VIRAL CLASSIFICATION
Virus classification is the process of naming viruses and placing them into a taxonomic system on the basis of their similarities. Similar to the classification systems used for cellular organisms, virus classification is the subject of ongoing debate and proposals. This is mainly due to the pseudo-living nature of viruses, which is to say they are non-living particles with some chemical characteristics similar to those of life, or non-cellular life. As such, they do not fit neatly into the established biological classification system in place for cellular organisms. Currently, two main schemes are used for the classification of viruses: the International Committee on Taxonomy of Viruses (ICTV) system and Baltimore classification system, which places viruses into one of seven groups. Other schemes are the Holmes Classification and The LHT System of Virus Classification.
INTERNATIONAL COMMITTEE ON TAXONOMY OF VIRUSES (ICTV) SYSTEM
This system was developed in 1962 by Lwoff, R.; Home, W. and Tournier, P. and it was called The hierarchical viral classification system. it consists of the following:
Order (-virales)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Species (-virus)
Later, The International Committee on Taxonomy of Viruses began to devise and implement rules for the naming and classification of viruses early in the 1970s based on this system of classification, an effort that continues to the present. They developed the current classification system and wrote guidelines that put a greater weight on certain virus properties to maintain family uniformity. A unified taxonomy (a universal system for classifying viruses) has been established. Viral classification starts at the level of realm and continues as follows, with the taxonomic suffixes in parentheses.
Realm (-viria)
Subrealm (-vira)
Kingdom (-virae)
Subkingdom (-virites)
Phylum (-viricota)
Subphylum (-viricotina)
Class (-viricetes)
Subclass (-viricetidae)
Order (-virales)
Suborder (-virineae)
Family (-viridae)
Subfamily (-virinae)
Genus (-virus)
Subgenus (-virus)
Species
The most important principle on which this system was based is that viruses should be grouped according to their shared properties rather than the properties of the host cell or organism they infect. The four characteristics used for this classification system are:
i. Nature of nucleic acids (RNA/DNA)
ii. Symmetry of the capsid (icosahedral/ helical)
iii. Presence or absence of an envelope
iv. Dimension of the virion or capsid
As of 2017, nine orders, 131 families, 46 subfamilies, 803 genera, and 4,853 species of viruses have been defined by the ICTV. The nine orders are the Caudovirales, Herpesvirales, Ligamenvirales, Mononegavirales, Nidovirales, Ortervirales, Picornavirales, Bunyavirales and Tymovirales.
BALTIMORE VIRAL CLASSIFICATION SYSTEM
This scheme was developed by a Nobel Laurate called David Baltimore. This system of classification provides a useful guide with regards to the various mechanisms of viral genome replication or mechanism for mRNA synthesis as well as the type of Nucleic Acid. The central theme in this classification system is that all viruses must generate +ve strand mRNA from their genomes in order to produce the viral specific protein and replicate themselves. The precise mechanism whereby this is achieved differs for each virus family.
The Baltimore classification of viruses is based on the mechanism of mRNA production. Viruses must generate mRNAs from their genomes to produce proteins and replicate themselves, but different mechanisms are used to achieve this in each virus family. Viral genomes may be single-stranded (ss) or double-stranded (ds), RNA or DNA, and may or may not use reverse transcriptase (RT). In addition, ssRNA viruses may be either sense (+) or antisense (−).The genomic RNA strand of single-stranded RNA viruses is called sense (positive sense, plus sense) in orientation if it can serve as mRNA, and antisense (negative sense, minus sense) if a complementary strand synthesized by a viral RNA transcriptase serves as mRNA. This classification places viruses into seven groups:
I: dsDNA viruses - These are viruses with double stranded DNA genome (e.g. Adenoviruses, Herpes viruses, Poxviruses).
II: ssDNA viruses – These are viruses with single strands of (+ strand or "sense") DNA genome (e.g. Parvoviruses).
III: dsRNA viruses – these are viruses with double stranded RNA genome (e.g. Reoviruses).
IV: (+)ssRNA viruses – These are viruses with single stranded (+ strand or sense) RNA genome (e.g. Picornaviruses, Togaviruses).
