29.0 Introduction

1. Viruses Are Not Living Organisms
1. Are Fragments of a Genome
1. Cannot grow or replicate on their own
2. Replicate only utilizing host cell's machinery

2. Important Due to Disease Producing Potential fig 29.1

29.1 Viruses are fragments of DNA or RNA that have detached from genomes

1. The Viruses
1. Viruses Are Unique Entities
1. Are strands of nucleic acid encased in protein coats
2. Cannot grow or replicate on their own, use machinery of host cell to reproduce
3. Possess only one form of nucleic acid, either DNA or RNA
4. True organisms contain both DNA and RNA
5. Could never have existed independently as preexisting organisms

2. Stanley Isolates the First Virus
1. Earliest indirect observations near end of nineteenth century
1. Concluded infectious agents of some diseases were not bacteria
2. Included tobacco mosaic and hoof-and-mouth disease
3. Infectious agents were not filtered out with fine porcelain filters

2. Purification on tobacco mosaic virus by Stanley in 1933
1. Purified virus formed crystals fig 29.2
2. Considered agent chemical matter rather than living organism

3. Viruses Are Made of Nucleic Acid and Protein
1. Structure of a virus: Tobacco mosaic virus fig 29.3
1. Protein coat in combination with a nucleic acid
2. Rod about 300 nanometers long

2. Tobacco mosaic virus specifically contained RNA
3. Plant viruses have similar composition
4. Most other viruses contain DNA
1. Nearly all viruses form a protein sheath or capsid around nucleic acid core
2. Many viruses form an envelope around capsid, rich in protein, lipid, glycoprotein

5. Simple structure of viruses enhance study of genetics and molecular biology
6. Viruses may be future means by which genetic traits are carried from one organism to another to treat human genetic diseases

2. The Nature of Viruses
1. Viruses Are Ubiquitous
1. May destroy cell or produce no disease or outward sign of presence
2. Viruses are often highly host-specific, reproduce only within a certain host
1. An organism may have more than one kind of virus
2. May be many more viruses than there are kinds of organisms

2. Viral Replication
1. Analogous to operation of a computer via a specific set of instructions
1. Introduction of a new program will cause all operations to cease
2. Computer will spend time making new copies of that introduced program
3. Introduced program is not a computer, but merely a set of instructions

2. Can reproduce only inside cells using host cell's machinery
1. Contain DNA or RNA that is translated into proteins to make more viruses
2. Lack ribosomes, enzymes for protein synthesis and energy production

3. Viruses Consist of a Genome in a Protein Shell
1. Size fig 29.4
1. Smallest are 17 nanometers in diameter
2. Largest are 1000 nanometers in greatest dimension
3. Few barely visible at light microscope level
4. Most are visible only through electron microscopy
5. Directly comparable to molecules in size

2. Variable in appearance
1. Simplest is single molecule of nucleic acid surrounded by capsid fig 29.3
2. More complex are many molecules surrounded by many different proteins
3. Two different shapes identified
1. Helical have rodlike or threadlike appearance
2. Isometric have spherical appearance
1. Form icosahedron structural pattern fig 29.4
2. Efficient symmetrical arrangement

29.2 Bacterial viruses exhibit two sorts of reproductive cycles

1. Bacteriophages
1. Infect Bacteria
1. Structurally and functionally diverse
1. Double-stranded DNA viruses important in molecular biology
2. Many are large, complex viruses
3. often named as part of a "T" series

2. T3 and T7 varieties are icosahedral with short tails
3. Structure of T-even (T2, T4, T6) varieties fig 29.5
1. Icosahedral head
2. Capsid composed of three primary proteins
3. Long tail
4. Connecting neck with collar, long whiskers and complex base plate

2. The Lytic Cycle
1. Progression of infection by T4 bacteriophage
1. One of tail fibers contacts bacterial cell wall lipoproteins
2. Other tail fibers set phage perpendicular to bacterial surface
3. Base plate contacts cell surface
4. Tail contracts, tail tube pierces bacterial cell wall
5. Contents of head (DNA) injected into host cell cytoplasm fig 29.6

2. T -series bacteriophages are all virulent

3. The Lysogenic Cycle
1. Many bacteriophages do not directly kill cells they infect
1. Integrate nucleic acid into host's genome
2. Called a prophage at this point

2. Example: Lambda () phage of Escherichia coli
1. Much known about its structure
2. Complete sequence of 48,502 bases identified, 23 proteins identified

3. Integration of genome called lysogeny
1. Prophage may exit genome later to initiate viral replication
2. Period of time called lysogenic cycle
3. Virus with stable integration called a lysogenic or temperate virus

