Virus

Virus can be defined as a genetic element containing either DNA or RNA that replicates in host cells as intracellular parasites but is characterized by having an extracellular state.

Virus can use the metabolic machinery of the host cell and can modify the genetics of the host cell. Virus has both extracellular and intracellular state.

Extracellular state: Outside the host cell, the virus is a minute particle containing nucleic acid surrounded by protein, which is referred as virions or virus particles.

Intracellular state: The active state in which the virus replicate in the host cell. When the virus nucleic acid is introduced to host cell and replication starts, the process is referred as infection.

As extracelluar particle, virions are metabolically inert. When infect the host cell, they can able to produce some enzymes which are essential for their replication.

• Nucleic acid polymerase – either DNA polymerase or RNA polymerase depends upon their genome.
• Reverse transcriptase – Some RNA viruses (ex. HIV like retrovirus) has this enzyme to produce DNA from RNA.
• Lysozyme – Especially bacteriophages produce lysozyme to make a hole in the bacterial cell wall for entry

Replication

Since, virus doesn’t have any system for replication by itself, it should induce the host cell to synthesize all essential components needed for complete virus. Then, these components must assemble into proper structure, and new virions must escape from the cell and infect the other cells. The sequence of virus replication is as follow:

• Attachment (adsorption) of virion to a susceptible host cell
• Penetration (injection) of virion or its nucleic acid into cell
• Early steps in replication – during which the host cell biosynthetic machinery is altered by virion as a prelude to virus nucleic acid synthesis. Virus specific enzymes are typically made.
• Replication of virus nucleic acid
• Synthesis of protein sub-units
• Assembly (Packing)

Attachment:

Attachment of virus particle with host cell is mainly based on the specific interaction between host and virus. The virus has one or two specific proteins on the outside of the virion with specific activity. This protein will recognize some host cell surface components such as proteins, polysaccharides, lipoproteins etc. These compounds are referred as receptors. If the receptor is removed in the host cell, the attachment of virus is not possible on the host cell.

Ex. For T2 bacteriophage, core polysaccharide of outer membrane of E.. coli acts as receptor.

Penetration:

The penetration of virus into the host cell is mainly based on the surface morphology of the host cell. The penetration varies from host to host (plant and bacteria have cell wall and animals don’t have cell wall). The bacteriophages (T2 phage) first attaches its tail fibres with receptor (core protein); By means of lysozyme, the phage make a hole in the cell wall and inject the nucleic acid by the help of tail.

Virus restriction & modification by host:

When the viral nucleic acid enters to cytoplasm of the host cell, as a protective mechanism host cell can able to digest the nucleic acid by means of restriction endonuclease (for DNA) or by RNAse (in case of RNA). To avoid that, the viral nucleic acid or genome modify its base pairs so that the restriction enzymes cannot react on it. By addition of glucose (glucosylation) or by addition of methyl group (methylation), the modification of viral genome is possible.

Replication of viral nucleic acid and proteins:

New viral proteins and nucleic acids should be synthesized with the help of host DNA. The genetic system of host is used by the viral nucleic acid to produce capsid and nucleic acid. Nucleic acids were synthesized by means of DNA or RNA replication using the enzymes DNA polymerase or RNA polymerase respectively.

The protein part of virions is synthesized as protein synthesis. The genetic information of virus (DNA or RNA) should be converted into mRNA (called as transcription).

The mRNA synthesis shows diversity among the viruses. Following diagram shows how the mRNA synthesis occurs from different viral genomes namely ssDNA, dsDNA, ssRNA and dsRNA.

After mRNA synthesized, viral protein sub-units were synthesized. The early proteins – synthesized soon after infection (enzymes) and late proteins – synthesized later part (coat protein).

The latent period refers the period which the presence of virus in the host cell cannot be detected. During that period, the synthesis of enzymes, nucleic acid and protein synthesis take place.

Package and Release

After the protein coat and nucleic acid synthesis, the assembly takes place leads to completion of viral particle which will lyse the host cell; escape and infect the next host cell. Above diagram shows the one step growth curve (means one lytic cycle) of virus against time. The population of virus is expressed as plaque forming units.

These types of viruses, which kill the host cell during release, are referred as lytic viruses and the cycle is referred as lytic cycle.

But some bacteriophages will multiply in side the host cell and release to the environment after assembly without killing the host cell are referred as temperate phage (Example: λ phage) and the cycle is referred as lysogenic cycle.

Latent period: The latent period is the shortest time required for virus reproduction and release.

Eclipse period: The initial part of the latent period in which infected host bacteria do not contain any complete virions.

Rise or bust period: The period during the onestep growth experiment when host cells lyse and release phage particles

burst size: The number of phages released by a host cell during the lytic life cycle.

Different replication methods of bacteriophages:

1. MS2 - This single strand RNA phage uses its RNA as mRNA and protein synthesized. The complimentary RNA also synthesized from which viral RNAs synthesized.
2. φX174 – This ssDNA phage has single strand circular DNA which duplicate by rolling circle replication.
3. M13 – This ssDNA phage has linear DNA. The DNA synthesized in cytoplasm and protein coats are synthesized and accumulated in the cytoplasmic membrane. The linear DNA when released from host covered by protein coat and released. This is a temperate phage which will not kill the host cell during replication. (A slight decline in the growth of bacteria will occur). The cycle is referred as lysogenic cycle and the phage is temperate phage and host bacterium is lysogen.
4. T2, T4, T3,T7 phages – They are ds DNA phages which are lytic phages and the cycle is lytic cycle. (25 minutes per cycle). The lytic cycle of these phages occurs as discussed earlier.
5. Lambda phage – This dsDNA phage is a temperate phage. After penetration, the lambda phage DNA will integrate with the bacterial DNA and will persist for ever. This state of phage is referred as prophage. When the prophage is induced (either by chemical or physical means) it become lytic phage and replicate in the host cell and by killing the host the virions will escape.
6. Mu Phage – This dsDNA phage is also a temperate phage like lambda phage. It has the unusual property like transposable elements (which can move from one portion of genomic DNA to another part) and thereby cause mutation. They are referred as biological mutagens.

Genome of Virus

The well-studied lytic phage, t-4 bacteriophage is a bacteriophage that infects E. coli bacteria. Its double-stranded DNA genome is about 169 kbp long and is held in an icosahedral head, also known as a capsid. It possess all the genes responsible for its replication in the host cells. The genome map of the T4 is as follows: