Msc Bub 103 Unit 9 Virus 51

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VIROLOGY

Viruses are smaller and less complex than bacteria. As science became aware of

the role of the viruses in human disease, the techniques of bacteriology were modified toaccomodate the viruses and the discipline of virology grew up within bacteriology.

Viruses are the cause of many diseases in humans ranging from AIDS and cancer

to the common cold. Microbiologists have developed vaccines for many viral diseases,

but haven not been as successful in discovery of treatments for the diseases. It is theopposite in bacteriology, at least since the discovery of antibiotics.

Virus Structure

Viruses consist of nucleic acid (DNA or RNA) surrounded by a protein coat

called a capsid. The capsid is made up of individual structural subunits

called capsomeres. Individual capsomeres are arranged to form a capsid which encloses

the nucleic acid (DNA or RNA) of the virus. Some viruses have additional structuralfeatures, such as the envelope of animal viruses or the tail of bacteriophages. Many

animal viruses also contain an envelope, which is partly derived from the host cellmembtrane but which always contains unique viral proteins (spikes).

poliovirus herpes virus tobacco mosaic

virus

influenza virus

Figure 9.1. The most common viral morphologies. A naked icosahedral virus, an

enveloped icosahedral virus, a naked helical virus and an enveloped helical virus.

General Features of Viruses

Viruses are considered obligate intracellular parasites because they require a hostcell in order to replicate. The host cell may be any form of eucaryote or procaryote.

Viruses are noncellular entities that are not considered as living by most

microbiologists. They are very different from cells. The viruses lack membranes andcannot produce their energy since, they lack enzymes for metabolic functions. They also

lack ribosomes required for protein synthesis.


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The general features of viruses are outlined in the table below.

Table 9. 1. General Features of Viruses

Viral Features Properties

1. Small size Viruses cannot be viewed with a light microscopepass through filters that retain bacteria. Viral sizes rangebetween 0.1-0.3 micrometers

2. Characteristic shapes Spherical (complex), helical, rod or polyhedral,sometimes with tails or envelopes. Most common

polyhedron is the icosahedron which as 20 triangular

faces.

3. Obligate intracellular

parasites

Viruses do not contain within their coats the machinery

for replication. For this they depend upon a host cell for

their existence as obligate intracellular parasites. Eachvirus can only infect certain species of cells. This refers

to the virus host range.4. No built-in metabolic

machinery

Viruses have no metabolic enzymes and cannot generate

their own energy.

5. No ribosome Viruses cannot synthesize their own proteins. Theyutilize host cell ribosomes for this during replication.

6. Only one type of nucleicacid

Viruses contain either DNA or RNA (never both) astheir genetic material. The nucleic acid can be single-

stranded or double stranded.

7. Do not grow in size Unlike cells, viruses do not grow in size and mass

leading to a division process. Rather viruses grow by

separate synthesis and assembly of their components

resulting in production of mature viruses.

Classification of Viruses

Viruses are classified on the basis of host range, morphology (size, shape), type of

nucleic acid (DNA, RNA, single-stranded, double-stranded, linear, circular, segmented,etc.) and occurrence of auxilliary structures such as tails or envelopes.

Host range refers to the type of host cell in which it grows. Depending upon the

host the viruses prefer, they can be broadly arranged into four groups. They are:

1. bacterial viruses (bacteriophage),2. animal viruses,

3. insect viruses (bacculoviruses) and

4. plant viruses.

Hosts of viruses

Hosts of viruses include all classes of cellular organisms described to date:


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General Host Range

Prokaryotes: Archaea Bacteria Mycoplasma Spiroplasma

Eukaryotes: Algae Plants Prortozoa Fungi

Invertebrates Vertebrates

Figure 2. Shapes and comparative sizes of different groups of viruses.A. Smallpox virus B. Orf virus C. Rhabdovirus D. Paramyxovirus

E. Bacteriophage T2 F. Flexuous-tailed

bacteriophage

G. Herpes virus H. Adenovirus

I. Influenza virus J. Filamentousflexuous virus

K. Tobacco mosaic virus L. Polyoma/papillomavirus

M. Alflafa mosaic virus N. Poliovirus O. Bacteriophage phiX174

Viruses have three fundamental morphology types:

1. Polygonal, the most common polygon being the icosahedron (E, F, G, H, L, N);

2. Helical, wherein the capsomeres assemble as a helix enclosing the nucleic acid)(B, D, I, J, K, M)

3. Complex, wherein the proteins are laid down in patches or layers (A). Some

animal viruses have envelopes which enclose their nucleocapsid (D, G, I). Theenvelopes are embedded with viral proteins that secure their entry and exit in

cells. Only bacteriophages have tails which are used for adsorption and

penetration of their host cell.


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Classification of Viruses

Classical virus classification schemes have been based on the consideration offour major properties of viruses:

1. The type of nucleic acid which is found in the virion (RNA or DNA)2. The symmetry and shape of the capsid

3. The presence or absence of an envelope

4. The size of the virus particle

More recent classification systems adopted by the International Committee on

Viral Taxonomy (ICTV) is based on the nature of viral genome as the primary

determinant. Furthermore, there is a drift towards the use of genomics for virusclassification that is sequence analysis of the viral genome, and comparison to other

known viral sequences.

The naming system for viruses that has been adopted by the ICTV is very usefulfor animal viruses, and is widely used. Latinized virus family names start with capital

letters and end with the suffix viridae (e.g., Herpesviridae). These formal names areoften used interchangably with the common names for viruses (e.g., herpesviruses).

The system makes use of a series of ranked taxons, with the:

Order (-virales) being the highest currently recognised.

Family (-viridae)

Subfamily (-virinae)

Genus (-virus)

Species (name of virus)

For example, the Ebola virus is classified as:

Order Mononegavirales

Family Filoviridae

Genus Filovirus

Species: Ebola virus Zaire

The most important taxonomic criteria are:

Host Organism(s)

Particle Morphology

Genome Typealthough a number of other criteria - such as disease symptoms, antigenicity, protein

profile, host range, etc. are important in precise identification, consideration of theabove three criteria are sufficient in most cases to allow identification of a virus down to

familial if not generic level.


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The Properties used for Classifying Viruses are as follows:

S.No Primary Characteristics Secondary Characteristics

1. Chemical nature of nucleic acid: RNA or

DNA; single or double stranded; single orsegmented genome; (+) or (-) strand ;molecular weight .

Host range:

Host species, specific hosttissues or cell types.

2. Structure of virion : Helical , icosahedral, or

complex; naked or enveloped, complexity;number of capsomers for icosahedral virions,

diameter of nucleo-capsids for helical viruses.

Mode of transmission:

Ex: faeces.

3.. Site of replication:Nucleus or cytoplasm Specific surface structures:Ex: antigenic properties

Certain virus families / groupings cross kingdom or phylum boundaries

The virus families infecting two kingdoms of organisms are:

Bunyaviridae (animals and plants)

Partitiviridae (plants and fungi)

Reoviridae (animals and plants)

Rhabdoviridae (animals and plants)

Phycodnaviridae (protozoa and plants)

Picornoviridae (plants and animals - tentative)

Totiviridae (protozoa / fungi and insects - tentative)

Virus families infecting across different phyla (all infecting insects and vertebrates)are:

Flaviviridae

Iridiviridae

Parvoviridae

Poxviridae

Togaviridae


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International Committee on Viral Taxonomy (ICTV) Classification System

Group I: dsDNA Viruses

OrderCaudovirales - Tailed BacteriophagesFamily(Subfamily) Genus Type Species H

Myoviridae T4-like viruses Enterobacteria phage

T4

Bacte

P1-like viruses Enterobacteria phage

P1

Bacte


P2

Bacte

Mu-like viruses Enterobacteria phage

Mu

Bacte

SP01-like viruses Bacillus phage SP01 Bacte

H-like viruses Halobacterium virusH

Bacte

Podoviridae T7-like viruses Enterobacteria phage

T7

Bacte


P22

Bacte

29-like viruses Bacillus phage 29 Bacte

N4-like viruses Enterobacteria phage

N4

Bacte

Siphoviridae -like viruses Enterobacteria phage

Bacte

T1-like viruses Enterobacteria phageT1

Bacte

T5-like viruses Enterobacteria phage

T5

Bacte

L5-like viruses Mycobacterium phage

L5

Bacte

c2-like viruses Lactococcus phage c2 Bacte

M1-like viruses Methanobacterium

virus M1

Bacte

C31-like viruses Streptomyces phage

C31

Bacte

N15-like viruses Enterobacteria phageN15

Bacte

Family(Subfamily) Genus Type Species H

Ascoviridae Ascovirus Spodoptera frugiperda

ascovirus

Inver

Adenoviridae Atadenovirus Ovine adenovirus D Verte

Aviadenovirus Fowl adenovirus A Verte


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Mastadenovirus Human adenovirus CVerte

Siadenovirus Frog adenovirus Verte

Asfarviridae Asfivirus African swine fever

virus

Verte

Baculoviridae Nucleopolyhedrovirus Autographa

californicanucleopolyhedrovirus

Inver

Granulovirus Cydia pomonella

granulovirus

Inver

Corticoviridae Corticovirus Alteromonas phage

PM2

Bacte

Fuselloviridae Fusellovirus Sulfolobus virus SSV1 Archa

Guttaviridae Guttavirus Sulfolobus virus

SNDV

Archa

Herpesviridae

:

Ictalurivirus Ictalurid herpesvirus 1 Verte

Alphaherpesvirinae Mardivirus Gallid herpesvirus 2 Verte

Simplexvirus Human herpesvirus 1VerteVaricellovirus Human herpesvirus 3 Verte

Iltovirus Gallid herpesvirus 1 Verte

Betaherpesvirinae Cytomegalovirus Human herpesvirus 5 Verte

Muromegalovirus Murine herpesvirus 1 Verte

Roseolovirus Human herpesvirus 6Verte

Gammaherpesvirina

e

Lymphocryptovirus Human herpesvirus 4 Verte

Rhadinovirus Simian herpesvirus 2Verte

Iridoviridae Iridovirus Invertebrate irid

virus 6

Inver

Chloriridovirus Invertebrate iridescent

virus 3

Inver

Ranavirus Frog virus 3 Verte

Lymphocystivirus Lymphocystis disease

virus 1

Verte

Megalocytivirus Infectious spleen and

kidney necrosis virus

Verte

Lipothrixviridae Alphalipothrixvirus Thermoproteus virus 1Archa

Betalipothrixvirus Sulfolobus

mislandicus

filamentous virus

Archa

Gammalipothrixvirus Acidianus filamentous

virus1

Archa

Nimaviridae Whispovirus White spot syndrome

virus 1

Inver

Mimivirus Acanthamoeba

polyphaga mimivirus

Proto

Verte

Polyomaviridae Polyomavirus Simian virus 40 Verte

Papillomaviridae Alphapapillomavirus Human Verte


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papillomavirus 32

Betapapillomavirus Human

papillomavirus 5

Verte

Gammapapillomavirus Human

papillomavirus 4

Verte

Deltapapillomavirus European elkpapillomavirus

Verte

Epsilonpapillomavirus Bovin papillomavirus

5

Verte

Zetapapillomavirus Equine papillomavirus

1

Verte

Etapapillomavirus Fringilla coelebs

papillomavirus

Verte

Thetapapillomavirus Psittacus erithacus

timneh papillomavirus

Verte

Iotapapillomavirus Mastomys natalensis

papillomavirus

Verte

Kappapapillomavirus Cottontail rabbit

papillomavirus

Verte

Lambdapapillomavirus Canine oral

papillomavirus

Verte

Mupapillomavirus Human

papillomavirus 1

Verte

Nupapillomavirus Human

papillomavirus 41

Verte

Xipapillomavirus Bovine papillomavirus

3

Verte

Omikronpapillomavirus

Phocoena spinipinnispapillomavirus

Verte

Pipapillomavirus Hamster oral

papillomavirus

Verte

Phycodnaviridae Chlorovirus Paramecium bursaria

Chlorella virus 1

Algae

Prasinovirus Micromonas pusilla

virus SP1

Algae

Prymnesiovirus Chryosochromomuli

a brevifilium virus

PW1

Algae

Phaeovirus Extocarpus siliculosusvirus 1

Algae

Coccolithovirus Emiliania huxleyi

virus 86

Algae

Raphidovirus Heterosigms akashiwo

virus 01

Algae

Plasmaviridae Plasmavirus Acholeplasma pha

L2

Myco


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Polydnaviridae Ichnovirus Campoletis sonor

ichnovirus

Inver

Bracovirus Cotesia melanoscela

brachovirus

Inver

Poxviridae: Chordopoxvirinae Orthopoxvirus Vaccinia virus Verte

Parapoxvirus Orf virus Verte Avipoxvirus Fowlpox virus Verte

Capripoxvirus Sheeppox virus Verte

Leporipoxvirus Myxoma virus Verte

Suipoxvirus Swinepox virus Verte

Molluscipoxvirus Molluscum

contagiosum virus

Verte

Yatapoxvirus Yaba monkey tumor

virus

Verte

Entomopoxvirinae Entomopoxvirus A Melolontha

melolontha

entomopoxvirus

Inver

Entomopoxvirus B Amsacta moorei

entomopoxvirus

Inver

Entomopoxvirus C Chironomus luridus

entomopoxvirus

Inver

Rhizidovirus Rhizidomyces virus Fungi

Rudiviridae Rudivirus Sulfolobus virus

SIRV1

Archa

Tectiviridae Tectivirus Enterobacteria phage

PRD1

Bacte

Group II: ssDNA Viruses

Family(Subfamily) Genus Type Species Hosts

Anellovirus Torque teno virus Vertebrates

Circoviridae Circovirus Porcine circovirus Vertebrates

Gyrovirus Chicken anemia virus Vertebrates

Geminiviridae Mastrevirus Maize streak virus Plants

Curtovirus Beet curly top virus Plants

Topocuvirus Tomato pseudo-curly

top virus

Plants

Begomovirus Bean golden mosaic

virus

Plants

Inoviridae Inovirus Enterobacteria phage

M13

Bacteria

Plectrovirus Acholeplasma phage

MV-L51

Bacteria

Microviridae Microvirus Enterobacteria X174 Bacteria

Spiromicrovirus Spiroplasma phage 4 Spiroplasma

Bdellomicrovirus Bdellovibrio phage

MAC1

Bacteria


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Chlamydiamicroviru

s

Chlamydia phage 1 Bacteria

Nanoviridae Nanovirus Subterranean clover

stunt virus

Plants

Babuvirus Banana bunchy top

virus

Plants

Parvoviridae

:

Parvovirinae Parvovirus Mice minute virus Vertebrates

Erythrovirus B19 virus Vertebrates

Dependovirus Adeno-associated virus

2

Vertebrates

Amdovirus Aleutian mink disease

virus

Vertebrates

Bocavirus Bovine parvovirus Vertebrates

Densovirina

e

Densovirus Junonia coenia

densovirus

Invertebrates

Iteravirus Bombyx mori

densovirus

Invertebrates

Brevidensovirus Aedes aegypti

densovirus

Invertebrates

Pefudensovirus Periplanta fuliginosa

densovirus

Invertebrates

Group III: dsRNA Viruses

Family

(Subfamily)

Genus Type Species Hosts

Birnaviridae Aquabirnavirus Infectious pancreatic necrosis

virus

Vertebrates

Avibirnavirus Infectious bursal disease virus Vertebrates

Entomobirnavirus

Drosophila X virus Invertebrates

Chrysoviridae Chrysovirus Penicillium chrysogenum virus Fungi

Cystoviridae Cystovirus Pseudomonas phage 6 Bacteria

Endornavirus Vicia faba endornavirus Plants

Hypoviridae Hypovirus Cryphonectria hypovirus 1-

EP713

Fungi

Partitiviridae Partitivirus Atkinsonella hypoxylon virus Fungi

Alphacryptovirus White clover cryptic virus 1 Plants

Betacryptovirus White clover cryptic virus 2 Plants

Reoviridae Orthoreovirus Mammalian orthoreovirus Vertebrates

Orbivirus Bluetongue virus Vertebrates

Rotavirus Rotavirus A Vertebrates

Coltivirus Colorado tick fever virus Vertebrates

Aquareovirus Golden shiner virus Vertebrates

Seadornavirus Banna virus Vertebrates

Cypovirus Cypovirus 1 Invertebrates

Idnoreovirus Idnoreovirus 1 Invertebrates


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Fijivirus Fiji disease virus Plants

Phytoreovirus Wound tumor virus Plants

Oryzavirus Rice ragged stunt virus Plants

Mycoreovirus Mycoreovirus 1 Fungi

Totiviridae Totivirus Saccharomyces cerevisiae virus

L-A

Fungi

Giardiavirus Giardia lamblia virus Protozoa

Leishmaniavirus Leishmania RNA virus 1-1 Protozoa

Group IV: (+)sense RNA Viruses

OrderNidovirales - "Nested" Viruses

Family

(Subfamily)


Arteriviridae Arterivirus Equine arteritis virus Vertebrates

Coronaviridae Coronavirus Infectious bronchitis virus Vertebrates

Torovirus Equine torovirus Vertebrates

Roniviridae Okavirus Gill-associated virus Vertebrates

Family

(Subfamily)


Astroviridae Avastrovirus Turkey astrovirus Vertebrates

Mamastrovirus Human astrovirus Vertebrates

Barnaviridae Barnavirus Mushroom bacilliform virus Fungi

Benyvirus Beet necrotic yellow vein virus Plants

Bromoviridae Alfamovirus Alfalfa mosaic virus Plants

Bromovirus Brome mosaic virus Plants

Cucumovirus Cucumber mosaic virus Plants

Ilarvirus Tobacco streak virus Plants

Oleavirus Olive latent virus 2 Plants

Caliciviridae Lagovirus Rabbit haemorrhagic disease virus Vertebrates

Norovirus Norwalk virus Vertebrates

Sapovirus Sapporo virus Vertebrates

Vesivirus Swine vesicular exanthema virus VertebratesCheravirus Cherry rasp leaf virus Plants

Closteroviridae Ampelovirus Grapevine leafroll-associated virus 3 Plants

Closterovirus Beet yellows virus Plants

Comoviridae Comovirus Cowpea mosaic virus Plants

Fabavirus Broad bean wilt virus 1 Plants


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Nepovirus Tobacco ringspot virus Plants

