Supplemental Lecture (98/04/18 update) by Stephen T. Abedon (abedon.1@osu.edu)

1. Chapter title: Virus Particles
1. A list of vocabulary words is found toward the end of this document
2. Most viruses do not cause human disease. In fact, the vast majority of viruses not only do not cause human disease, but are incapable of replicating in or on humans. The study of viruses, therefore, is not necessarily one associated, in any specific way, with a study of human disease. Furthermore, just because something is a virus does not mean that it might be capable, in any way, of interacting with your body.
3. On the other hand, of those viruses which people study and lay persons are aware, the vast majority cause human disease (simple self interest is no doubt the cause of this bias). Virus diseases range from mild to usually fatal. The difference is very often between what kind of virus is doing the infecting though also can include whether the infected person (the host) is especially sensitive or resistant.
4. In many cases, once infected by a given type of virus, the body memorizes an immune response which prevents future infection by a virus of that type. Sometimes the type is fairly broadly defined (or, stated more precisely, only a narrow spectrum of viruses is able to cause a specific disease, all recognized interchangeably by the immune system). These viruses consequently tend to be ones that strike early in life and for which lifetime immunity results (chickenpox, measles, etc.). In other cases a given disease is caused by a multitude of viruses and, consequently, susceptibility to the disease declines only slowly with time and exposure (common cold, influenza).
5. Treatment of virus disease is often limited due to the virus producing few target proteins upon which a "magic bullet," one capable of killing the virus while sparing the host, might act. In fact, viral treatments often target normal functions of virus harboring (as well as non-harboring) cells and consequently can cause severe side effects. As a result, usually the very best "treatment" for viral infection is the widespread use of prophylactic vaccination. Such vaccines immunologically mimic the effects of virus disease and, at best, render lifetime immunity similar to that acquired through actual infection.
6. Although not covered here, it should be kept in mind when considering the physiology of viruses that much of the work involved in elucidating an understanding of this physiology was done in conjunction with the use of viruses as simple, model systems. These model systems were employed to characterize eucaryotic and bacterial cell physiology. In other words, very often there is little difference between the means by which a virus employs a cell's biochemical machinery and the way an uninfected cell uses it. Particularly, virus infected cells often can be much easier to work with and specifically characterize than are uninfected cells.
7. My intention with this lecture (and the next two, titled virus growth and virus types) is to give an overview of virology which will lead to a general understanding of what a virus is . Elsewhere we will go through the various types of viruses that exist, as well as additional concerns of virus disease including the mechanisms of virus induced cell damage, cellular antiviral i
2. Obligate intracellular parasite
1. An obligate intracellular parasite is a parasite that is incapable of replicating except when inhabiting the inside of a cell.
2. All viruses are obligate intracellular parasites.
3. There exist a number of bacterium which are also obligate intracellular parasites (i.e., the chlamydias and the rickettsias).
3. What is a virus?
1. Simple living/complex non-living:
1. Viruses are either:
1. the most complex of not living things or
2. the simplest of living things
2. I, as a microbiologist with a strong interest in viruses, prefer to think of viruses as the latter.
2. Viruses:
1. are obligate intracellular parasites

have RNA or DNA genome(s) protect their genome while in the acellular state by employing a protein coat^*

2. an absence of metabolic machinery including (in most cases) no ribosomes (and, certainly, no currently functioning ribosomes)
3. *In many cases this "coat" additionally contains lipid and carbohydrate

Viruses may also be described as infectious, acellular particles which:

1. display a metabolically active state during infection
2. display a metabolically inactive state during extracellular passage
3. Viruses may also be described as genetic parasites:
1. it is more or less bare nucleic acid which does the parasitizing
2. a protein, etc. shell serves as a disposable transfer vehicle that delivers the nucleic acid from cell to cell.
4. Virus origins:
1. Whether viruses are more closely related to their hosts than to other viruses (or higher taxonomic categories) is really not well understood (or, at least, not completely generalizable).
2. Mainly, the answer to the question of virus origins depends on:
3. just where viruses came from evolutionarily (i.e., phylogenetically)
4. how capable viruses are of switching to new species of hosts
5. Note that this fuzziness about just where viruses come from is due to the limits of phylogenetic classification.
6. However, virus lineages probably cannot be traced backward without passing through cellular lineages (which is another way of saying that first their were cells, and viruses were created by cells---i.e., out of control genetic material capable of transmission to new hosts).