V: (−)ssRNA viruses – These are viruses with single stranded (− strand or antisense) RNA genome (e.g. Orthomyxoviruses, Rhabdoviruses).
VI: ssRNA-RT viruses - These are viruses with single strands (+ strand or sense) RNA with DNA intermediate in life-cycle (e.g. Retroviruses).
VII: dsDNA-RT viruses – These are viruses with double strands of DNA genome with RNA intermediate in life-cycle (e.g. Hepadnaviruses).
As an example of viral classification, the chicken pox virus, varicella zoster (VZV),
Based on ICTV system, belongs to the
• ORDER Herpesvirales
• FAMILY Herpesviridae
• SUBFAMILY Alphaherpesvirinae
• GENUS Varicellovirus.
Based on Baltimore system
VZV is in Group I of the Baltimore Classification because it is a dsDNA virus that does not use reverse transcriptase.
Fig. 1: Seven Groups Viruses are classified based on Viral genome
VIRAL CLASSIFICATION BASED ON HOST RANGE
Holmes Classification
Holmes (1948) used Carl Linnaeus's system of binomial nomenclature to classify viruses into 3 groups under one order, Virales. Holmes separated viruses based on their host tropisms and ignored the considerable morphological similarities of the particles produced by all of the viruses that he separated into the 3 suborders. They are placed as follows:
• Group I: Phaginae (attacks bacteria)
• Group II: Phytophaginae (attacks plants)
• Group III: Zoophaginae (attacks animals)
Viruses are by far the most abundant entities on the face of the earth as they outnumbered all other forms of life put together. They infect all types of cellular life including animals, plants, bacteria and fungi. However, different types of viruses can infect only a limited range of host and many viruses are species specific. e.g. small pox virus can infect only one species which is man and so, they are said to have a narrow host range. Other viruses such as the rabies virus can infect different species of mammals (Dogs and Man), So these are said to have broad range of host.
The viruses that infect plants are harmless to animals and most viruses that infect animals are harmless to man or human. Although, we have seen lately some very few viruses that do not conform to this group and are called zoonotic virus e.g. the flu virus.
The host range of bacteriophage is limited to a single strain of bacteria and this can be used to trace the source of infection by a method called Phage-typing.
Group I - Viruses that infect Microorganisms
1. Actinophages: these are phages that attack and kill actinomycetes and such phages are abundant in the soil.
2. Phycoviruses: This family consists of phages that attack and kill algae. Viruses that attack the blue –green algae Lyngbya was later discovered to infect other algae like Plectonema and phornidium. This virus was code named LPP-1 virus.
3. Mycovirus or Fungal viruses: These are viruses that affect and control fungi especially parasitic ones that destroy crops. The first record of an economic impact of mycoviruss on fungi was recorded in a cultivated mushroom called Agaricus biosporus and the disease was called x-disease or watery stripe disease. However, the best known mycovirus is Hypoviruses that causes disease in Cryphonectra parasitica (A parasitic fungus of chestnut).
4. Bacteriophages: Bacteriophages are virus that infect and reproduce in side bacteria.
EXAMPLES OF BACTERIA VIRUSES
S/N FAMILY NUCLEIC ACID TYPE DESCRIPTION
1. Myoviridae dsDNA Elongated/Isometric head/Contractile tail
2. Siphorviridae dsDNA Isometric head, long contractile tail
3. Podoviridae dsDNA Isometric head, very short tail
4. Lipothrixviridae dsDNA No clear head & tail tubular
5. Plasmaviridae dsDNA Pleomorphic
6. Corticoviridae dsDNA Lipid containing capsid
7. Fuselloviridae dsDNA Shaped like a fusel
8. Tectiviridae dsDNA Have distinctive double capsid
9. Rudiviridae dsDNA Rod shaped
10. Microviridae ssDNA Isometric head and no tail
11. Inoviridae(plectovirus) ssDNA Rod shaped
12. Inoviridae(inovirus) ssDNA Long rod shaped
13. Cystoviridae dsRNA Isometric head no tail
14 Leviviridae ssRNA Small isometric head no tail
Group II - Viruses that infect Plants
These are viruses that infect plants. Plant viruses are grouped into 73 genera and 49 families. Despite this huge number, there is one plant virus that is iconic which is Tobacco Mosaic Virus (TMV). Plants do not move from one place to another, so for plant virus to be transmitted from one plant to another, plants make use of strategies that are different from those of animal viruses in that they always involve vectors which are usually insects.