Dicistroviridae Cripavirus Cricket paralysis virus Invertebrates

Flaviviridae Flavivirus Yellow fever virus Vertebrates

Pestivirus Bovine diarrhea virus 1 Vertebrates

Hepacivirus Hepatitis C virus Vertebrates

Flexiviridae Potexvirus Potato virus X Plants

Mandarivirus Indian citrus ringspot virus Plants

Allexivirus Shallot virus X Plants

Carlavirus Carnation latent virus Plants

Foveavirus Apple stem pitting virus Plants

Capillovirus Apple stem grooving virus Plants

Vitivirus Grapevine virus A Plants

Trichovirus Apple chlorotic leaf spot virus Plants

Furovirus Soil-borne wheat mosaic virus Plants

Hepevirus Hepatitis E virus Vertebrates

Hordeivirus Barley stripe mosaic virus Plants

Idaeovirus Rasberry bushy dwarf virus Plants

Iflavirus Infectious flacherie virus Invertebrates

Leviviridae Levivirus Enterobacteria phage MS2 Bacteria

Allolevivirus Enterobacteria phage Q Bacteria

Luteoviridae Luteovirus Cereal yellow dwarf virus-PAV Plants

Polerovirus Potato leafroll virus Plants Enamovirus Pea enation mosaic virus-1 Plants

Machlomovirus Maize chlorotic mottle virus Plants

Marnaviridae Marnavirus Heterosigma akashiwo RNA virus Fungi

Narnaviridae Narnavirus Saccharomyces cerevisiae narnavirus 20SFungi

Mitovirus Cryphonectria parasitica mitovirus 1-NB631

Fungi

Nodaviridae Alphanodoavirus Nodamura virus Invertebrates

Betanodovirus Striped jack nervous necrosis virus Vertebrates

Pecluvirus Peanut clump virus Plants

Ourmiavirus Ourmia melon virus Plants

Picornaviridae Enterovirus Poliovirus Vertebrates

Rhinovirus Human rhinovirus A Vertebrates

Hepatovirus Hepatitis A virus Vertebrates

Cardiovirus Encephalomyocarditis virus Vertebrates


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Aphthovirus Foot-and-mouth disease virus O Vertebrates

Parechovirus Human parechovirus Vertebrates

Erbovirus Equine rhinitis B virus Vertebrates

Kobuvirus Aichi virus Vertebrates

Teschovirus Porcine teschovirus Vertebrates

Pomovirus Potato mop-top virus Plants

Potyviridae Potyvirus Potato virus Y Plants

Ipomovirus Sweet potato mild mottle virus Plants

Macluravirus Maclura mosaic virus Plants

Rymovirus Ryegrass mosaic virus Plants

Tritimovirus Wheat streak mosaic virus Plants

Bymovirus Barley yellow mosaic virus Plants

Sadwavirus Satsuma dwarf virus Plants

Sequiviridae Sequivirus Parsnip yellow fleck virus Plants

Waikavirus Rice tungro spherical virus Plants

Sobemovirus Southern bean mosaic virus Plants

Tetraviridae Betatetravirus Nudaurelia capensis virus Invertebrates

Omegatetravirus Nudaurelia capensis virus Invertebrates

Tobamovirus Tobacco mosaic virus Plants

Tobravirus Tobacco rattle virus Plants

Tombusviridae Tombusvirus Tomato bushy stunt virus Plants

Avenavirus Oat chlorotic stunt virus Plants Aureusvirus Pothos latent virus Plants

Carmovirus Carnation mottle virus Plants

Dainthovirus Carnation ringspot virus Plants

Machlomovirus Maize chlorotic mottle virus Plants

Necrovirus Tobacco necrosis virus Plants

Panicovirus Panicum mosaic virus Plants

Togaviridae Alphavirus Sindbis virus Vertebrates

Rubivirus Rubella virus Vertebrates

Tymoviridae Maculavirus Grapevine fleck virus Plants

Marafivirus Maize rayado fino virus Plants

Tymovirus Turnip yellow mosaic virus Plants

Umbravirus Carrot mottle virus Plants

Group V: (-)sense RNA Viruses


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Order Mononegavirales


Bornaviridae Bornavirus Borna disease virusVertebrates

Filoviridae Marburgvirus Lake Victoria

marburgvirus

Vertebrates

Ebolavirus Zaire ebolavirus Vertebrates

Paramyxoviridae Paramyxovirinae Avulavirus Newcastle disease virus Vertebrates

Henipavirus Hendra virus Vertebrates

Morbillivirus Measles virus Vertebrates

Respirovirus Sendai virus Vertebrates

Rubulavirus Mumps virus Vertebrates

Pneumovirinae Pneumovirus Human respiratorysyncytial virus

Vertebrates

Metapneumovirus Avian pneumovirus Vertebrates

Rhabdoviridae Vesiculovirus Vesicular stomatitis

Indiana virusVertebrates,Invertebrates

Lyssavirus Rabies virus Vertebrates

Ephemerovirus Bovine ephemeral fevervirus

Vertebrates,

Invertebrates

Novirhabdovirus Infectious haematopoetic

necrosis virusVertebrates

Cytorhabdovirus Lettuce necrotic yellows

virus

Plants,

Invertebrates

Nucleorhabdovirus Potato yellow dwarf

virusPlants,

Invertebrates


Arenaviridae Arenavirus Lymphocytic

choriomeningitis virus

Vertebrates

Bunyaviridae Orthobunyavirus Bunyamwera virus Vertebrates

Hantavirus Hantaan virus Vertebrates

Nairovirus Nairobi sheep disease

virusVertebrates

Phlebovirus Sandfly fever Sicilian

virus

Vertebrates

Tospovirus Tomato spotted wilt virus Plants

Deltavirus Hepatitis delta virusVertebrates

Ophiovirus Citrus psorosis virus Plants

Orthomyxoviridae Influenza A virus Influenza A virus Vertebrates


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Influenza B virus Influenza B virus Vertebrates

Influenza C virus Influenza C virus Vertebrates

Isavirus Infectious salmonanemia virus

Vertebrates

Thogotovirus Thogoto virus VertebratesTenuivirus Rice stripe virus Plants

Varicosaivirus Lettuce big-vein

associated virusPlants

Group VI: RNA Reverse Transcribing Viruses

Family

(Subfamily)Genus Type Species Hosts

Retroviridae Alpharetrovirus Avian leukosis virus Vertebrates

Betaretrovirus Mouse mammary tumor virus Vertebrates

Gammaretrovirus Murine leukemia virus VertebratesDeltaretrovirus Bovine leukemia virus Vertebrates

Epsilonretrovirus Walley dermal sarcoma virus Vertebrates

Lentivirus Human immunodeficiency virus 1 Vertebrates

Spumavirus Human spumavirus Vertebrates

Metaviridae Metavirus Saccharomyces cerevisiae Ty3 virus Fungi

Errantivirus Drosophila melanogaster gypsy virus Invertebrates

Pseudoviridae Pseudovirus Saccharomyces cerevisiae Ty1 virus Invertebrates

Hemivirus Drosophila melanogaster copia virus Invertebrates

Group VII: DNA Reverse Transcribing Viruses

Family

(Subfamily)


Hepadnaviridae Orthohepadnavirus Hepatitis B virus Vertebrates

Avihepadnavirus Duck hepatitis B virus Vertebrates

Caulimoviridae Caulimovirus Cauliflower mosaic virus Plants

Badnavirus Commelina yellow mottle virus Plants

Cavemovirus Cassava vein mosaic virus Plants

Petuvirus Petunia vein clearing virus Plants

Soymovirus Soybean chlorotic mottle virus Plants

Tungrovirus Rice tungro bacilliform virus Plants

Subviral Agents: Viroids



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Pospiviroidae Pospiviroid Potato spindle tuber viroid Plants

Hostuviroid Hop stunt viroid Plants

Cocadviroid Coconut cadang-cadang viroid Plants

Apscaviroid Apple scar skin viroid Plants

Coleviroid Coleus blumei viroid 1 Plants

Avsunviroidae Avsunviroidae Avocado sunblotch viroid Plants

Pelamonviroid Peach latent mosaic viroid Plants

The Bacteriophages

Viruses that attack bacteria were observed by Twort and d'Herelle in 1915 and1917. They observed that broth cultures of certain intestinal bacteria could be dissolved

by addition of a bacteria-free filtrate obtained from sewage. The lysis of the bacterial

cells was said to be brought about by a virus.

Every known bacterium is subject to an infection by viruses orbacteriophages("phage" from Gr. "phagein" meaning "to eat"). But at research level more

work has been done on the phages that infectE. coli. Ex: the T-phages and phage lambda.

Like most viruses, bacteriophages carry only the genetic information needed for

replication of their nucleic acid and synthesis of their protein coats. When phages infecttheir host cell they utilize the bacterial precursors, energy and ribosomes to replicate their

nucleic acid and to produce the protective protein coat.

Bacterial cells can undergo one or two types of infections by bactriophages. They

are termed as lytic infections or lysogenic (temperate) infections. A group seven phagesknown as the T-phages cause lytic infections inE. coli. Whereas, phage lambda causes

lysogenic infections.

Composition and Structure of Bacteriophage

A. Composition

Although different bacteriophages may contain different materials they all contain

nucleic acid and protein.

Depending upon the phage, the nucleic acid can be either DNA or RNA but not

both and it can exist in various forms. The nucleic acids of phages often contain unusualor modified bases. These modified bases protect phage nucleic acid from nucleases that

break down host nucleic acids during phage infection. The size of the nucleic acid varies

depending upon the phage. The simplest phages only have enough nucleic acid to codefor 3-5 average size gene products while the more complex phages may code for over

100 gene products.


