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 to accomodate 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 the opposite 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 structural features, 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 cell membtrane but which always contains unique viral proteins (spikes).

tobacco mosaic influenza virus 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 host cell 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 and cannot produce their energy since, they lack enzymes for metabolic functions. They also lack ribosomes required for protein synthesis.

poliovirus

herpes virus

The general features of viruses are outlined in the table below. Table 9. 1. General Features of Viruses 1. 2. Viral Features Small size Properties Viruses cannot be viewed with a light microscope pass through filters that retain bacteria. Viral sizes range between 0.1-0.3 micrometers Characteristic shapes Spherical (complex), helical, rod or polyhedral, sometimes with tails or envelopes. Most common polyhedron is the icosahedron which as 20 triangular faces. Obligate intracellular Viruses do not contain within their coats the machinery parasites for replication. For this they depend upon a host cell for their existence as obligate intracellular parasites. Each virus can only infect certain species of cells. This refers to the virus host range. No built-in metabolic Viruses have no metabolic enzymes and cannot generate machinery their own energy. No ribosome Viruses cannot synthesize their own proteins. They utilize host cell ribosomes for this during replication. Only one type of nucleic Viruses contain either DNA or RNA (never both) as acid their genetic material. The nucleic acid can be singlestranded or double stranded. 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.

3.

4. 5. 6. 7.

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:

General Host Range Prokaryotes: Archaea Eukaryotes: Algae Invertebrates

Bacteria Plants

Mycoplasma Prortozoa Vertebrates

Spiroplasma Fungi

Figure 2. Shapes and comparative sizes of different groups of viruses.

A. Smallpox virus E. Bacteriophage T2 I. Influenza virus M. Alflafa mosaic virus B. Orf virus F. Flexuous-tailed bacteriophage J. Filamentous flexuous virus N. Poliovirus C. Rhabdovirus G. Herpes virus K. Tobacco mosaic virus O. Bacteriophage phiX174 D. Paramyxovirus H. Adenovirus L. Polyoma/papilloma virus

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). The envelopes 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.

Classification of Viruses Classical virus classification schemes have been based on the consideration of four 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 virus classification 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 useful for 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 are often 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 Type although a number of other criteria - such as disease symptoms, antigenicity, protein profile, host range, etc. are important in precise identification, consideration of the above three criteria are sufficient in most cases to allow identification of a virus down to familial if not generic level.

The Properties used for Classifying Viruses are as follows: S.No 1. Primary Characteristics Chemical nature of nucleic acid: RNA or DNA; single or double stranded; single or segmented genome; (+) or (-) strand ; molecular weight . Structure of virion : Helical , icosahedral, or complex; naked or enveloped, complexity; number of capsomers for icosahedral virions, diameter of nucleo-capsids for helical viruses. Site of replication: Nucleus or cytoplasm Secondary Characteristics Host range: Host species, specific host tissues or cell types. Mode of transmission: Ex: faeces. Specific surface structures: Ex: antigenic properties

2.

3..

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

International Committee on Viral Taxonomy (ICTV) Classification System Group I: dsDNA Viruses Order Caudovirales - Tailed Bacteriophages Genus Type Species T4-like viruses Enterobacteria phage T4 P1-like viruses Enterobacteria phage P1 P2-like viruses Enterobacteria phage P2 Mu-like viruses Enterobacteria phage Mu SP01-like viruses Bacillus phage SP01 H-like viruses Halobacterium virus H T7-like viruses Enterobacteria phage T7 P22-like viruses Enterobacteria phage P22 29-like viruses Bacillus phage 29 N4-like viruses Enterobacteria phage N4 -like viruses Enterobacteria phage T1-like viruses Enterobacteria phage T1 T5-like viruses Enterobacteria phage T5 L5-like viruses Mycobacterium phage L5 c2-like viruses Lactococcus phage c2 M1-like viruses Methanobacterium virus M1 C31-like viruses Streptomyces phage C31 N15-like viruses Enterobacteria phage N15 Genus Type Species Ascovirus Spodoptera frugiperda ascovirus Atadenovirus Ovine adenovirus D Aviadenovirus Fowl adenovirus A

Family (Subfamily) Myoviridae

Hosts Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria

Podoviridae

Siphoviridae

Family (Subfamily) Ascoviridae Adenoviridae

Hosts Invertebrates Vertebrates Vertebrates

Asfarviridae Baculoviridae

Mastadenovirus Siadenovirus Asfivirus Nucleopolyhedrovirus Granulovirus

Corticoviridae Fuselloviridae Guttaviridae Herpesviridae : Alphaherpesvirinae

Corticovirus Fusellovirus Guttavirus Ictalurivirus Mardivirus Simplexvirus Varicellovirus Iltovirus Cytomegalovirus Muromegalovirus Roseolovirus Lymphocryptovirus Rhadinovirus Iridovirus Chloriridovirus Ranavirus Lymphocystivirus Megalocytivirus

