Viruses and Prions Book

Media Under The Microscope: Racing to Save Her Own Life

• This case study examines an article from the NIH Record (January 2020) titled "Couple Turns Hand of Fate into Hand of Hope" to assess its factual accuracy and potential to mislead.

• The article discusses Sonia Vallabh, a former Harvard-trained lawyer, who discovered she carried the mutation for a prion disease after her mother's diagnosis and subsequent death.

• Prions are misfolded proteins that can be infectious or arise spontaneously, leading to fatal brain diseases with no known cure.

• Vallabh and her husband pursued PhDs and became scientists at MIT and Harvard, researching prion diseases.

• The article claims they found a potential treatment: synthetic RNA nucleotides (oligonucleotides) that bind to misfolded prion proteins, inactivating them.

• The treatment has received investment from a major pharmaceutical company, and the FDA is showing encouragement for its approval.

Introduction to Viruses

• Viruses infect all types of cells (bacteria, algae, fungi, protozoa, plants, and animals) and are abundant.

• Ocean waters contain approximately $10^7$ viruses per milliliter, while lake water has up to $2.5 * 10^8$ viruses per milliliter.

• Viruses are described as either active or inactive, rather than alive or dead.

• Viruses have shaped the evolution of cells, tissues, bacteria, plants, and animals.

• Between 40% and 80% of the human genome may consist of remnants of ancient viral infections.

• Viruses are obligate intracellular parasites that rely on host cell machinery to multiply.

• Viruses differ from host cells in structure, behavior, and physiology.

Table 7.1 Properties of Viruses

• Not cells

• Obligate intracellular parasites

• Inactive macromolecules outside the host cell; active inside host cells

• Basic structure: protein shell (capsid) surrounding a nucleic acid core

• Found everywhere in nature; major impact on biological life

• Ultramicroscopic in size (20 nm to 1,500 nm)

• Contain either DNA or RNA (not both)

• Can have double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA

• Surface molecules determine specificity for host cell attachment

• Multiply by taking control of the host cell’s genetic material

• Usually lack enzymes for most metabolic processes and protein synthesis machinery

Microbiome: Viruses as Part of the Microbiome

• The virome is the sum total of viruses associated with the body.

• Viruses in the microbiome are often dormant within cells.

• Bacteriophages infect bacteria in the microbiome ($10^{15}$ viruses in the microbiome).

• The human body contains approximately $10^{13}$ to $10^{14}$ cells, with slightly more bacterial cells.

• Most viruses in the human body are non-pathogenic.

• Viruses have influenced the development of the mammalian placenta.

• Bacteriophages in the intestinal mucosa may protect against bacterial infection.

• Medical research has historically focused on disease-causing viruses.

• "Quiet" viruses are categorized as seemingly always quiet or intermittently quiet but becoming pathogenic.

• The Epstein-Barr virus (EBV) is a herpesvirus, and most adults are infected with one or more herpesviruses.

• Over 50% of people are infected with the virus causing genital herpes, though most are unaware.

• Most adults are infected with cytomegalovirus (CMV), which can cause serious birth defects.

The General Structure of Viruses

• Viruses range in size from small parvoviruses (around 0.02 μm in diameter) to larger viruses (0.4–1 μm in length), some even larger than bacteria.

• Viruses consist of genetic material (DNA or RNA) and a protein coat (capsid).

• Some viruses can form large aggregates or crystals.

• Viruses lack protein-synthesizing machinery.

Viral Components: Capsids, Envelopes, and Nucleic Acids

• Viruses contain only the essentials to invade and control a host cell: an external coating (capsid or envelope) and a core containing nucleic acid (DNA or RNA).

• Some contain enzymes.

Size Range

• Viruses are much smaller than bacteria.

• Over 2,000 bacterial viruses could fit into an average bacterial cell.

• More than 50 million polioviruses can be found inside an infected human cell.

Table 7.1 Properties of Viruses

• Are not cells

• Are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals (some exceptions have been found)

• Are inactive macromolecules outside the host cell and active only inside host cells

• Have basic structure of protein shell (capsid) surrounding nucleic acid core

• Are everywhere in nature and have had major impact on the development of biological life

• Are often ultramicroscopic in size, ranging from 20 nm to 1,500 nm

• Can have either DNA or RNA but not both

• Can have double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA

• Carry molecules on their surface that determine specificity for attachment to host cell

• Multiply by taking control of host cell’s genetic material and regulating the synthesis and assembly of new viruses

• Usually lack enzymes for most metabolic processes

• Usually lack machinery for making proteins

Viral Components: Capsids, Envelopes, and Nucleic Acids

• Viruses possess an external coating (capsid or envelope) and a core containing nucleic acid (DNA or RNA).