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The number of different kinds of protein and the amount of each kind of protein

in the phage particle will vary depending upon the phage. The simplest phage have many

copies of only one or two different proteins while more complex phages may have manydifferent kinds. The proteins function in infection and to protect the nucleic acid from

nucleases in the environment.

B. Structure

Bacteriophage come in many different sizes and shapes. The basic structural

features of bacteriophages (Ex: phage T4).

Figure 4. Bacteriophage T4

1. Size - T4 is among the largest phages; it is approximately 200 nm long and 80-100 nm

wide. Other phages are smaller. Most phages range in size from 24-200 nm in length.

2. Head or Capsid - All phages contain a head structure which can vary in size and shape.Some are icosahedral (20 sides) others are filamentous. The head or capsid is composed

of many copies of one or more different proteins. Inside the head is found the nucleicacid. The head acts as the protective covering for the nucleic acid.

3. Tail - Many but not all phages have tails attached to the phage head. The tail is ahollow tube through which the nucleic acid passes during infection. The size of the tail

can vary and some phages do not even have a tail structure. In the more complex phages

like T4 the tail is surrounded by a contractile sheath which contracts during infection ofthe bacterium. At the end of the tail the more complex phages like T4 have a base plate


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and one or more tail fibers attached to it. The base plate and tail fibers are involved in the

binding of the phage to the bacterial cell. Not all phages have base plates and tail fibers.

In these instances other structures are involved in binding of the phage particle to thebacterium.

Phage multiplication cycle

Lytic or Virulent Phages

1. Definition - Lytic or virulent phages are phages which can only multiply on bacteriaand kill the cell by lysis at the end of the life cycle.

2. Life cycle - The life cycle of a lytic phage is illustrated:

Eclipse period - During the eclipse phase, no infectious phage particles can be foundeither inside or outside the bacterial cell. The phage nucleic acid takes over the host

biosynthetic machinery and phage specified m-RNA's and proteins are made. There is anorderly expression of phage directed macromolecular synthesis. Early m-RNA's code forearly proteins needed for phage DNA synthesis and for shutting off host DNA, RNA and

protein biosynthesis. In some cases the early proteins actually degrade the host

chromosome. After phage DNA is made late m-RNA's and late proteins are made. Thelate proteins are the structural proteins of the phage as well as the proteins needed for

lysis of the bacterial cell.


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Intracellular Accumulation Phase - In this phase the nucleic acid and structural

proteins that have been made are assembled and infectious phage particles accumulate

within the cell.

Lysis and Release Phase - After a while the bacteria begin to lyse due to the

accumulation of the phage lysis protein and intracellular phage are released into themedium. The number of particles released per infected bacteria may be as high as 1000.

The lytic infections

Before phage infection, the bacterial cell is involved in replication of its own

DNA and transcription and translation of its own genetic information to carry out

biosynthesis, growth and cell division. After phage attack, the viral DNA takes over the

machinery of the host cell and uses it to produce the nucleic acids and proteins needed for

production of new virus particles. Viral DNA replaces the host cell DNA as a templatefor both replication (to produce more viral DNA) and transcription (to produce viral

mRNA). Viral mRNAs are then translated, using host cell ribosomes, tRNAs and aminoacids, into viral proteins such as the coat or tail proteins. The process of DNA replication,

synthesis of proteins, and viral assembly is a carefully coordinated.

The overall process of lytic infection and discussion is diagrammed below:


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Figure 4. The lytic cycle of a bacterial virus, e.g. bacteriophage T4.

The first step in the replication of the phage in its host cell is called adsorption.The phage particle undergoes a chance collision at a chemically complementary site on

the bacterial surface, then adheres to that site by means of its tail fibers.

Following adsorption, the phage injects its DNA into the bacterial cell. The tailsheath contracts and the core is driven through the wall to the membrane. This process is

called penetration and it may be both mechanical and enzymatic. Phage T4 packages a

bit of lysozyme in the base of its tail from a previous infection and then uses thelysozyme to degrade a portion of the bacterial cell wall for insertion of the tail core. The

DNA is injected into the periplasm of the bacterium.

Immediately after injection of the viral DNA there is a process initiatedcalled synthesis of early proteins. This refers to the transcription and translation of asection of the phage DNA to make a set of proteins that are needed to replicate the phage

DNA. Among the early proteins produced are a repair enzyme to repair the hole in the

bacterial cell wall, a DNAase enzyme that degrades the host DNA into precursors of

phage DNA, and a virus specific DNA polymerase that will copy and replicate phageDNA. During this period the cell's energy-generating and protein-synthesizing abilities


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are maintained, but they have been subverted by the virus. The result is the synthesis ofseveral copies of the phage DNA.

The next step is the synthesis of late proteins. Each of the several replicatedcopies of the phage DNA can now be used for transcription and translation of a second

set of proteins called the late proteins. The late proteins are mainly structural proteinsthat make up the capsomeres and the various components of the tail assembly. Lysozyme

is also a late protein that will be packaged in the tail of the phage and be used to escapefrom the host cell during the last step of the replication process.

Having replicated all of their parts, there follows an assembly process. The

proteins that make up the capsomeres assemble themselves into the heads and "reel in" a

copy of the phage DNA. The tail and accessory structures assemble and incorporate a bitof lysozyme in the tail plate. The viruses arrange their escape from the host cell during

the assembly process.

While the viruses are assembling, lysozyme is being produced as a late viralprotein. Part of this lysozome is used to escape from the host cell by lysing the cell wall

peptiodglycan from the inside. This accomplishes the lysis of the host cell and the

release of the mature viruses, which spread to nearby cells, infect them, and complete

the cycle. The life cycle of a T-phage takes about 25-35 minutes to complete. Because thehost cells are ultimately killed by lysis, this type of viral infection is referred to a lytic

infection.

Lysogenic Infections

Lysogenic or temperate infection rarely results in lysis of the bacterial host cell.

Lysogenic viruses, such as lambda which infectsE. coli, have a different strategy thanlytic viruses for their replication. After penetration, the virus DNA integrates into the

bacterial chromosome and it becomes replicated every time the cell duplicates itschromosomal DNA during normal cell division. The life cycle of a lysogenic

bacteriophage is illustrated below.


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Figure 7. The lysogenic cycle of a temperate bacteriophage such as lambda.

Temperate viruses usually do not kill the host bacterial cells they infect. Their

chromosome becomes integrated into a specific section of the host cell chromosome.Such phage DNA is called prophage and the host bacteria are said to be lysogenized. In

the prophage state all the phage genes except one are repressed. None of the usual early

proteins or structural proteins are formed.

The phage gene that is expressed is an important one because it codes for thesynthesis of a repressor molecule that prevents the synthesis of phage enzymes and

proteins required for the lytic cycle. If the synthesis of the repressor molecule stops or if

the repressor becomes inactivated, an enzyme encoded by the prophage is synthesizedwhich excises the viral DNA from the bacterial chromosome. This excised DNA (the

phage genome) can now behave like a lytic virus, that is to produce new viral particlesand eventually lyse the host cell. This spontaneous derepression is a rare event

occurring about one in 10,000 divisions of a lysogenic bacterium., but it assures that newphage are formed which can proceed to infect other cells.

Usually it is difficult to recognize lysogenic bacteria because lysogenic and nonlysogenic

cells appear identical. But in a few situations, the prophage supplies genetic information


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such that the lysogenic bacteria exhibit a new characteristic (new phenotype), not

displayed by the nonlysogenic cell, a phenomenon called lysogenic conversion.

Significance of Lysogeny

Model for animal virus transformation - Lysogeny is a model system for virustransformation of animal cells

Lysogenic conversion - When a cell becomes lysogenized, occasionally extra

genes carried by the phage get expressed in the cell. These genes can change the

properties of the bacterial cell. This process is called lysogenic or phage conversion. Thiscan be of significance clinically. e.g. Lysogenic phages have been shown to carry genes

that can modify the Salmonella O antigen, which is one of the major antigens to which

the immune response is directed. Toxin production by Corynebacterium diphtheriae ismediated by a gene carried by a phage. Only those strains that have been converted by

lysogeny are pathogenic.

Plant Viruses

With plant viruses, the term specificity (or host-specificity) has a very narrow

meaning, since no plant virus as such exists. Instead, plant viruses can be grouped in anumber of varieties. The tobacco mosaic-virus (TMV), for example, multiplies withinNicotiana-species, several other solanaceous plants, and a few species of other plant

families.

The name of a virus is usually derived from the name of its main host plant. The

genetic information of plant viruses is either encoded by single-stranded RNA (most

plant viruses), double-stranded RNA (wound tumor viruses), single-stranded DNA(gemini-viruses) or double-stranded DNA (cauliflower mosaic-virus: CaMV).

Based on the shape of the virus particle, plant viruses can be distinguished as rod-

shaped and icosaedrical viruses with a capsid which is almost spherical.

TMV has helically arranged protein capsomers enclosingRNA. The RNA has a molecular weight of 2.1 x 106.

The protein coat consists of 2130 identical

polypeptide chains, each with a molecular weight of17.500. The polypeptide is made up of 158 amino

acid residues. The molecular weight of the TMV

virus particle (virion) is 40 x 106.

