in contact with the host cell.
• Other enzymes include neuraminidase in Influenza Virus, RNA polymerase, RNA transcriptase, reverse transcriptase.

Replication of Virus

Viruses can only replicate in living organisms. For the synthesis of viral proteins and nucleic acids, the host cell must provide the energy, synthetic machinery, and low-molecular-weight precursors.

The virus replicates in seven distinct stages:

1. Attachment
2. Entry,
3. Uncoating,
4. Transcription / mRNA production,
5. Synthesis of virus components,
6. Virion assembly and
7. Release (Liberation Stage).

Attachment

• This is the initial stage of viral replication. Attachment of the virus to the cell membrane of the host cell. The virus then initiates infection by injecting its DNA or RNA into the host.
• In animal cells, these viruses enter via the process of endocytosis, which involves the fusion of the virus and the viral envelope with the cell membrane, whereas in plant cells, they enter via the process of pinocytosis, which involves the pinching of the viruses.

Entry

• The virus particle is encased in a pinocytotic vacuole by the invagination of the cell membrane of the host cell. This protects the cell against antibodies, such as those produced by the HIV virus.

Uncoating

• Lysosome-derived enzymes remove the virus’ protein envelope. This releases or makes available the nucleic acid or genome of the pathogen.

Transcription / mRNA production

• The infecting RNA of certain RNA viruses generates messenger RNA (mRNA), which can translate the genome into protein products. Viruses with negative-stranded RNA or DNA are produced through transcription followed by translation.
• The mRNA instructs the host cell to synthesize virus components. The virus utilizes preexisting cellular structures to replicate itself.

Synthesis of virus components

The virus manufactures the components using the host’s existing organelles:

• Viral proteins: On cellular ribosomes, viral mRNA is translated into two types of viral proteins:
  • Structural: the proteins that compose the virus particle
  • Nonstructural: proteins not detected in the virus particle, primarily replication enzymes.
• Viral nucleic acid (genome replication): In the synthesis of new viral genomes, the progenitor genome or newly formed complementary strands serve as templates for single-stranded genomes. In rapidly dividing cells, these genomes are produced by either a viral polymerase or (in the case of some DNA viruses) a cellular enzyme.

Virion assembly

• A virion is any viral particle that is alive and well. Here, the genome (nucleic acid) and proteins that were just created come together to form infectious virus particles.
• For most evolved viruses, this can occur in the nucleus, the cytoplasm, or the plasma membrane of the host cell.

Release (liberation stage)

• Both rapid cell rupture and slow extrusion (force out) of encapsulated viruses through the cell membrane can result in the release of mature viruses.
• These novel viruses can either replicate outside the host cell or launch an attack on healthy cells. Lysis of the infected bacterium is the mechanism through which bacterial viruses release their offspring virions into the environment. In animals, however, viruses are typically released without the need for cell lysis.

Different Diagnosis Methods of Virus

There are various methods used to diagnose viruses. Here are some of them:

1. Molecular tests: These tests detect the genetic material of the virus, such as RNA or DNA, using a technique called polymerase chain reaction (PCR). Molecular tests are highly accurate and can detect viruses even in low concentrations.
2. Serological tests: These tests detect the presence of antibodies produced by the body in response to a viral infection. Serological tests can determine if a person has been infected with a virus in the past, but they may not be able to detect a current infection.
3. Antigen tests: These tests detect proteins produced by the virus in the body. Antigen tests are faster than molecular tests, but they may not be as accurate and can miss some infections.
4. Viral culture: This method involves growing the virus in a laboratory from a sample taken from the patient. Viral culture is a slow process and requires special equipment and expertise.
5. Imaging tests: Imaging tests, such as X-rays or CT scans, can help identify the presence of viral infections in certain parts of the body, such as the lungs.
6. Clinical presentation: In some cases, a doctor may be able to diagnose a viral infection based on the patient’s symptoms and physical examination.

It’s important to note that different viruses may require different diagnostic methods, and the choice of method may depend on the severity of the illness, the stage of the infection, and other factors.

Application of Virus

Viruses have a range of applications in various fields, including:

1. Research: Viruses are commonly used in scientific research to study their genetic makeup, structure, and behavior. This research has led to a better understanding of viruses and the development of treatments and vaccines.
2. Gene therapy: Viruses can be used to deliver therapeutic genes into cells to treat genetic disorders. In this approach, the virus is modified so that it does not cause disease but can still deliver the therapeutic gene to the targeted cells.
3. Biotechnology: Viruses can be used in biotechnology to produce vaccines, therapeutic proteins, and other products. For example, the flu vaccine is produced using the influenza virus.
4. Pest control: Some viruses can be used to control pests and insect populations. These viruses are harmless to humans but can infect and kill certain insects, such as the baculovirus used to control caterpillar populations.
5. Nanotechnology: Viruses can be used as templates for creating nanoscale materials and structures. This approach has led to the development of new materials and technologies with unique properties.
6. Biosensors: Viruses can be used in biosensors to detect the presence of specific molecules, such as proteins or DNA. This approach has applications in medical diagnosis and environmental monitoring.

Examples of a Virus

1. Polio Virus

• It is a Class III virus with double-stranded RNA, which encodes 12 proteins.
• They release mRNA strands into the host cell’s cytosol during reproduction which codes for new virus molecules.
• They are not fatal until people start treating their water. 

2. Rabies Virus

• It is a Class V virus and contains a bullet-shaped protein coat.
• They are composed of linear, single-stranded RNA and their genome codes for five proteins, from 12,000 nucleotides.
• The accumulation of assembled rabies virus occurs in the saliva thus they are transmitted through the bite of infected animals.
• This virus is fatal to humans if not treated immediately.

3. The Influenza (Flu) Virus

• Influenza or “the flu” is responsible for the common cold, and they create respiratory infection.
• Their symptoms are fever, headache, fatigue, muscle weakness and pain, sore throat, dry cough, and a runny or stuffy nose. 

4. The Human Immunodeficiency Virus (HIV)

• In 1983, Robert Gallo and Luc Montagnier first isolated the HIV virus.
• HIV is the causative agent of AIDS.
• They are also called retroviruses; contain reverse transcriptase enzymes; and they maintain their genetic information in the form of ribonucleic acid (RNA).
• They have the ability to produce DNA from RNA.

FAQ

References

• https://www.sparknotes.com/biology/microorganisms/viruses/section1/
• https://www.immunology.org/public-information/bitesized-immunology/pathogens-and-disease/viruses-introduction
• https://www.britannica.com/science/virus#ref32740
• https://biologydictionary.net/virus/#examples-of-a-virus
• https://micro.magnet.fsu.edu/cells/virus.html
• https://courses.lumenlearning.com/boundless-microbiology/chapter/structure-of-viruses/
• https://en.wikipedia.org/wiki/Virus
• https://www.khanacademy.org/test-prep/mcat/cells/viruses/a/are-viruses-dead-or-alive
• https://morgridge.org/outreach/teaching-resources/virology-immunology/virus-structure/
• https://www.biologydiscussion.com/viruses/components-viruses/components-of-viruses-4-components/44608