• Some viruses may carry one or two enzymes.

The Viral Capsid: The Protective Outer Shell

• The capsid is a protein shell that surrounds the nucleic acid core.

• The capsid and nucleic acid together form the nucleocapsid.

• Many animal viruses have an additional covering external to the capsid called an envelope.

• Viruses consisting only of a nucleocapsid are called naked viruses.

• Naked and enveloped viruses have proteins (spikes) on their outer surfaces for docking with host cells.

• A fully formed virus able to establish infection is called a virion.

• Capsids are constructed from identical subunits called capsomeres, which self-assemble.

• Animal viruses have two main capsid types: helical and icosahedral.

Helical Capsids

• Rod-shaped capsomeres bond together to form hollow cylinders.

• Cylinders link to form a continuous helix, with the nucleic acid strand coiled inside.

• Naked helical viruses are rigid and tightly wound (e.g., tobacco mosaic virus).

• Enveloped helical viruses are flexible and arranged as a looser helix within the envelope (e.g., influenza, measles, rabies).

• Rabies virus has a distinctive bullet shape due to a matrix protein between the helical capsid and the envelope.

Icosahedral Capsids

• Icosahedron: a 20-sided figure with 12 evenly spaced corners.

• Capsomeres can be made of a single type or several types of proteins.

• The number of capsomeres varies among viruses (e.g., poliovirus has 32, adenovirus has 252).

• Capsomeres can be ring- or dome-shaped.

• Icosahedral viruses can be naked (e.g., papillomavirus) or enveloped (e.g., herpes simplex).

Complex Capsids

• Found in viruses infecting bacteria; have multiple types of proteins and irregular shapes (e.g., T4 bacteriophage).

The Viral Envelope

• Enveloped viruses take a piece of the host cell membrane when released.

• The viral envelope contains viral proteins, some of which attach to the capsid, and glycoproteins (spikes) that remain exposed.

• Spikes are essential for attachment to the next host cell.

• Envelopes make viruses pleomorphic, ranging from spherical to filamentous.

Nucleic Acids: At the Core of a Virus

• The genome is the sum total of genetic information carried by an organism.

• Viruses contain either DNA or RNA, but not both.

• The number of viral genes varies (4 in hepatitis B virus to over 2,500 in pandoraviruses).

• Escherichia coli has approximately 4,000 genes, and a human cell has approximately 23,000 genes.

• DNA viruses can have single-stranded (ss) or double-stranded (ds) DNA, arranged linearly or in circles.

• RNA viruses can be double-stranded, but are more often single-stranded.

• Single-stranded RNA genomes ready for immediate translation are called positive-sense RNA (e.g., SARS-CoV-2).

• RNA genomes needing conversion are called negative-sense RNA.

• RNA genomes may be segmented, with genes on separate RNA pieces (e.g., influenza virus).

• Retroviruses are a special type of RNA virus.

• Viruses are genetic parasites, needing the host cell's internal environment to multiply.

Other Substances in the Virus Particle

• Viruses can contain enzymes for specific operations within the host cell.

• Viruses may come with preformed enzymes that are required for viral replication; examples include polymerases that synthesize DNA and RNA and replicases that copy RNA.

• HIV comes equipped with reverse transcriptase (RT) for synthesizing DNA from RNA.

• Some viruses can carry away substances from their host cell. For instance, arenaviruses pack along host ribosomes, and retroviruses “borrow” the host’s tRNA molecules.

Disease Connection

• Hand sanitizer typically contains ethyl alcohol or isopropyl alcohol.

• Enveloped viruses are inactivated by alcohols, UV light, desiccation, and soap.

• Nonenveloped (naked) viruses are generally not affected by alcohol.

• Examples of enveloped viruses: HIV, hepatitis B, influenza virus.

• Examples of nonenveloped viruses: hepatitis A, enteroviruses.

How Viruses Are Classified and Named

• Viruses are classified based on structure, chemical composition, and genetic makeup.

• The International Committee on the Taxonomy of Viruses lists 59 orders and 189 families of viruses.

• Virus orders end in -virales, families end in -viridae, and genera end in -virus.

• Common names are used rather than precise species names (not italicized).

Table 7.7 Important Human Virus Families, Genera, Common Names, and Types of Diseases

How Viruses Multiply

• Viruses seize control of the synthetic and genetic machinery of cells.