Structure of a tobacco mosaic-virus (TMV)


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Plant viruses have no specific mechanism for entering the host cell. Cell wall and

cuticle are difficult obstacles for them. Plant viruses depend therefore on injuries or ontransmission via invertebrates (insects, nematodes, etc.). The animal transmitter does in

some cases also act as an intermediate host. This means that some plant viruses are ableto multiply within animal tissue.

Viruses cause many important plant diseases and are responsible for huge lossesin crop production and quality in all parts of the world. Infected plants may show a range

of symptoms depending on the disease but often there is leaf yellowing (either of the

whole leaf or in a pattern of stripes or blotches), leaf distortion (e.g. curling) and/or other

growth distortions (e.g. stunting of the whole plant, abnormalities in flower or fruitformation).

Plant Viral Diseases

Virus diseases of plants are relatively rare. Infection is scarcely strong enough to

kill the plant. Monoculture favours spreading, and agricultural losses of profit.

Lettuce mosaic virus

LMV is a virus with flexuous filamentous particles approximately 750 x 13 nm. It

is sap-transmissible to a wide range of species, often seed-borne in lettuce and

transmitted by several aphid species in the non-persistent manner.

Grapevine fanleaf virus

This is an isometric virus particle with angular outline, about 30 nm in diameter,occurring worldwide in Vitis species. They are composed of a single protein of Mr

56,000. The virus causes fanleaf and yellow mosaic diseases of grapes. Fanleaf disease is

characterized by malformations of leaves (open marginal and petiolar sinuses, prominentmarginal teeth, asymmetrical blades, irregular veins).

Tomato Bushy Stunt Virus

TBSV is a soil-borne virus with isometric particles of about 30 nm diameter and

rounded outline found infecting economically important crops. Virus particles contain

one major linear positive sense, ssRNA species of c. 4.7 kb and a single coat protein ofMr 41,000. The virus is readily transmitted by mechanical inoculation to a wide range of

experimental hosts.

Natural transmission is through seed and soil, apparently without a vector. The

virus causes stunting and bushy growth, chlorotic spots, crinkling, deformation and

necrosis of leaves of tomato. Sometimes the virus is restricted to certain parts of the plant


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(e.g. the vascular system; discrete spots on the leaf) but in others it spreads throughout

the plant causing a systemic infection.

Infection does not always result in visible symptoms (as witnessed by names such

as Carnation latent virus and Lily symptom-less virus, both members of the genus

Carlavirus). Occasionally, virus infection can result in symptoms of ornamental value,such as breaking of tulips or variegation of Abutilon.

Spread of Plant Viruses

Since plant cells have a robust cell wall the viruses cannot penetrate them

unaided. Most plant viruses are therefore transmitted by a vector organism that feeds on

the plant or (in some diseases) are introduced through wounds made, for example, duringcultural operations (e.g. pruning). A small number of viruses can be transmitted through

pollen to the seed (e.g. Barley stripe mosaic virus, genus Hordeivirus) while many that

cause systemic infections accumulate in vegetatively propagated crops. The major

vectors of plant viruses are:

Insects: This forms the largest and most significant vector group and particularlyincludes:

Aphids: transmit viruses from many different genera, including Potyvirus,Cucumovirus and Luteovirus.

Whiteflies: transmit viruses from several genera but particularly those in thegenus Begomovirus.

Hoppers: transmit viruses from several genera, including those in the familiesRhabdoviridae and Reoviridae.

Thrips: transmit viruses in the genus Tospovirus. Beetles: transmit viruses from several genera, including Comovirus and

Sobemovirus

Control of Plant Viruses

Plant viruses cannot be directly controlled by chemical application. The major

means of control (depending on the disease) include:

Chemical or biological control of the vector (the organism transmitting thedisease, often an insect): this can be very effective where the vectors need to feed

for some time on a crop before the virus is transmitted but are of much less valuewhere transmission occurs very rapidly and may already have taken place before

the vector succumbs to the pesticide.

Growing resistant crop varieties: in some crops and for some viruses there arehighly effective sources of resistance that plant breeders have been using for

many years. However, no such natural resistance has been identified for manyothers.


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Transgenic resistance has shown considerable promise for many plant-viruscombinations following the discovery that the incorporation of part of the virus

genome into the host plant may confer a substantial degree of resistance.

Use of virus-free planting material: in vegetatively propagated crops (e.g.potatoes, many fruit crops) and where viruses are transmitted through seed major

efforts are made through breeding, certification schemes etc., to ensure that the

planting material is virus-free.

Exclusion: the prevention of disease establishment in areas where it does not yetoccur. This is a major objective of plant quarantine procedures throughout theworld as well as more local schemes.

Moreover, viroids were detected. Viroids are small, circular RNA molecules that

do not encode proteins themselves. Instead, virions interfere with the transcription ofcells due to their similarity with certain areas of recognition of primary transcription

products. It seems that viroids prevent the correct cutting out of the introns. They are

presumably multiplied with the aid of the cellular DNA-dependent RNA-polymerase II.Viroids occur mainly in warm climates and cause significant loss of profit as the

causative agents of the potato disease or the Cadang-Cadang disease of palms.

The virus concentration within plant cells is high, although a virus like the TMV

does not harm the host seriously. Infected cells contain often voluminous virus crystals.

Plants are far from being defenceless against viruses. Only a few virus species are

able to penetrate meristematic tissues or to infect a number of successive plantgenerations (vertical transmission). Hypersensitivity is an effective protection where viral

infection proceeds with dying of plant cells in the immediate surrounding of the primarysite of infection, thus stopping the spreading of the virus. The symptom a virus causes at

the primary site of infection is called primary symptom. Symptoms caused by its

spreading throughout the rest of the plant are called secondary symptoms.

Virus infections can usually be recognized by mosaic-like leaf patterns of lightand dark green. The infection spreads often over the whole leaf beginning at the leaf

veins. Leaves that had been infected during their development are usually deformed or

involute.

Frequently, lightened leaf areas, called chloroses, develop around the primary siteof infection. Withered areas are called necroses . Chloroses are caused by a breakdown of

the chlorophyll resulting in a decreased rate of photosynthesis. Heavy infections are

characterized by a complete local loss of chlorophyll. Affected areas have a yellowishlook as only the carotenoids remain. Some TMV strains, for example, can be recognized

by yellow leaf areas ("yellow strains").


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Some viruses multiply within the plant without causing symptoms. This

phenomenon is called latent infection. In contrast, wound tumor virus cause the

development of tumors. The symptoms of most viruses are dependent on both virus andhost, and do thus present an important diagnostic feature.

The TMV virus uses the plants vascular system for spreading. As a result, fullydifferentiated, old leaves and roots, and young leaves are equally infected. A number of

TMV wild types differing, for example, in their host range or in the primary structure oftheir coat proteins exist. The classic strain that at the same time is the one that proliferates

best on tobacco plants is called vulgare. A strain from tomatoes that proliferates equally

well on tobacco plants is called dahlemense. A third strain gained from plantain is knownas Holmes ribgrass.

Spherical (icosaedrical) Viruses

The densely packed nucleic acid of many spherical viruses is enclosed by a

protein coat also called capsid. The capsid is a polyhedral, i.e. it has many sides. Theexact number is specific for the respective species. The aggregated polypeptides form

morphological units often composed of several identical polypeptide chains. The crystal

structures of a number of different RNA-containing plant viruses are known, among them

are:

the tomato bushy stunt virus (TBSV),

the southern bean mosaic-virus (SBMV),

the satellite of the tobacco necrosis virus (STNV),

and the turnip crinkle-virus (TCV).

All of them have an icosaedrical structure. They consist of 60 (= 5 x 12) identicalpolypeptide copies of with the same building pattern assembled to form a hollow sphere.Simple examples of this type of architecture are the SBMV and the TBSV.

RNA-Viruses with Split Genomes

A number of RNA plant viruses contain more than just one molecule of RNA per

virion. In others, the genome is distributed among several virus particles.

The cucumber mosaic virus (CMV) is an example of the first type. It contains five

molecules of RNA, four of which are required for the replication of the virus, the fifth is

likely to have a helper function and can be classified as satellite-RNA (CARNA 5).

Incomplete viruses, satellite viruses: The multiplication of viruses leads often toincomplete infectious particles. They contain often cellular RNA instead of a complete or

partial viral-RNA. This frequently high proportion of non-infectious particles makes it

very difficult to determine the plating efficiency of the virus.
http://www.biologie.uni-hamburg.de/b-online/e35/icosaed.htmhttp://www.biologie.uni-hamburg.de/b-online/e35/icosaed.htm


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The genome of the alfalfa mosaic virus (AMV) consists of three molecules of

RNA contained in three capsids (the B, M, and Tb-particle). All three particles together

are infectious, the RNA isolated from them alone is not infectious.

In satellite viruses, the infectiousness depends on the presence of a helper virus.

The tobacco-necrosis virus (TNV) and its satellite (STNV) are a typical example. Themultiplication of the TNV is not dependent on the presence of STNV. TNV alone

produces large lesions in tobacco plants. These lesions are small if STMV is present.

Double-Stranded RNA-Viruses; Wound Tumor Viruses

The genome of wound tumor viruses (WTV) consists of 12 double-stranded RNA

segments. Neither of them is infectious. The wound tumor viruses of plants and animals

(reoviruses) are related and are characterized by a number of common activities. Theycontain, for example, the enzyme transcriptase that transcribes single-stranded RNA or,

in other words, produces an mRNA complementary to the transcribed strand. Each of the

12 segments can be transcribed and it is assumed that each of them encodes one protein.Replication occurs within the cytoplasm. Infection takes place via insects (e.g. aphids)

that function both as a vector and an intermediate host, i.e. the virus multiplies in their

tissue, too.

