Structure and Composition of Viruses

1.            Defining Features of Viruses

a.         Viruses are entities whose genomes are elements of nucleic acid that replicate inside living cells using the cellular synthetic machinery and causing the synthesis of specialized elements that can transfer the viral genome to other cells.

b.         Viruses must replicate within cells, because they cannot generate energy or synthesize proteins.

c.            Because they can only reproduce within cells, viruses are ‘obligate intracellular parasites.’

2.         Size and Shape

a.         Viruses range from 20 to 300nm in diameter.

b.         They are complex structures of precise geometric symmetry.

c.         The shape of the virus particles is determined by the arrangement of the repeating subunits that form the protein coat (capsid) of the virus.

3.         Capsid and Symmetry

a.         The nucleic acid is surrounded by a protein coat called a capsid, made up of subunits called capsomers.

b.            Capsomeres:

i.          they are held together by noncovalent bonds.

ii.          each capsomer, consisting of one or several proteins, can be seen in the electron microscope as a spherical particle, sometimes with a central hole.

iii.         within an infected cell, the capsomers undergo self-assembly to form the capsid.

iv.         the manner of assembly is strictly defined by the nature of the bonds formed between individual capsomers, which imparts symmetry to the capsid.

c.         There are 2 forms of symmetry in virus capsids:

i.            icosahedral: the capsomers are arranged in 20 triangles that forms a symmetric figure (an icosahedron) with the approximate outline of a sphere.

ii.          helical, in which the capsomers are arranged in a hollow coil that appears rod-shaped.

d.         Both the icosahedral and the helical forms can exist either as a ‘naked’ nucleocapsid or with an outer envelope layer.

e.            Advantages of building virus particle from identical protein subunits:

i.          it reduces the need for genetic information.

ii.          it promotes self-assembly, i.e. no enzyme or energy is required.

4.         Viral Envelope

a.         Virions acquire an envelope during maturation by the process known as ‘budding’ from cellular membranes.

b.         The viral envelope is a lipoprotein membrane composed of lipid derived from the host cell membrane and protein that is virus-specific (encoded by the virus itself).

c.         Viral envelope proteins:

i.            glycoproteins (peplomer) in form of spikelike projections on the surface, which attach to host cell receptors during the entry of the virus into the cell.

ii.          matrix protein mediates the interaction between the capsid proteins and the envelope.

d.            Instability:

i.          the presence of an envelope confers instability on the virus.

ii.            enveloped viruses are more sensitive to heat, detergents, and lipid solvents such as alcohol and ether than are nonenveloped viruses.

e.         Surface antigens:

i.          the surface proteins of the virus, be they capsid proteins or envelope glycoproteins, are the principal antigens against which the host mounts its immune response to viruses.

ii.          they are also determinants of type specificity.

iii.         for example, poliovirus types 1, 2, and 3 are distinguished by the antigenicity of their capsid proteins.

5.         Viral Nuclei acids

a.         With the exception of the retroviruses, which are diploid, viruses are haploid; i.e. they contain only one copy of their genes.

b.         The viral nucleic acid is located internally and can be either single- or double-stranded DNA or single- or double-stranded RNA.

c.         The nucleic acid can be either linear or circular.

d.         The DNA is always a single molecule; the RNA can exist either as a single molecule or in several pieces.

e.         DNA:

i.          the genome of all DNA viruses consists of a single molecule, which is double-stranded except in the case of the parvoviruses, and may be linear or circular.

ii.          the DNA of papovaviruses and hepadnaviruses is circular; the circular DNA of hepadnaviruses is only partially double-stranded.

f.          RNA:

i.          while some RNA genomes occur as a single molecule, others are segmented.

ii.          except for the small circular ssRNA of hepatitis D virus, no animal virus RNA genome is a covalently linked circle.

g.         Single-stranded RNA:

i.          single-stranded genome RNA can be defined according to its sense (polarity).

ii.          positive (plus) sense: of the same sense as mRNA – togaviruses, coronaviruses, retroviruses.

iii.            negative (minus) sense: nucleotide sequence is complementary to that of mRNA – paramyxoviruses, orthomyxoviruses, all of which have an RNA-dependent RNA polymerase (transcriptase) in the virion.

6.         Viral Proteins

a.         Some virus-coded proteins are structural, that is, they are part of the virion; some are nonstructural and are concerned with various aspects of the replication cycle.

b.         Outer capsid proteins:

i.          protect the genetic material and mediate the attachment of the virus to specific receptors on the host cell surface.

ii.          this interaction of the viral proteins with the cell receptor is the major determinant of species and organ specificity.

iii.         they are important antigens that induce neutralizing antibody and activate cytotoxic T cells to kill virus-infected cells.

c.         Internal proteins:

i.          various types of transcriptases which transcribe mRNA from dsDNA or dsRNA viral genomes or from genomes of viruses with minus sense ssRNA.

ii.          reverse transcriptase, which transcribes DNA from RNA, is found in retroviruses and hepadnaviruses.

iii.         other enzymes found in retrovirus particles are involved in the integration of the transcribed DNA into the cellular DNA.

iv.            histonelike proteins, which may have a regulatory function or may neutralize the negative charge on the nucleic acid during assembly of the virus particle.

7.            Atypical Viruslike agents

a.            Defective viruses:

i.          they are composed of viral nucleic acid and proteins but cannot replicate without a ‘helper’ virus, which provides the missing function.

ii.          they usually have a mutation or a deletion of part of their genetic material.

iii.            because they can interfere with the growth of the infectious particles, they may aid in recovery from an infection by limiting the ability of the infectious particles to grow.

b.            Pseudovirions:

i.          contain host cell DNA instead of viral DNA within the capsid.

ii.          formed during infection with certain viruses when the host cell DNA is fragmented and pieces of it are incorporated with the capsid protein.

iii.         can infect cells, but they do not replicate.

c.         Viroids:

i.          consist solely of a single molecule of circular RNA without a protein coat or envelope.

ii.          small RNA does not code for any protein.

d.         Prions:

i.          they are infectious protein particles made solely of proteins encoded by a single cellular gene.

ii.          they are implicated as the cause of certain diseases such as Creutzfeldt-Jakob disease.

iii.            because prion proteins are found associated with cell membranes, their pathogenicity may be related to alterations of membrane function.