·        1: Virus Types

·        A list of vocabulary words is found toward the end of this document

·        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

a:Similarity plus host:

·        A virus species is a population of viruses with similar characteristics plus which infect the same (or nearly so) range of host species .

·        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.

·        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

a :Common name nomenclature:

·        Note that virus species names have not been established; consequently viruses are described by their common names.

·        Note that common names are not italicized.

·        Influenza virus or varicella-zoster virus (chickenpox) are both examples of common names.

b :Subspecies nomenclature:

·        Virus subspecies are often described by adding numbers to the common name.

·        HIV-1 and HIV-2 are both considered subspecies of HIV (human immunodeficiency virus).

·        6 :Viral permutations

·        Viruses may be distinguished in a number of ways beyond into different species.

·        Distinguishing features include:

tropism (target cell)

host range

virion morphology

genetic material

genome structure

genome sequence

7 :Target cell [tropism]

a :Cells which may be infected:

·        Target cells are those which a given virus may infect.

·        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).

·        Particularly, viruses may fail to adsorb and likely are not compatible with the biochemistry of all types of cells.

b :Cell types which may be infected:

·        The type of cell within a given individual host cell, which a virus can infect, is referred to as a virus' tropism.

·        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

a:Enteric viruses are viruses which infect cells lining the gastrointestinal tract.

b:Mouth portal of entry:

·        Additonally, viruses which have a gastrointestinal portal of entry (particularly one beginning with ingestion at the mouth) are termed Enteric viruses.

·        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

a ;Range of host species that may be infected:

·        A virus' host range is the range of cell types and, particularly, host species a virus is able to infect.

·        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).

b :Between species variation:

·        As with virus tropism, viruses can vary in terms of the breadth of their host range.

·        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.

c :Change in host range (or tropism) can occur through virus mutation.

d :Example: distemper on the Serengeti:

·        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:

·        "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

Arboviruses are viruses which are transmitted by an insect vector (arbo stands for arthropod-borne).

11 :Bacteriophage [phage]

a :Bacteriophage (phage) are viruses that infect bacteria .

b   :T-even bacteriophage:

·        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):

·        "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

a :Viruses, as viewed through the electron microscope , come in a variety of shapes (i.e., morphologies) that may be divided into:

helical viruses

polyhedral viruses

enveloped viruses

enveloped polyhedral viruses

complex viruses

13 :Helical viruses

·        Helical viruses are nonenveloped with capsomeres which are arranged helically around the virus genome .

·        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.

·        :See Tobacco Mosaic Virus in figure 11.2, p. 273 of Black, 1996.

14 :Polyhedral viruses [icosahedral]

a :Polyhedral viruses are nonenveloped viruses whose capsids form geometric shapes with flat sides (i.e., faces) and edges.

b :Icosahedral:

·        An example is an icosahedron which has 20 equilateral triangle faces and 12 corners.

·        Though apparently complex, a very large number of otherwise unrelated viruses are icosohedral.

·        See Reovirus, Adenovirus, and Picornavirus in figure 11.2, p. 273 of Black, 1996.

15 :Enveloped helical virus

·        Enveloped helical viruses are enveloped viruses whose envelope surrounds a capsid with helical virus morphology.

·        See Paramyxovirus in figure 11.2, p. 273 of Black, 1996.

16 :Enveloped polyhedral virus

·        Enveloped polyhedral viruses are enveloped viruses whose envelope surrounds a capsid with polyhedral virus morphology.

·        See Herpesvirus and Togavirus in figure 11.2, p. 273 of Black, 1996.

17 :Complex virus

·        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.

·        Tailed bacteriophage are complex viruses.

·        See T4 Bacteriophage and Poxvirus in figure 11.2, p. 273 of Black, 1996.

18 :Virus genome [plus strand, minus strand]

·        Though the genome of many viruses consists of DNA just like cellular organisms, many other viruses instead have genomes made up of RNA .

·        RNA viruses employ special, virus coded polymerases to transcribe and replicate their genomes.

·        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:

RNA or DNA genome

may be short or long* 

may be haploid or diploid **

may be segmented or not segmented***

may be linear or circular

may be single- or double-stranded

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).

·        See Illustration below.

·        Animal virus structural generalizations:

a :Among DNA viruses which infect animals, all are double-stranded except those known as parvoviruses (which have single-stranded DNA genomes).

b :Among RNA viruses which infect animals, all are single stranded except those known as reoviruses (which have double-stranded RNA genomes

20 :Virus taxonomy

Morphological classification:

·        Host range aside, viruses traditionally are distinguished by their morphologies (at least, of course, in the present electron microscopy era).

·        Much of virus classification has consequently been done mostly via the study of morphologies and is called virus taxonomy.

Genomic classification:

Viruses are also differentiated by similarities and differences in their genomes . See virus species.

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

Standard nomenclature:

·        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.

·        "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)

Double-stranded, enveloped, DNA viruses of animals:

·        Hepadnaviridae (hepa-DNA-virus) infect the liver and includes hepatitis B virus (HBV). All health workers should be vaccinated against HBV.

·        Herpesviridae include:

herpes simplex 1 (oral herpes)

herpes simplex 2 (genital herpes)

herpes zoster (varicella-zoster, a.k.a., chickenpox)

cytomegalovirus (CMV)

Epstein-Barr virus (EBV)

etc.

·        Herpesviruses have a tendency toward latent and recurrent infections, and have an associated tendency to incorporate their genome into that of their host.

·        Latent herpes infections lead to complications particularly in the immunosuppressed.

·        Poxviridae are the largest and most complex of viruses. The Poxviruses incluce the smallpox virus (Variola major and minor), vaccinia virus, etc.

Double-stranded, non-enveloped, DNA viruses of animals:

·        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.

·        Papovaviridae include those which cause warts (papillomaviruses).

Single-stranded, nonenveloped, DNA viruses of animals:

·        Parvoviridae cause some human disease, though in most cases symptoms are mild.

Segmented, single-stranded, enveloped, negative sense, RNA viruses of animals:

·        Arenaviridae

·        Bunyaviridae includes California encephalitis virus, Hanta virus (hemorrhagic fever).

·        Orthomyxoviridae includes influenza virus.

Non-segmented, single-stranded, enveloped, negative sense RNA viruses of animals:

·        Filoviridae includes Ebola fever virus, Marburg virus.

·        Paramyxoviridae includes:

measles virus

mumps virus

respiratory syncytial virus

·        Rhabdoviridae includes the rabies virus.

Non-segmented, single-stranded, nonenveloped, positive sense RNA viruses of animals:

·        Caliciviridae includes Norwalk virus.

·        Picornaviridae includes hepatitis A virus, polio virus, rhinoviruses.

Retroviridae are animal viruses with the following characteristics:

nonsegmented

single-stranded

enveloped

positive sense

diploid

reverse transcriptase using

RNA genomes

Examples include:

human immunodeficiency virus (HIV, a.k.a., HTLV-III)

human T-cell leukemia virus (HTLV-I)

hairy cell leukemia virus (HTLV-II)

etc.

Reoviridae:

Reoviridae are segmented, double-stranded, nonenveloped (double capsid) positive sense, RNA viruses of animals.

Examples include tick fever virus and rotavirus gastroenteritis.