More than 50 plant species are known to be susceptible for wound tumor viruses.Among the symptoms are small tumors at the stem and larger and more numerous ones at

the roots. WTV-induced wound tumors of leguminosae can be clearly distinguished from

the nodules caused by nodule bacteria. In some plant species, like the lobelia, the

infection induces the development of organs from otherwise normal organs, e.g. a leafcan develop at the lower leaf surface of another leaf.

Plant Viruses with Circular, Single-Stranded DNA: Gemini Viruses

The particles of gemini viruses are quasi-isometric. They are called gemini (twin)

viruses, because they are usually found in pairs. Each particle has a diameter of just 15 20 nm. Gemini viruses belong to the smallest virus particles able to multiply without a

helper virus. They have a circular DNA with a molecular weight of 0.7 0.8 x 106 (about

2,500 base pairs). In the case of some gemini viruses the genome consists of twomolecules of DNA of almost equal size, but different sequence.

Isolated circular DNA alone is not infectious. In infected host cells, the nucleus

holds the chief amount of viral DNA. It is therefore assumed that the nucleus is also theplace of its replication. It looks as if analogous to the TMV double-strandedintermediates would exist (= replication state: RF), since double-stranded DNA has been

isolated from infected cells. The bean golden mosaic-virus (BGMV), the cassava latend-

virus (CLV), the tomato golden-mosaic-virus (TGMV), the maize-streak virus (MSV),and the abutilon mosaic-virus belong all to the Gemini-virus family.


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Insects (greenhouse whitefly, grasshoppers, and others) help usually in spreading

Gemini-viruses in nature. These viruses can cause considerable damage to agriculture.

Double-Stranded DNA Viruses

The prototype of a plant virus with double-stranded DNA is the cauliflower

mosaic-virus (CaMV). CaMV-DNA is normally not incorporated constantly into the host

cell genome. CaMV is the collective name for a group of tightly related viral speciesusually transmitted by aphids. Each species has a narrow host specificity, overlapping

with that of other species is rare. The virion is spherical with a diameter of about 50 nm.

Most likely, the capsid consists of 420 identical subunits with molecular weights of

42,000. The DNA contains about 8,000 base pairs.

Symptoms occur two to three weeks after infection and can be recognized by the

mosaic-like lesions of infected leaves. The virus spreads systemically, its secondary

symptoms are similar to those of the primary infection. Leaves that were infected duringtheir development display deformed leaf blades.

Viroids

Viroids are infectious units that cause a number of plant diseases. They are

circular molecules of RNA. Ex: Potato spindle tuber virus (PSTV). It consists of 359

ribonucleotides and is characterized by numerous intramolecular base-pairings that lendstability to the structure. They are organized in a sequence of helices separated from each

other by loops. The resulting structure resembles a dumb-bell with an axis ratio of 1:20.

They are all single stranded covalent circles There is extensive intramolecular base pairing A DNA-directed RNA polymerase makes both plus and minus strands

Replication does not depend on the presence of a helper virus

No proteins are encoded

Several more viroids have been sequenced in the meantime. All of them havestructures similar to that of the PSTV. They are ~240 380 nucleotides long and all of

them have dumb-bell structures. The fact that a central portion of the molecule that is

responsible for the pathogenicity of the viroids, is structurally conserved is especiallyinteresting.


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Viroids multiply even at relatively high temperature (about 35C). Most likely,

they have adapted to their host plants that have so-far strictly been found to inhabit

tropical, subtropical, and continental climates. The viroids are localized within thechromatin fraction of the nucleus. The DNA-dependent RNA-polymerase II and I use the

viroids as templates and produce strands that again serve as templates for the synthesis of

the + strand.

Slow Viruses and DI Viruses

The plants infected with DNA viruses (other than the full length viral genomes),

often contain one or more types of smaller DNAs (subviral molecules) derived fromthem. These smaller versions of the viral DNAs accumulate to significant levels in the

infected tissues. In most cases they interfere with viral multiplication resulting in

symptom amelioration and hence, interference. In many cases, their interfering naturesare not well-established and are consequently called defective DNA or subgenomic DNA.

To undergo a complete infectious cycle such defective genomes need original/helper

virus to provide the missing functions, like replication and encapsidation.

Plant viruses with circular double-stranded DNA (dsDNA) which replicate by

reverse transcription through an RNA intermediate (caulimoviruses and badnaviruses),

and those with circular single-stranded DNA (ssDNA), which replicate through a dsDNAintermediate (the geminiviruses, nanoviruses and associated DNA satellites) by rolling

circle replication in the nuclei of infected cells and also by recombination-dependent

replication are occurring. Defective DNA molecules have been reported for both the

above types, which fall into three families, namely Geminiviridae,Nanoviridae andCaulimoviridae. In addition, geminivirus-associated satellite DNAs also give rise to

defective DNAs.

General Features of Animal Viruses

Animal viruses consist of nucleic acid (DNA or RNA) surrounded by a protein

coat called a capsid. The capsid is made up of individual structural subunits called

capsomeres. The combination of the nucleic acid genome enclosed in the capsid is called

the nucleocapsid. In addition, the animal viruses have an envelope, which is amembranous lipid structure that surrounds the nucleocapsid.

The structural components of a Herpes virus are illustrated below.


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Herpes simplex Virus 1, (HSV1) is an enveloped, icosahedral DNA virus. The regionbetween the outer lipid envelope and the nucleocapsid is called the tegument. The DNA

of the virus resides in the core. The envelope proteins ("Glycoprotein Spikes") are unique

viral proteins, but the envelope itself is derived from the virus host cell.

Classification of Animal Viruses

The primary criteria for taxonomic classification of animal viruses are based on

morphology (size, shape, etc.), type of nucleic acid (DNA, RNA, single-stranded,

double-stranded, linear, circular, segmented, etc.), and occurrence of envelopes. ssRNAviruses possess either (+)RNA (if it serves as messenger RNA) or (-)RNA (if it serves as

a template for messenger RNA). Host range is not a particularly reliable criterion forclassification. Although some animal viruses exhibit a very narrow or specific host range,

such as HIV in humans or canine distemper virus (CDV) in dogs. But for classification

purposes, host range cannot be a criterion because each animal species is subject toinfection by a wide variety of viral agents, and numerous viruses infect several different

animal species. West Nile virus, for example, has a primary host of birds, but it infects

and causes disease in horses and humans. Some viruses, such as the influenza virus, are

able to change their structure in such a way that they can shift from one primary host toanother, for example birds to humans.

Morphologic similarity among animal viruses correlates closely with similarity of

viral components, particularly with the type and size of the viral nucleic acid (genome).

For example, all viruses with the morphology of adenoviruses contain dsDNA genomeswith a molecular weight of about 23 million daltons; all reoviruses contain segmented

dsRNA genomes. In fact, a system of virus classification based on structure and size of

viral genomes yields that same grouping as one based on morphology.


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This information is organized in two ways.

According to the Baltimore method of classification, animal viruses are be

separated into several classes, grouped by type of nucleic acid. Class I. dsDNA viruses;

Class II. ssDNA viruses; Class III. dsRNA viruses; Class IV. (+)RNA viruses; Class V.

(-)RNA viruses: Class VI. RNA reverse transcribing viruses; Class VII. DNA reversetranscribing viruses.

The Baltimore method of classification


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On the basis of morphology alone, animal viruses are organized into a

hierarchical scheme consisting of virus families and constitutive genera based on size,

shape, type of nucleic acid and the presence or absence of an envelope. Some families ofviruses generated in this scheme are described and illustrated below.

Some families of Animal Viruses


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Replication of Animal Viruses

Outside its host cell a virus is an inert particle. However, when it encounters a

host cell it becomes a highly efficient replicating machine. After attachment and gaining

entry into its host cell, the virus subverts the biosynthetic and protein synthesizing

abilities of the cell in order to replicate the viral nucleic acid, make viral proteins andarrange its escape from the cell. The process occurs in several stages and differs in its

details among DNA-containing and RNA-containing viruses.

The Stages of Replication

1. The first stage in viral replication is called the attachment (adsorption) stage.

Animal viruses attach to host cells by means of a complementary association

between attachment sites on the surface of the virus and receptor sites on the host cell

surface. This accounts for specificity of viruses for their host cells. Attachment sites onthe viruses (called virus receptors) are distributed over the surface of the virus coat

(capsid) or envelope, and are usually in the form of glycoproteins or proteins. Receptorson the host cell (the host cell receptors) are generally glycoproteins imbedded into thecell membrane. Cells lacking receptors for a certain virus are resistant to it and cannot be

infected.

Attachment can be blocked by antibody molecules that bind to viral attachment

sites or to host cell receptors. Since antibodies block the initial attachment of viruses to

their host cells, the presence of these antibodies in the host organism are the mostimportant basis for immunization against viral infections.

2. The penetration stage follows attachment.

Penetration of the virus occurs either by engulfment of the whole virus, or byfusion of the viral envelope with the cell membrane allowing only the nucleocapsid of the

virus to enter the cell. Animal viruses generally do not "inject" their nucleic acid into host

cells as do bacteriophages, although occasionally non enveloped viruses leave theircapsid outside the cell while the genome passes into the cell.

