Introduction to Virology

The Search for the Elusive Virus

• Louis Pasteur suggested rabies was caused by something smaller than bacteria in 1884
• Dmitri Ivanoski first proposed the term "virus" in Latin meaning "poison"
• Ivanovski and Beijerinck showed a disease in tobacco was caused by a virus in the 1890s
• Virology in the 1950s: Viruses are noncellular particles with a definite size, shape, and chemical composition

Viruses in the Biological Spectrum

• No universal agreement exists on the origin of viruses
• Viruses are the most abundant microbes on earth
• Viruses influenced the evolution of Bacteria, Archaea, and Eukarya
• Viruses are obligate intracellular parasites, requiring a host to reproduce
• Viruses are obligate intracellular parasites of bacteria, protozoa, fungi, algae, plants, and animals
• Viruses range in ultramicroscopic size from 20 nm to 450 nm in diameter
• Viruses are non-cellular with a compact and economical structure
• Viruses cannot independently fulfill the characteristics of life
• Viruses are inactive macromolecules outside of host cells and active only inside host cells
• Viruses consist of a protein shell (capsid) surrounding a Nucleic acid core
• The viral genome's nucleic acid is either DNA or RNA, but not both
• Viral nucleic acid can be double-stranded DNA, single-stranded DNA, single-stranded RNA, or double-stranded RNA
• Molecules on the virus surface impart specificity for attachment to a host cell
• Viruses primarily function by taking control of the host cell's genetic material, regulating the synthesis and assembly of new viruses – They lack enzymes for most metabolic processes
• Viruses also lack the machinery for synthesizing proteins

General Size of Viruses

• Most viruses require an electron microscope and are ultramicroscopic, measuring less than 0.2 µm
• Megaviruses and Pandaviruses, are the largest, averaging 500-1,000 nanometers, being 20-50 times larger than an average virus

Viral Structure

• Viruses do not resemble cells and lack protein-synthesizing machinery
• Viruses contain only the parts needed to invade and control a host cell
• A virus particle comprises a covering, capsid, envelope(not in all viruses) and a central core
• A virus particle's central core also contains nucleic acid molecule(s) (DNA or RNA) and matrix proteins enzymes (not found in all viruses)
• Virus molecular structure is crystalline and consists of regular, repeating molecules
• When purified viruses can form crystals or large aggregates

General Structure of Viruses: Capsids

• All viruses have capsids, which are protein coats enclosing and protecting their nucleic acid
• A nucleocapsid is the capsid together with the nucleic acid
• Some viruses have an external covering called an envelope; viruses lacking one are called naked
• Capsomers are identical protein subunits make each capsid
• Helical capsids continuously form helix of capsomers forming a cylindrical nucleocapsid
• Icosahedral capsids are symmetrical polygons in three-dimensions, with 20 sides and 12 evenly spaced corners
• An arrangement of capsomers vary among icosahedral viruses and in the number of capsomers
• During assemblage nucleic acids gets packed into the center of the icosahedron to form nucleocapsid
• Icosahedral viruses can lack an outer envelope, or can be naked (Rotavirus), or enveloped (Herpes Simplex)

Functions of Capsid/Envelope

• The capsid or envelope protects the nucleic acid when the virus is outside of the host cell
• The capsid or envelope assists the penetration of the viral DNA or RNA into a suitable host cell

General Structure of Viruses: Complex Viruses

• Atypical viruses, such as Poxviruses, lack a typical capsid and are covered by a dense layer of lipoproteins
• Some bacteriophages have a polyhedral nucleocapsid plus a helical tail and attachment fibers

Basic Types of Viral Morphology

• Complex viruses include poxvirus (a large DNA virus) and flexible-tailed bacteriophages
• Enveloped viruses with a helical nucleocapsid include mumps and rhabdoviruses
• Enveloped viruses with as icosahedral nucleocapsid include herpesvirus and human immunodeficiency virus (HIV) (AIDS)
• Naked viruses with a helical capsid includes plum poxvirus
• Naked viruses with icosahedral capsid includes Poliovirus and papillomavirus

General Structure of Viruses: Nucleic Acids

• The viral genome may be DNA or RNA but never both
• Viral genome carries genes necessary to invade a the host cell and redirect its activity to make new viruses
• The number of genes varies for each type of virus, varying from a few to hundreds
• DNA viral nucleic acids are usually double stranded (ds), but may be single-stranded (ss), and can be circular or linear
• RNA viral strands are usually single-stranded, may be double stranded, may be segmented into separate sections .
• ssRNA genomes ready for immediate translation are positive-sense RNA; ssRNA genomes needing conversion are negative-sense RNA