Betaherpesvirinae Gammaherpesvirina e Iridoviridae

Lipothrixviridae

Alphalipothrixvirus Betalipothrixvirus Gammalipothrixvirus

Nimaviridae Mimivirus Polyomaviridae Papillomaviridae

Whispovirus

Polyomavirus Alphapapillomavirus

Human adenovirus C Frog adenovirus African swine fever virus Autographa californica nucleopolyhedrovirus Cydia pomonella granulovirus Alteromonas phage PM2 Sulfolobus virus SSV1 Sulfolobus virus SNDV Ictalurid herpesvirus 1 Gallid herpesvirus 2 Human herpesvirus 1 Human herpesvirus 3 Gallid herpesvirus 1 Human herpesvirus 5 Murine herpesvirus 1 Human herpesvirus 6 Human herpesvirus 4 Simian herpesvirus 2 Invertebrate iridescent virus 6 Invertebrate iridescent virus 3 Frog virus 3 Lymphocystis disease virus 1 Infectious spleen and kidney necrosis virus Thermoproteus virus 1 Sulfolobus mislandicus filamentous virus Acidianus filamentous virus 1 White spot syndrome virus 1 Acanthamoeba polyphaga mimivirus Simian virus 40 Human

Vertebrates Vertebrates Vertebrates

Invertebrates

Invertebrates Bacteria Archaea Archaea

Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Invertebrates

Invertebrates Vertebrates Vertebrates Vertebrates Archaea Archaea Archaea

Invertebrates Protozoa, Vertebrates Vertebrates Vertebrates

Betapapillomavirus Gammapapillomavirus Deltapapillomavirus Epsilonpapillomavirus Zetapapillomavirus Etapapillomavirus Thetapapillomavirus Iotapapillomavirus Kappapapillomavirus Lambdapapillomavirus Mupapillomavirus Nupapillomavirus Xipapillomavirus Omikronpapillomaviru s Pipapillomavirus Phycodnaviridae Chlorovirus Prasinovirus Prymnesiovirus Phaeovirus Coccolithovirus Raphidovirus Plasmaviridae Plasmavirus

papillomavirus 32 Human papillomavirus 5 Human papillomavirus 4 European elk papillomavirus Bovin papillomavirus 5 Equine papillomavirus 1 Fringilla coelebs papillomavirus Psittacus erithacus timneh papillomavirus Mastomys natalensis papillomavirus Cottontail rabbit papillomavirus Canine oral papillomavirus Human papillomavirus 1 Human papillomavirus 41 Bovine papillomavirus 3 Phocoena spinipinnis papillomavirus Hamster oral papillomavirus Paramecium bursaria Chlorella virus 1 Micromonas pusilla virus SP1 Chryosochromomulin a brevifilium virus PW1 Extocarpus siliculosus virus 1 Emiliania huxleyi virus 86 Heterosigms akashiwo virus 01 Acholeplasma phage L2

Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Algae Algae Algae Algae Algae Algae Mycoplasma

Polydnaviridae

Ichnovirus Bracovirus

Poxviridae:

Chordopoxvirinae

Orthopoxvirus Parapoxvirus Avipoxvirus Capripoxvirus Leporipoxvirus Suipoxvirus Molluscipoxvirus Yatapoxvirus

Entomopoxvirinae

Entomopoxvirus A Entomopoxvirus B Entomopoxvirus C

Rhizidovirus Rudiviridae Tectiviridae Rudivirus Tectivirus

Campoletis sonorensis ichnovirus Cotesia melanoscela brachovirus Vaccinia virus Orf virus Fowlpox virus Sheeppox virus Myxoma virus Swinepox virus Molluscum contagiosum virus Yaba monkey tumor virus Melolontha melolontha entomopoxvirus Amsacta moorei entomopoxvirus Chironomus luridus entomopoxvirus Rhizidomyces virus Sulfolobus virus SIRV1 Enterobacteria phage PRD1

