An Introduction to Viruses, Virions and Prions

The Elusive Virus

• Louis Pasteur (1884) postulated rabies was caused by a "living thing" smaller than bacteria.

• Dmitri Ivanoski first proposed the term "virus" (L. "poison").

• Ivanovski and Beijerinck (1890s) showed a disease in tobacco was caused by a virus.

• By the 1950s, virology became a multifaceted discipline.

• Viruses are defined as noncellular particles with a definite size, shape, and chemical composition.

Viruses in the Biological Spectrum

• There is no universal agreement on how and when viruses originated.

• Viruses are considered the most abundant microbes on earth.

• Viruses played a role in the evolution of Bacteria, Archaea, and Eukarya.

• Viruses are obligate intracellular parasites.

Properties of Viruses (TABLE 6.1)

• Obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals.

• Ultramicroscopic size, ranging from $20$ nm up to $450$ nm in diameter.

• Not cellular in nature; structure is very compact and economical.

• Do not independently fulfill the characteristics of life.

• Inactive macromolecules outside the host cell and active only inside host cells.

• Basic structure consists of a protein shell (capsid) surrounding a nucleic acid core.

• The nucleic acid of the viral genome is either DNA or RNA, but not both.

• Nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA.

• Molecules on the virus surface impart high specificity for attachment to the host cell.

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

• Lack enzymes for most metabolic processes.

• Lack machinery for synthesizing proteins.

General Size of Viruses

• Ultramicroscopic - most < $0.2$ $μm$; require an electron microscope.

• Bacterial cells:

  • Streptococcus: $1$ $μm$ wide

  • Escherichia coli: $2$ $μm$ long

  • Rickettsias: $0.5$ $μm$ wide

• Yeast cell: $7$ $μm$

• Viruses:

  • Megavirus: $800$ nm

  • Poxvirus: $400$ nm

  • Herpes simplex: $150$ nm

  • Rabies: $125$ nm

  • HIV: $110$ nm

  • Influenza: $100$ nm

  • Adenovirus: $75$ nm

  • T2 bacteriophage: $65$ nm

  • Poliomyelitis: $30$ nm

  • Yellow fever: $22$ nm

• Protein Molecule

  • Hemoglobin molecule: $15$ nm

• Largest viruses: average $500$ to $1,000$ nanometers (20 to 50 times larger than an average virus).

  • Megaviruses

  • Pandaviruses

Viral Structure

• Viruses bear no resemblance to cells.

• Lack protein-synthesizing machinery.

• Viruses contain only the parts needed to invade and control a host cell.

Virus Particle Components

• Covering:

  • Capsid

  • Envelope (not found in all viruses)

• Central core:

  • Nucleic acid molecule(s) (DNA or RNA)

  • Matrix proteins

  • Enzymes (not found in all viruses)

• Crystalline Nature:

  • Their molecular structure consists of regular, repeating molecules that give rise to their crystalline appearance.

  • When purified, many can form large aggregates or crystals.

General Structure of Viruses: Capsids

• All viruses have capsids (protein coats that enclose and protect their nucleic acid).

• The capsid together with the nucleic acid is the nucleocapsid.

• Some viruses have an external covering called an envelope; those lacking an envelope are naked.

• Each capsid is made of identical protein subunits called capsomers.

Two structural capsid types:

• Helical – continuous helix of capsomers forming a cylindrical nucleocapsid

• Icosahedral –three-dimensional, symmetrical polygon, with $20$ sides and $12$ evenly spaced corners

Helical Capsids

• Nucleocapsid Assembly:

  • Rod-shaped capsomers assemble into hollow discs

  • The nucleic acid is inserted into the center of the disc

  • Elongation of the nucleocapsid progresses from both ends, as the nucleic acid is coiled inside

• Appearance varies with the type of virus (naked versus enveloped)

Icosahedral Capsids

• Arrangements of capsomers vary among icosahedral viruses

• They can also vary in the number of capsomers

• During assembly of the virus, the nucleic acid is packed into the center of the icosahedron, forming the nucleocapsid

• Icosahedral viruses can lack an outer envelope

  • Rotavirus (naked)

  • Herpes simplex (enveloped)

General Structure of Viruses: Envelope

• Mostly in animal viruses

• Acquired when the virus leaves the host cell

• Exposed proteins on the outside of the envelope, called spikes, are essential for attachment of the virus to the host cell

Functions of Capsid/Envelope

• Protects the nucleic acid when the virus is outside of the host cell

• Helps the virus bind to a cell surface and assists the penetration of the viral DNA or RNA into a suitable host cell

General Structure of Viruses: Complex Viruses

• Atypical viruses

  • Poxviruses lack a typical capsid and are covered by a dense layer of lipoproteins

