January 2010


Viruses are "particles" composed of nucleic acid, protein, and (for some viruses) lipid. The surface proteins allow the virus particle to attach to and enter into a susceptible host cell, and once inside, the nucleic acid can somehow get replicated and expressed. Many new virus particles may get produced and released from the (usually dying) cell. This virus life cycle, which typically takes less than 24 hours for viruses that infect humans, may repeat over and over as long as there are host cells available or until the host organism's immune system successfully counters the infection. Pathology to the host can result directly from the destruction of many millions of host cells and/or indirectly from the overall effects of the immune response.

1. What is the simplest possible virus life cycle?

Figure 1 (below) shows a hypothetical virus with a genome of just one gene, which codes for a protein which aggregates to form the capsid of the virion. For a virus to be this simple, it would have to depend completely on host cell enzymes and machinery for viral genome replication, transcription, and translation.
There is no known virus that is this simple.

2. What are the genomes of the major viruses infecting humans?

Table 1 (link) describes the genomes of some of the major viruses infecting humans.

A good "order of magnitude estimate" for virus genomes is that one gene takes up about a thousand bases. Thus, we see that all of the RNA genome viruses have about ten genes. Some of the DNA viruses also have about ten genes, while others, particularly the herpesviruses and the poxviruses, have about a hundred genes.

3. What are the basic geometries of virions (virus particles)?

Some figures from A. J. Cann's 2001 book Principles of Molecular Virology show examples of viruses with helical and icosahedral capsid structures.

As shown in Figure 2.3, the rhabdoviruses (such as rabies) have a helical nucleocapsid surrounded by a lipid-protein envelope. Most of the other group V viruses also have a virion structure consisting of a helical nucleocapsid surrounded by an envelope. In terms of structure and the mechanism of assembly, the most highly characterized viral helical capsid is that of Tobacco Mosaic Virus, TMV, as shown in Figure 2.16.

Figures 2.4 and 2.5 show basic icosahedral geometry, and Figure 2.6 shows the "triangulation number 3" icosahedral structure of picornavirus virions (poliovirus, rhinovirus, and hepatitis A virus).

Some other viruses have an icosahedral-based structure that is significantly more complex. In the reoviruses, there is a complicated "doubled-shelled" icosahedral structure surrounding an inner core (Figure 2.14). In the herpesviruses, there is an icosahedral capsid surrounded by an amorphous layer called the "tegument" and a lipid-bilayer envelope (membrane) that contains numerous glycoproteins.

The largest and most complex virions are those of the poxviruses, as shown in Figure 2.11.
Poxvirus virions contain two lipid bilayer envelopes, and an overall shape that is distinctly different from other viruses.


4. What do some of these more complicated virus structures look like when analyzed by the most recent electron microscopy techniques?

A new technique called cryo-electron tomography has been applied to the study of several complicated enveloped viruses within the past few years. The links below take you to the abstracts of four articles. Go to the full length articles and look at the figures in some detail prior to class. In addition, look for links to more recent journal articles that have cited these papers.

Herpes Simplex Virus: Grunewald et al. Science, 2003

Poxvirus (Vaccinia): Cyrklaff et al., Proc. Nat. Acad. Sci., 2005

Influenza Virus: Harris et al., Proc. Nat. Acad. Sci., 2006

Human Immunodeficiency Virus: Zhu et al., Nature, 2006

One can imagine the simplest possible virus and its life cycle; but no known virus is this simple. Of the viruses that infect us and other animals, there is a wide variety of structural and genome variation. Virions have capsid proteins packed in either helical or icosahedral symmetry, and about half have a lipid-protein envelope. Viral genomes are either DNA or RNA, single stranded or double stranded. DNA viruses have genome sizes of anywhere from several thousand bases to about two hundred thousand bases, while RNA viruses have genomes that fall into a much narrower range, from about 8 to 20 thousand bases.


Figure 1