Invertebrates

Invertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates

Invertebrates

Invertebrates

Invertebrates Fungi Archaea Bacteria

Family (Subfamily) Circoviridae Geminiviridae

Inoviridae

Microviridae

Group II: ssDNA Viruses Genus Type Species Anellovirus Torque teno virus Circovirus Porcine circovirus Gyrovirus Chicken anemia virus Mastrevirus Maize streak virus Curtovirus Beet curly top virus Topocuvirus Tomato pseudo-curly top virus Begomovirus Bean golden mosaic virus Inovirus Enterobacteria phage M13 Plectrovirus Acholeplasma phage MV-L51 Microvirus Enterobacteria X174 Spiromicrovirus Spiroplasma phage 4 Bdellomicrovirus Bdellovibrio phage MAC1

Hosts Vertebrates Vertebrates Vertebrates Plants Plants Plants Plants Bacteria Bacteria Bacteria Spiroplasma Bacteria

Nanoviridae

Parvoviridae :

Family (Subfamily) Birnaviridae

Subterranean clover stunt virus Babuvirus Banana bunchy top virus Parvovirinae Parvovirus Mice minute virus Erythrovirus B19 virus Dependovirus Adeno-associated virus 2 Amdovirus Aleutian mink disease virus Bocavirus Bovine parvovirus Densovirina Densovirus Junonia coenia e densovirus Iteravirus Bombyx mori densovirus Brevidensovirus Aedes aegypti densovirus Pefudensovirus Periplanta fuliginosa densovirus Group III: dsRNA Viruses Genus Type Species Aquabirnavirus Infectious pancreatic necrosis virus Infectious bursal disease virus Drosophila X virus Penicillium chrysogenum virus Pseudomonas phage 6 Vicia faba endornavirus Cryphonectria hypovirus 1EP713 Atkinsonella hypoxylon virus White clover cryptic virus 1 White clover cryptic virus 2 Mammalian orthoreovirus Bluetongue virus Rotavirus A Colorado tick fever virus Golden shiner virus Banna virus Cypovirus 1 Idnoreovirus 1

Chlamydiamicroviru s Nanovirus

Chlamydia phage 1

Bacteria Plants Plants Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Invertebrates Invertebrates Invertebrates Invertebrates

Hosts

Vertebrates Vertebrates Invertebrates Fungi Bacteria Plants Fungi Fungi Plants Plants Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Invertebrates Invertebrates

Avibirnavirus Entomobirnaviru s Chrysoviridae Chrysovirus Cystoviridae Cystovirus Endornavirus Hypoviridae Hypovirus Partitiviridae Reoviridae Partitivirus Alphacryptovirus Betacryptovirus Orthoreovirus Orbivirus Rotavirus Coltivirus Aquareovirus Seadornavirus Cypovirus Idnoreovirus

Totiviridae

Fijivirus Phytoreovirus Oryzavirus Mycoreovirus Totivirus Giardiavirus Leishmaniavirus

Fiji disease virus Wound tumor virus Rice ragged stunt virus Mycoreovirus 1 Saccharomyces cerevisiae virus L-A Giardia lamblia virus Leishmania RNA virus 1-1

Plants Plants Plants Fungi Fungi Protozoa Protozoa

Family

Group IV: (+)sense RNA Viruses Order Nidovirales - "Nested" Viruses Genus Type Species

Hosts

(Subfamily) Arteriviridae Arterivirus Coronaviridae Coronavirus Torovirus Roniviridae Okavirus Family Genus (Subfamily) Astroviridae Avastrovirus Mamastrovirus Barnaviridae Barnavirus Benyvirus Bromoviridae Alfamovirus Bromovirus Cucumovirus Ilarvirus Oleavirus Caliciviridae Lagovirus Norovirus Sapovirus Vesivirus Cheravirus Closteroviridae Ampelovirus Closterovirus Comoviridae Comovirus Fabavirus

Equine arteritis virus Infectious bronchitis virus Equine torovirus Gill-associated virus Type Species

Vertebrates Vertebrates Vertebrates Vertebrates Hosts

Turkey astrovirus Human astrovirus Mushroom bacilliform virus Beet necrotic yellow vein virus Alfalfa mosaic virus Brome mosaic virus Cucumber mosaic virus Tobacco streak virus Olive latent virus 2 Rabbit haemorrhagic disease virus Norwalk virus Sapporo virus Swine vesicular exanthema virus Cherry rasp leaf virus Grapevine leafroll-associated virus 3 Beet yellows virus Cowpea mosaic virus Broad bean wilt virus 1

Vertebrates Vertebrates Fungi Plants Plants Plants Plants Plants Plants Vertebrates Vertebrates Vertebrates Vertebrates Plants Plants Plants Plants Plants

