VIROLOGY

Virology

• Virology is the scientific discipline concerned with the study of the biology of viruses and viral diseases, including the distribution, biochemistry, physiology, molecular biology, ecology, evolution, and clinical aspects of viruses.

Virus

• The name "virus" comes from a Latin word meaning "slimy liquid" or "poison"

• A virus is a small infectious agent that replicates only inside the living cells of an organism.

• Viruses can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.

• Viruses are acellular organisms whose genomes consist of nucleic acid, either RNA or DNA. They cannot be grown on sterile media and require the presence of specific host cells.

• Virology - is the study of viruses.

Virus History

• SMALL POX

  • Edward Jenner (1798)

    • Experiments on virology began with the experiments

    • He inoculated a 13-year-old boy with vaccinia virus (cowpox) and demonstrated immunity to smallpox.

    • Jenner found that individuals exposed to cowpox did not suffer from smallpox.

      • Sarah Nelmes - diarymaid

      • James Phipps - 13 y/o boy who got vaccinated

      • blossom - name of cow

  • On May 8, 1980, the WHO announced that the world was free of smallpox.

  • In the summer of 1978, the last known case of smallpox was reported, claiming the life of 40-year-old medical photographer Janet Parker.

• RABIES

  • Louis Pasteur (1881-1885) first used animals as models for growing and studying viruses.

    • He found that the rabies virus could be cultured in rabbit brains and discovered the rabies vaccine.

    • However, Pasteur DID NOT try to identify the infectious agent.

  • On July 6, 1885, the vaccine was administered to Joseph Meister, a 9-year-old boy who had been attacked by a rabid dog. The boy survived and avoided contracting rabies.

  • Rabies - from latin word rebere means rave or mad

• TABACCO MOSAIC DISEASE

  • In 1879, Adolf Mayer first observed the dark and light spots on infected leaves of the tobacco plant and named it tobacco mosaic disease.

    • He showed the infectious nature of the disease after inoculating the juice extract of the diseased plant into a healthy one.

  • Dimitri Ivanovsky in 1890 demonstrated that sap of leaves infected with tobacco mosaic disease retains its infectious property even after filtration through a Chamberland filter.

• FILTRATION

  • In 1898, Martinus Beijerinck (Coined the term virus) independently replicated Ivanovsky's experiments and became convinced that the filtered solution contained a new form of infectious agent, which he named virus.

    • He surmised that the virus under study was a new kind of infectious agent, which he designated contagium vivum fluidum.

• Friedrich Loeffler and Paul Frosch discovered an animal virus that causes foot-and-mouth disease in cattle (1898).

  • Foot-and-mouth disease (FMD) - is a highly contagious virus disease of animals caused by foot-and-mouth virus, a picornavirus.

• Walter Reed and his team discovered the yellow fever virus, the first human virus, from Cuba in 1901.

  • In 1900, yellow fever was the first human disease shown to be caused by a filterable agent by Walter Reed.

  • He found the yellow fever virus present in the blood of patients during the fever phase and that the virus spread via mosquitoes.

• Poliovirus was discovered by Karl Landsteiner and Erwin Popper in 1909.

  • Poliovirus itself would not be visible to researchers until the 1950s when the electron microscope was available.

• In 1911, Francis Peyton Rous discovered the solid tumor virus, which he called Rous sarcoma virus.

  • This finding, that cancer could be transmitted by a virus (now known as the Rous sarcoma virus, a retrovirus), was widely discredited at the time.

  • RSV causes sarcoma in chickens.

• Frederick William Twort - was the original discoverer of bacteriophages (viruses that infect bacteria).

• Felix d'Herelle - co-discovered bacteriophages and developed the assay to titrate viruses by plaques.

• Wendell Stanley (1935) - first crystallized the tobacco mosaic virus (TMV) and described its molecular structure.

Discoveries by Date:

• 1796: Cowpox virus used to vaccinate against smallpox by Edward Jenner.

• 1892: Description of filterable infectious agent (TMV) by Ivanovsky.

• 1898: Concept of the virus as a contagious living form by Beijerinck.

• 1901: First description of a yellow fever virus by Dr. Reed and his team.

• 1909: Identification of poliovirus by Landsteiner and Popper.

• 1911: Discovery of Rous sarcoma virus.

• 1923: Alexander Glenny perfected a method to inactivate tetanus toxin with formaldehyde.

