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Chapter 6 an Introduction to Viruses Introduction All Life-Forms Can Be Infected by Viruses

Chapter 6 An Introduction to Introduction All life-forms can be infected by viruses.

Some viruses generate serious epidemics, from dengue fever to to AIDS.

Others fill essential niches in the environment, particularly in marine ecosystems.

In research, viruses have provided both tools and model systems in . This 11-inch-high limestone Egyptian funerary stele is from Saqqara, 10 miles south of Cairo; Amarna Period, 18th Dynasty (1403-1365 BCE), Glyptotek Museum, Copenhagen.

The stele portrays Roma (or Rema), an Egyptian doorkeeper, and his family giving offerings to the Goddess Astarte.

Thought to be the earliest depiction of a victim of poliomyelitis, the man adeptly carries a goblet while supporting himself with a staff.

His withered right leg and deformed right foot are characteristic of poliomyelitis. Ramses V, Pharaoh of Egypt

He died ~1145 BCE, presumably of . His mummified head and torso bear the characteristic lesions of the disease.

Smallpox victims included many other rulers throughout history, among them Louis XV of France, Mary II of England, and the Holy Roman Emperor Joseph I. The search for the elusive

Louis Pasteur postulated that was caused by a virus (1884)

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

Viruses: non-cellular particles with a definite size, shape, and chemical composition

Viral diseases led to the development of some of the first . causes poliomyelitis, which can lead to paralysis. President Franklin Roosevelt established the March of Dimes. With its support, Jonas Salk developed the first in 1952. What Is a Virus?

A virus is a non-cellular particle that must infect a (obligate intracellular parasite), where it reproduces.

It typically subverts the cell’s machinery and directs it to produce viral particles.

The virus particle, or virion, consists of a single nucleic acid (DNA or RNA) contained within a protective . The position of 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 of , , and Eukarya

Viruses are obligate intracellular parasites Viruses infect all forms of life Viruses are ubiquitous in all environments and part of our daily lives

Most frequent infections of college students: 1) Respiratory such as rhinovirus (the ) and Epstein-Barr virus (infectious mononucleosis) 2) Sexually transmitted viruses such as virus (HSV) and papillomavirus (genital warts)

Different viruses infect every group of

Each of virus infects a particular group of host species, or host range

Viroids Viroids are RNA molecules that infect plants. They have no protein capsid. Are replicated by host RNA polymerase. Some have catalytic ability.

Prions are that infect animals. They have no nucleic acid component. Have an abnormal structure that alters the conformation of other normal proteins Extremely resistant to usual sterilization techniques

Prions Diseases Common in animals

Scrapie in sheep and goats

Bovine spongiform encephalopathies (BSE), a.k.a. mad cow disease - transmissible and fatal neurodegenerative disease

Humans – Creutzfeldt-Jakob Syndrome (CJS) 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 structure

The viral capsid is the protein shell of a virus.

The capsid encloses the viral genome

The capsid delivers the viral genome into the host cell.

Different viruses make different capsid forms.

Capsids All viruses have (protein coats that enclose and protect their nucleic acid)

The capsid together with the nucleic acid is the nucleocapsid

Each capsid is made of identical protein subunits called capsomers

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

Structural types of capsids

Helical – Rod or thread-like continuous helix of capsomers forming a cylindrical nucleocapsid

Structural types of capsids

Icosahedral - Polyhedral with 20 identical triangular faces

Have a structure that exhibits rotational symmetry Envelope In some icosahedral viruses, the capsid is enclosed in an envelope, formed from the cell membrane. The envelope contains glycoprotein spikes, which are encoded by the virus. Spikes are essential for attachment of the virus to the host cell Between the envelope and capsid, tegument proteins may be found.

Viruses lacking an envelope are naked

Dr.Stepehen Fuller Functions of capsid

1. Protect genome from atmosphere (May include damaging UV-light, shearing forces, nucleases either leaked or secreted by cells).

2. Virus-attachment protein- interacts with cellular receptor to initiate infection.

3. Delivery of genome in infectious form. May simply “dump” genome into (most +ssRNA viruses) or serve as the core for replication ( and ). Viruses with unusual structures These have complex multipart structures T4 : Have an icosahedral “head” and helical “neck”

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

Viruses with unusual structures Filamentous viruses The capsid consists of a long tube of protein, with the genome coiled inside Vary in length, depending on genome size Include bacteriophages (e.g. M13) as well as animal viruses () Ebola virus M13 Bacteriophage Bacterial viruses (phages)

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

Are called T-even phages as T2, T4 & T6 of the 7 phages studied have similar structures Types of viruses Nucleic acids

Viral genome – either DNA or RNA but never both

Carries 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

RNA genomes ready for immediate are positive-sense RNA

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

Viral

Pre-formed enzymes may be present

– Polymerases – DNA or RNA

– Replicases – copy RNA

– – synthesis of DNA from RNA (HIV-1) - rules All viruses require a host cell for .

Thus, they all face the same needs for host infection:

Host recognition and attachment

Genome entry

Assembly of progeny virions

Exit and transmission

Replication cycle of Bacteriophages

Multiplication goes through similar stages as animal viruses

Only the nucleic acid enters the cytoplasm - uncoating is not necessary (Hershey- Chase experiment)

Release is a result of cell induced by viral enzymes and accumulation of viruses - lytic cycle Hershey- Chase experiment

http://scarc.library.oregonstate.edu/coll/pauling/dna/index.html 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 – viruses leave the cell to infect other cells Bacteriophages attach to host cells

Contact and attachment are mediated by cell-surface receptors.