2. Cell Transformation
1. Expression of Viral Genes
1. May occur when virus is integrated during lysogenic cycle
1. RNA polymerase reads viral genes as if host genes
2. Expression may have novel effect on host cell

2. Alteration of host genome called transformation

2. Transforming the Cholera-Causing Bacterium
1. Cholera is often fatal bacterial disease caused by Vibrio cholerae
1. Exists in two forms, harmless and virulent, disease-causing
2. Change from one form to other not known until recently

2. Bacteriophage infecting V. cholerae inserts gene into bacterial genome
1. Gene produces cholera toxin
2. Gene translated along with other bacterial genes
3. Transforms benign bacterium to disease-causing one
4. Transfer occurs through bacterial pili
5. Bacteria without pili are resistant to transformation

3. Important implication in developing vaccine against disease

29.3 HIV is a typical animal virus

1. AIDS
1. A Viral Case Study
1. Acquired immunodeficiency syndrome (AIDS) is a viral disease
2. AIDS first reported in U.S. in 1981
1. Infectious agent: Human immunodeficiency virus (HIV) fig 29.7
2. Closely related to African chimpanzee virus

3. Etiology of the disease
1. Affected individuals have no resistance to infection
2. Rarely survive more than a few years, die of otherwise nonlethal diseases
3. Transfer of disease by day-to-day contact essentially nonexistent
4. Transfer of body fluids poses most significant threat
5. Incidence growing rapidly

2. How HIV Compromises the Immune System
1. Normally a series of cells patrols bloodstream for invaders
2. These cells are destroyed in AIDS patients, most specifically CD4+ T cells
1. Virus infects and kills cells fig 29.8
2. AIDS patient dies of relatively normal infections

3. Clinical symptoms do not develop until after long period of latency
1. Makes spread difficult to control
2. Reason for latency period puzzling
1. Herpes virus inserts into host chromosomes as a provirus
2. Remains inactive, future event causes it to be removed and become active

3. HIV does not follow this kind of cycle
1. HIV infection cycle continues throughout latent period
2. Immune system suppresses ongoing infection
3. Random mutation in virus eventually, but quickly overcomes immune system

2. The HIV Infection Cycle fig 29.9
1. Attachment
1. HIV infects only CD4+ cells
1. Other animal viruses are similarly limited in scope
2. Examples: Polio virus to nerve cells, hepatitis to liver, rabies to brain

2. Infects cell by recognizing glycoprotein surface marker gp120
1. Precisely fits CD4 protein on surface of macrophages and T cells
2. Macrophages infected first

2. Entry into Macrophages
1. Virus docks onto CD4 receptor
2. Second receptor, CCR5, used to pull HIV across cell membrane
1. gp120 binding to CD4 causes conformational change
2. Allows binding to CCR5
3. Penetrates cell membrane, enters cell via endocytosis

3. Cell membrane folds inward, forms deep cavity around virus

3. Replication
1. Protein coat shed
2. Single strand RNA and reverse transcriptase enzyme now inside cell
3. Viral RNA made into double-stranded DNA via reverse transcriptase
1. Double-stranded DNA directs host cell to produce copies of virus
2. Does not cause cell to rupture and be killed
3. Viruses released by exocytosis
4. Causes synthesis of far greater numbers of viruses
5. Challenges immune system for years

4. Entry into T Cells
1. HIV constantly replicating and mutating over time
1. By chance, gp120 gene becomes altered
2. New form of gp120 protein prefers to bind to different second receptor
3. Binds to CXCR4 on surface of T lymphocyte CD4+ cells

2. T lymphocytes become infected
1. New viruses exit by rupturing and killing cells
2. Shift to CXCR4 receptor precipitates drop in T cell numbers
3. Drop in T cells debilitates body's immune response
4. Leads directly to onset of AIDS
5. Cancers and opportunistic infections invade defenseless body

3. The Future of HIV Treatment fig 29.10
1. Combination Drug Therapy
1. AZT and analogs inhibit nucleic acid replication
2. Protease inhibitors inhibit cleavage of large polyproteins preventing viral replication
3. Combination of drugs improved ability to fight infection
1. Protease inhibitor and two AZT analogs eliminated HIV from many patients' blood
2. Drugs received early to reduce developing tolerance to them
3. Early treatment increases chances for fighting infection
4. Reduce time available for virus to mutate to drug-resistant forms

4. Combination treatment did not remove virus completely
1. Traces still found in lymph tissue
2. Scientists hope copies of virus may be defective, unable to reproduce