• 1931: Virus propagation in embryonated chicken eggs by Woodruff and Goodpasture.

• 1933: Induction of carcinomas in other species by rabbit papillomavirus by Rous and Beard.

• 1936: Identification of rabbit papillomavirus.

• 1947: Zika virus was first discovered and is named after the Zika Forest in Uganda.

• 1948: Poliovirus replication in cell culture by Enders, Weller, and Robbins.

• 1954: Polio vaccine development by Jonas Salk.

• 1958: Bacteriophage lambda regulation paradigm by Pardee, Jacob, and Monod.

• 1963: Discovery of hepatitis B virus by Blumberg.

• 1967: Description of viroids (Diener).

• 1976: Discovery of Ebola virus by Peter Piot and his colleagues in a blood sample taken from a sick nun working in Zaire.

• 1983: Description of human immunodeficiency virus (HIV) as the causative agent of acquired immunodeficiency syndrome (AIDS) by Montagnier and Gallo.

• 1997: HAART treatment for AIDS (HAART - Highly active antiretroviral therapy, also known as antiretroviral therapy).

• 2003: Severe acute respiratory syndrome (SARS) is caused by a novel coronavirus.

• 2005: Hepatitis C virus propagation in tissue culture by Chisari, Rice, and Wakita.

• 2006: Influenza virus genome sequencing, vaccine against human papillomavirus.

Virus Characteristics

• Viruses bear no real resemblance to cells, and they lack any of the protein-synthesizing machinery found in even the simplest cells.

• Their molecular structure is composed of regular, repeating subunits that give rise to their crystalline appearance.

• Viruses contain only those parts needed to invade and control a host cell: an external coating and a core containing one or more nucleic acid strands of either DNA or RNA.

  

Viral Structure

Viral Capsid

• Function:

  • Protects nucleic acid

  • Aids in transfer to host

• Structure:

  • Protein coat

  • Capsomeres (protein subunits)

• Covering:

  • Envelope (not found in all viruses)

• Central Core:

  • Nucleic acid molecule (DNA or RNA)

  • Various proteins (enzymes)

• Capsomeres determine the shape of the virus.

• The arrangement and composition of the capsomeres varies with virus families.

Morphology

• Depending on how the capsomers are shaped and arranged, this results in two different types:

  • Helical

  • Icosahedral

Helical

• The simpler helical capsids have rod-shaped capsomers that bond together to form a series of hollow discs resembling a bracelet.

• During the formation of the nucleocapsid, these discs link with other discs to form a continuous helix into which the nucleic acid strand is coiled.

• Examples: influenza, measles, and rabies

Icosahedral

• A three-dimensional, 20-sided figure with 12 evenly spaced corners.

• In theory, the icosahedral symmetry may sometimes be referred to as spherical based on the external morphology.

• Some viruses have major variations in the capsids of icosahedral viruses (e.g., poliovirus has 32 capsomers, and adenovirus has 240 capsomers).

• Individual capsomers can look either ring- or dome-shaped, and the capsid itself can appear spherical or cubical.

Complex Viruses

• Atypical viruses are more intricate than the helical, icosahedral, naked, or enveloped viruses.

  • The poxviruses (including the agent of smallpox) are very large viruses that contain a DNA core but lack a regular capsid and have in its place several layers of lipoproteins and coarse surface fibrils.

  • Bacteriophages are another group of very complex viruses.

Bacteriophages

• Viruses that parasitize bacteria.

• Have a polyhedral head, a helical tail, and fibers for attachment to the host cell.

Envelope

• An additional covering external to the capsid, which is actually a modified piece of the host's cell membrane.

• Acquired from the host cell during viral release; the envelope is a portion of the membrane system of the host.

• Also contains proteins and virally-coded glycoproteins (spikes), which often play a role in host recognition.

• If a virus doesn't have an envelope, it is considered to be a naked virus.

• The envelope sometimes contains glycoprotein (protein with carbohydrate) in the form of spikes, which helps them in the attachment during the time of infection to the host cell surface (gp120 in HIV).

Viral Nucleic Acids (Genome)

• Viruses contain either DNA or RNA but not both.

• The size of the viral genome is quite small compared with that of a cell.

• Shape: Circular or linear

• Number: One or more

• Strands: Single-stranded (ss), double-stranded (ds), + or - RNA

Virus Size

• Viruses are generally much smaller than bacteria, and their average size varies from 10-400 nm in diameter.

• They are visible under an electron microscope, and only the largest and complex viruses are seen under a light microscope with high resolution.

• The smallest viruses belong to the families Circoviridae, Parvoviridae, and Picornaviridae, which measure about 20-30 nm in diameter, while some large viruses, such as those that belong to Poxviridae, measure around 250-300 nm in diameter.

• Parvovirus: smallest known viruses (Latin parvus meaning small).

  • The common name applied to all the viruses in the Parvoviridae.

  • Parvovirus B19 causes Fifth disease (Erythema infectiosum), which is transmitted primarily by respiratory secretions but can also be spread by contact with infected blood.

• Giant virus (girus): a very large virus, some of which are larger than typical bacteria.

  • They have extremely large genomes compared to other viruses and contain many unique genes not found in other life forms.

  • Examples: Megavirus chilensis, Mamavirus, and Mimivirus.

• Pithovirus: largest known virus.

  • First described in 2014, is a genus of giant virus known from one species, Pithovirus sibericum, which infects amoebas.

  • A specimen of Pithovirus measures approximately 1.5 μm (1500 nm) in length and 0.5 μm (500 nm) in diameter, making it the largest virus yet found.

• Pandoravirus:

  • The second largest in physical size of any known viral genus.

  • A genus of giant virus, first discovered in 2013 by a team of French scientists.

  • It has the largest viral genome, containing 1.9 to 2.5 megabases of DNA.

  • They are mostly found in marine environments, infecting amoeba.

• Cafeteria roenbergensis virus (CroV): the largest known marine virus.

Classifying & Naming of Viruses

ICTV Classification

• Viruses are not classified as members of the kingdoms but are diverse enough to require their own classification scheme.

• To group new emerging viruses in a specific group by specifying certain parameters was initiated in 1966 when the International Committee on the Taxonomy of Viruses (ICTV) was formed to classify the viruses.

• Names for genera, subfamilies, families, and orders must all be a single word, ending with the suffixes -virus, -virinae, -viridae, and -virales, respectively.

• In written usage, the name should be capitalized and italicized.

• Total of 19 animal viruses.

  • 6 DNA virus families.

  • 13 RNA virus families.

• Although the ICTV nomenclature is used to classify animal viruses, plant virologists do not place their viruses into families and genera but use group names derived from the prototype virus.

• Viral classification starts at the level of order and continues as follows, with the taxon suffixes:

  • Order (-virales)

  • Family (-viridae)

  • Subfamily (-virinae)

  • Genus (-virus)

  • Species

• Species names generally take the form of [Disease] virus.

• Characteristics used for placement in a particular 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.

• Examples include rhabdoviruses, which have a bullet-shaped envelope, and togaviruses, which have a cloak-like envelope.

• Anatomical or geographic areas have also been used in naming. For instance, adenoviruses were first discovered in adenoids (one type of tonsil), hantaviruses were originally isolated in an area in Korea called Hantaan, and Rift Valley Fever Virus (RVFV) was first reported in livestock by veterinary officers in Kenya's Rift Valley.

• Viruses can also be named for their effects on the host. Lentiviruses tend to cause slow, chronic infections.

• Acronyms are also used such as in picornaviruses, hepadnavirus, and reoviruses.

Baltimore Classification

• First defined in 1971, a virus classification system that groups viruses into families, depending on their type of genome (DNA, RNA, single-stranded (ss), double-stranded (ds), etc.) and their method of replication.

• These groups are designated by Roman numerals (I to VII).

• Named after David Baltimore, a Nobel Prize-winning biologist.

Holmes Classification

• Holmes (1948) used Carl Linnaeus's system of binomial nomenclature to classify viruses into 3 groups under one order, Virales.

  • Group 1: Phaginae (attacks bacteria).

  • Group 2: Phytophaginae (attacks plants).

  • Group 3: Zoophaginae (attacks animals).

Modes of Viral Multiplication

• Adsorption: a recognition process between a virus and the host cell that results in virus attachment to the external surface of the host cell.

• Penetration: entrance of the virion (either a whole virus or just its nucleic acid) into the host cell.

• Replication: copying and expression of the viral genome at the expense of the host's synthetic equipment, resulting in the production of the various components.

• Assembly and maturation: of these individual viral parts into whole, intact virions.