7. Viruses probably also cannot be described as a monophyletic lineage (which is another was of saying that viruses probably were created by cells more than once).
8. One method for distinguishing viruses are by the kingdoms they infect. Particularly, viruses are differentiated into those which infect:
1. plants (plant viruses)
2. animals (animal viruses)
3. bacteria (bacteria viruses, a.k.a., bacteriophage or phage)
4. fungi (mycoviruses)
5. etc.
4. Size of viruses
1. Ultramicroscopic:
1. Most viruses are so small they are considered ultramicroscopic.
2. Particularly, most viruses are not visible, under even the best of circumstances, even through the best light microscopes (i.e., one must employ and electron microscope to "see" most viruses).
3. Exceptional are pox viruses which cause such things as smallpox---they are nearly as large as the smallest bacteria).
2. Difficult to filter:
1. This small size allows viruses to pass through filters which trap bacteria.
2. This lack of filterability of viruses was the initial manner in which viruses were distinguished from infections caused by bacteria and other cellular forms.
3. (Note that this is not to say that viruses cannot be filtered, only, for example, that their filtration requires filters with smaller holes than those necessary to filter bacteria.)
3. Observing the unobservable:
1. Because of their small size, virologists employ a number of tricks to allow them to keep track of, or follow virus replication.
2. Usually these tricks involve observation of the host cell or tissue in which in the virus is growing.
4. example: plaque assay:
1. A simple means of making viruses visible to the naked eye is through the plaque assay which works in a manner analogous to bacterial colonies grown on solid medium.
2. Alternatively, for example, viruses may be followed in terms of their microscopic cytopathic effects on host cells.
5. Virion [virus particle]
1. A virion or virus particle is a mature virus potentially capable of surviving in the extracellular state.
6. Free virus
1. A free virus is a virion which has been released from the intracellular state.
7. Utility of nucleic acid packaging
1. The nucleic acid containing coat of a virion particle (called an envelope and/or capsid) play at least three roles in the virus life cycle:
1. protection
2. attachment
3. penetration
2. Packaged genomes in free viruses are protected from extracellular degradants.
3. The capsids of enteric viruses tend to be both resistant to and protect their virus genomes from stomach acid and digestive enzymes.
4. Proteins on the surface of free viruses serve as a means of virus-to-cell attachment.
5. Proteins on the surface of free viruses also serve to transfer virus genomes into cells to effect infection (i.e., adsorption and entry ).
8. Adsorption [attachment, penetration]
1. Binding cell:
1. The binding of a virus to the outside of a potential host cell is termed adsorption.
2. Often adsorption follows an extracellular search period which involves little more than virion diffusion and random collision with potential host cells.
3. Adsorption typically constitutes the first step of viral infection.
2. Multistep process:
1. Adsorption may occur in more than one step.
2. The first steps of adsorption often are reversible and involve only the transient binding of a coat protein or envelope protein to a cell receptor.
3. Subsequent steps are irreversible at least in part because they involve irreversible changes in the conformation of virus capsid or envelope proteins. In other words, at some point in the adsorption process a virus must irrevocably commit to the adsorption of a particular cell.
3. Adsorption is mediated by proteins displayed by the capsid (in nonenveloped viruses) or envelope proteins (in enveloped viruses).
9. Virus genes
1. Viruses vary greatly in number of genes . This leads directly to great differences in degree of complexity (the more genes, the more complex a virus may be, either morphologically, in terms of life history, or both).
2. Variation in number of genes/complexity:
1. Minimally, a virus must have whatever genes are necessary to replicate and package its genome , i.e., to synthesize new virions .
2. Some viruses thus only have a few genes .
3. There exist viruses which contain hundreds genes , many of which code for much more than these basic functions.
10. Virus protein
1. Virus proteins are protein products of virus genes , i.e., genes found on the virus genome .
2. Virus enzymes:
1. In addition to structural genes used in the virus coat, viruses may produce numerous enzymes.
2. Most of the virus proteins that are enzymes are used only inside of cells, i.e., they are not packaged into the virus particles.
3. Some virus enzymes, however, are intentionally packaged within capsids. These enzymes may be employed during and after entry and include nucleic acid polymerases as well as various enzymes involved in hydrolyzing host macromolecules.
11. Receptor molecule(s)
1. Products of host cells:
1. Receptor molecule(s) are molecules, often proteins , that a virus recognizes and binds to effect adsorption or entry .
