Chapter 3. Virology

Viruses are the smallest obligate intracellular infective agents containing only one type of nucleic acid (DNA or RNA) as their genome. They have no metabolic activity outside the living cells. They do not possess a cellular organization and lack the enzymes necessary for protein and nucleic acid synthesis. Viral genome (nucleic acid) diverts the host’s metabolism to synthesize a number of virus specific macromolecules required for the production of virus progeny. They multiply by a complex process and not by binary fission. They do not grow in inanimate media. They are resistant to antibiotics.

Morphology of viruses

Size. Viruses are much smaller than other organisms. The extracellular infectious virus particle is called the virion. The size of viruses ranges from 20 to 300 nm in diameter. The largest virus is the smallpox virus (300 nm) and the smallest is the parvovirus (20 nm). In earlier days the virus particles were measured by passing them through the collodion membrane filters of different pore sizes (gradocol membranes). With the development of ultracentrifuge, the virus size could be calculated from the rate of sedimentation of virus in the ultracentrifuge. The latest and the most direct method for measuring virus size is electron microscopy. By this method, both size and the shape of viruses can be made out.

Structure. The virion consists of a nucleic acid core (genome) surrounded by a protein coat, the capsid. The capsid together with the enclosed nucleic acid is known as the nucleocapsid. The capsid is composed of a large number of protein subunits (polypeptides) which are known as capsomers. Two major functions of capsid are, forming an impenetrable shell around the nucleic acid core and to introduce viral genome into the host cells by adsorbing readily to cell surfaces. Certain viruses also contain envelope that surrounds the nucleic acid. The envelope is acquired by the progeny virus during release by budding through the host cell membrane. It is lipoprotein in nature. The lipid is largely of host cell origin while the protein is virus coded. Protein subunits are exposed as ­projectile spikes on the surface of the envelope. These structures are called peplomers from peplos meaning envelope. Enveloped viruses are susceptible to the action of lipid solvents like ether and chloroform. Envelopes confer antigenic, biological and chemical properties on viruses.

Symmetry. Three types of symmetry are determined by the arrangement of capsid around the nucleic acid core.

1. Icosahedral (cubical) symmetry: an icosahedron is a polygon with 12 vertices or corners and 20 facets in the shape of equilateral triangular faces. Icosahedral symmetry has a rigid structure. This type of symmetry is found in papova, picorna, adenoviruses (all naked or non-enveloped) and herpes, togaviruses (enveloped).
2. Helical symmetry: the nucleic acid and the capsomers are wound together to form a helical or spiral tube). Most of the helical viruses are enveloped and all are RNA viruses.
3. Complex symmetry: some viruses do not show either icosahedral or helical symmetry due to the complexity of their structures. These are referred to have complex symmetry, e.g., poxvirus.

Shape. The overall shape of virus particles varies in different groups. Poxvirus is brick-shaped, rabies virus is bullet-shaped and tobacco mosaic virus is rod-shaped. Some are irregular and pleomorphic in shape.

Replication of viruses

Due to lack of biosynthetic enzymes, viruses replicate by taking over the biochemical machinery of the host cell to synthesize virus specific macromolecules required for the production of virus progeny. The genetic information necessary for viral replication is contained in the viral nucleic acid. The replicative cycle can be divided into six sequential phases: adsorption, penetration, uncoating, biosynthesis, maturation, release.

1. Adsorption or attachment. The viruses come in contact with the cells by random collision but adsorption or attachment is mediated by the binding of virus surface structures, known as ligands, to the receptors on cell surface. In case of influenza virus, the hemagglutinin (a surface glycoprotein) binds specifically to sialic acid residue of glycoprotein receptor sites on the surface of respiratory epithelium. With the human immunodeficiency virus (HIV), attachment is between the viral surface glycoprotein GP 120 and the CD4 receptor on host cells.
2. Penetration. After attachment, the virus particles may be engulfed by a mechanism resembling phagocytosis, a process known as viropexis. Alternatively, in case of the enveloped viruses, the envelope may fuse with the plasma membrane of the host cell releasing the nucleocapsid into the cytoplasm.
3. Uncoating. This is the process of stripping the virus of its outer layers and capsid to release the nucleic acid into the cell. With most viruses, uncoating is affected by the action of lysosomal enzymes of the host cells.
4. Biosynthesis. After uncoating, the viral genome directs the biosynthetic machinery of the host cell to shut down the normal cellular metabolism and direct the sequential production of viral components. In general, the nucleic acid genome of most DNA viruses is synthesized in the host cell nucleus. Nucleic acid genome of most RNA viruses is synthesized in the cytoplasm. Viral protein is synthesized only in the cytoplasm. Biosynthesis consists of the following steps. 
   1. Transcription of messenger RNA (mRNA) from viral nucleic acid.
   2. Translation of the mRNA into «early proteins» or «nonstructural proteins». These are enzymes which initiate and maintain synthesis of virus components. They may also induce shutdown of host protein and nucleic acid synthesis.
   3. Replication of viral nucleic acid.
   4. Synthesis of «late proteins» or «structural proteins» which constitute daughter virion capsids.
5. Retroviruses exhibits a unique replicative cycle. Virus genome (single stranded RNA) is converted into an RNA: DNA hybrid by the viral enzyme, RNA directed DNA polymerase (reverse transcriptase). Double stranded DNA is synthesized from the hybrid (RNA: DNA). The double stranded DNA form of the virus (provirus) integrates into the host cell genome. The provirus acts as the template for the synthesis of progeny viral RNA. The integration of the provirus into the host cell genome may lead to transformation of the cell and development of neoplasia.
6. Maturation. The viral nucleic acid and capsid polypeptide assemble together to form the daughter virions. The assembly takes place in either the nucleus (herpes and adenoviruses) or cytoplasm (picorna and pox viruses). In case of enveloped viruses, the envelope is derived from the nuclear membrane (herpes virus) and from plasma membrane when the assembly occurs in the cytoplasm of host cell (orthomyxoviruses and paramyxoviruses).
7. Release. Enveloped viruses are released by a process of budding from the cell membrane over a period of time. The host cell is usually not affected but there are exceptions, e.g., polioviruses not only damage host cell but may also be released by the lysis of the host cell. In case of bacterial viruses (e.g., bacteriophages), they are usually released by lysis of the infected bacterium.