EXAMPLES OF SOME PLANT VIRUSES
S/N GENERA VIRUS HOST
1.
Caulimovirus Cauliflower virus Cauliflower
2. Geminivirus Whitefly disease virus Leafhopper
3. Luteovirus Barley yellow dwarf, Maize chlorotic dwarf virus Barley, maize
4. Necrovirus Tobacco Necrosis Tobacco
5. Tombusvirus Tomato busfly stunt Tomato
6. Bromovirus Brome mosaic Brome
7. Cucumovirus Cucumber mosaic Cucumber
8. Alfamovirus Alfalfa mosaic Alfalfa
9. Comovirus Cowpea mosaic Cowpea
10. Nepovirus Tobacco ringspot Tobacco
11. Tobamovirus Tobacco mosaic virus Tobacco
12. Potyvirus Potato yellow virus, Lettuce necrotic yellow Potato, lettuce
13. Oryzavirus Rice ragged stunt disease Rice
Group III - Viruses that infect Animals
This can be divided into viruses that infect vertebrates and invertebrates.
A) Viruses that infect vertebrates: are informally distinguished between those that primarily cause infection in human beings and those that infect other vertebrates. The two belong to the fields called clinical and veterinary virology.
Different viruses can infect all the organs and tissues of the human body causing infection from mild or no symptoms to a life-threatening disease. Human beings or man cannot be infected by plant or insect viruses but are susceptible to infections with viruses from other vertebrates. A good example of this is rabies virus and such infection is called zoonotic infections.
B) Viruses that infect Invertebrates: there are many viruses that infect invertebrates. Baculo viruses are among the best studied invertebrate viruses. Most viruses that infect invertebrates are attractive alternatives to chemical pesticides because they are safe to be used on insects as they leave no residue.
EXAMPLES OF SOME ANIMAL VIRUSES
S/N FAMILY VIRUS HOST
1. Poxviridae Vaccinia; molluscum, contagiosum, fowl pox Man, Fowl
2. Herpesviridae Herpesvirus 1-5 Man
3. Adenoviridae Adenovirus, Aviadenovirus Man, birds
4. Parvoviridae Parvovirus B19 Man
5. Papovaviridae Polyoma, Papilillomavirus Man
6. Plaviviridae Yellow fever, Hog cholera, Hepatitis C Man, swine
7. Picornaviridae Enterovirus; Hepatitis A, Foot & Mouth disease virus, Polio Man, cattle
8 Togaviridae Arbovirus, Rubella Insect, man
9. Retroviridae HIV, SIV, FIV Man, rat, cat
10. Orthomyxoviridae Influenza, A, B, C Man
11. Paramyxoviridae Measles, canine distemper, Newcastle Man, dog, fowl
12. Rhabdoviridae Rabies Man, dog
13. Reoviridae Rotavirus Man
14. Bunyaviridae Hantavirus Man
15. Hepardnaviridae Hepatitis B Man
16. Calciviridae Norwalk, Hepatitis E Man
17. Filoviridae Marburg, Ebola Man
18. Iridoviridae Ramavirus Frog
19. Coronaviridae Coronavirus Frog, Man
20. Baculoviridae Baculovirus Insects
VIRAL CLASSIFICATION BASED ON MODE OF TRANSMISSION
S/N ROUTE OF TRANSMISSION VIRUS TARGET ORGAN
1. Air borne (Respiratory) Influenza A
i. H5N1-Avian
ii. H1N1 – swine
iii. H3N2- Human
iv. Coxsackie A&B
v. Parainfluenza
vi. Echovirus
vii. Severe Acute respiratory Syndrome (SARS)
viii. Reovirus
Respiratory Organs
Mumps virus Parotid glands/Testes
Chicken pox (varicella) Respiratory organ + Skin
Measles (Rubeola) Respiratory organ + Skin
German Measles (Rubella) Respiratory organ + Skin
Small pox (variola) Respiratory organ + Skin
2. Enteric or Food/ water borne or Fecal-oral Polio, hepatitis A, C, E, Coxsackie, Echo, Rotavirus CNS, Liver, Kidney & Spleen,
Intestinal mucosa (diarrhea)
3. Direct contact
i. Formites
ii. Blood
iii. Sexual
iv. Sweat, Urine, faeces, dead body
Herpes virus -1
Herpes virus -5(cytomegalovirus)
Herpes virus -4(Epstein Barr)
Herpes virus -6
HTLV (Human T-cell lymphotropic virus)
Hepatitis B
Human Immunodeficiency Virus (HIV)
Human Papilloma Virus
HSV-2
HTLV, Hepatitis B
Ebola Mouth, lips & face
All body cells, Nodes & lymph & spleen
Blood Leukemia
Serum