2. Receptors may also consist of, for example, carbohydrate displayed on the surface of eucaryotic cells.
3. These molecules are host, not virus products (i.e., products of host rather than virus genes).
4. They are a property of the cells which are subsequently (potentially) infected by viruses.
2. Cell surface molecules:
1. Receptor molecules, especially those first seen by free virus are called primary receptors and tend to be cell surface molecules.
2. Interaction with these primary receptors generally constitutes the first step of viral infection.
3. There may exist subsequent cell macromolecules with which the virus interacts in the course of adsorption. These subsequent molecules may be termed secondary receptors and may be found in various locals on or within the cell envelope.
12. Capsid [capsomer]
1. Virus protein coat:
1. Capsids are the virus proteins (here called capsomers) that surround the virus genome as it is found in the virion particle .
2. The proteins from which make up these coats spontaneously self assemble intracellularly and incorporate the virus genome.
3. Incorporation occurs either during or following this self assembly. For virus particle viability, this incorporation must occur prior to the release of free virus from the cell.
2. These are the proteins associated with protecting the free virus from extracellular physical and chemical degradants, as well as the proteins involved in cell recognition and entry.
3. Viral defining structure:
1. By the definition of virus, a virus genome must be found at least from time to time within a capsid (depending on the degree to which a virus bypasses an extracellular state during its replication---i.e., see latent infection).
2. For many viruses the virus genome is packed within a capsid at least once per life cycle.
4. Complex variations on the capsid theme:
1. An exception in detail if not in spirit is found among the poxviruses which display more complex nucleic acid packaging than the relatively simple protein capsids displayed by many viruses.
2. In addition, bacteriophage can display amazingly complex protein-based capsids.
13. Nucleocapsid
1. A nucleocapsid is a viral capsid which has a virus genome packaged within it.
14. Envelope [enveloped virus]
1. Lipid bilayer surrounding capsid:
2. An enveloped virus is a virion whose capsid is surrounded by a lipid bilayer .
3. The lipid bilayer is called an envelope.
4. Host membrane derived:
1. The virus envelope may be derived from:
2. the cytoplasmic membrane
3. the nuclear membrane
4. the endoplasmic reticulum
5. of the host cell, which one depending on the type of virus.
15. Envelope protein [spike, peplomer] ---
1. Membrane proteins:
1. Found in the lipid bilayer are virus proteins (envelope proteins) that are involved in virus adsorption and entry .
2. These virus proteins are membrane proteins.
16. nonenveloped virus [naked nucleocapsid]
1. Non-membraned:
1. Nonenveloped viruses are virions whose activity is not dependent on the presence of an envelope, i.e., these viruses lack envelopes .
2. The capsids of nonenveloped viruses consequently form the only layer of defense between the virus genome and the extracellular environment.
2. Functional differences:
1. Among animal viruses, the nonenveloped and enveloped viruses differ in how they enter and leave the host cell.
2. In contrast to enveloped proteins, it is upon the capsids of nonenveloped viruses that the virus proteins responsible for effecting adsorption and entry are found.
3. Generalizations:
1. Bacteriophage tend to be nonenveloped viruses while a great deal of enveloped viruses are found among the viruses of eucaryotes.
2. Among animal viruses, most RNA viruses are nonenveloped.
3. "Environmental conditions that destroy membranes---increased temperature, freezing and thawing, pH below 6 or above 8, lipid solvents, and some chemical disinfectants such as chlorine, hydrogen peroxide, and phenol---will also destroy the envelope. Naked viruses generally are more resistant to such environmental conditions." (p. 272, Black, 1996)
17. Inactivation by antibody binding [inactivating antibody]
1. Interference with adsorption:
1. The mechanisms of adsorption (and entry ) may be interfered with through antibody binding.
2. Such interference, if complete, is called virus inactivation.
2. Immune system selective pressure:
1. Inactivation by antibody binding represents powerful selection against virus variants which are easily recognized by host antibodies which are capable of effecting inactivation.
2. Many viruses have evolved envelope proteins (or capsomers) which are somewhat resistant to recognition by inactivating antibodies.
3. Within a population of virus infecting a single individual who exhibits an anti-virus humoral (antibody) immune response, there can exist virus variations which display envelope proteins (or capsomers) which are not inactivated by any antibodies currently produced by the host.
4. Such viruses, all else being equal, may display a selective advantage associated with their ability to avoid inactivation by antibody binding.