Nepovirus Dicistroviridae Cripavirus Flaviviridae Flavivirus Pestivirus Hepacivirus Flexiviridae Potexvirus Mandarivirus Allexivirus Carlavirus Foveavirus Capillovirus Vitivirus Trichovirus Furovirus Hepevirus Hordeivirus Idaeovirus Iflavirus Leviviridae Levivirus Allolevivirus Luteoviridae Luteovirus Polerovirus Enamovirus Machlomovirus Marnaviridae Marnavirus Narnaviridae Narnavirus Mitovirus

Tobacco ringspot virus Cricket paralysis virus Yellow fever virus Bovine diarrhea virus 1 Hepatitis C virus Potato virus X Indian citrus ringspot virus Shallot virus X Carnation latent virus Apple stem pitting virus Apple stem grooving virus Grapevine virus A Apple chlorotic leaf spot virus Soil-borne wheat mosaic virus Hepatitis E virus Barley stripe mosaic virus Rasberry bushy dwarf virus Infectious flacherie virus Enterobacteria phage MS2 Enterobacteria phage Q Cereal yellow dwarf virus-PAV Potato leafroll virus Pea enation mosaic virus-1 Maize chlorotic mottle virus Heterosigma akashiwo RNA virus Saccharomyces cerevisiae narnavirus 20S Cryphonectria parasitica mitovirus 1NB631 Nodaviridae Alphanodoavirus Nodamura virus Betanodovirus Striped jack nervous necrosis virus Pecluvirus Peanut clump virus Ourmiavirus Ourmia melon virus Picornaviridae Enterovirus Poliovirus Rhinovirus Human rhinovirus A Hepatovirus Hepatitis A virus Cardiovirus Encephalomyocarditis virus

Plants Invertebrates Vertebrates Vertebrates Vertebrates Plants Plants Plants Plants Plants Plants Plants Plants Plants Vertebrates Plants Plants Invertebrates Bacteria Bacteria Plants Plants Plants Plants Fungi Fungi Fungi Invertebrates Vertebrates Plants Plants Vertebrates Vertebrates Vertebrates Vertebrates

Aphthovirus Parechovirus Erbovirus Kobuvirus Teschovirus Pomovirus Potyviridae Potyvirus Ipomovirus Macluravirus Rymovirus Tritimovirus Bymovirus Sadwavirus Sequiviridae Sequivirus Waikavirus Sobemovirus Tetraviridae Betatetravirus Omegatetravirus Tobamovirus Tobravirus Tombusviridae Tombusvirus Avenavirus Aureusvirus Carmovirus Dainthovirus Machlomovirus Necrovirus Panicovirus Togaviridae Alphavirus Rubivirus Tymoviridae Maculavirus Marafivirus Tymovirus Umbravirus

Foot-and-mouth disease virus O Human parechovirus Equine rhinitis B virus Aichi virus Porcine teschovirus Potato mop-top virus Potato virus Y Sweet potato mild mottle virus Maclura mosaic virus Ryegrass mosaic virus Wheat streak mosaic virus Barley yellow mosaic virus Satsuma dwarf virus Parsnip yellow fleck virus Rice tungro spherical virus Southern bean mosaic virus Nudaurelia capensis virus Nudaurelia capensis virus Tobacco mosaic virus Tobacco rattle virus Tomato bushy stunt virus Oat chlorotic stunt virus Pothos latent virus Carnation mottle virus Carnation ringspot virus Maize chlorotic mottle virus Tobacco necrosis virus Panicum mosaic virus Sindbis virus Rubella virus Grapevine fleck virus Maize rayado fino virus Turnip yellow mosaic virus Carrot mottle virus

Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Plants Plants Plants Plants Plants Plants Plants Plants Plants Plants Plants Invertebrates Invertebrates Plants Plants Plants Plants Plants Plants Plants Plants Plants Plants Vertebrates Vertebrates Plants Plants Plants Plants