  • Some bacteriophages have a polyhedral nucleocapsid along with a helical tail and attachment fibers

Basic Types of Viral Morphology

• A. Complex viruses:

  • poxvirus, a large DNA virus

  • flexible-tailed bacteriophage

• B. Enveloped viruses:

  • With a helical nucleocapsid:

    • mumps virus

    • rhabdovirus

  • With an icosahedral nucleocapsid:

    • herpesvirus

    • HIV (AIDS)

• C. Naked viruses:

  • Helical capsid:

    • plum poxvirus

  • Icosahedral capsid:

    • Poliovirus

    • papillomavirus

General Structure of Viruses: Nucleic Acids

• Viral genome – either DNA or RNA but never both

• Carries genes necessary to invade host cell and redirect cell’s activity to make new viruses

• Number of genes varies for each type of virus – few to hundreds

Nucleic Acids

• DNA viruses

  • Usually double stranded (ds) but may be single stranded (ss)

  • Circular or linear

• RNA viruses

  • Usually single stranded, may be double stranded, may be segmented into separate RNA pieces

  • ssRNA genomes ready for immediate translation are positive-sense RNA

  • ssRNA genomes that must be converted into proper form are negative-sense RNA

General Structure of Viruses: Other Substances

• Pre-formed enzymes required for viral replication:

  • Polymerases – synthesize DNA or RNA

  • Replicases – copy RNA

  • Reverse transcriptase – synthesis of DNA from RNA (HIV virus)

How Viruses Are Classified

• Main criteria presently used are structure, chemical composition, and genetic makeup

• The International Committee on the Taxonomy of Viruses lists: 7 orders, 104 families, and 505 genera of viruses.

Nomenclature

• Families italicized and given the suffix -viridae

• Genera likewise italicized and end in -virus

• Viral species: Distinct virus types that share a collection of properties such as host range, pathogenicity, and genetic makeup

• Characteristics for placement in a virus family include:

  • type of capsid, nucleic acid strand number, presence and type of envelope, overall viral size, and area of the host cell in which the virus multiplies

  • Microscopic appearance (that is rhabdoviruses),

  • Anatomical or geographic areas (that is adenoviruses and hantaviruses)

  • Effects on the host (that is lentiviruses)

  • Acronyms blending several characteristics (that is picornaviruses)

Important Human Virus Families: DNA Viruses

TABLE 6.2a Important Human Virus Families, Genera, Common Names, and Types of Diseases: DNA Viruses

Important Human Virus Families: RNA Viruses

TABLE 6.2b Important Human Virus Families, Genera, Common Names, and Types of Diseases: RNA Viruses

Modes of Viral Multiplication

• General phases in animal virus multiplication cycle:

  • Adsorption – binding of virus to specific molecules on the host cell

  • Penetration – genome enters the host cell

  • Uncoating – the viral nucleic acid is released from the capsid

  • Synthesis – viral components are produced

  • Assembly – new viral particles are constructed

  • Release – assembled viruses are released by budding (exocytosis) or cell lysis

Adsorption and Host Range

• Virus coincidentally collides with a susceptible host cell and adsorbs specifically to receptor sites on the membrane

• Spectrum of cells a virus can infect – host range

  • Hepatitis B – human liver cells

  • Poliovirus – primate intestinal and nerve cells

  • Rabies – various cells of many mammals

Penetration/Uncoating

• Animal viruses must penetrate the cell membrane of the host cell and deliver the viral nucleic acid into its interior.

• Most viruses enter through one of two means:

  • Fusion (envelope viruses) – viral envelope fuses directly with host membrane by rearrangement of lipids

  • Endocytosis (enveloped or naked)– entire virus is engulfed and enclosed in a vacuole or vesicle.

• Once inside, the virus is uncoated and viral nucleocapsid or nucleic acid is released.

Synthesis: Replication and Protein Production

• Varies depending on whether the virus is a DNA or RNA virus

• DNA viruses generally are replicated and assembled in the nucleus

• RNA viruses generally are replicated and assembled in the cytoplasm

  • Positive-sense RNA contain the message for translation

  • Negative-sense RNA must be converted into positive- sense message

Assembly

• Mature virus particles are constructed from the growing pool of parts

• In general, the capsid is first laid down as an empty shell that will serve as a receptacle for the nucleic acid strand

• Electron micrographs taken during this time show cells with masses of viruses, often enclosed in packets

Release

• Assembled viruses leave the host cell in one of two ways:

  • Budding or exocytosis (enveloped): nucleocapsid binds to membrane which pinches off and sheds the viruses gradually; the cell is not immediately destroyed

  • Cell lysis or rupturing (nonenveloped and complex): viruses released when cell dies and ruptures

Damage to Host Cell

• Cytopathic effects – cell damage altering microscopic appearance

  • Disorientation of individual cells

  • Gross changes in shape or size

  • Intracellular changes (inclusion bodies, syncytium)

TABLE 6.3 Cytopathic Changes in Selected Virus-Infected Animal Cells

Persistent Infections

• Persistent infections - cell harbors the virus and is not immediately lysed

• Can last weeks or host’s lifetime; several can periodically reactivate – chronic latent state

  • Measles virus – may remain hidden in brain cells for many years

  • Herpes simplex virus – cold sores and genital herpes

  • Herpes zoster virus – chickenpox and shingles

Viral Damage

• Some animal viruses enter the host cell and permanently alter its genetic material resulting in cancer

• These viruses are termed oncogenic, and their effect on the cell is called transformation

• Transformed cells have an increased rate of growth, alterations in chromosomes, and the capacity to divide for indefinite time periods resulting in tumors

• Mammalian viruses capable of initiating tumors are called oncoviruses

  • Papillomavirus – cervical cancer

  • Epstein-Barr virus – Burkitt’s lymphoma

Multiplication Cycle in Bacteriophages

• Bacteriophages – bacterial viruses (phages)

  • Most widely studied are those that infect Escherichia coli – complex structure, DNA

• Multiplication goes through similar stages as animal viruses

• Only the nucleic acid enters the cytoplasm - uncoating is not necessary

• Release is a result of cell lysis induced by viral enzymes and accumulation of viruses - lytic cycle

Steps in Phage Replication

1. Adsorption – binding of virus to specific molecules on host cell

2. Penetration – genome enters host cell

3. Replication – viral components are produced

4. Assembly – viral components are assembled

5. Maturation – completion of viral formation

6. Lysis & Release – The lytic cycle involves full completion of viral infection through lysis and release of virions

   • Occasionally the virus enters a reversible state of lysogeny and its DNA is incorporated into the host’s genetic material

Bacteriophage versus Animal Viral Multiplication (TABLE 6.4)

Lysogeny: The Silent Virus Infection

• Not all phages complete the lytic cycle

• Some DNA phages, called temperate phages, undergo adsorption and penetration but don’t replicate

• The viral genome inserts into bacterial genome and becomes an inactive prophage – the cell is not lysed

• Prophage is retained and copied during normal cell division resulting in the transfer of temperate phage genome to all host cell progeny – lysogeny

• Induction can occur resulting in activation of lysogenic prophage followed by viral replication and cell lysis

• Lysogeny results in the spread of the virus without killing the host cell

• Phage genes in the bacterial chromosome can cause the production of toxins or enzymes that cause pathology – lysogenic conversion

  • Corynebacterium diphtheriae

  • Vibrio cholerae

  • Clostridium botulinum

Cultivating and Identifying Animal Viruses

• Primary goals of viral cultivation:

  1. Isolate and identify viruses in clinical specimens

  2. Prepare viruses for vaccines

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

Methods

• “In vitro”:

  • Cell (tissue) cultures – cultured cells support viral replication and permit observation of cytopathic effects

• “In vivo”

  • Bird embryos –intact and self-supporting unit, complete with its own sterile environment and nourishment, with embryonic tissues that support viral multiplication

  • Live animal inoculation – the animal is exposed by injection of a viral preparation or specimen into the brain, blood, muscle, body cavity, skin, or footpads

Medical Importance of Viruses

• Viruses are the most common cause of acute infections

• Several billion viral infections per year

• Some viruses have high mortality rates

• Possible connection of viruses to chronic afflictions of unknown cause

• Viruses are major participants in the earth’s ecosystem

Detection and Treatment of Animal Viral Infections

• More difficult than other agents

• Consider overall clinical picture

• Take appropriate sample

  • Infect cell culture – look for characteristic cytopathic effects

  • Screen for parts of the virus

  • Screen for immune response to virus (antibodies)

• Antiviral drugs can cause serious side effects

Prions and Other Nonviral Infectious Particles

• Prions - misfolded proteins, contain no nucleic acid

  • Extremely resistant to usual sterilization techniques

  • Cause transmissible spongiform encephalopathies – fatal neurodegenerative diseases

  • Common in animals:

    • Scrapie in sheep and goats

    • Bovine spongiform encephalopathies (BSE), also known as mad cow disease

    • Wasting disease in elk

  • Humans – Creutzfeldt-Jakob Syndrome (CJS)

Other Noncellular Infectious Agents

• Satellite viruses – dependent on other viruses for replication

  • Adeno-associated virus – replicates only in cells infected with adenovirus

  • Delta agent – naked strand of RNA expressed only in the presence of hepatitis B virus

• Viroids – short pieces of RNA, no protein coat; only been identified in plants