THE VIRUSES- IMMUNO {ST1} BY RANJEET RAMAN

General Characteristics: virus means poison; someone once called them “a piece of bad news wrapped in a protein;" obligate intracellular parasites (can reproduce/replicate only inside a host cell) not cells; debate over whether or not they are considered “alive” consist of nucleic acids (DNA or RNA) in a protein coat, called a capsid (no cell membrane)

they insert themselves into a host cell & direct the host cell's metabolic machinery to make more virus; the virus supplies information (the plan) in the form of its nucleic acid - raw materials and driving force (ATP & reducing power) are supplied by the host cell. all cellular organisms can be attacked by viruses; however, viruses are very specific for the organisms & cells they infect.

Are Viruses Alive? Characteristics of living things: reproduction, metabolism, organized as cells, contain all organic molecules (lipids, enzymes, nucleic acids, carbs), evolution & adaptation to changing environments.

Viruses have some of these char's: they can evolve, they contain some macromolecules, they direct their own reproduction; However, they are not cells - they do not have cytoplasm, a cell membrane, organelles, ribosomes, or a nucleus.

They have DNA or RNA, unlike prokaryotic and eukaryotic cells, which have both. In addition, they lack a metabolism of their own (they cannot produce ATP, etc.) - raw materials and driving force (ATP & reducing power) are supplied by the host cell.

I. HOW ARE THEY CLASSIFIED I. HOW ARE THEY CLASSIFIED? (4 ways: size, structure, host range, life cycles) A. Size - range from about 1/10th to 1/3rd the size of a small bacterial cell.

B. Structure - basic structure of a virus is a nucleic acid surrounded by a protein capsid; a membrane envelope may also be present outside of the capsid, but this is acquired from host cell. A complete viral particle (= capsid + nucleic acid + envelope if it is present) is called a virion.

1. Nucleic Acid - Viruses can store their genetic info 1. Nucleic Acid - Viruses can store their genetic info. in different types of nucleic acid (each virus has only type). Viruses can have DNA or RNA. Their nucleic acid can be double stranded (ds) or single stranded (ss); they can even have double stranded RNA! RNA viruses can have a (-) sense strand or a (+) sense strand of RNA.

(+) sense RNA acts like mRNA and can be translated into proteins by the host cell’s ribosomes. (-) sense RNA does not make sense to the host cell’s ribosomes. After the virus containing this type of RNA enters the host cell, a complementary (+) sense strand is made from its (-) sense strand. Only (+) sense strand RNA can be read by the host cell’s ribosomes!

2. Capsids - protein coat that surrounds the nucleic acid; the constituent protein molecules making up the capsids are called capsomeres; there are 3 basic shapes based on how the capsomeres are arranged. See diagrams of these shapes!!

a. helical - proteins fit together as a spiral to form a rod- shaped structure. b. polyhedral - proteins are arranged in equilateral triangles that fit together to form a geodesic dome-shaped structure; some appear almost spherical; you may have seen architectural structures that have this shape.

c. complex - combination viruses with a helical portion (tail) attached to a polyhedral portion (head); ex. many bacteriophages; may also have a tail sheath (participates in injecting the viral nucleic acid into the host cell), plate, pins, & tail fibers (help virus attach to host cell).

3. Viral Envelopes - pieces of the host cell's cell membrane that the virus acquires as it emerges from its host cell; the virus pushes out of the cell membrane, forming a bud that encloses the virus - then the bud pinches off behind, resealing the cell - as a result the host cell is not lysed. Glycoprotein spikes from the host cell’s glycocalyx may stick out of the envelope.

Viruses that lack envelopes are called naked viruses Viruses that lack envelopes are called naked viruses. Because envelopes are acquired from host’s cell membranes, viruses may be hidden from attach by the host’s immune system. Envelopes also help viruses infect new cells by fusion of the envelope with the host’s cell membrane. On the other hand, enveloped viruses are damaged easily by physical and chemical antimicrobial agents.

C. Host Range - defined as the spectrum of organisms a virus attacks; viruses exhibit considerable specificity for hosts and even cells within that host; viral specificity is determined by whether or not a virus can attach to a cell. Attachment depends on the presence specific receptor sites on the surface of host cell and on specific attachment structures on the viral capsid or envelope. Examples of receptor sites are proteins, LPS’s, glycolipids, or glycoproteins.

D. Life Cycles of Bacteriophages (viruses that infect bacteria – means “bacteria eating”) 1. Replication [= Lytic Cycle] See diagram Events: a. Adsorption - the virion attaches itself to a specific receptor site on the surface of the host cell.

b. Penetration - the viral nucleic acid penetrates the host cell c. Uncoating - removing the capsid & envelope; basically 2 ways it can happen: 1.) during penetration, the virion disassembles so that only the viral nucleic acid enters host cell

2.) the entire virion enters the host cell & uncoating occurs later d. Viral Synthesis (Latent Period) (also called biosynthesis) - more viral components (nucleic acids & proteins for capsids) are synthesized by the host cell. d. Maturation (Assembly) - components are assembled into new viruses f. Release (Burst Period) - hundreds of intact virions exit host cell; 2 ways:

1.) If the virus is of the naked type, an encoded protein, lysozyme, dissolves the cell membrane &/or cell wall of the host cell, causing the cell to lyse & releasing the hundreds of viruses inside it. 2.) If the virus is to be an enveloped virus, it pushes out the cell membrane, forming a bud that encloses the virus - then the bud pinches off behind, resealing the host cell; as a result the host cell is not lysed.

2. Lysogenic Cycle (Lysogeny or Temperance) - Temperence involves the capacity of certain viruses to set up long-term relationships with their host cells - the virus remains latent for many cellular generations by becoming integrated into a host cell's chromosome (the integrated viral DNA is called a prophage). In this case no new viral components are synthesized & the host cell is not harmed.

The virus may remain latent for long periods of time before initiating a lytic cycle. The problem with this type of cycle is that the viral nucleic acid that becomes integrated into the host cell's chromosome gets replicated along with the host cell's chromosome and is passed to daughter cells during cell division.

In the prophage state, some viral genes are expressed, which may slightly change the host cell's phenotype (ex. only lysogenic strains of Corynebacterium diphtheriae cause the disease diphtheria because the disease-causing toxin is encoded in the prophage of the infecting virus). Something (ex. temperature change) may trigger prophages to go into the lytic cycle. Released virions cannot infect cells that are carrying the same prophage - it makes the cell immune to attack by a virion of the same phage.

II. TAXONOMY Family names all end in viridae ; family names are often converted into English (ex. Retroviridae are called retroviruses). Genus names end in virus - species names are English words.

Ex. Retroviridae, Lentivirus, Human Immunodeficiency Virus (HIV) Groupings reflect only common characteristics and are not intended to represent evolutionary relationships.

III. ANIMAL VIRUSES A. Cultivating Animal Viruses & Diagnosing Viral Illnesses At one time animal viruses had to be cultivated & counted by infecting animals. In the 1930's it was discovered that embryonated chicken eggs could be used to culture animal viruses; embryonated eggs are inoculated with dilutions of a virus sample to determine the highest dilution that kills the embryo; this procedure was more economical & efficient than using adult animals.

In the 1950's cell culture & tissue culture methods were developed In the 1950's cell culture & tissue culture methods were developed. This solved the problem of viral specificity. Ex. Before cell cultures it was impossible to culture viruses in mice or chicken eggs that only infected humans (ex. HIV); continuous cell lines are usually derived from cancerous tissue & grow indefinitely in culture;

regular cell lines grow increasingly slowly after 20-30 subcultures & eventually lose their ability to support viral replication; the most famous c.c.l. is the HeLa cell line (named after Helen Lack, the donor - from cervical cancer).

Important Note: Physicians rely on symptoms to diagnose most viral illnesses. Culturing viruses takes too long & antibodies in the blood can usually be detected only after patient has recovered. Viral infections sometimes affect human cells in ways that can be seen under the microscope. For ex. the measles virus causes the membranes of neighboring cells to fuse, creating giant, multinucleated cells.

Some virus-infected cells can be id Some virus-infected cells can be id. because they contain inclusion bodies, collections of viral components such as capsids and nucleic acid, waiting to be assembled into new viral particles. For example, the rabies virus produces inclusion bodies called negri bodies in infected nerve cells (this is what we look for in suspected cases of rabid animals - have to look for negri bodies in brain - animals have to be euthanized).