Group V: (-)sense RNA Viruses

Order Mononegavirales Family (Subfamily) Genus Type Species Hosts Bornaviridae Bornavirus Borna disease virus Vertebrates Filoviridae Marburgvirus Lake Victoria Vertebrates marburgvirus 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 respiratory Vertebrates syncytial virus Metapneumovirus Avian pneumovirus Vertebrates Rhabdoviridae Vesiculovirus Vesicular stomatitis Vertebrates, Indiana virus Invertebrates Lyssavirus Rabies virus Vertebrates Ephemerovirus Bovine ephemeral fever Vertebrates, virus Invertebrates Novirhabdovirus Infectious haematopoetic Vertebrates necrosis virus Cytorhabdovirus Lettuce necrotic yellows Plants, virus Invertebrates Nucleorhabdovirus Potato yellow dwarf Plants, virus Invertebrates Family (Subfamily) Genus Type Species Hosts Arenaviridae Arenavirus Lymphocytic Vertebrates choriomeningitis virus Bunyaviridae Orthobunyavirus Bunyamwera virus Vertebrates Hantavirus Hantaan virus Vertebrates Nairovirus Nairobi sheep disease Vertebrates virus Phlebovirus Sandfly fever Sicilian Vertebrates virus Tospovirus Tomato spotted wilt virus Plants Deltavirus Hepatitis delta virus Vertebrates Ophiovirus Citrus psorosis virus Plants Orthomyxoviridae Influenza A virus Influenza A virus Vertebrates

Influenza B virus Influenza C virus Isavirus Thogotovirus Tenuivirus Varicosaivirus

Influenza B virus Influenza C virus Infectious salmon anemia virus Thogoto virus Rice stripe virus Lettuce big-vein associated virus

Vertebrates Vertebrates Vertebrates Vertebrates Plants Plants

Family (Subfamily) Retroviridae

Group VI: RNA Reverse Transcribing Viruses Genus Type Species Alpharetrovirus Betaretrovirus Gammaretrovirus Deltaretrovirus Epsilonretrovirus Lentivirus Spumavirus Metavirus Errantivirus Pseudovirus Hemivirus Avian leukosis virus Mouse mammary tumor virus Murine leukemia virus Bovine leukemia virus Walley dermal sarcoma virus Human immunodeficiency virus 1 Human spumavirus Saccharomyces cerevisiae Ty3 virus Drosophila melanogaster gypsy virus Saccharomyces cerevisiae Ty1 virus Drosophila melanogaster copia virus

Hosts Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Vertebrates Fungi Invertebrates Invertebrates Invertebrates Hosts

Metaviridae Pseudoviridae

Family

Group VII: DNA Reverse Transcribing Viruses Genus Type Species

(Subfamily) Hepadnaviridae Orthohepadnavirus Avihepadnavirus Caulimoviridae Caulimovirus Badnavirus Cavemovirus Petuvirus Soymovirus Tungrovirus Family (Subfamily)

Hepatitis B virus Duck hepatitis B virus Cauliflower mosaic virus Commelina yellow mottle virus Cassava vein mosaic virus Petunia vein clearing virus Soybean chlorotic mottle virus Rice tungro bacilliform virus

Vertebrates Vertebrates Plants Plants Plants Plants Plants Plants Hosts

Subviral Agents: Viroids Genus Type Species

Pospiviroidae

Avsunviroidae

Pospiviroid Hostuviroid Cocadviroid Apscaviroid Coleviroid Avsunviroidae Pelamonviroid

Potato spindle tuber viroid Hop stunt viroid Coconut cadang-cadang viroid Apple scar skin viroid Coleus blumei viroid 1 Avocado sunblotch viroid Peach latent mosaic viroid

Plants Plants Plants Plants Plants Plants Plants

The Bacteriophages Viruses that attack bacteria were observed by Twort and d'Herelle in 1915 and 1917. 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 or bacteriophages("phage" from Gr. "phagein" meaning "to eat"). But at research level more work has been done on the phages that infect E. 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 infect their 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 phages known as the T-phages cause lytic infections in E. 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 unusual or 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 code for 3-5 average size gene products while the more complex phages may code for over 100 gene products.

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 many different 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 nucleic acid. 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 a hollow 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 of the bacterium. At the end of the tail the more complex phages like T4 have a base plate

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 the bacterium.

Phage multiplication cycle Lytic or Virulent Phages 1. Definition - Lytic or virulent phages are phages which can only multiply on bacteria and 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 found either 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 an orderly expression of phage directed macromolecular synthesis. Early m-RNA's code for early 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. The late proteins are the structural proteins of the phage as well as the proteins needed for lysis of the bacterial cell.

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 the medium. 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 template for both replication (to produce more viral DNA) and transcription (to produce viral mRNA). Viral mRNAs are then translated, using host cell ribosomes, tRNAs and amino acids, 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:

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 tail sheath 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 the lysozyme 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 initiated called synthesis of early proteins. This refers to the transcription and translation of a section 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 phage DNA. During this period the cell's energy-generating and protein-synthesizing abilities

are maintained, but they have been subverted by the virus. The result is the synthesis of several copies of the phage DNA. The next step is the synthesis of late proteins. Each of the several replicated copies 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 proteins that 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 escape from 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 bit of 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 viral protein. 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 the host 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 infects E. coli, have a different strategy than lytic viruses for their replication. After penetration, the virus DNA integrates into the bacterial chromosome and it becomes replicated every time the cell duplicates its chromosomal DNA during normal cell division. The life cycle of a lysogenic bacteriophage is illustrated below.

