Supplemental Lecture (98/04/22 update) by Stephen T. Abedon (

  1. Chapter title: Virus Types
    1. A list of vocabulary words is found toward the end of this document
    2. A great variety of viruses are known. It is often said, in fact, that all cellular species likely have at least one associated virus. This statement, though not necessarily true, is nevertheless a reflection of the confidence microbiologists have in how successfully exploited the "virus niche" must be. Certainly all phyla have their associated viruses. In fact, the virus niche is sufficiently broad that even many viruses have viruses: defective viruses which are only able to reproduce when they coinfect with another specific virus. In this lecture we consider various means by which viruses, especially those which infect animals, may be differentiated.
  2. Some human diseases caused by viruses
    1. AIDS
    2. Burkitt's lymphoma
    3. chicken pox
    4. colds
    5. Colorado tick fever
    6. dengue
    7. encephalitis
    8. fever blisters
    9. genital warts
    10. gastroenteritis
    11. genital herpes
    12. German measles
    13. hepatitis
    14. influenza
    15. leukemia
    16. liver cancer
    17. measles
    18. mononucleosis
    19. mumps
    20. oral herpes
    21. polio
    22. rabies
    23. shingles
    24. smallpox
    25. virus hemorrhagic fever
    26. warts
    27. yellow fever .
  3. Animal virus classification
    1. Adenoviridae
    2. Arenaviridae
    3. Bunyaviridae
    4. Caliciviridae
    5. Coronaviridae
    6. Filoviridae
    7. Hepadnaviridae
    8. Herpesviridae
    9. Orthomyxoviridae
    10. Papovaviridae
    11. Paramyxoviridae
    12. Parvoviridae
    13. Picornaviridae
    14. Poxviridae
    15. Reoviridae
    16. Retroviridae
    17. Rhabdoviridae
    18. Togaviridae
  4. Virus species
    1. Similarity plus host:
      1. A virus species is a population of viruses with similar characteristics plus which infect the same (or nearly so) range of host species .
      2. Notice how virus species are defined much more in terms of their host niche than bacterial species are defined in terms of their niche or niches.
      3. This is likely at least in part an artifact of how bacterial vs. virus species are identified in the laboratory:
        1. bacteria are identified based on growth and morphological characteristics in artificial environments
        2. viruses are identified in terms of what host is infected (in a sense, the host upon which a virus grows is simply an important virus growth characteristic)
  5. Nomenclature
    1. Common name nomenclature:
      1. Note that virus species names have not been established; consequently viruses are described by their common names.
      2. Note that common names are not italicized.
      3. Influenza virus or varicella-zoster virus (chickenpox) are both examples of common names.
    2. Subspecies nomenclature:
      1. Virus subspecies are often described by adding numbers to the common name.
      2. HIV-1 and HIV-2 are both considered subspecies of HIV (human immunodeficiency virus).
  6. Viral permutations
    1. Viruses may be distinguished in a number of ways beyond into different species.
    2. Distinguishing features include:
      1. tropism (target cell)
      2. host range
      3. virion morphology
      4. genetic material
      5. genome structure
      6. genome sequence
  7. Target cell [tropism]
    1. Cells which may be infected:
      1. Target cells are those which a given virus may infect.
      2. Cells from different species, conspecifics, or even different cell types within the same individual can display significant variation in receptivity to virus infection (i.e., may or may not serve as target cells).
      3. Particularly, viruses may fail to adsorb and likely are not compatible with the biochemistry of all types of cells.
    2. Cell types which may be infected:
      1. The type of cell within a given individual host cell, which a virus can infect, is referred to as a virus' tropism.
      2. Different species of viruses tend to vary both in their specific tropisms as well as in the breadth of their tropisms (i.e., they differ both in what cells they can infect and in how many different kinds of cells they can infect).
  8. Enteric virus
    1. Enteric viruses are viruses which infect cells lining the gastrointestinal tract.
    2. Mouth portal of entry:
      1. Additonally, viruses which have a gastrointestinal portal of entry (particularly one beginning with ingestion at the mouth) are termed Enteric viruses.
      2. The polio virus, for example, has a fecal-oral portal of exit and entry, is an enteric virus. However it does its most harm (polio myelitis) when infecting cells other than those of the gastrointestinal tract.