3. Constraints on evolution:
1. At the same time there will be constraints on the evolutionary change these proteins can undergo because virus envelope proteins and capsomers must retain their abilities to effect virus adsorption and entry .
2. Thus one finds compromise in the mutational variation among viruses between
1. avoidance of the host immune response
2. retention of viability, independent of immune response
4. Example: HIV in vivo:
1. Mutational variation among envelope proteins exhibited by the Human Immunodeficiency Virus (HIV) has been exhaustively studied.
2. HIV appears to sequester its receptor protein binding sites deep within clefts in their envelope protein.
3. This sequestering makes these sites resistant to antibody binding and presumably make such viruses resistant to inactivating antibody when propagating in vivo.
5. Example: HIV in vitro:
1. In HIV populations maintained in vitro (cell culture) where they are not under antibody selection, evolution seems to favor a decline in the degree to which these receptor protein binding sites are hidden.
2. This makes in vitro propagated HIV often much easier to inactivate with antibodies than wild isolates.
3. These evolutionarily modified viruses appear to be more capable of rapidly adsorbing to the cells employed for in vitro propagation (i.e., domesticated virus appears to adapt, often quite rapidly, to replication within the tissue culture environment).
18. Inactivation of free virus [HIV vs. HBV]
1. Durability affects transmissability:
1. The susceptibility of free virus to inactivation, especially when found outside of the body, varies considerably.
2. All else being equal, the durability of a virion particle can have dramatic effects on the likelihood of infection given indirect exposure to persons harboring virus.
2. Example: HIV:
1. The HIV particle is very unstable outside of the body.
2. It is, in fact, difficult to acquire an HIV infection under any circumstances except for intimate contact with fresh body fluids.
3. Example: HBV:
1. The hepatitis B virus (HBV), on the other hand, can remain infective for days in dried blood, months in serum stored at room temperature, and even decades when frozen.
2. Exposure to 60°C for four hours does not destroy it!
3. Boiling, halogen disinfectants, and aldehyde disinfectants are effective at killing it.
4. Autoclaving, however, is the most reliable of methods.
4. Identical portals of entry:
1. HIV and HBV are transmitted via the same routes.
2. Health care workers concerned about avoiding HBV transmission will automatically avoid HIV transmission.
3. HBV vaccination, however, serves as a way out for health care workers from the high infectivity and durability of HBV virions.
5. immunity, and antiviral vaccination.
19. Vocabulary
1. Adsorption
2. Attachment
3. Capsid
4. Capsomer
5. Envelope
6. Envelope protein
7. Enveloped virus
8. Free virus
9. Inactivating antibodies
10. Inactivation by antibody
11. Inactivation of free virus (HIV vs. HBV)
12. Naked nucleocapsid
13. Nonenveloped virus
14. Nucleocapsid
15. Obligate intracellular parasite
16. Penetration
17. Peplomer
18. Receptor molecule
19. Spike
20. Utility of nucleic acid packaging
21. Virion
22. Virus genes
23. Virus particle
24. Virus protein
25. What is a virus?
20. Practice questions
1. The cell surface receptor molecule recognized by a virus (circle only one correct answer) [PEEK]
1. may be a protein
2. may be a carbohydrate
3. is a character belonging to the host
4. is recognized during the first step of adsorption
5. all of the above
6. none of the above
2. What is an obligate intracellular parasite (give definition, not example)? [PEEK]
3. Give one reason that some scientists are disposed to arguing that viruses are not alive. [PEEK]
4. Other than that viruses can exist in an acellular state, what principle means historically has been used to distinguish viruses from cellular infectious particles? [PEEK]
5. Which of the following typically consists of just protein? (circle best answer) [PEEK]
1. viral genome.
2. viral capsid.
3. viral envelope.
4. viral receptor molecules.
5. virion particle.
6. virus genes.