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 the synthesis 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 synthesized which 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 particles and 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 new phage 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

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 virus transformation 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. This can 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 is mediated 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 a number of varieties. The tobacco mosaic-virus (TMV), for example, multiplies within Nicotiana-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 rodshaped and icosaedrical viruses with a capsid which is almost spherical.

TMV has helically arranged protein capsomers enclosing RNA. 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 of 17.500. 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)

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 on transmission 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 able to multiply within animal tissue. Viruses cause many important plant diseases and are responsible for huge losses in 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 fruit formation). 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, prominent marginal 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 of Mr 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

(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, during cultural 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 particularly includes: Aphids: transmit viruses from many different genera, including Potyvirus, Cucumovirus and Luteovirus. Whiteflies: transmit viruses from several genera but particularly those in the genus Begomovirus. Hoppers: transmit viruses from several genera, including those in the families Rhabdoviridae 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 the disease, 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 value where 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 are highly effective sources of resistance that plant breeders have been using for many years. However, no such natural resistance has been identified for many others.

Transgenic resistance has shown considerable promise for many plant-virus combinations 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 yet occur. This is a major objective of plant quarantine procedures throughout the world 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 of cells 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 plant generations (vertical transmission). Hypersensitivity is an effective protection where viral infection proceeds with dying of plant cells in the immediate surrounding of the primary site 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 light and 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 site of 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 yellowish look as only the carotenoids remain. Some TMV strains, for example, can be recognized by yellow leaf areas ("yellow strains").

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 and host, and do thus present an important diagnostic feature. The TMV virus uses the plants vascular system for spreading. As a result, fully differentiated, 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 of their 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 known as 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. The exact 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) identical polypeptide 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 to incomplete 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.

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. The multiplication 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. They contain, 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 leaf can 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 10 6 (about 2,500 base pairs). In the case of some gemini viruses the genome consists of two molecules 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 the place of its replication. It looks as if analogous to the TMV double-stranded intermediates would exist (= replication state: RF), since double-stranded DNA has been isolated from infected cells. The bean golden mosaic-virus (BGMV), the cassava latendvirus (CLV), the tomato golden-mosaic-virus (TGMV), the maize-streak virus (MSV), and the abutilon mosaic-virus belong all to the Gemini-virus family.

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 species usually 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 during their 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 lend stability 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 have structures 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 especially interesting.

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 the chromatin 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 from them. 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 natures are 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 dsDNA intermediate (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 and Caulimoviridae. 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 a membranous lipid structure that surrounds the nucleocapsid. The structural components of a Herpes virus are illustrated below.

Herpes simplex Virus 1, (HSV1) is an enveloped, icosahedral DNA virus. The region between 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. ssRNA viruses 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 for classification. 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 to infection 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 to another, 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 genomes with 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.

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 reverse transcribing viruses. The Baltimore method of classification

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 of viruses generated in this scheme are described and illustrated below. Some families of Animal Viruses

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 and arrange 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 on the 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. Receptors on the host cell (the host cell receptors) are generally glycoproteins imbedded into the cell 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 most important 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 by fusion 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 their capsid 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 the cell 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.

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 with replication 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 also transported 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 the replication 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 stage begins. 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 that envelope 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 the mature 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, the nucleocapsid 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 that envelope which become unique viral antigens and which will be used by the virus to gain entry into a new host cell.

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 cell membrane. 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 the translation 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 newly replicated genomes. The envelope proteins are imbedded in the nuclear membrane. 6. The nucleocapsids are enveloped by budding through the nuclear membrane, and the mature viruses are released from the cell through cytoplasmic channels.

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 mediated endocytosis. 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 transported into 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. The nucleocapsid recognizes specific points on cell membrane where viral proteins have become inserted and buds off of the membrane to be released during enclosure in the viral envelope.

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 they infect. 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. Fever blisters (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 of stress 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 in replication which determine the nature of the disease they produce.

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 possess sophisticated 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.