  9. Host range
    1. Range of host species that may be infected:
      1. A virus' host range is the range of cell types and, particularly, host species a virus is able to infect.
      2. As with tropism, host range is usually a function of either or both:
        1. an inability of the virus to successfully adsorb and/or enter cells because of an incompatibility between virus capsid proteins (or virus envelope proteins ) and the host receptor molecule
        2. an incompatibility between the biochemistry of the virus and the biochemistry of the host. Very often, for closely related hosts, the biochemical differences can be quite subtle (i.e., difficult to pin down).
    2. Between species variation:
      1. As with virus tropism, viruses can vary in terms of the breadth of their host range.
      2. Thus, some viruses infect one or only a few species while others (such as the rabies virus or poxviruses) are capable of infecting a broad range of species.
    3. Change in host range (or tropism) can occur through virus mutation.
    4. Example: distemper on the Serengeti:
      1. For example, in the Serengeti a 1994 die off of lions apparently was caused by a canine distemper virus (CDV) variant which jumped from domestic dogs. Cats normally are thought to be not susceptible to CDV. This variant apparently changed both host range and tropism:
      2. "Between 1993 and 1994, a CDV epidemic swept through villages to the west o f the Serengeti, killing thousands of domestic dogs. Monoclonal antibody tests show similarities between this strain and the one that infected the lions. The researchers propose that the virus then entered the park, perhaps via jackals and spotted hyenas, which frequently scavenge near humans. Because CDV is shed in mucus, these animals, in turn, probably infected lions at kill sites, where there is often a lot of biting and snarling between species. . . at least 1000 of the park's 3000 lions are thought to have died of the disease." Other variants of CDV-like viruses have also been identified which infect dolphins, horses, and seals. (p. 596, Morell, 1996)
  10. Arbovirus
    1. Arboviruses are viruses which are transmitted by an insect vector (arbo stands for arthropod-borne).
  11. Bacteriophage [phage]
    1. Bacteriophage (phage) are viruses that infect bacteria .
    2. T-even bacteriophage:
      1. Bacteriophage were very important model organisms during the the 1950's and 1960's. They can also be rather amazing to behold. Referring to T-even bacteriophage (which includes bacteriophage T4):
      2. "Momentarily setting aside a strictly scientific and objective tone, it is tempting to think of these extraordinary viruses as minute spacecrafts docking on an alien planet to unload their genetic cargo." (p. 172, Talaro and Talaro)
  12. Virus morphology
    1. Viruses, as viewed through the electron microscope , come in a variety of shapes (i.e., morphologies) that may be divided into:
      1. helical viruses
      2. polyhedral viruses
      3. enveloped viruses
      4. enveloped polyhedral viruses
      5. complex viruses
  13. Helical viruses
    1. Helical viruses are nonenveloped with capsomeres which are arranged helically around the virus genome .
    2. That is, like a spiral staircase or, better, one of those helical parking lot ramps, with the genome arranged up the hole in the middle.
    3. See Tobacco Mosaic Virus in figure 11.2, p. 273 of Black, 1996.
  14. Polyhedral viruses [icosahedral]
    1. Polyhedral viruses are nonenveloped viruses whose capsids form geometric shapes with flat sides (i.e., faces) and edges.
    2. Icosahedral:
      1. An example is an icosahedron which has 20 equilateral triangle faces and 12 corners.
      2. Though apparently complex, a very large number of otherwise unrelated viruses are icosohedral.
      3. See Reovirus, Adenovirus, and Picornavirus in figure 11.2, p. 273 of Black, 1996.
  15. Enveloped helical virus
    1. Enveloped helical viruses are enveloped viruses whose envelope surrounds a capsid with helical virus morphology.
    2. See Paramyxovirus in figure 11.2, p. 273 of Black, 1996.
  16. Enveloped polyhedral virus
    1. Enveloped polyhedral viruses are enveloped viruses whose envelope surrounds a capsid with polyhedral virus morphology.
    2. See Herpesvirus and Togavirus in figure 11.2, p. 273 of Black, 1996.
  17. Complex virus
    1. The morphology of complex viruses consists of complex combinations of structures that may or may not be completely consistent between viruses of the same species.
    2. Tailed bacteriophage are complex viruses.
    3. See T4 Bacteriophage and Poxvirus in figure 11.2, p. 273 of Black, 1996.
  18. Virus genome [plus strand, minus strand]
    1. Though the genome of many viruses consists of DNA just like cellular organisms, many other viruses instead have genomes made up of RNA .