• Release: escape from the host cell of active, infectious viral particles.

• Eclipse: the early stages of viral replication, a period during which no mature virions can be detected within the host cell.

  • This corresponds with the period of penetration, replication, and early assembly, and if the cell were disrupted at this time, no infective virus would be released.

Two Stages of Viral Multiplication

• Lytic and Lysogenic

Lytic

• Lytic infection: an active, infectious stage. Example: Influenza (flu virus).

• A virus cannot reproduce by itself; it must invade a host cell and take over the cell activities, eventually causing destruction of the cell and killing it.

• The virus enters a cell, makes copies of itself, and causes the cell to burst, releasing more viruses.

• Some viruses like HIV do NOT go straight into the lytic cycle.

• Rapid: Causes disease right away

• Does NOT involve integration of viral genetic material into the host genetic material.

• Result in host destruction.

Lysogenic

• Lysogenic infection: A dormant (sleeping) stage - period between an infection and the onset of disease. Example: Human Immunodeficiency Virus

• Viral genetic material (DNA) incorporates into a host's DNA and is called a prophage.

• Lysogeny: the potential ability to produce phage.

• The virus replicates its genetic material without destroying the host.

• Every time the host divides, it copies the viral DNA and passes the copies.

• Various factors such as UV light can trigger a virus to enter the LYTIC CYCLE → cell bursts.

• Long period between infection and onset off disease (dormant period).

• Involves integration of viral genetic material into the host's genetic material forming a prophage.

• Eventually enters the Lytic Cycle and host cell lyses.

Bacteriophage Life Cycle:

• Attachment: Phage attaches to host cell.

• Penetration: Phage penetrates host cell and injects its DNA.

• Biosynthesis: Phage DNA directs synthesis of viral components by the host cell.

• Maturation: Viral components are assembled into virions.

• Release: Host cell lyses and new virions are released.

Lysogeny: The Silent Virus Infection

• Temperate phages: special DNA phages that undergo adsorption and penetration in the bacterial host but are not replicated or released.

• Instead, the viral DNA enters an inactive prophage state, in which it is inserted into the bacterial chromosome.

• The viral DNA will be retained by the bacterial cell and copied during its normal cell division so that the cell's progeny will also have the temperate phage DNA.

• Lysogeny: condition in which the host chromosome carries bacteriophage DNA.

• Transduction: the process by which foreign DNA is introduced into a cell by a virus or viral vector (e.g., the viral transfer of DNA from one bacterium to another).

Multiplication Cycles in Animal Viruses

1. Adsorption (attachment):

   • Invasion begins when the virus encounters a susceptible host cell and adsorbs specifically to receptor sites on the cell membrane.

   • The virus attaches to a protein or polysaccharide molecule (receptor) on the surface of a host cell.

2. Penetration

   • Unlike bacteriophages, animal viruses have no mechanism to inject their nucleic acids. Instead, the flexible cell membrane of the host is penetrated by the whole virus or its nucleic acid.

   • The entire virus enters the host cell, in some cases because it was phagocytized by the cell.

3. Uncoating

   • When enzymes in the vacuole dissolve the envelope and capsid, the virus is said to be uncoated.

   • The viral nucleic acid escapes from the capsid.

4. Biosynthesis

   • Viral genes are expressed, resulting in the production of pieces or parts of viruses (i.e., viral DNA and viral proteins).

5. Assembly

   • The viral pieces or parts are assembled to create complete virions.

6. Release

   • The complete virions escape from the host cell by lysis or budding (or exocytosis).

   • Budding and exocytosis are interchangeable. They mean the release of a virus from an animal cell by enclosing it in a portion of membrane derived from the cell.

Comparison of Bacteriophage and Animal Virus Multiplication

Damage to Host Cell and Persistent Infections

• Cytopathic effects are defined as virus-induced damage to the cell that alters its microscopic appearance.

• Individual cells can become disoriented, undergo gross changes in shape or size, or develop intracellular changes.

• Inclusion bodies: compacted masses of viruses or damaged cell organelles in the nucleus and cytoplasm.

• Examination of cells and tissues for cytopathic effects is an important part of the diagnosis of viral infections.

• Although accumulated damage from a virus infection kills most host cells, some cells maintain a carrier relationship, in which the cell harbors the virus and is not immediately lysed.