• The multiplication cycle dictates transmission, effects on the host, immune responses, and control strategies.

Multiplication Cycles in Animal Viruses

• The general phases: adsorption, penetration, uncoating, synthesis, assembly, and release.

• The cycle length varies (8 hours in polioviruses to 72 hours in some herpesviruses).

Adsorption and Host Range

• The virus attaches to receptor sites on the cell membrane.

• Membrane receptors are usually glycoproteins (e.g., rabies virus binds to acetylcholine receptor of nerve cells, HIV attaches to CD4 protein on certain white blood cells).

• Host range is limited by the virus's ability to make an exact fit with a specific host molecule.

• Hepatitis B infects only liver cells of humans; poliovirus infects intestinal and nerve cells of primates; rabies virus can infect various cells of all mammals.

• Cells lacking compatible receptors are resistant to the virus.

• Viruses have tropisms for certain cells in the body (e.g., hepatitis B virus targets the liver, mumps virus targets salivary glands).

Penetration/Uncoating of Animal Viruses

• Animal viruses enter cells via penetration by endocytosis or direct fusion of the viral envelope with the host cell membrane.

• In penetration by endocytosis, the entire virus is engulfed and enclosed in a vacuole or vesicle; enzymes dissolve the envelope and capsid, releasing nucleic acid.

• Direct fusion involves the viral envelope merging with the cell membrane, releasing the nucleocapsid into the cell’s interior where uncoating will occur later.

Synthesis: Genome Replication and Protein Production

• The virus makes new genomic material and new proteins for replication.

• Viral nucleic acid controls the host’s synthetic and metabolic machinery.

• DNA viruses (except poxviruses) replicate and assemble in the host cell’s nucleus.

• RNA viruses (except retroviruses) replicate and assemble in the cytoplasm.

• Coronaviruses: +ssRNA acts as mRNA and is translated into viral proteins, + strand is replicated into –ssRNA, which becomes the template for new +ssRNAs.

• Retroviruses turn their RNA genomes into DNA using reverse transcriptase (RT).

Assembly of Animal Viruses: Host Cell as Factory

• Mature virus particles are constructed from a growing pool of parts.

• Empty capsid shells are constructed as receptacles for the nucleic acid strand.

• Viral spikes are inserted into the host’s cell membrane.

Release of Mature Viruses

• Nonenveloped and complex viruses lyse the cell.

• Enveloped viruses bud off via exocytosis from the membranes of the cytoplasm, nucleus, endoplasmic reticulum, or vesicles, picking up viral spikes.

• Budding allows gradual shedding without sudden destruction.

• Active viral infections are typically lethal to the cell.

• 3,000-4,000 virions are released from a single cell infected with poxviruses, whereas a poliovirus-infected cell can release over 100,000 virions.

Damage to the Host Cell

• Virus-induced damage altering the microscopic appearance is termed cytopathic effects (CPEs).

• Cells lose positional orientation, undergo shape/size changes, or develop intracellular changes.

• Inclusion bodies: compacted masses of viruses or damaged cell organelles.

• Syncytia: fusion of multiple host cells into single large cells containing multiple nuclei, resulting from some viruses’ ability to fuse membranes.

Persistent Infections

• Some cells maintain a carrier relationship without immediate lysis (persistent infections), lasting weeks to the host's life.

• Viruses can remain latent in the cytoplasm or incorporate into the host DNA (provirus).

• Herpes simplex viruses (cold sores and genital herpes) and herpes zoster virus (chickenpox and shingles) can go into latency in nerve cells and reemerge.

Viruses and Cancer

• Some animal viruses alter the host's genetic material, leading to cancer (oncoviruses, oncogenic effect = transformation).

• Experts estimate up to 13% of human cancers are caused by viruses.

• Viruses carry genes that directly cause cancer or produce proteins that induce a loss of growth regulation.

• Transformed cells have increased growth rate, chromosome alterations, changes in surface molecules, and indefinite division.

• Some oncoviruses are DNA viruses (papillomavirus, herpesviruses, hepatitis B virus).

• HTLV-I (related to HIV) is involved in one type of human leukemia.

Viruses That Infect Bacteria

• Bacteriophages (phages) infect bacteria.

• Most bacteriophages contain double-stranded DNA.

• Every bacterial species is parasitized by at least one specific bacteriophage.

• Bacteriophages can make bacteria more pathogenic.

• T-even phages (T2, T4) of Escherichia coli are complex, with an icosahedral capsid head containing DNA, a central tube, collar, base plate, tail pins, and fibers.