    2. RNA viruses employ special, virus coded polymerases to transcribe and replicate their genomes.
    3. Extreme structural variation:
      1. Beyond whether a virus has an RNA or DNA genome, viruses differ in the structure of their genomes .
      2. Below is a list of viral structural permutations:
        1. RNA or DNA genome
        2. may be short or long*
        3. may be haploid or diploid **
        4. may be segmented or not segmented***
        5. may be linear or circular
        6. may be single- or double-stranded
        7. if single stranded, may be plus-stranded or minus-stranded****
      3. *Number of genes tends to be a function of length which, in turn, determines the degree of complexity displayed by a viruses .
      4. **Note that very few viruses have diploid genomes.
      5. ***Segmented means broken up into more than on section.
      6. **** The strand from which mRNA is templated (i.e., transcribed ) is called the minus or antisense strand. The complementary strand is equivalent to, or in some cases actually is the mRNA (and is called the plus or sense strand).
    4. See Illustration below.
    5. Animal virus structural generalizations:
      1. Among DNA viruses which infect animals, all are double-stranded except those known as parvoviruses (which have single-stranded DNA genomes).
      2. Among RNA viruses which infect animals, all are single stranded except those known as reoviruses (which have double-stranded RNA genomes).
  19. Illustration, variation in virus genomes
  20. Virus taxonomy
    1. Morphological classification:
      1. Host range aside, viruses traditionally are distinguished by their morphologies (at least, of course, in the present electron microscopy era).
      2. Much of virus classification has consequently been done mostly via the study of morphologies and is called virus taxonomy.
    2. Genomic classification:
      1. Viruses are also differentiated by similarities and differences in their genomes . See virus species.
      2. The morphologies of various families of human-infecting viruses are shown in tables 11.1 and 11.2 (p. 276, Black, 1996) along with a listing of representative virus genera and common names.
  21. Virus types
    1. Standard nomenclature:
      1. Viruses are first classified as having animal, plant, bacterial, etc. hosts. Within each large host-based phylogenetic grouping there exist numerous schemes of virus classification.
      2. "A widely used scheme for classifying animal viruses first assigns them to one of two superfamilies, either those containing DNA or those containing RNA. DNA viruses can be further subdivided into six families, and RNA viruses into 17 families, for a total of 19 families. Virus families are given a name comprised of a Latin root followed by -viridae. Characteristics used for placement in a particular family include type of capsid, nucleic acid strand number, presence and type of envelope, overall viral size, and area of the host cell in which the virus multiplies. . . Each different type of virus is also assigned genus status according to its host, target tissue, and the type of disease it causes. Viral genera are denoted by a special Latinized root followed by the suffix -virus (for example, Enterovirus and Herpesvirus). Because the use of standardized species names has not been widely accepted, the genus or common English vernacular names (for example, poliovirus and rabies virus) predominate in discussions of specific viruses." (p. 169, Talaro and Talaro, 1996; see also pp. 170-171 in Talaro and Talaro, 1996)
    2. Double-stranded, enveloped, DNA viruses of animals:
      1. Hepadnaviridae (hepa-DNA-virus) infect the liver and includes hepatitis B virus (HBV). All health workers should be vaccinated against HBV.
      2. Herpesviridae include:
        1. herpes simplex 1 (oral herpes)
        2. herpes simplex 2 (genital herpes)
        3. herpes zoster (varicella-zoster, a.k.a., chickenpox)
        4. cytomegalovirus (CMV)
        5. Epstein-Barr virus (EBV)
        6. etc.
      3. Herpesviruses have a tendency toward latent and recurrent infections, and have an associated tendency to incorporate their genome into that of their host.
      4. Latent herpes infections lead to complications particularly in the immunosuppressed.
      5. Poxviridae are the largest and most complex of viruses. The Poxviruses incluce the smallpox virus (Variola major and minor), vaccinia virus, etc.
    3. Double-stranded, non-enveloped, DNA viruses of animals:
      1. Adenoviridae are one of the etiologies of the common cold. About 30 adenovirus strains are known. They can also cause conjunctivitis as well as chronic respiratory infections.