• These so-called persistent infections can last from a few weeks to the rest of one's life.

• One of the more serious complications occurs with the measles virus. It may remain hidden in brain cells for many years, causing progressive damage and loss of function.

• Several viruses remain in a chronic latent state, periodically becoming reactivated. Examples of this are herpes simplex viruses (fever blisters and genital herpes) and herpes zoster virus (chickenpox and shingles).

• Some animal viruses enter their host cell and permanently alter its genetic material, leading to 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; changes in the cell's surface molecules; and the capacity to divide for an indefinite period, unlike normal animal cells.

Oncoviruses

• Viruses capable of initiating tumors.

• Some are DNA viruses such as papillomavirus (genital warts are associated with cervical cancer), herpesviruses (Epstein-Barr virus causes Burkitt's lymphoma), and hepatitis B virus.

• Retroviruses: an unusual family of RNA viruses that can program the synthesis of DNA using their single-stranded RNA as a template. They can then insert their DNA into a host chromosome, where it can remain for the life of the cell.

  • One type of retrovirus is HIV, the cause of AIDS. Other viruses related to HIV—HTLV I and II—are involved in human cancers.

Prions

• Misfolded proteins with the ability to transmit their misfolded shape onto normal variants of the same protein.

• They characterize several fatal and transmissible neurodegenerative diseases in humans and many other animals.

• Prions are so small that they are even smaller than viruses and can only be seen through an electron microscope when they have aggregated and formed a cluster.

• Prions are also unique in that they do not contain nucleic acid, unlike bacteria, fungi, viruses, and other pathogens.

• PRNP (prion protein): the human gene encoding for the major prion protein PrP (protease-resistant-protein, Pr for prion, and P for protein), also known as CD230 (cluster of differentiation 230).

• Expression of the protein is most predominant in the nervous system but occurs in many other tissues throughout the body.

• Proteinaceous infectious agents.

• Causes Bovine Spongiform Encephalopathy (BSE).

• Also causes Creutzfeldt-Jacob Disease (CJD).

Human Prion Diseases

• Creutzfeldt-Jacob Disease (CJD)

• Kuru

• Mad Cow Disease

• Variant Creutzfeldt-Jakob Disease (vCJD)

• Gerstmann-Straussler-Scheinker Syndrome

• Fatal Familial Insomnia

Animal Prion Disease

• Bovine Spongiform Encepalopathy

• Chronic Wasting Disease

• Scrapie

• Feline Spongiform Encepalopathy

• Transmissible mink encephalopathy

• Ungulate spongiform encephalopathy

Prion Protein Forms

• The normal form of the protein is called PrPC, while the infectious form is called Prpsc.

  • C refers to 'cellular' PrP

  • Sc refers to 'scrapie', the prototypic prion disease, occurring in sheep.

• Scrapie is a neurodegenerative disease of sheep and goats and is also caused by prions. Experimental scrapie has been extensively studied in hamsters and mice.

• The scrapie prion protein (PrPSc) is the only component of the infectious scrapie prion identified to date.

Families of DNA Viruses

Families of RNA Viruses

Rabies virus is an RNA virus that attacks the nervous system in mammals including humans and later secreted in the saliva

| Rhabdoviridae | Rabies virus |
| Togaviridae | Causes Encephalitis |

Classification by Symptomalogy

Generalized Diseases

• Measles, Rubella, Chicken Pox, Dengue, Enteroviruses

Specific Organs

• Nervous System:

  • Poliomyelitis, Rabies, Herpes Simplex, Meningoencephalitis of Mumps, Measles, Slow Viral Infections

• Respiratory Tract:

  • Influenza, RSV, Adenovirus, Coronavirus, Rhinovirus

• Skin or Mucous Membrane:

  • HSV Types 1 and 2, Molluscum Contagiosum, Enteroviruses (coxsackie)

• Diseases of the Eye:

  • Adenovirus conjunctivitis, herpes keratoconjunctivitis, Epidemic hemorrhagic conjunctivitis (enterovirus)

• Liver:

  • Hepatitis, Enteroviruses, Herpesviruses (Epstein-Barr, CMV)

• Salivary Glands:

  • Mumps, CMV

• Gastrointestinal Tract:

  • Rotavirus, Norwalk, Enteric Adenovirus

• Sexually Transmitted:

  • HSV, Hep B, papillomavirus, molluscum contagiosum, HIV