6. Name something that a viral envelope protein and a capsid protein of a non-enveloped virus might have in common. [PEEK]
7. Name a specific parasite, other than a member of genera Bdellovibrio, Chlamydia, or Richettsia, which is an obligate intracellular parasite. [PEEK]
8. The collision of a virus with a cell and subsequent attachment to the cell is called ___________. These processes are steps by which the nucleic acid of a virus is subsequently deposited in the cell cytoplasm. [PEEK]
9. The molecule on the surface of a cell to which an incoming virus attaches is called a __________. [PEEK]
10. Why do you suppose an animal virus grown in (and then isolated from) tissue culture might be more susceptible to inactivation by antibody than a similar virus propagated (and then isolated from) in an animal? That is, assume you do the assay by isolating the viruses grown in these two different environments from antibody (pariticularly in the case of the animal-grown virus) and then seek to compare in a controlled environment which virus particle is inactivated more readily by the presence of appropriate antibody. [PEEK]
11. You discover that the virus you are working with experimentally, one that you have been propagating in vitro (tissue culture using serum-free tissue culture medium), has, over time, been showing less and less virulence upon propagation in live animals. In terms of differences between your in vitro growth conditions and those likely to be present in live animals, why might this be so? (hint: the live animal virulence assay is done with new animals, i.e., ones not previously exposed to the virus). [PEEK]
12. __________ is the technical term for the binding of a virus to the outside of a potential host cell. [PEEK]
13. Where does one usually find receptor molecules used by viruses? [PEEK]
14. A component of all viruses is __________. [PEEK]
1. DNA
2. an envelope
3. a protein capsid
4. one or more envelope proteins
5. a lipid bilayer
6. a nucleus
15. Which of the following is not an obligate intracellular parasite? [PEEK]
1. Mycobacterium tuberculosis
2. Rickettsia rickettsia
3. bacteriophage T4
4. Chlamydia trachomatis
5. human immunodeficiency virus
6. a non-enveloped, double-stranded DNA virus
16. A virion (or virion particle) is a mature virus capable of existing (and functioning) outside of its parental, host cell. A virion particle which is no longer contained within a cell (i.e., has been released by some mechanism) may be referred to additionally as a __________ virus. [PEEK]
21. Practice question answers
1. v, all of the above
2. obligate = necessarily so, can't do it any other way; intracellular = lives or exists within a cell; parasite = half of a symbiotic relationship, the species that does the harm. An obligate intracellular parasite is a generally-net-destructive class of organisms (there are some exceptions) which can replicate only when found on the inside of a cell. An example is a virus.
3. They are capable of existing in an acellular state.
4. Most viruses are capable of passing through filters which are capable of trapping most cellular life forms.
5. ii, viral capsid.
6. (i) responsibility for attachment to host; (ii) site of antibody binding to effect inactivation; protection is not a good answer.
7. HIV, HBV, influenza virus, bacteriophage T4, bacteriophage lambda, etc. That is, viruses.
8. Adsorption.
9. Receptor molecule, viral receptor.
10. In tissue culture inactivation by antibody binding does not occur (unless antibody is actually added to the culture which is usually not done). Therefore, any suppression of capsomer activity (such as adsorption rate or efficiency) caused by selection against antibody inactivation is removed. Variants which display enhanced function at the expense of increased susceptibility to antibody inactivation can preferentially accumulate. Tissue culture propagated viral stocks consequently tend to be become more susceptible to antibody inactivation as compared with their animal propagated counterparts
11. The easy answer to this question is simply that your virus has adapted to tissue culture growth and therefore is no longer as well adapted to growth in an animal. This is a way in which live-attenuated vaccines may be acquired. An alternative, more specific answer might have something to do with immune system evasion, i.e., the organism grown in tissue culture displays less resistance to the onslaught of both humoral and cell-mediated immunity. For example: Your in vitro conditions lack selection by an immune system. Increased growth efficiency in vitro therefore evolves at the expense of immune system evasion (which is irrelevant in tissue culture). Following repeated propagation in tissue culture this acquired mitigation of immune system evading adaptations become the virus' Achilles' heal. Upon propagation with an animal host the virus shows a reduced ability to cause disease because of increased susceptibility to the host immune response. It therefore displays a reduced pathogen virulence. Note that other explanations which are less immune system related can also explain such a decline in virulence such as a change in virus tropism to one favoring propagation in the cells found in tissue culture over those present in live animals. By the way, the use of serum-free medium assures that it lacks antibody.
12. adsorption.
13. The molecule (or molecules) to which a virus initially attaches upon adsorption are typically found on the surface of cells.
14. iii, a protein capsid.
15. i, Mycobacterium tuberculosis
16. free
22. References
1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. 270-274.
2. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 573-588.
3. Talaro, K., Talaro, A. (1996). Foundations in Microbiology. Second Edition. Wm. C. Brown Publishers. pp. 160-188, 741-766, 767-813 .
4. Tortora, G.J., Funke, B.R., Case, C.L. (1995). Microbiology. An Introduction. Fifth Edition. The Benjamin/Cummings Publishing, Co., Inc., Redwood City, CA, pp. 332-363.