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. Virus: Rhinoviruses Rotaviruses Papillomaviruses Virus: Enteroviruses (poliovirus) Herpesvirus (HSV types 1 and 2) Rabies virus 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 viruses in 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 site of infection. Once in peripheral nerves, the virus can spread to the CNS by axonal Localized Infections: Primary Replication: Upper respiratory tract Intestinal epithelium Epidermis Systemic Infections: Primary Secondary Replication: Replication: Intestinal epithelium Lymphoid tissues, CNS Oropharynx or urogenital tract Muscle cells and connective tissue Lymphoid cells, peripheral nervous system, CNS CNS

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. The interaction 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 the production 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 is capable 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 complication of 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 cell lysis, 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 of synthesis 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 from two main mechanisms:

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 of latency 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 induce a 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 to attack or eliminate the virus. List of important virus families that contain genera that infect humans and the symptoms that they cause DNA- containing viruses Adenoviridae Human Adenoviruses - primarily respiratory and conjunctival infections Astroviridae Astrovirus - flulike symptoms Herpesviridae Herpes simplex virus type 1 - stomatitis; upper respiratory infections Herpes simplex virus type 2 - genital infections Varicella-zoster - chicken pox; herpes zoster; shingles , Human Cyotmegalovirus - jaundice; hepatosplenomegaly, brain damage, death Epstein-Barr Virus - Burkitt's lymphoma; nasopharyngeal carcinoma; infectious mononucleosis Papovaviridae Human papilloma viruses- benign tumors (warts); cervical cancer Human polyoma viruses - progressive leukoencephalopathy (PML); transform cells in tissue culture Poxviridae Orthopoxvirus Variola - smallpox Cowpox - vesicular lesions on skin Unclassified Round-structured viruses Norwalk agent "Noroviruses" - gastroenteritis

RNA - containing viruses Arenaviridae Lymphocytic choriomeningitis virus (LCM) - fatal meningitis Lassa virus - hemorrhagic fever, frequently fatal Bunyaviridae Hanta virus Coronaviridae Human Coronavirus - SARS - severe acute respiratory syndrome Filoviridae Ebola - acute hemorrhagic fever almost 90% case mortality Marburg - hemorrhagic fever, frequently fatal Flaviviridae Yellow 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 disease Influenza 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, meningoencephalitis Measles - 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 Enteroviruses Poliovirus - poliomyelitis Coxsackie virus A - aseptic meningitis, paralysis, and common cold syndrome Coxsackie virus B - aseptic meningitis, paralysis, severe systemic illness of newborns Hepatitis A virus - infectious hepatitis Human Rhinoviruses - common cold, bronchitis, croup, bronchopneumonia

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) Rhabdoviridae Rabies virus - encephalitis, usually fatal Togaviridae Eastern Equine Encephalitis virus - encephalitis Western 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 this method 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 and method gives unique insight into virus pathogenesis. Embryonated eggs have been used as alternative models.

Cell culture This method is currently the most common way to study the viruses. Sterility is an 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 abnormal chromosome 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 or suspension cells. The monolayer cells can be obtained on a solid surface like plastic or glass. 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 double every 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.

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 10 10 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 the plaques 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. The visualization can be improved with histochemical stains. The viral titer is usually expressed as plaque forming units (PFU).

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 virus results 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 useful in some respects. Infectious Center Assay This a modification of the plaque assay where infected cells are mixed with noninfected 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 of transformed cells (small piles). The measurement is expressed in terms of focus- forming units (FFU). Endpoint dilution assay This method is employed with animal models. The virus to be tested is diluted into replicate animals and disease or death is monitored. The endpoint is measured as the dilution which causes death of 50 percent of experimental animals or disease in 50 percent of experimental animals (ID50 = Infective dose 50%).

Chemotherapy of Viral Infections Basic Mechanisms Antiviral drugs specifically inhibit one or more steps of virus replication without causing unacceptable side effects. Approved Antiviral Drugs The approved antiviral drugs and the viruses and diseases they treat are amantadine and rimantadine (influenza A virus), ribavirin (respiratory syncytial virus), idoxuridine and trifluridine (topical treatment of herpetic keratitis), vidarabine and acyclovir (systemic treatment of herpes simplex virus and varicella-zoster virus infections), famciclovir and valaciclovir (oral treatment of varicella-zoster virus infections), ganciclovir and foscarnet (cytomegalovirus), and zidovudine, didanosine, zalcitabine and stavudine (human immunodeficiency virus). Future Antiviral Drugs To overcome the limitations of current antiviral drugs, more effective compounds are being developed that allow greater inhibition of viruses, greater selectivity for virusspecific functions, and fewer side effects, and may avoid emergence of resistant mutants. Main Targets for Antiviral Drugs Specific events in virus replication identified as targets for antiviral agents are viral adsorption, penetration, uncoating, and viral nucleic acid synthesis as well as viral protein synthesis. Specificity for infected cells may occur when virus-specified enzymes (e.g., thymidine kinase-induced by herpes simplex virus or varicella-zoster virus) activate drugs (e.g., acyclovir). Limitations of Antiviral Drugs Limitations include a narrow antiviral spectrum, ineffectiveness against the latent virus, development of drug-resistant mutants and toxic side effects. Interferon Interferons play an important role in the first line of defense against viral infections. They are part of the non-specific immune system and are induced at an early stage in viral infection before the specific immune system has had time to respond. Interferons are made by cells in response to an appropriate stimulus, and are released into the surrounding medium; they then bind to receptors on target cells and induce transcription of approximately 20-30 genes in the target cells, and this results in an anti-viral state in the target cells.