3. Once the nucleocapsid gains entry into the host cell cytoplasm, the process of

uncoating occurs.

The viral nucleic acid is released from its coat. Uncoating processes are

apparently quite variable and only poorly understood. Most viruses enter the host cell in

an engulfment process called receptor mediated endocytosis and actually penetrate thecell contained in a membranous structure called an endosome. Acidification of the

endosome is known to cause rearrangements in the virus coat proteins which probably

allows extrusion of the viral core into the cytoplasm.

Some antiviral drugs such as amantadine exert their antiviral effect my preventing

uncoating of the viral nucleic acid.


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4. Immediately following uncoating, the viral synthesis stage begins.

Exactly how these events will unfold depends upon whether the infecting nucleic

acid is DNA or RNA.

In DNA viruses, such as Herpes, the viral DNA is released into the nucleus of the

host cell where it is transcribed into early mRNA for transport into the cytoplasm where

it is translated into early viral proteins. The early viral proteins are concerned withreplication od the viral DNA, so they are transported back into the nucleus where they

become involved in the synthesis of multiple copies of viral DNA. These copies of the

viral genome are then templates for transcription into late mRNAs which are alsotransported back into the cytoplasm for translation into late viral proteins. The late

proteins are structural proteins (coat envelope proteins) or core proteins (certain

enzymes) which are then transported back into the nucleus for the next stage of thereplication cycle.

In the case of some RNA viruses (picornaviruses), the viral genome (RNA) stays

in the cytoplasm where it mediates its own replication and translation into viral proteins.In other cases (orthomyxoviruses), the infectious viral RNA enters into the nucleus where

it is replicated before transport back to the cytoplasm for translation into viral proteins.

5. Once the synthesis of the various viral components is complete, the assembly stagebegins.

The capsomere proteins enclose the nucleic acid to form the viral nucleocapsid.

The process is called encapsidation. If the virus contains an envelope it will acquire thatenvelope and asssociated viral proteins in the next step.

6. The release stage is the final event in viral replication, and it results in the exit of themature virions from their host cell.

Virus maturation and release occurs over a considerable period of time. Some

viruses are released from the cell without cell death, by egestion, whereas others are

released when the cell dies and disintegrates. In the case of enveloped viruses, thenucleocapsid acquires its final envelope from the nuclear or cell membrane by a budding

off process (envelopment) before egress (exit) out of the host cell. Whenever a virus

acquires a membrane envelope, it always inserts specific viral proteins into the thatenvelope which become unique viral antigens and which will be used by the virus to gain

entry into a new host cell.


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Replication of enveloped double stranded DNA virus: Herpes simplex virus (HSV)

The replication cycle of Herpes Simplex virus

1. Specific proteins in the viral envelope attach to host cell receptors on the cellmembrane. 2. Penetration is achieved when the viral envelope fuses with the cell

membrane releasing the nucleocapsid directly into the cytoplasm. 3. The virion is

uncoated and the viral DNA is transported into the nucleus. 4. In the nucleus, the viral

DNA is transcribed into early mRNAs which are transported to the cytoplasm for thetranslation of early proteins. These early proteins are brought back into the nucleus and

participate in the replication of the virus DNA into many copies. The viral DNA is then

transcribed into the late mRNAs which exit to the cytoplasm for translation into the late

(nucleocapsid and envelope) proteins. 5. The capsid proteins encapsidate the newlyreplicated genomes. The envelope proteins are imbedded in the nuclear membrane. 6. The

nucleocapsids are enveloped by budding through the nuclear membrane, and the matureviruses are released from the cell through cytoplasmic channels.


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Replication of Influenza virus is an enveloped, single stranded (-)RNA virus that

contains a segmented genome:

The replication cycle of Influenza A Virus.

1. The virus adsorbs to the cell surface by means of specific receptors. 2. The virus is

taken up in a membrane enclosed endosome by the process of receptor mediatedendocytosis. 3. Uncoating takes place in the endosome and the viral RNA (genome) is

released into the cytoplasm. 4. The (-)RNA of the viral genome is transported into the

nucleus where it is replicated and copied by a viral enzyme into (+)RNA which is both

messenger RNA and serves as a template for more (-)RNA. The (+)RNA is transportedinto the cytoplasm for translation into early and late viral proteins. 5. The viral core

proteins are transported back into the nucleus to assemble as the capsid around the viral

(-) RNA forming the "ribonucleoprotein core" or the genome-containing nucleocapsid of

the virus. The viral envelope proteins assemble themselves in the cell membrane. 6. Thenucleocapsid recognizes specific points on cell membrane where viral proteins have

become inserted and buds off of the membrane to be released during enclosure in theviral envelope.


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How Viruses Cause Disease

There are several possible consequences to a cell that is infected by a virus, and

ultimately this may determine the pathology of a disease caused by the virus.

Lytic infections result in the destruction of the host cell. Lytic infections are

caused by virulent viruses, which inherently bring about the death of the cells that theyinfect.

When enveloped viruses are formed by budding, the release of the viral particles

may be slow and the host cell may not be lysed. Such infections may occur over

relatively long periods of time and are thus referred to as persistent infections.

Viruses may also cause latent infections. The effect of a latent infection is that

there is a delay between the infection by the virus and the appearance of symptoms. Feverblisters (cold sores) caused by herpes simplex type 1 result from a latent infection; they

appear sporadically as the virus emerges from latency, usually triggered by some sort ofstress in the host.

Some animal viruses have the potential to change a cell from a normal cell into a

tumor cell, the hallmark of which is to grow without restraint. This process is called

transformation. Viruses that are able to transform normal cells into tumor cells are

referred to as oncogenic viruses.

The vast majority of viral infections in humans are inapparent or asymptomatic.

Viral pathogenesis is the abnormal situation and it is of no particular value to the virus,although it typically results in the multiplication of the viruses that can be transmitted to

other individuals. For pathogenic viruses, there are a number of critical stages inreplication which determine the nature of the disease they produce.


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The possible effects that animal viruses may have on the cells that they infect.

The Stages of Viral Infections

1. Entry into the Host

The first stage in any virus infection, irrespective of whether the virus is pathogenic or

not. In the case of pathogenic infections, the site of entry can influence the disease

symptoms produced.

Infection can occur via several portals of entry:

Skin - Most viruses which infect via the skin require a breach in the physical integrity of

this effective barrier, (cuts or abrasions). Some viruses employ vectors (ticks, mosquitos)

to breach the skin.

Respiratory tract - The respiratory tract and all other mucosal surfaces possesssophisticated immune defense mechanisms, as well as non-specific inhibitory

mechanisms (ciliated epithelium, mucus secretion, lower temperature) which viruses

must overcome. This is the most common point of entry for most viral pathogens.


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Gastrointestinal tract - a fairly protected mucosal surface, but some viruses (e.g.

enteroviruses, including polioviruses) enter at this site.

Genitourinary tract - less protected than the GI tract, but less frequently exposed to

extraneous viruses.

Conjunctiva - an exposed site and relatively unprotected.

2. Primary Replication

Having gained entry to a potential host, the virus must initiate an infection by

entering a susceptible cell. Some viruses remain localized after primary infection, but

others replicate at a primary site before dissemination and spread to a secondary site.

Examples are given in the table below.

Localized Infections:

Virus: Primary Replication:Rhinoviruses Upper respiratory tract

Rotaviruses Intestinal epithelium

Papillomaviruses Epidermis

Systemic Infections:

Virus: Primary

Replication:

Secondary Replication:

Enteroviruses

(poliovirus)

Intestinal epithelium Lymphoid tissues, CNS

Herpesvirus (HSV

types 1 and 2)

Oropharynx or

urogenital tract

Lymphoid cells, peripheral

nervous system, CNS

Rabies virus Muscle cells andconnective tissue

CNS

3. Dissemination Stage

There are two main mechanisms for viral spread throughout the host: via the

bloodstream and via the nervous system.

The virus may get into the bloodstream by direct inoculation - arthropod vectors, blood transfusion or I.V. drug abuse. The virus may travel free in the plasma

(Togaviruses, Enteroviruses), or in association with red cells (Orbiviruses), platelets

(HSV), lymphocytes (EBV, CMV) or monocytes (Lentiviruses). The presence of virusesin the bloodstream is referred to as a viremia. Primary viremia may be followed by

more generalized secondary viremia as the virus reaches other target tissues or replicates

directly in blood cells.

In some cases, spread to nervous system is preceded by primary viremia, as

above. In other cases, spread occurs directly by contact with neurons at the primary siteof infection. Once in peripheral nerves, the virus can spread to the CNS by axonal


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transport along neurons (HSV). Viruses can cross synaptic junctions since these

frequently contain virus receptors, allowing the virus to jump from one cell to another.

4. Tissue/Cell tropism

Tropism is the ability of a virus to replicate in particular cells or tissues. It is

influenced partly by the route of infection but largely by the interaction of a virus

attachment sites (virus receptors) with specific receptors on the surface of a cell. Theinteraction of the virus receptors with the host cell receptors may have a considerable

effect on pathogenesis.

5. Host Immune Responses

There are several ways that the host immune responses may contribute to viral

pathology. The mechanisms of cell mediated immunity are designed to kill cells which

are infected with viruses. If the mechanisms of antibody mediated immunity result in theproduction of antibodies that cross-react with tissues, an autoimmune pathology may

result.