General Structure of Viruses: Other Substances

• Pre-formed enzymes are required for viral replication.
• Polymerases synthesize DNA or RNA
• Replicases copy RNA
• Reverse transcriptase synthesizes DNA from RNA (as in HIV)

How Viruses Are Classified

• Main criteria for classifying viruses presently include 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 are italicized and given the suffix -viridae
• Genera are also italicized and end in -virus

How Viruses Are Named

• Viral species are 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 capsid type, nucleic acid strand number, presence and type of envelope, virus size, and host cell area of multiplication
• Characteristics for placement in a virus family also include microscopic appearance (rhabdoviruses), anatomical or geographic areas (adenoviruses, hantaviruses), and effects on the host (lentiviruses)
• Acronyms blending several characteristics (picornaviruses)

Important Human Virus Families: DNA Viruses

• (Poxviridae, Orthopoxvirus, Simplexvirus): Variola and vaccinia, Smallpox, cowpox, Fever blister, cold sores, Genital herpes
• (Herpesviridae, Varicellovirus, Cytomegalovirus): Varicella zoster virus, Chickenpox, shingles, CMV infections (Adenoviridae, Mastadenovirus): Human adenoviruses, Adenovirus infection
• (Papillomaviridae, Papillomavirus): Human papillomavirus, Several types of warts Polyomaviridae, Polyomavirus: JC virus (JCV), Progressive multifocal leukoencephalopathy Hepadnaviridae, Hepadnavirus: Hepatitis B virus, Serum hepatitis
• (Parvoviridae, Erythrovirus): Parvovirus B19, Erythema infectiosum

Important Human Virus Families: RNA Viruses

• (Picornaviridae, Enterovirus): Poliovirus, Hand-foot-mouth disease
• (Picornaviridae, Hepatovirus): Hepatitis A virus, Short-term hepatitis
• (Picornaviridae, Rhinovirus): Human rhinovirus, Common cold, bronchitis
• (Caliciviridae, Calicivirus): Norwalk virus, Viral diarrhea, Norwalk virus syndrome
• (Togaviridae, Alphavirus): Eastern equine encephalitis virus (EEE), Western equine encephalitis (WEE), Yellow fever, Saint Louis encephalitis
• (Flaviviridae, Rubivirus and Flavivirus): Rubella, Dengue fever, West Nile fever, Zika fever; California encephalitis, Respiratory syndrome
• Rift Valley fever virus: Rift Valley fever; Crimean-Congo hemorrhagic fever (CCHF) virus, Ebola and Marburg virus, Human and Colorado rotavirus
• Influenza (Flu), Paramyxovirus, measles, red measles, common cold

Modes of Viral Multiplication

• Adsorption: virus binds to specific molecules on the host cell, the genome enters the host cell during penetration
• Uncoating is when the viral nucleic acid is released from the capsid
• Synthesis: viral components are produced and new viral particles are constructed during assembly,
• Release occurs when viruses are released by budding (exocytosis) or cell lysis

Adsorption and Host Range

• Virus collides with a susceptible host cell and adsorbs specifically to receptor sites on the membrane
• Host range represents the spectrum of cells that a virus can infect
• Hepatitis B infects human liver cells
• Poliovirus infects primate intestinal and nerve cells
• Rabies infects various cells of many mammals

Penetration/Uncoating

• Animal viruses penetrate the host cell membrane, delivering the nucleic acid into its interior
• Most viruses enter via Fusion, in which the viral envelope of envelope viruses fuses with the host membrane and rearranges lipids
• Most viruses enter by Endocytosis, where the entire virus (enveloped or naked) is engulfed in to a vacuole or vesicle

Synthesis: Replication and Protein Production

• Synthesis varies depending on whether the virus is a DNA or RNA virus
• DNA viruses are generally replicated and assembled in the nucleus
• RNA viruses are generally 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
• The capsid is first laid down as an empty shell that acts as a receptacle for the nucleic acid strand
• Electron micrographs show cells with masses of viruses, often found enclosed in packets

Release

• Assembled viruses leave the host cell in one of two ways:
• Budding or exocytosis (enveloped): The nucleocapsid binds to the membrane, which pinches off; the cell may not be destroyed right away
• Cell lysis or rupturing (non-enveloped or complex): viruses are released when cell dies and ruptures