B. Replication of Animal Viruses (Lytic cycle) proceeds through similar stages as bacteriophage replication. 1. Adsorption - Proteins in cell membrane act as receptor sites for a virus; remember, no cell walls in animal cells; adsorption is largely responsible for tissue specificity of animal viruses - only cells with a complementary receptor are attacked by a particular virus.

2. Penetration can occur in 3 ways: a. Viral envelope fuses with cell membrane, emptying the rest of the virion inside the cell. b. other enveloped viruses enter by being phagocytized by a host cell c. most naked animal viruses enter as most bacteriophages do the capsid adsorbs to cell surface & only the viral nucleic acid enters cell.

3. Uncoating - Envelopes/capsids are often removed in the penetration process; viruses that enter the cell partially or completely intact are uncoated inside the cell by the host cell's own hydrolytic enzymes, sometimes those in its lysosomes.

4. Viral Synthesis - The specifics of this process depend on which of the 5 types of nucleic acids is present in the virus. 5. Maturation - Assembly not really understood

6. Release - Enzymes cause lysis of the host cell or viruses "bud 6. Release - Enzymes cause lysis of the host cell or viruses "bud." Viruses that kill the host cell by causing lysis are called cytocidal. Viruses that damage the host cell but do not kill it are called cytopathic. Persistent viral infections can last for years, producing new virus particles by budding without killing the infected cell.

C. Latency (similar to temperance or lysogeny) - Sometimes the viral nucleic acid is integrated in the host cell's DNA (called a provirus), allowing the infected animal cells to function normally for years (just as a lysogenic bacteriophage or prophage does).

Ex. Typical of DNA viruses belonging to Herpesvirus family - herpes simplex 1 (causes fever blisters) causes a symptomless latent infection of nerve cells of mouth & lips - infection can be reactivated by a fever, a cold, too much sun, or stress.

Ex. Varicella Zoster (another Herpesvirus) causes chickenpox as the primary infection & shingles as the reactivation. Ex. HIV (Human Immunodefiency Virus) – belongs to the Retrovirus family; causes AIDS (Acquired Immune Deficiency Syndrome).

D. Some Animal RNA Viruses Retroviruses (Retroviridae) large group of RNA viruses; includes HIV (Human Immunodeficiency Virus) which causes AIDS (acquired immune deficiency syndrome); infects T cells (type of white blood cell). capsid contains 2 copies of the same (+) sense RNA molecule (called a diploid virus); capsid also contains the enzyme reverse transcriptase.

Retro means "backward." This virus uses the enzyme reverse transcriptase to make DNA from its RNA. This DNA can be integrated into the host cell's chromosome. The proviral DNA can now be transcribed into mRNA and translated into viral proteins to assemble new viruses for release; As with prophages, the provirus can stay in a latent stage in which it is replicated along with host cell DNA, causing the host cell no damage.

AZT (azidothymidine), which is used against HIV, helps stop reverse transcription by targeting the enzyme reverse transcriptase. Flaviviridae enveloped; polyhedral capsid; (+) sense RNA includes Yellow Fever (hemorrhagic fever)

Togaviridae enveloped; polyhedral capsid; (+) sense RNA includes Rubella virus (Rubella or German measles) Picornaviridae, naked; polyhedral capsid includes Enteroviruses (causes polio); Rhinovirus (common cold); Hepatovirus (Hepatitis A)

Orthomyxoviridae - Influenza Viruses Flu viruses; 3 types (A, B, C); A is the most common, infecting many species of animals, including humans; A is responsible for many pandemics (worldwide epidemics); B & C only infect humans & do not cause pandemics; Outbreaks of B occur every 2-3 years; C causes mild cold-like illnesses.

enveloped RNA viruses; protein spikes in envelope; its (-) sense RNA is divided into 8 separate pieces, each one packaged in a helical capsid This virus exhibits antigenic shift- sudden changes in properties that id. the virus as a foreign invader to the defenses of the human immune system;

occurs from genetic changes that can occur when 2 different flu viruses infect the same cell; when this happens it is likely that the RNA molecules of the 2 infecting virions recombine in various ways among the new virions, producing a virus that is significantly different from either of the original infecting strains. This is why you can get the flu over and over again!

