1. Classification and Taxonomy
Or the grouping of viruses into an ordered system that indicates relationships
There are multiple ways that you can goupr viruses and none of them all have there advantages and disadvantages
Add slide about spliiters and lumpers.
Reference site:

2. Naming viruses Animal viruses
Diseases that they cause:
small pox, foot and mouth disease, hepatitis
Places where virus was first identified
Norwalk virus, West Nile virus, Hanta virus
3) Other
Organ virus was isolated from: adnoids -Adenovirus
Sin Nombre
Plant viruses an many insect viruses (two components)
Host
Disease
Tomato bushy stunt virus
Cricket paralysis virus

3. Classification and Taxonomy
Classical: morphology
Physical and chemical composition
Genetic relatedness
Modern: Phylogenetic, based on nucleic acid sequence analysis.

4. Classical criteria for classification of animal viruses
Disease symptoms
Useful in clinical situations
Host organism
implies a fixed link between virus and host-Small pox, HBV
Physical structure of the virus particle
Envelope vs no envelope
Helical or isocahedral
Example-
1)hepatitis, colds, pneumonia---disimilar viruses casue similar disease states
2) Some viruses cause more than one disease state
90-100% of people in this room are infected with HSV-1
For some of us this infection is asympomatic
Others will have reoccuring cold soars as a result of the infection.
and Approximately 3 in 100,000 people HSV will develop encephalitis from HSV , which is an infection of the brain.
erpes virus common cold sore and e ncephalitits, chicken pox
Many viruses that don’t cause disease in humans
Problems : This approach focus mainly on human viruses and some live stock- ignores viruses that do not cause disease
Why not use the type of cell that a virus infects or disease as a criteria for basic science
Unrelated viruses can cause similar disease states
HAV-ssRNA nonenveloped
HBV - dsDNA
HCV- (+) RNA, envoloped
Related viruses can very different diseases
HCV
WNV
dengue virus
However grouping viruses passed on disease is useful in clinical and epidemiological studies
Host
Small host range Poio and HCv humans and primates
Large host range- WNv mosquitos, birds, humans , horsed, cats, dogs etc,
Does not imply any other similarity in terms of disease of genetics
Structure tell you nothing of the biology, pathology or molecular biology of the virus
Classification methods
1 disease
focuses on viruses that infect humans and animals
many viruses do not cause disease
single virus may cause different disease-chickenpox
different viruses cause similar diseases
some viruses infect multiple a range of hosts-WNV-insects, birds,horses
humans, cat etc,
infection of a single host does not imply similarities in genetic makeup
Morp
when first visualized this method was used
helica, iscohedron, filamentous
similar structure does not allow you to predict anything about the biology,pathology or
molecular biology of the virus.
Genome-baltimore
Sat,viriods,prions
Alls these approaches fail to predict fundamental features of the viruses

5. Baltimore classification
Modern Criteria for classification
Based on genome composition and structure
allows you to:
1) deduce the basic steps that must take place to produce mRNA
2) simplifies comprehension of the life cycle of virus
Baltimore classification
The first method of sequencing were developed in 1970 and were extremely inefficient.
Still use the balitmore classification but add the perameter of genome structure

6. Traditional classification generate thousands of distinct entities but based on genomes can be classified into 7 groups

7. Note-all animal viruses that are helical are enveloped
Compare old vs new

8. Classification and Nomenclature
ICTV-International Committee on Taxonomy of Viruses (meets every 4 years).
Considerations:
Host range (eukaryote or prokaryote, animal, plant etc.)
Morphological features (enveloped, shape of capsid)
Nature of genome
Add current total to emphasize that these number are subject to change

9. Taxonomy scheme Present totals: Family: 73 Subfamily: 9 Genus: 287
Species:

10. Family A group of genera with common characteristics.
Capitalized, Italicized, and end in -viridae.
Examples:
Picornaviridae (picornavirus family is also acceptable).
Herpesviridae (herpesvirus family).
Flaviviridae (flavivirus family)

11. Origins of family names
1) Symptoms or disease caused by viruses
Herpes: produce scaly (snake skin) lesions
Pox: infections produce pox lesions
Papilloma:infections result in papilla (bumps on skin), e.g. warts
Flavi: Latin for yellow
2) Sites of infection
Adeno: infections of respiratory tract
3) Physical characteristics of the viruses
Picorna: Pico (small) + RNA
Toga: wearing a toga
Corona: wearing a crown
Retro: use retrotransposition
Filo: Look fibrous
4) Combination
Hepadna: hepatitis + DNA

12. Subfamilies Groups within some large families.
Capitalized, Italicized, end in -virinae.
Examples
Alphaherpesvirinae
Betaherpesvirinae
Gammaherpesvirinae.