Immune system
Genital organ(cancer)
Genital herpes
Blood (Leukemia)
Vascular system
4. Zoonotic
1. Animal bite or secretion or faeces or urine of infected animal
2. Insect Bite
Rabies,
Ebola,
Marburg,
Hanta and
Lassa
Yellow fever
Dengue fever
Colorado Tick fever
CNS,
vascular system
CNS
CNS
CNS
Liver
Liver
Skin
VIRAL CLASSIFICATION BASED ON PATHOLOGY
The range of structural and biochemical effects that viruses have on cells that they infect is extensive. Most virus infection usually results in the death of the host cells. The causes of the death include:
1. cell lysis (ii) Alteration of cell surface (iii) Apoptosis
CELL LYSIS: when this occur, the cellular content are released to the immediate environment thereby causing death of the cell.
ALTERATION OF THE CELL SURFACE: when this occurs, the cell membrane may be so altered that the water can move into the infected cell from surrounding cells by osmosis which eventually leads to cell lysis.
APOPTOSIS: many viruses induce apoptosis or programmed cell death I.e.; the cell dies before the completion of viral reproduction cycle. This can be an important part of host self-defense. However, if viral replication is completed in an infected cell, it often results in detectable changes which are known as cytopathic Effects (CPE). Viruses use a variety of mechanisms to cause CPE which in some cases brings about cytocidal effects.
The following are some of the CPE that are commonly produced as a result of viral pathology:
i. POLYKARYCYTOSIS: this is a type of CPE that is characterized by multinucleated masses of cells produced by fusion of many cells resulting in a syncytium which leads to cell death. A good example of virus that causes polykarycytotic CPE is the measles virus and also the HIV infection that has resulted into AIDS, when the envelope glycoproteins of the HIV binds to the CD4 antigen of the uninfected neighboring T cells.
ii. INCLUSION BODY FORMATION (IBF): this can be nuclear or cytoplasmic. IBF are usually aggregates of stainable substances usually proteins that typically represents the site of viral replication in the cell. Some good examples of IBF are
Negri Bodies – what are Negri Bodies? They are intracytoplasmic inclusion bodies that are formed by virions in the neurons as in Rabies virus infection
Cowdry Bodies: these are intranuclear inclusion bodies formed by Herpes Simplex Virus and Varicella Zoster virus during infection. Measles virus can form inclusion bodies that can either be intranuclear or intracytopathic. Other viral infections that form inclusion bodies include Rinderpest virus and Canine Distemper Virus. Inclusion bodies are sometimes formed in plants as well. Example of inclusion body found in plant includes the aggregation of viral particles in the cucumber mosaic virus infection.
iii. VACUOLATION: this CPE is characterized by the presence of vacuoles within the cell. These vacuoles can be in the cytoplasm as in the case of Simian virus (SV40) infection. Or it can be in the nucleus as in the case of the Pig Pox Virus.
iv. NECROSIS: this simply means death of tissue by eating it up. The cellular necrosis is usually focal in nature and pus is never observed in necrosis except there is a secondary bacterial infection. For example viruses that cause necrosis are smallpox virus that causes pocks on the face of the infected individual or yellow fever virus.
The characteristic jaundice of yellow fever infection is as a result of reduced liver functions due to necrosis of the liver by the yellow fever virus.
v. LATENCY: This occurs when viral genome resides in a suppressed or inactive state within the host cell. Latency can be either Intermittent or Quiescence.
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virology STM326