Rhabdoviridae enveloped; helical capsid; (-) sense RNA includes Rabies virus Paramyxoviridae enveloped; helical capsid; (-) sense RNA includes viruses that cause Mumps, Measles, Viral pneumonia, Bronchitis

Bunyaviridae enveloped; segmented RNA; (-) sense RNA includes Hantavirus (“4 corners disease”) Filoviridae enveloped; filamentous capsid; (-) sense RNA includes Ebola virus

Reoviridae naked; polyhedral capsid; ds RNA includes Rotavirus (most common cause of diarrhea in infants and young children under the age of 2) E. Some Animal DNA Viruses Adenoviridae naked; polyhedral capsid; ds DNA mainly responsible for human respiratory diseases; also causes diarrhea in babies and young children

Herpesviridae - enveloped; polyhedral capsid; dsDNA Simplex virus – Herpes simplex 1 (oral) and 2 (genital & neonatal) Varicellovirus – Varicella zoster – chicken pox and shingles Roseolovirus – Roseola infantum – roseola in infants (rash and fever) Lymphocryptovirus – Epstein Barr virus – causes infectious mononucleosis and Burkitt’s lymphoma; also linked to Hodgkin’s disease.

Poxviridae enveloped; brick shaped capsid; ds DNA; largest of all viruses includes Orthopoxvirus – small pox & cow pox Papovaviridae naked; polyhedral capsid; ds DNA; replicate in nuclei of host’s cells. Includes Papillomavirus – warts (some associated with cervical cancer)

Hepadnaviridae enveloped; mostly ds DNA; hepa = liver Hepatitis B virus Parvoviridae naked; ssDNA; uses a helper virus to supply necessary component to produce more viruses. Includes Canine parvovirus – causes severe and sometimes fatal gastroenteritis in dogs.

Also includes Erythrovirus (B19) – causes 5th disease (erythema infectiosum) – deep red rash on children’s cheeks and ears and both a rash and arthritis in adults; can cross placenta and damage fetus.

F. Viruses and Cancer 1. Tumors - uncontrolled growth of tissue (cells are dividing out of control); most are benign (non-life threatening); some are malignant (they spread or metastasize to surrounding tissues).

2. Cancer – malignant tumors that metastasize to surrounding tissues. 3. Cause – Most human cancers arise form genetic mutations or cellular damage caused by environmental factors (chemicals - nicotine, pesticides; radiation - UV, X-rays, etc.; diet). About 15% are attributed to viral infections.

4. Examples: a. Human T-cell leukemia (blood cancer), b. Epstein-Barr virus causes Burkitt's lymphoma c. Hepatitis B virus causes hepatocellular carcinoma (liver cancer) d. human papillomavirus causes skin & cervical cancers. e. Kaposi’s sarcoma – thought to be associated with Herpesvirus

5. How? Some tumor viruses are retroviruses; they convert a normal cell to a tumor cell by introducing an oncogene into it (oncogenic provirus). Some researchers believe even normal retroviruses might cause tumors - merely inserting a normal provirus into the host chromosome near a normal gene might alter its expression and convert it to an oncogene.

G. Viruses and Teratogenesis Teratogenesis – the induction of defects during embryonic development. A teratogen is a drug or other agent that induces such defects. Viruses are teratogens that can be transmitted across the placenta and infect the fetus. Cytomegalovirus (CMV), Herpes Simplex virus (HSV), and Rubella account for a large number of teratogenic effects. TORCH series is a series of blood tests used to detect antibodies to these viruses.

IV. VIROIDS Defined - a circular molecule of ssRNA without a capsid; don’t produce proteins Cause several economically important plant diseases; none known to infect animals 1/10 the size of the smallest plant virus How it causes disease is a mystery; one theory is that it interacts in some way with the host genome, changing the expression of the host genes to cause disease.

V. PRIONS Defined: infectious agent composed only of protein Affect the central nervous system. Ex. scrapie of sheep, Creutzfeldt-Jakob disease (CJD) of humans, mad cow disease. Not known exactly how it causes disease.