Virus:features, structure ,clasification of virus, genetic analysis of phage, animal virus and plant virus.

Viruses 

  • features
  • structure
  • clasification of virus
  • genetic analysis of phage
  • animal virus
  • plant virus

Features

  • Simple, noncéllular (consisting of one or more molecules of either DNA or RNA enclosed in of protein).
  • Reproduce only within living cells ( obligate Intracellular parasites).
  • Smalle than prokaryotic cells( ranging in size from 0.02 to 0.3 um).         
              Smallpox virus is largest virus (200 nm in diamete) . 
               Polio virus is the smallest virus (28 nm in diameter).

A fully assembled infectious virus is called a virion (function of the virion is to deliver its DNA or RNA genome into the host cell so that the genome can be expressed) .

Structure

  • Very diverse,
  • Varying widely in size, shape and chemical composition
  •  Nucleocapsid composed of nucleic acid surrounded by a protein capsid.

protein capsid.

  • Capsids- formed as single or double protein shells and consist of only one or a few structural protein species. 
  • The proteins used to build the capsid are called capsomeres. 
  • The nucleic acid together with the capsid forms the nucleocapsid (Some viruses have a membranous envelope that lies outside the nucleocapsid). 
Enveloped viruses ( virions having an envelope) and Naked viruses (lacking an envelope)
  •  The nucleocapsid is surrounded by a lipid bilayer and glycoprotein derived from the modified host cell membrane. 
  • Outerside of viruses exhibit a fringe of glycoprotein spikes, also called peplomers (which budding through the plasma membrane or another intracellular cell membrane.)

 Functions :- shell to protect the viral genome from nucleases and which during infection attaches the virion to specific receptors exposed on the prospective host cell.

Viral genomes 

  • Smaller in size. (The largest known viral genome, that of bacteriophage G, is 670 kbs.)
  • Consist of DNA or RNA,( may be single stranded (ss) or double stranded (ds), linear or circu ) 
  • Two type of genomes

Segmented genomes ( which are divided into two or more physically separate molecules of nucleic acid, all of which are then packaged into a single viral particle)

Multipartite genomes (Which segmented, but each genome segment is packaged into separate virus particle.) Multipartite viruses are only found in plants.

Types of viral nucleic acids

nucelc acid type               Nucleic acid structure

DNA 
Single stranded     -          Linear, single-stranded DNA Circular, single-stranded DNA    

Double stranded    -          Linear, double-stranded DNA
                                          Linear double-strand DNA with single chain breaks
                                          Circular, double-strand DNA


RNA

Single stranded     -     Linear, single-stranded, positive-strand RNA
                                      Linear, single-stranded, negative-strand RNA
                                       Linear, single-stranded, segmented RNA

Double stranded    -  Linear, double-stranded, segmented RNA


Shape/symmetry

  • All viruses have a nucleocapsid (nucleic acid and protein) structure. 
  • Two type shape\symmetry
                 Icosahedral (spherical shape)
                      Regular polyhedron with 20 equilateral triangular faces and 12 vertices.
 
                  Helical (rod shape)
                       Helical nucleocapsids consist of a helical array of capsomeres wrapped around a helical                           filament of nucleic acid.
                      A typical virus with helical symmetry is TMV.

                     Complex structures have capsid symmetry that is neither purely icosahedral nor helical.
                                      As for example T4 virus of E. coli.




Classification of viruses

based on their host, virion structure and composition, mode of reproduction and the nature of any diseases caused.
Classification of viruses
bacterial virus
animal virus
plant virus
 insect virus 

Bacteriophage (Bacterial virus) (or simply phage) 

  • First observed in 1915 by F. Twort in England and in 1917 by F.Herelle in France( used tearm bacteriophage) 
  • Type of phage - polyhedral, filamentous, and complex. 
  • Complex phages have polyhedral heads to which talls and sometimes other appendages (tail plates, tall fibers, etc.) are attached. (Example Phage T4 - linear double-stranded DNA genome (172 kb) enclose in a capsid and attached to a tail , icosahedron.and the core and sheath are attached to a hexagonal base plate). 

Phage genome
Nature of genome                                               Example     

Single stranded DNA                                             4X174, fd

Double stranded DNA                                            T-phages, A-phages

Single-stranded RNA genome of plus sense             MS2

Double-stranded RNA                                              06

T phages are classified into Treven (T2, T4 and T6) and T-odd phages (T1, T3, T5 and T7). The Trever and Todd phages differ in several parameters such as tall structure and chemical composition.

Life cycle of bacteriophage

  1.  Binding to the bacterial cell surface.
  2.  Inject its genome and the genome must be protected from the bacterial nucleases in the cytoplasm. 
  3.  Genome must be replicated, transcribed, and translated. 
  4.  Then assembled into new virions and  infect other cells.

There are two different types of viral life cycles: Lytic and Lysogenic cycle.

LYTIC CYCLE
The lytic life cycle consists of five steps. These are attachment, penetration, synthesis, assembly and release.






LYSOGENIC CYCLE

In the lysogenic cycle, the viral DNA is inserted into the host into the host;s DNA and replicates as the host into the hosts DNA replicates.then replications of host cell DNA  undergoes a lytic life cycle. When the genetic material of these phages is inserted into the DNA of host cells, it is said to be in the prophage state( lysogen ). When a cell becomes lysogenized, occasionally extra genes carried by the phage get expressed in the cell. These genes can change the properties of the bacterial cell. This process is called lysogenic or phage conversion.