      2. Papovaviridae include those which cause warts (papillomaviruses).
    4. Single-stranded, nonenveloped, DNA viruses of animals:
      1. Parvoviridae cause some human disease, though in most cases symptoms are mild.
    5. Segmented, single-stranded, enveloped, negative sense, RNA viruses of animals:
      1. Arenaviridae
      2. Bunyaviridae includes California encephalitis virus, Hanta virus (hemorrhagic fever).
      3. Orthomyxoviridae includes influenza virus.
    6. Non-segmented, single-stranded, enveloped, negative sense RNA viruses of animals:
      1. Filoviridae includes Ebola fever virus, Marburg virus.
      2. Paramyxoviridae includes:
        1. measles virus
        2. mumps virus
        3. respiratory syncytial virus
      3. Rhabdoviridae includes the rabies virus.
    7. Non-segmented, single-stranded, enveloped, positive sense RNA viruses of animals:
      1. Coronaviridae includes common cold viruses.
      2. Togaviridae includes:
        1. dengue fever virus
        2. equine encephalitis viruses
        3. rubella virus
        4. yellow fever virus
    8. Non-segmented, single-stranded, nonenveloped, positive sense RNA viruses of animals:
      1. Caliciviridae includes Norwalk virus.
      2. Picornaviridae includes hepatitis A virus, polio virus, rhinoviruses.
    9. Retroviridae are animal viruses with the following characteristics:
      1. nonsegmented
      2. single-stranded
      3. enveloped
      4. positive sense
      5. diploid
      6. reverse transcriptase using
      7. RNA genomes
    10. Examples include:
      1. human immunodeficiency virus (HIV, a.k.a., HTLV-III)
      2. human T-cell leukemia virus (HTLV-I)
      3. hairy cell leukemia virus (HTLV-II)
      4. etc.
    11. Reoviridae:
      1. Reoviridae are segmented, double-stranded, nonenveloped (double capsid) positive sense, RNA viruses of animals.
      2. Examples include tick fever virus and rotavirus gastroenteritis.
  22. Vocabulary
    1. Arbovirus
    2. Bacteriophage
    3. Complex virus
    4. Enteric virus
    5. Enveloped helical virus
    6. Enveloped polyhedral virus
    7. Helical virus
    8. Host range
    9. Human diseases
    10. Nomenclature
    11. Phage
    12. Polyhedral virus
    13. Target cell
    14. Tropism
    15. Variation in virus genomes, illustration
    16. Virus genomes
    17. Virus morphology
    18. Virus species
    19. Virus taxonomy
    20. Virus types
  23. Practice questions
    1. Name the virus morphological types represented by each of the above. [PEEK]
    2. Contrast enveloped and non-enveloped virus. [PEEK]
    3. What kind of diseases do HTLV-1 and HTLV-2 cause? [PEEK]
    4. What is the main difference between the viral species concept and the bacterial species concept.[PEEK]
    5. Cellular surface incompatibilities (such as absence of a receptor or receptor existing in appropriate conformation) or (often subtle) cellular biochemical differences serve to define ________. (choose best answer) [PEEK]
      1. the host range of viruses
      2. viral tropisms
      3. what target cells viruses are able to infect
      4. the host species a virus is able to infect
      5. all of the above
      6. none of the above
    6. Which of the following would you expect not to be a property of a virus: (choose best answer) [PEEK]
      1. segmented genome
      2. RNA genome
      3. lack of capsid while in extracellular state
      4. DNA genome
      5. single stranded DNA genome
      6. double stranded RNA genome
    7. Give me the common name of one type of complex virus. [PEEK]
    8. One fortunate thing about AIDS is that it is caused by a virus which has a number of unusual, chemotherapeutically targetable properties. Name four properties of this virus' (HIV's) particle or infection cycle which are distinct from that exhibited by viruses in general (i.e., are not properties of all viruses but are a property of HIV). [PEEK]
    9. Define tropism. [PEEK]
    10. Other than that they cause different diseases, name a feature of human immunodeficiency virus which distinguishes it from hepatitis B virus. [PEEK]
    11. Why is it that the viruses which infect bacteria are described as bacteriophage rather than as bacterial viruses?[PEEK]
    12. How many equilateral triangles make up an icosahedron? [PEEK]
    13. How does the term "tropism" differ in meaning from the term "host range"? [PEEK]
    14. What does it mean for a single-stranded RNA virus to be plus stranded? [PEEK]
    15. Other than that they are both viruses, what do cytomegalovirus and Epstein-Barr virus have in common? [PEEK]