2. Using a Defective HIV Gene to Develop Vaccines and Drug Therapy
1. Patients in Australia haven't developed AIDS after 14 years of HIV infection
1. All infected when transfused with blood from same person
2. Defect found in one of nine genes, virus cannot completely disable immune system
3. Defective gene is "negative factor" nef gene
4. Gene is missing pieces, may not be able to reproduce as much
5. Virus kept in check by immune system

2. Implications to develop vaccine
1. Scientists previously unable to produce AIDS strain to elicit immune response
2. Australian strain with defective nef gene may be solution

3. May also help develop drugs to inhibit HIV proteins that speed viral replication
1. Protein produced by nef is a critical HIV protein
2. Viruses with defective nef do not reproduce
3. Now looking for drug that targets nef protein

3. Chemokines and CAF
1. Chemokine chemicals inhibit HIV infection
1. Bind to and block CCR5 and CXCR4 coreceptors
2. Persons infected with HIV without AIDS have high levels of chemokines

2. Intense search for HIV-inhibiting chemokines
3. Have found differences in levels of CAF, CD8⁺ antiviral factor
1. CAF not yet isolated
2. Does not block entry receptors
3. Prevents replication of virus once it has entered cells

4. Problems associated with chemokine therapy
1. Chemokines also associated with inflammatory response of immune system
2. Attract white blood cells to sight of infection
3. Work fine in small amounts, in large amounts treatment is worse than infection
4. Injections may hinder body's response to local chemokines, trigger massive response
5. May increase susceptibility to infections

4. Disabling Chemokine Receptors
1. Mutation in gene coding for CCR5 receptor blocks or inhibits HIV infection
1. Individuals with homozygous defect exposed to HIV have not developed AIDS
2. Individuals heterozygous may also be protected

2. Allele more common in Caucasians, absent in African and Asian populations
1. Defect shows survival is possible without CCR5
2. Looking for agents to block or disable CCR5

29.4 Viruses are responsible for many important human diseases

1. Disease Viruses
1. Many Human Diseases Caused by Viruses tbl 29.1
1. Include: Smallpox, chickenpox, measles, German measles, viral encephalitis,
2. mononucleosis, mumps, shingles, influenza, colds, infectious hepatitis, yellow fever,
3. polio, rabies, AIDS
4. Implicated in some cancers, leukemias
5. Associated with some cases of autoimmune diseases like multiple sclerosis, rheumatoid arthritis
6. Specific viruses associated with certain cases of diabetes
7. Also affect agriculture, forestry, productivity of natural ecosystems
8. Most lethal virus
1. Influenza virus of 1918
2. Killed 22 million Americans and Europeans

2. Emerging Viruses
1. Viruses may develop in one organism and transfer to another fig 29.8
1. HIV arose in chimpanzees, passed to humans
2. Disease may be virulent in new host

2. New pathogens represent public health danger in light of rapid world transportation
3. Filamentous viruses of Africa cause some of most lethal diseases known to man
1. Include Ebola virus with lethality of over 90% fig 29.12
2. Outbreak in 1995 threatened to spread worldwide

2. Prions and Viroids
1. Prions
1. Existence of prions demonstrated and under great study
1. Infectious proteins not associated with nucleic acids
2. Implicated as infectious agents in Alzheimer's disease

2. Puzzling how prions are maintained and passed between cells without nucleic acids
1. Different types of prion proteins (PrP) are actually same one folded differently
2. Abnormally shaped proteins can infer misfolding to normal ones fig 29.13
3. This is a heritable process without genes

3. Cause of PrP misfolding is unknown
1. May be caused by mutation initially
2. Transfer occurs by contact, can be caused by injection of abnormal prions

2. How Prions May Cause Disease
1. Prions associated with several serious brain diseases
2. May transmit diseases from animals to humans
3. Example: Bovine spongiform encephalopathy (BSE), mad-cow disease
1. May infect humans, causing Creutzfeldt-Jakob disease (CJD)
2. 1996 outbreak in England, entered cattle herds from sheep
3. Sheep develop prion-caused brain disease called scrapie
4. Cows feed pellets containing ground-up sheep brains
5. May have passed to four humans that died of CJD

4. Link hard to prove due to long latent period before developing disease

3. Viroids
1. Tiny, naked molecules of RNA, infectious disease agents in plants
2. Recent outbreak in coconut palms in Philippines
3. Not clear how disease is caused
1. Viral nucleotide sequences resemble introns in ribosomal RNA genes
2. Sequences capable of catalyzing excision from DNA
3. Viroids may catalyze destruction of chromosomal integrity