Proteins that are specific to the host species and which bind to a specific viral component.

Bacterial cell receptors are normally used for important functions for the host cell. Example: sugar uptake

Phage reproduction within host cells Bacteriophages (phages) inject only their genome into a cell through the cell envelope.

The phage capsid remains outside, attached to the cell surface (ghost).

Orlova EV. How viruses infect bacteria? The EMBO Journal 2009;28(7):797-798. doi:10.1038/emboj.2009.71. Bacteriophages can undergo two different types of life cycles

1) Lytic cycle Bacteriophage quickly replicates, killing host cell

2) Lysogenic cycle Bacteriophage is quiescent. Integrates into cell chromosome, as a prophage. Can reactivate to become lytic.

The “decision” between the two cycles is dictated by environmental cues In general, events that threaten host cell survival trigger a lytic burst 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 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

• 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 – lysogenic conversion

– Corynebacterium diphtheriae

– Vibrio cholerae

– Clostridium botulinum

Animal Virus replication cycles

The primary factor determining the life cycle of an is the form of its genome.

DNA viruses Can utilize the host replication machinery RNA viruses Use an RNA-dependent RNA-polymerase to transcribe their mRNA Retroviruses Use a reverse transcriptase to copy their genomic (RNA) sequence into DNA for insertion in the host chromosome Modes of animal viral multiplication General phases in animal virus multiplication cycle:

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

2.Penetration – genome enters the host cell

3.Uncoating – the viral nucleic acid is released from the capsid

4.Synthesis – viral components are produced

5.Assembly – new viral particles are constructed

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

Animal viruses show tropism

Animal viruses bind specific receptor proteins on their host cell.

Receptors determine the viral tropism.

Ebola virus exhibits broad tropism, infecting many kinds of host tissues. Papillomavirus shows tropism for only epithelial tissues. Most animal viruses enter host as virions.

Internalized virions undergo uncoating, where genome is released from its capsid. 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 – – human liver cells – Poliovirus – primate intestinal and nerve cells – Rabies – various cells of many mammals

Envelope spike Host cell membrane Capsid spike

Receptor

Host cell membrane

Receptor Penetration/Uncoating

• Flexible cell membrane is penetrated by the whole virus by:

– – entire virus is engulfed and enclosed in a or vesicle

– Fusion – envelope merges directly with membrane resulting in nucleocapsid’s entry into cytoplasm Variety in penetration and uncoating Replication and protein production

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

• DNA viruses generally replicate and assemble in the nucleus

• RNA viruses generally replicate and assemble in the cytoplasm

– Positive-sense RNA contain the message for translation

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

Papillomavirus (DNA) Life Cycle

HPV, a double-stranded DNA virus, enters the cytoplasm, where the protein coat disintegrates.

The viral DNA enters the nucleus for replication and by host polymerases.

Viral mRNA returns to the cytoplasm for translation of capsid proteins, which return to the nucleus for assembly of virions. Picornavirus (RNA) Life Cycle Picornavirus life cycle. A picornavirus inserts its (+) strand RNA into the cell.

Reproduction occurs entirely in the cytoplasm.

A key step is the early translation of a viral to make RNA-dependent RNA polymerase.

The polymerase uses the picornavirus RNA template to make (–) strand RNA, which then serves as a template for other viral mRNAs, as well as progeny genomic RNA. HIV () Life Cycle

Retrovirus life cycle.

A retrovirus such as human virus (HIV) uses reverse transcriptase to copy its RNA into double-stranded DNA.

The DNA then enters the nucleus to integrate in the host genome.

Host RNA polymerase generates viral mRNA and viral genomic RNA.

The viral mRNA enters the cytoplasm for translation.

Virions assemble near cell membrane and bud out. Release • Assembled viruses leave the host cell in one of two ways:

– Budding – exocytosis; nucleocapsid binds to membrane which pinches off and sheds the viruses gradually; cell is not immediately destroyed

– Lysis – nonenveloped and complex viruses released when cell dies and ruptures

Late Uta von Schwedler Damage to host cell Cytopathic effects - virus-induced damage to cells

1. Changes in size and shape

2. Cytoplasmic inclusion bodies

3. Inclusion bodies

4. Cells fuse to form multinucleated cells

5. Cell lysis

6. Alter DNA

7. Transform cells into cancerous cells

Effects of some human viruses 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 – and shingles

Viral damage

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

• 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 or oncogenic viruses

– Papillomavirus – cervical cancer

– Epstein-Barr virus – Burkitt’s lymphoma

– virus – Liver cancer

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 Oncogenic viruses Oncogenic viruses transform the host cell to become cancerous.

Mechanisms of oncogenesis include:

1) Insertion of an oncogene into the host genome

2) Integration of the entire viral genome

3) Expression of viral proteins that interfere with host cell cycle regulation Techniques in cultivating and identifying animal viruses

Methods used:

– Cell (tissue) cultures – cultured cells grow in sheets that support viral replication and permit observation for cytopathic effects

– Bird embryos – incubating egg is an ideal system; virus is injected through the shell

– Live animal inoculation – occasionally used when necessary

Methods for growing viruses Tissue culture of animal viruses

Animal viruses can be cultured within whole animals by serial inoculation Ensures that the virus strain maintains its original , but process is expensive and laborious. They can also be grown in human cell tissue culture. Plaque assay of bacteriophages Plaque assay of animal viruses 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 to virus ()

• Antiviral drugs can cause serious side effects

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

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