6. Secondary Replication

This occurs in systemic infections when a virus reaches other tissues in which it iscapable of replication. For example, polioviruses initiate infection in the GI where the

produce an asymptomatic infection. However, when disseminated to neurons in the brain

and spinal cord, where the virus replicates secondarily, the serious paralytic complicationof poliomyelitis occurs. If a virus can be prevented from reaching tissues where

secondary replication can occur, generally no disease results.

7. Direct Cell and Tissue Damage

Viruses may replicate widely throughout the body without any disease symptoms

if they do not cause significant cell damage or death. Although retroviruses (e.g. HIV) do

not generally cause cell death, being released from the cell by budding rather than by celllysis, they cause persistent infections and may be passed vertically to offspring if they

infect the germ line. Conversely, most other viruses, referred to as virulent viruses,

ultimately damage or kill their host cell by several mechanisms, including inhibition ofsynthesis of host cell macromolecules, damage to cell lysosomes, alterations of the cell

membrane, development of inclusion bodies, and induction of chromosomal aberrations.

8. Persistence versus Clearance

The eventual outcome of any virus infection depends on a balance between the

ability of the virus to persist or remain latent (persistence) and the forces of the host to

completely eliminate the virus (clearance).

Long term persistence is the continued survival of a critical number of virus

infected cells sufficient to continue the infection without killing the host. It results fromtwo main mechanisms:


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a. Regulation of lytic potential. For viruses that do not kill their host cells, this is not

usually a problem. But for lytic (virulent) viruses, there may be ways to down

regulate their replicative and lytic potential so that they can persist in a state oflatency without replication and damage to their host cell. This is the case with herpes

viruses.

b. Evasion of immune surveillance.

This may be due to several conditions that are properties of the host or the virus.

Some viruses, such as influenza, can undergo antigenic shifts or antigenic drift that

allows them to bypass a host immune response. Some viruses, e.g., measles, may inducea form of immune tolerance such that the host is unable to undergo an effective immune

response to the virus. Other viruses, such as HIV, may set up a direct attack against cells

of the immune system such that the immune system is compromised in its ability toattack or eliminate the virus.

List of important virus families that contain genera that infect humans and the

symptoms that they cause

DNA- containing viruses

AdenoviridaeHuman Adenoviruses - primarily respiratory and conjunctival infections

Astroviridae

Astrovirus - flulike symptoms

Herpesviridae

Herpes simplex virus type 1 - stomatitis; upper respiratory infectionsHerpes simplex virus type 2 - genital infections

Varicella-zoster - chicken pox; herpes zoster; shingles ,

Human Cyotmegalovirus - jaundice; hepatosplenomegaly, brain damage, deathEpstein-Barr Virus - Burkitt's lymphoma; nasopharyngeal carcinoma; infectious

mononucleosis

PapovaviridaeHuman papilloma viruses- benign tumors (warts); cervical cancer

Human polyoma viruses - progressive leukoencephalopathy (PML); transform cells

in tissue culture

Poxviridae

OrthopoxvirusVariola - smallpox

Cowpox - vesicular lesions on skin

Unclassified Round-structured viruses

Norwalk agent "Noroviruses" - gastroenteritis


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RNA - containing viruses

Arenaviridae

Lymphocytic choriomeningitis virus (LCM) - fatal meningitisLassa virus - hemorrhagic fever, frequently fatal

BunyaviridaeHanta virus

Coronaviridae

Human Coronavirus - SARS - severe acute respiratory syndrome

Filoviridae

Ebola - acute hemorrhagic fever almost 90% case mortality

Marburg - hemorrhagic fever, frequently fatal

FlaviviridaeYellow Fever - hemorrhagic fever, hepatitis, nephritis

Dengue - fever, arthralgia, rash

West Nile - fever, arthralgia, rash

Hepatitis C virus - hepatitis

Orthomyxoviridae

Influenza virus type A - acute respiratory diseaseInfluenza virus type B - acute respiratory disease

Influenza virus type C - acute respiratory disease

Paramyxoviridae

Parainfluenza viruses - croup, common cold syndrome, mild respiratory disease

Mumps - parotitis, orchitis, meningoencephalitisMeasles - measles

Subacute sclerosing panencephalitis (SSPE) - chronic degeneration of CNS

Respiratory syncytial virus (RSV) - pneumonia and bronchiolitis in infants and

children, common cold syndrome

Picornaviridae

Human EnterovirusesPoliovirus - poliomyelitis

Coxsackie virus A - aseptic meningitis, paralysis, and common cold syndrome

Coxsackie virus B - aseptic meningitis, paralysis, severe systemic illness ofnewborns

Hepatitis A virus - infectious hepatitis

Human Rhinoviruses - common cold, bronchitis, croup, bronchopneumonia


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Reoviridae

Colorado Tick fever virus - encephalitis

Human Rotaviruses - diarrhea in infants

Retroviridae (RNA-tumor viruses)

Human immunodeficiency virus - acquired immune deficiency syndrome (AIDS)Human T-lymphotrophic virus (HTLV)

RhabdoviridaeRabies virus - encephalitis, usually fatal

Togaviridae

Eastern Equine Encephalitis virus - encephalitisWestern Equine Encephalitis virus - encephalitis

Rubella (Measles) - severe deformities of fetuses in first trimester of pregnancy

Cultivation and enumeration of viruses

Laboratory animals

The laboratory animals are considered equivalent animal models of human

infection. Historically the only way to study viruses was from animal to animal. But thismethod of analysis faced several problems: 1) They are inconvenient and expensive, 2)

not defined system- leads to generation of virus mutants, 3) animal welfare issues.

However, these methods have advantages like some viruses can only be studied andmethod gives unique insight into virus pathogenesis.

Embryonated eggs have been used as alternative models.


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Cell culture

This method is currently the most common way to study the viruses. Sterility isan important aspect in employing them. The cells can be infected synchronously to obtain

viruses on large scale.

The different types of cells employed for virus infection are:

Primary cells- These are derived directly from animal tissue. Ex: Chick embryo,human foreskin, monkey kidney, etc.

Diploid cell lines- These cells maintain the diploid number of chromosomes but

can divide up to 100 times. Ex: usually cells from human embryos

Continuous cell lines- Such cells can be propagated indefinitely. They are

derived usually from a tumor tissue or by treating primary or diploid cells with mutagens

or tumor viruses. These cells have little resemblance to original cell and posses abnormalchromosome numbers (aneupoloid), and can be tumorigenic. Ex: HeLa, Vero, L929,

CHO, etc.

Also the diploid and continuous cells can be frozen in liquid nitrogen for later use.

The different cell types can be cultured in the laboratory as monolayer cells orsuspension cells. The monolayer cells can be obtained on a solid surface like plastic orglass. Where as if cells are required on a large scale, the cells can be cultured (spinner

culture) as suspension cell cultures.

In any case the culture of cells in laboratory requires the supply of food in the

form of chemically defined media. The designed medium is an isotonic solution of salts,glucose, vitamins, coenzymes, amino acids, buffered to 7.3 (with CO2) and antibiotics.

An important constituent of cell culture medium is the serum, it provides the growth

factors required for the cells to grow in culture. On cell culturing most cell lines doubleevery 24-48 hours and must be passaged(divided) into new cultures every 3-4 days. The

adherent monolayers of cells are removed from the containers by treating with trypsin

(proteolytic enzyme) and versene (EDTA).

The viral infection of cell cultures generates typical cytophathic effects (CPE).

Some viruses kill the cells in which they replicate. Such an incident is often easily visible

as CPE in some viral infections, but other viral infections do not show any visible CPE.The other type of CPE is in the form of typical rounding or detaching of cells and cell

fusion called syncytia. Thus cytophatic effects due to viral infections of animal cells vary

from virus to virus and they can be diagnostic in nature.


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Table. 9. Some cytophathic effects

Detection and quantification of infectious viruses

Here the amount of virus that causes infection in the system is detected. The

measure of virus is referred to as titer. Thus virus titer is a measure of the concentration

of the virus. The virus titer can be determined by several methods: Plaque assay,fluorescent focus assay, infectious center assay, transformation assay, endpoint dilution

assay, etc. The virus titers can be as high as 1010 infections/ml, or very low.

The plaque assay

The monolayers of cells are exposed to a defined dilution of virus, such that the

virus is adsorbed. The inoculum is removed and the cells covered with medium that

includes a gelling substance like agar. The gel prevents long range spread of virus but

allows virus to infect neighboring cells- thus causing a localized infection. With time theplaques become visible with naked eye, or can be seen after staining the cells (with neural

red, crystal violet). A plaque assay will work with viruses that cause CPE. Thevisualization can be improved with histochemical stains. The viral titer is usuallyexpressed as plaque forming units (PFU).


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Make serial dilutions of virus

Plate dilutions onto susceptible cells, after

virus attachment, overlay cells with

semisolid medium which restricts

diffusion of viral particles

Restricted cell-to-cell spread of virusresults in localized destruction of cell

monolayer visible as plaques.

Fluorescent focus assay

Infection is scored by addition of virus-specific antibody, and fluorescent

secondary antibody and visualization under the microscope usually after a single round of

infection. The infectivity can be scored as FFU/cell. This assay is not accurate but usefulin some respects.

Infectious Center Assay

This a modification of the plaque assay where infected cells are mixed with non-

infected cells before plating. This method is useful for persistently infected cells.

Transformation assay

It is considered as inverse plaque assay. It measures the production of foci oftransformed cells (small piles). The measureme

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