• Bacteriophages adsorb to host bacteria using specific receptors on the bacterial surface, then inject their nucleic acid.

• Host cell DNA replication and protein synthesis stop.

• The host cell machinery is used for viral replication and synthesis of viral proteins.

• Parts spontaneously assemble into bacteriophages.

Lytic vs. Lysogenic Cycles

• The host cell lyses, releasing the virions (lytic phase).

• Temperate phages can enter an inactive prophage state, inserting into the bacterial chromosome (lysogenic cycle).

• Viral DNA is retained and copied during cell division.

• In induction, the prophage is activated and progresses into viral replication and the lytic cycle.

• Viruses can contribute permanent traits to bacteria, creating hybrids.

The Danger of Lysogeny in Human Disease

• Lysogenic conversion: a bacterium acquires a new trait from its temperate phage.

• Diphtheria toxin produced by Corynebacterium diphtheriae is a bacteriophage product; C. diphtheriae without the phage are harmless.

• Other bacteria made virulent by prophages: Vibrio cholerae (cholera), Clostridium botulinum (botulism).

Disease Connection

• Streptococcus pyogenes with bacteriophage genes can cause greater damage, leading to scarlet fever.

Table 7.9 Comparison of Bacteriophage and Animal Virus Multiplication

Virophages

• Virophages are viruses that parasitize other viruses.

• A virophage utilizes genes from the other virus for its own replication and production.

Techniques in Cultivating and Identifying Animal Viruses

• In vivo methods use living embryos or animals.

• In vitro methods use cells or tissues cultivated in the lab (cell culture/tissue culture).

Purposes for Viral Cultivation

1. Isolate and identify viruses in clinical specimens.

2. Prepare viruses for vaccines.

3. Do detailed research on viral structure, multiplication cycles, genetics, and effects on host cells.

Using Live Animal Inoculation

• Specially bred strains of white mice, rats, hamsters, guinea pigs, and rabbits are commonly used.

• The animal is exposed to the virus by injection.

Using Bird Embryos

• Bird eggs provide an intact, self-supporting unit for viral propagation.

• Chicken, duck, and turkey eggs are common choices.

• The virus solution is injected through the shell, using sterile techniques.

Using Cell (Tissue) Culture Techniques

• Populations of isolated animal cells are grown in culture dishes.

• Animal cell cultures are grown in sterile dishes or bottles with special media.

• The cultured cells grow as a monolayer, a single sheet of cells that supports viral multiplication.

• Primary cell cultures are prepared from fresh animal tissue and have a limited existence.

• Continuous cell lines have altered chromosome numbers and can be continuously subcultured.

Detecting Virus Growth

• Degeneration and lysis of infected cells in the monolayer can be observed.

• Plaques are clear, well-defined patches where virus-infected cells have been destroyed.

Virus and Human Health

• It is impossible to measure accurately the number of viral infections that occur worldwide.

• Most viral infections do not result in death, however some of them, such as COVID-19, colds, chickenpox and influenza can cause long-term debility.

• So far, we know of 268 different viruses that can infect humans

• Viruses are difficult to target with therapies (antibiotics don't work).

• Many antiviral drugs block virus replication by targeting the function of host cells (severe side effects).

• Almost all currently used antiviral drugs are designed to target one of the steps in the viral multiplication cycle

• Interferon (IFN) can be used to treat/prevent viral infections.

• Vaccine development is aimed at preventing viral diseases.

• Viruses cause some human cancers but clinical trials are testing the use of viruses to target cancer.

Prions and Other Noncellular Infectious Agents

• Prions are implicated in chronic, persistent diseases in humans and animals (spongiform encephalopathies).

• These infections have a long latency period (several years) before clinical signs appear.

• A common feature is the deposition of distinct protein fibrils in brain tissue.

• Creutzfeldt-Jakob disease (CJD) afflicts the central nervous system, causing gradual degeneration and death.

• Bovine spongiform encephalopathy (BSE), or “mad cow disease,” is a prion disease transmitted from animals to humans.

• Prions lack nucleic acid, which revolutionizes ideas of infectious agents.

• Multiple-system atrophy (MSA), a rare brain disease, is possibly caused by prions.

Satellite Viruses

• Satellite viruses (defective forms) are dependent on other viruses for replication (e.g., adeno-associated virus (AAV), delta agent).

Viroids

• Viroids are naked strands of RNA that parasitize plants (tomatoes, potatoes, cucumbers, citrus trees, chrysanthemums).