Genetic analysis of phage

They have short generation time and large number can be propagated on pes or in small volumes of liquid media. 
Complementation
A complementation test can reveal if mutations are in the same gene or in different genes. 

Intragenic mapping

In the early 1950s, S. Benzer conducted a fine genetic mapping of the rII locus known as intragenic
mapping (also known as fine-structure mapping). Intragenic mapping is performed to establish distances between two or more mutations within the same gene.
These intragenic recombinants were produced at a very low rate.



Animal viruses

Variety of shapes, sizes, and nature of the genome. 
The genome be DNA or RNA, ss or ds, linear or circular, segmented or non-segmented. 
According to the Baltimore system virus classification, which is based on characteristics such as genome type and mRNA synthesis pathway ,viruses are classified into seven classes. 
 
CLASS 1 (Genome-dsDNA)
 Viral DNA enters the cell nucleus, where cellular enzymes transcribe the DNA and process the     resulting RNA into viral mRNA.
              Class Ia:-DNA replicates in host-cell nucleus; use host enzymes for DNA replication.
                              Example: Adenoviruses, Herpesviruses (Herpes simplex, Varicella zoster and                                                             Epstein  Barr virus) and Papovaviruses (Papilloma and Polyoma).

              Class Ib:- DNA replicates in host-cell cytoplasm using viral enzymes.
                               Example: Pox virus (Smallpox, Vaccinia and Cow pox)



CLASS 2(Genome-ssDNA)

Example: Parvoviruses (from Latin parvo, poor), 

simple viruses that contain one molecule of single-stranded DNA (ssDNA). Some parvoviruses encapsidate (enclose) both plus and minus stran of DNA, but in separate virions; others encapsidate only the minus strand. In both cases, the ssDNA is copied inside the cell into dsDNA, which is then itself copied into mRNA.


CLASS 3(Genome- dsRNA) 

Example: Reoviruses

CLASS 4(Genome-Plus sense ssRNA)

Example-plcornaviruses (Poliovirus and Rhinovirus) and Togavirus (Rubella virus).

CLASS 5 (Genome- Minus sense ssRNA)
Contain a single negative strand of genomic RNA, whose sequence is complementary to that of the viral mRNA. The genomic RNA in the virion acts as a template for synthesis of mRNA but does not itself encode proteins,
Example: Rhabdovirus (Rables), Paramyxovirus (Measles and Mumps) and Orthomyxovirus (Influenza)

CLASS 6(Genome Plus sense ssRNA that replicates with DNA intermediate)
 Example: Retroviruses

CLASS 7 (Genome-dsDNA that replicates with RNA intermediate)

Example: Hepadnavirus such as human hepatitis B virus.





Effect of animal virus on animal cells

Animal viruses can have several different effects on animal cells:

Lytic infection:- Lytic infection results in the host cell lysis.
Persistent infection:- In persistent infections, the infected cell remains alive and continue to produce
virus indefinitely
 Latent infection:- Transformation: In a latent infection, there is a delay between infection by
the virus and lytic events. Co sores caused by the herpes simplex virus are a typical example of latent
viral infection 
Transformation -Certain animal viruses can change the normal cell into a tumor cell, process called
transformation

Life cycle of animal viruses

A generalized productive life cycle for animal viruses consisting of the following steps:

  1. Viral adsorption or attachment to the host cell
  2. Viral entry into the host cell
  3. Replication of the viral genome within the host cell
  4. Viral assembly
  5. Viral release


  1. Viral adsorption or attachment to the host cell
  • Attach to cell via specific cell surface receptors
  • Adsorption involves the binding of attachment sites on the viral surface with receptor sites on the host cell cytoplasmic membrane.



        2.Viral entry into the host cell

  •  viruses must enter cells.

        3.Replication of the viral genome within the host cell

DNA viruses
  • DNA viruses after penetration, the viral nucleic acid is prepared for expression and replication. 
  •  In DNA viruses, early viral mRNA and proteins usually occurs in the host nucleus; poxviruses are exceptions since their genomes are replicated in the cytoplasm. 

RNA viruses
  • The RNA viruses are much more diverse in their reproductive strategies than are the DNA viruses. 

             4.Viral assembly

Some viral genes direct the synthesis of capsid proteins, and these spontaneously self-assemble to form
the capsid The nucleic acid is then inserted into the capsid. The assembly of enveloped virus capsids is
generally similar to that naked virions.

            5.Viral release

Mechanisms of virion release differ between naked and enveloped viruses. naked viruses are predominantly release by host cell lysis. 


Plant viruses
  • Plant viruses exist in rod and polyhedral shape.
  • Most plant viruses have genomes consisting of a single RNA strate of plus (+) sense type. 
  • The best-known plant virus is the rod-shaped tobacco mosaic virus (TMV). Relatively ant viruses have DNA genomes. 
  • There are only two classes of DNA containing plant viruses. The cauliflower most virus belongs to the first class, which contains a double-stranded DNA genome in a polyhedral capsule.
  •  The sector class of DNA containing plant viruses are the geminivirusesgemini twins), characterized by a connected pair d capsids, each containing a circular, single-stranded
  • DNA molecule of about 2500 nucleotides.




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