Types of interferon Type I interferon Interferon-alpha (leukocyte interferon) is produced by virus-infected leukocytes, etc Interferon-beta (fibroblast interferon) is produced by virus-infected fibroblasts, or virus-infected epithelial cells, etc Interferon- (a family of about 20 related proteins) and interferon- are particularly potent as antiviral agents. They are not expressed in normal cells, but viral infection of a cell causes interferons to be made and released from the cell (that cell will often eventually die as a result of the infection). The interferon binds to target cells and induces an antiviral state. Both DNA and RNA viruses induce interferon but RNA viruses tend to induce higher levels. Double-stranded RNA produced during viral infection may be an important inducing agent. Other stimuli will also cause these interferons to be made: e.g. exogenous double-stranded RNA, lipopolysaccharide, other components of certain bacteria. Type II inteferon Interferon-gamma (immune interferon) is produced by certain activated T-cells and NK cells. Interferon- is made in response to antigen (including viral antigens) or mitogen stimulation of lymphocytes.

Interferon-alpha and interferon-beta (type I Interferons) These interferons induce about 20-30 proteins, and the function of many of these is not fully understood. However, three of the proteins that appear to play an important role in the induction of the anti-viral state have been intensively studied. Expression of one of these proteins (25 oligo A synthase) results in activation of the second of these proteins (a ribonuclease) which can break down mRNA, and expression of the third protein (a protein kinase) results in inhibition of the initiation step of protein synthesis. These activities target viral protein synthesis, but also result in inhibition of host protein synthesis. Thus it is important that these proteins are only made and activated when needed. Interferon treatment induces the synthesis of the inactive form of these proteins in the target cell. Double-stranded RNA is needed for activation of these proteins. It directly activates 25 oligo A synthase and protein kinase R, and indirectly activates ribonuclease L (since this needs 2'5'oligo A, the product of 25 oligo A synthase, for activation). Thus, these potentially toxic pathways are only activated in the interferon-treated cell if double-stranded RNA is made, this will usually only happen if virus infection actually occurs. The activation of these proteins may sometimes result in the death of the cell, but at least the progress of the infection is prevented.

Other effects of interferons The pathway described above is by no means the only way that interferons protect cells against viruses and other pathogens.

All three interferons increase expression of class I MHC molecules and thus promote recognition by cytotoxic T cells. All three interferons can activate NK cells which can then kill virus-infected cells. Interferon-gamma increases expression of class II MHC molecules on antigenpresenting cells and thus promotes presentation of antigens to helper T cells. Interferongamma can also activate the ability of macrophages to resist viral infection (intrinsic antiviral activity) and to kill other cells if they are infected (extrinsic antiviral activity). Interferons have many other effects on gene expression, not all of which are understood. Therapeutic uses of interferons Interferons-alpha and beta have been used to treat various viral infections. One currently approved use for various types of interferon- is in the treatment of certain cases of acute and chronic hepatitis C and chronic hepatitis B. Interferon-gamma has been used to treat a variety of disease in which macrophage activation might play an important role in recovery, Ex: lepromatous leprosy, leishmaniasis, toxoplasmosis. Since interferons have anti-proliferative effects, they have also been used to treat certain tumors such as melanoma and Kaposis sarcoma. Side effects of interferons Common side effects of interferons are fever, malaise, fatigue, muscle pains High levels of interferons can cause kidney, liver, bone marrow and heart toxicity. Viral defenses against the non-specific and specific immune systems Not surprisingly, some viruses have developed defenses against the interferoninduced antiviral response and other aspects of the immune defense system. For example, viruses may code for proteins which block interferon binding to cells, inhibit the action of the interferon-induced protein kinase, inhibit NK function, interfere with cell surface expression of MHC, block complement activation, prevent the host cell committing apoptosis, etc.