13. Genus A group of virus species sharing common characteristics.
Capitalized, Italicized, ends in -virus.
type member: a single virus designated by the ICTV that serves as a reference for the genus
Example from Flaviviridae:
Flavivirus-yellow fever virus
Pestivirus- Bovine Diarrhea virus 1
Hepacivirus-Hepatitis virus C (HCV)
Flavivirus
5’ NTR
Structural
Non-Structural
3’ NTR C
prM 1 E 2 B 3 5 A 4
cap 1)
Hepacivirus E1 E2 p7
A B
IRES 3)
Pestivirus
Npro
ERNS
NS2/3 NS 2)
HCV as example of classification based on sequence.
Give two examples; go over flavivirus in detail.

14. Hepacivirus
Pestivirus
Flavivirus

15. Species A cluster of strains from a variety of sources
or a population of strains from one particular source, all of which have in common a set pattern of stable properties that separates the cluster from other clusters or strains.
Not capitalized, unless a geographical location.
Not italicized.
Examples:
poliovirus
human immunodeficiency virus
West Nile virus
Add slide on names- disease, place of isolation-
Plants- plant infected and disease.

16. Taxonomy: two examples
Example 1: herpes simplex virus 1
Family: Herpesviridae or herpesvirus family
Subfamily: Alphaherpesvirinae;
Genus: Simplexvirus;
Species: herpes simplex virus 1.

17. Taxonomy: two examples
Example 2: Poliovirus
Family: Picornaviridae or picornavirus family;
Subfamily: None;
Genus: Enterovirus;
Species: poliovirus

18. Further breakdowns not recognized by the ICTV
Strain- different lines of isolates of the same virus.
Example: Isolated from different geographical locations.
Type- different serotype (different antigenic specificity) of the same virus.
Example: Influenza type A or B. There may also be “subtypes” within a particular type.
Group- sub-category of species, division often based on genomic sequence similarities or origin.
Example: HIV group M (Main), N (Neither M or O), or O (Outlier).
There may also be “subgroups” (sometimes called clades) within a particular group (subgroups A-J of group M HIV).
Varient-Virus whose phenotype differs from original wild type strain but where the genetic basis for the difference is not known.
Add or isolated at different times; example 1918 flu.
Spend more time on this.
Type or serogroups-switch to WNV as a sampe and include the whole description of classification-

19. Satellites,DI particles,viriods & prions.
Special cases
Satellites,DI particles,viriods & prions.
Satellites and viriods-subviral agents
Hbv enhnced pathology in HBV infectins

20. Satellite virus and nucleic acids
Common features :
1) do not encodes enzymes required for replication
2)therefore require coinfection with a conventional (helper) virus
3) Satellite genome is significantly different from the helper virus
4) May affect replication of the helper virus.
5) May increase or decrease severity of disease
Require both the host cell and another virus for replciaton
Add DI particles to lecture
Most common in plants

21. www-ermm.cbcu.cam.ac.uk/ fig002bbr.gif
Satellites viruses
Encodes structural proteins which form the viral capsid
They rely on the helper virus replicative machinery to replicate their genomes.
Examples : adeno associated virus (helper: adenovirus)
Aav-used in gene therapy
HDv- associated with increase disease state in HVB infections
www-ermm.cbcu.cam.ac.uk/ fig002bbr.gif

22. Satellite nucleic acids
encode only nonstructural proteins or no proteins at all.
rely upon a helper virus for replication, and caspid formation.
often found in plants.

23. DI Particles
Defective interfering particle: A virus that lacks part of its genome and interferes with the replication of a standard virus.
Require helper virus
Derived from helper virus: They tend to be deletion mutants that have lost their ability to encode proteins, but retain their ability to be replicated by the helper virus replicative machinery. (defective)
Interfere with helper virus replication by their ability to out compete for helper virus resources.

24. Viroids: Novel agent of disease in plants
Single circular ssRNA molecule with no protein component
70% base-paired
Disease from RNA interfering with essential host cell mechanisms
emu.arsusda.gov/ typesof/images/viroid.jpg

25. Prions
Agents of disease characterized by slow progressive neurological degeneration
Aberrant form of normal cellular proteins that induce changes in the shape of the normal homologs