Damage to Host Cell

• Cytopathic effects represents the cell damage altering microscopic appearance
• Indicators of cell damage include the disorientation of individual cells and gross changes in shape or size, as well as intracellular changes like inclusion bodies and/or syncytium

Persistent Infections

• Persistent infections occur when a cell harbors the virus without immediate lysis
• Persistent infections can last weeks or a host's lifetime, and several can reactivate periodically into a chronic latent state
• Measles virus may remain hidden in brain cells for many years
• Herpes simplex virus causes cold sores and genital herpes
• Herpes zoster virus causes chickenpox and shingles

Viral Damage

• Some animal viruses enter the host cell, permanently altering its genetic material and potentially resulting in cancer
• These oncogenic viruses cause transformation effects on the cell
• Transformed cells have an increased rate of growth and alteration in chromosomes
• Mammalian viruses capable of initiating tumors are called oncoviruses
• Papillomavirus – cervical cancer
• Epstein-Barr virus – Burkitt's lymphoma

Multiplication Cycle in Bacteriophages

• Bacteriophages infect bacteria and have a complex DNA structure
• Multiplication goes through similar phases as animal viruses
• Only the nucleic acid enters the cytoplasm, thus uncoating is not necessary
• Viral enzymes induce cell lysis, which results in the release of viruses into a lytic cycle

Steps in Phage Replication

• Adsorption involves the binding of virus to specific molecules on the host cell
• Penetration involves the genome entering the host cell
• Replication involves in the production of viral components
• Assembly and Maturation involve the assembling of viral components and the completion of viral formation
• The lytic cycle ends in Lysis and Release with full completion of viral infection
• Occasionally, the virus enters a reversible state of lysogeny with its DNA incorporates into the host's genetic material

Lysogeny: The Silent Virus Infection

• Not all phages complete the lytic cycle-
• The temperate phages, that are some DNA phages, undergo adsorption and penetration
• The inactive prophage occurs as the viral genome inserts into the bacterial genome
• During normal cell division prophage is retained and copied, transferring temperate phage genome to all host cell progeny - lysogeny
• The lysogenic prophage is followed by viral replication and cell lysis occur as a result of induction

Lysogeny

• Lysogeny results in the spread of the virus without killing the host cell
• Toxins or enzymes result from Phage genes in the bacterial chromosome - lysogenic conversion
• Corynebacterium diphtheriae, Vibrio cholerae, Clostridium botulinum are lysogenic bacteria

Cultivating and Identifying Animal Viruses

• Isolating and identifying viruses in clinical specimens
• Preparing viruses for vaccines
• Allowing intensive research on the viral structure, genetics, effects on host cells and multiplication cycles, are the Primary goals of viral cultivation –
• "In vitro" cultivation involves cells undergoing replication in tissue culture with the observation of cytopathic effects
• "In vivo cultivation involves bird embryos used for the multiplication, complete with its own sterile environment and nourishment
• "In vivo cultivation can also involve live animal inoculation by injecting a viral preparation into an animal's brain, blood, skin, or footpads

Medical Importance of Viruses

• Acute infections commonly result from viruses
• There are several billion viral infections per year
• Some viruses have high mortality rates
• Afflictions, viruses potentially have connections to chronic
• Viruses partake as major participants in the earth's ecosystem

Detection and Treatment of Animal Viral Infections

• Viral infections are more difficult to detect than other agents and require considering the overall clinical picture and taking appropriate samples
• Diagnostic tests can determine and identify, infecting a cell culture or testing a sample of bodily tissues
• Diagnostic tests can also screen for parts of the virus, or for the immune response to the virus in antibodies
• Antiviral drugs may cause serious side effects

Prions and Other Nonviral Infectious Particles

• Prions are misfolded proteins that contain no nucleic acid
• Prions are extremely resistant to usual sterilization techniques
• Prions can also cause transmissible spongiform encephalopathies such as fatal neurodegenerative diseases
• Common in animals: scrapie in sheep, bovine spongiform encephalopathies in cattle named "mad cow disease", and wasting disease in elk
• Creutzfeldt-Jakob Syndrome (CJS) occurs in humans

Other Noncellular Infectious Agents

• Satellite viruses depend on other viruses for replication
• Adeno-associated virus replicates only in cells infected with adenovirus
• Delta agent is a naked strand of RNA expressed only in the presence of hepatitis B virus
• Viroids are short pieces of RNA with no protein coat and have only been identified in plants