    16. The genomes of different species of viruses can display a great deal of structural variation. Name five general ways in which the virion-packed genomes of viruses may differ structurally (note: by saying "virion-packed" I am implying that I am not looking for differences which may be observed in the course of a viruses life cycle; for example, the genome of a retrovirus is converted from one type to another to another, until finally integrating into the host's genome, etc., all in the course of a single infectious cycle. Instead, for example, consider how genomes of retroviruses, as found in the virion particle, differ structurally from those of other types of viruses). [PEEK]
    17. Give the common name of a plus-stranded RNA virus. [PEEK]
    18. In terms of tropism, distinguish a virus which is capable of causing viral pneumonia from one which is incapable of causing viral pneumonia. [PEEK]
    19. Give two specific examples (i.e., common names) of positive-sense, single-stranded RNA viruses. [PEEK]
    20. Describe a hypothetical virus genome such that it displays five structural characteristics each of which may be shared with some but none of which are shared with all other viruses. [PEEK]
    21. Contrast arbovirus and bacteriophage. [PEEK]
  24. Practice question answers
    1. A. polyhedral, B. enveloped polyhedral, C. helical, D. enveloped helical, E. complex
    2. An enveloped virus has its capsid surrounded by a lipid bilayer derived from a membrane of the host cell. An enveloped virus also has membrane proteins involved in adsorption found in the envelope. Non-enveloped viruses lack this lipid bilayer surrounding their capsid and have the proteins associated with adsorption found directly on (or part of) the capsid. Among animal viruses, DNA viruses tend to be enveloped and RNA viruses non-enveloped (retroviruses are exceptions). In addition, non-enveloped tend to be lytic while enveloped viruses are chronic infectors.
    3. Leukemia
    4. Viral species, unlike bacterial species, are usually defined in terms of the species of hosts they infect. Note, though, that this difference is extraneous because the virus host requirement is essentially just another, albeit complex, growth requirement.
    5. all of the above
    6. iii, lack of capsid while in extracellular state
    7. Lambda, phage T4, ebola, etc., but not HIV.
    8. (i) Diploid, (ii) RNA genome, (iii) positive strand genome, (iv) polyhedral capsid, (v) enveloped virus, (vi) integrates into its host's genome, (vii) uses reverse transcriptase, (viii) single stranded genome, (ix) genome consists of single mRNA, (x) capable of latent infections, (xi) CD4 lymphocyte tropism, (xii) host range limited to humans and chimpanzees, etc.
    9. The range of specific cell types within a single species that a virus is capable of successfully infecting.
    10. A: significantly greater virion particle fragility for HIV; also, HIV but not HBV is a retrovirus so consequently integrates into its host genome.
    11. Bacteriophage were initially characterized as infectious agents which are capable of lysing ("eating") cells and only subsequently was it understood that they additionally are viruses. That is, they were named before they were shown to be viruses.
    12. 20
    13. Tropism refers to the type of cells within a given organism a virus can infect while host range refers to the species (or strains) of host organism a virus can infect.
    14. The strand of RNA is equivalent to a messenger RNA (i.e., as opposed to be complementary to the messenger RNA).
    15. Both are herpes viruses.
    16. RNA vs. DNA, short vs. long, segmented vs. not segmented, single stranded vs. double stranded, circular vs. linear, plus stranded vs. minus stranded.
    17. HIV, the HTLVs, polio virus, hepatitis A virus, equine encephalitis virus, yellow fever virus, rubella virus, etc.
    18. The virus capable of causing viral pneumonia must have a tropism for cells found in the lung, i.e., can successfully infect them, while the latter presumably does not.
    19. HIV, HTLV-I, HTLV-II
    20. For example, RNA, single-stranded, linear, plus-stranded, segmented, haploid, short .
    21. An arbovirus is a virus which is transmitted by an insect while a bacteriophage is a virus that infects a bacterium.
  25. References
    1. Black, J.G. (1996). Microbiology. Principles and Applications. Third Edition. Prentice Hall. Upper Saddle River, New Jersey. pp. 274-280.
    2. Morell, V. (1996). New virus variant killed Serengeti cats. Science 271:596.
    3. Raven, P.H., Johnson, G.B. (1995). Biology (updated version). Third Edition. Wm. C. Brown publishers, Dubuque, Iowa. pp. 572-588.
    4. Talaro, K., Talaro, A. (1996). Foundations in Microbiology. Second Edition. Wm. C. Brown Publishers. pp. 160-188, 741-766, 767-813 .
    5. 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.