Chapter 10. Viruses

General Characteristics

Viral Components 

• Viruses are non-cellular, obligate intracellular parasites
• Genetic materials
• Viral particle contains a single type of nucleic acid, either DNA or RNA, not both (bacteria have both)
• Single- or double-stranded
• Positive (+) or Negative (-) RNA: (+) RNA is used directly for protein synthesis
• Viral nucleic acids are enclosed in a capsid (protein coat) and (in enveloped viruses) an envelop derived from host membrane

Viral morphology and host range

• Sizes: small relative to bacterial or human cells
• Shapes
• Helical: helical capsid; e.g., tobacco mosaic virus
• Polyhedral: many-sided; e.g., polio virus
• Enveloped: e.g., influenza virus, herpes simplex virus, HIV
• Complex: e.g., T-even bacteriophage, composed of a polyhedral head and a helical tail
• Most viruses are tissue-specific and species-specific, determined by viral receptor on cell surfaces

Viral replication

• Viruses multiply by taking over the metabolic machinery of the host cell
• Key steps in a viral replication cycle
• Adsorption and attachment to specific receptor sites on a host cell surface
• Penetration of viral DNA or RNA into the host cell
• Biosynthesis of viral components using the metabolic machinery of the host cell
• Release of new viral particles from the host cell
• Cytopathic effects (CPE) of viral infection: e.g., multi-nucleation (formation of cell with multiple nuclei) and transformation (becoming cancer cells)

Viral Taxonomy

• Viral classification is based NOT on symptomatology (the disease they cause), but on:
• Nucleic acid type (e.g., DNA or RNA viruses)
  
• Morphology (e.g., enveloped or non-enveloped)
  
• Strategy for replication (e.g., retroviruses uses reverse transcriptase)

Examples of RNA viruses

• (+) Sense RNA viruses
• Picornaviruses: small, naked, polyhedral, (+) RNA, e.g., poliovirus, hepatitis A virus, and rhinoviruses (causing common cold and SARS)
• Togaviruses: small, enveloped, polyhedral, (+) RNA, e.g., rubella virus
• Flaviviruses: enveloped, polyhedral, (+) RNA, often transmitted by arthropods ("arbovirus"), e.g., yellow fever virus, hepatitis C virus, and West Nile virus
• Retroviruses: enveloped, (+) RNA, uses reverse-transcriptase (much lower fidelity than normal DNA polymerase) for replication, e.g., HIV-1 (human immunodeficiency virus, type 1) and HTLV (human T-cell leukemia viruses)
• (-) Sense RNA viruses
• Paramyxoviruses: enveloped, (-) RNA, e.g., viruses causing mumps and measles
• Rhbdoviruses: e.g., rabies virus
• Orthomyxoviruses: enveloped, containing multiple RNA segments, e.g., influenza A virus

Examples of DNA viruses

• Adenviruses: naked, linear dsDNA
• Herpesviruses: large, enveloped, linear dsDNA, often existing as latent infection in nerve cells, e.g., Herpes simplex viruses (causing cold sores and genital warts) and viruses causing chickenpox and shingles
• Poxviruses: large, enveloped, linear dsDNA, e.g., smallpox virus
• Hepadnaviruses: small, enveloped, e.g., hepatitis B virus

Emerging Viruses

• HIV-1
• Is closely related to SIV (simian immunodeficiency virus) and likely evolved from SIV recently (about 100 years ago) by gaining human specificity
• Infects the CD4 type of T-helper cells, using CCR5 molecule on the cell surface as receptor
• There is rapid turnover of viral populations during the course of infection, due to the killing of viruses by the host immune response and rapid re-generation of new viral particles
• AIDS develops when viral replication overcomes T cell re-generation
• Patients die from opportunistic infections (pathogens suppressed in healthy individuals)
• Influenza viruses
• Three main types (A, B, C)
• Viral types determined by spikes on the viral envelop: H spike (hemagglutinin is used for attachment to host cells) and N spike (neuraminidase is an enzyme used for cutting the new viral particles loose from the host cell, to release the virus)
• Reservoirs (non-symptomatic carriers) include human, birds (wild migratory birds or domestic poultry), and swine
• Rapid evolution due to antigenic "drift" (point mutations in spikes) and antigenic "shift" (reassortment of RNA segments)
• SARS (Sever acute respiratory syndrome) virus
• Caused by a new type of coronavirus (similar to the common cold virus)
• Maintained in wild life reservoir-species like civet cats and recently gained human infectivity
• Summary: Causes of emerging viruses
• Ecological disruption: increasing contact with wild life creating opportunities for viruses to jump hosts from wild animals to humans. HIV, SARS, "bird flu" are examples of "zoonosis" (infectious diseases originated from wild animals)
• "Boeing Effect": increasing global transportation of goods and people facilitate rapid dissemination (e.g., SARS and West Nile viruses)
• Rapid evolution: HIV evolves within a single individual due to a high mutation rate, flu viruses change from year to year due to antigenic drift and antigenic shift.

Viral multiplication

• Multiplication of bacteriophages

• T4 Phage-The lytic cycle (resulting in cell death)
1. Attachment (at a cell "receptor site")
   
2. Penetration (breaks down part of cell wall and injects DNA)
3. Biosynthesis (using protein and DNA synthesizing machinery of the host cell)
4. Maturation (viral particle assembly)
5. Release (result in the lysis and death of the host cell)
• Lambda Phage-The lysogenic cycle (causing NO cell lysis or death)
1. Attachment
2. Penetration
3. Phage DNA incorporates into host cell DNA, becoming a "prophage"
4. Replicates with host chromosome.  Prophage remain latent (inactive), but could pop out from chromosome and enter the lytic cycle, causing cell death under stress

• Multiplication of animal viruses
• DNA viruses
1. Attachment: "receptor sites" are on cell membrane; individuals less susceptible to a virus may not have the right receptors on their cell membrane.
2. Penetration: viral particles taken in by endocytosis or fusion
   
3. Uncoating: enzymatic removal of viral capsid
4. Biosynthesis: viral DNA enters into nucleus, where viral DNA replication and new viruses are assembled
5. Maturation and release: "budding" out (enveloped viruses, host cells may survive) or rupture (non-enveloped viruses, host cells die)
• (+) RNA viruses (example: polioviruse): (+) RNA is used for translation of viral proteins, as well as for making a complementary (-) RNA, which is used for replicating new copies of (+) RNA
• Retroviruses (example: HIV-1): (+) RNA is reverse-transcribed into ssDNA, which replicates into dsDNA; viral dsDNA is incorporated into host cell chromosome, becoming "provirus"; new viral (+) RNA is made from incorporated DNA

Isolation and Culturing of Viruses

• Culturing of bacteriophages: the plaque method.  Phages growing on a lawn of bacteria create clear spots on a Petri plate, called "plaques".  After sufficient dilution, each plaque corresponds to a single viral particle in the original sample.
• Culturing animal viruses
• Cell cultures: Primary cells (differentiated cells, e.g., muscle cells), cell strains (actively dividing cells, e.g., fibroblasts), and cell lines (tumor-derived, immortal, indefinitely dividing cells)
• Embronated chicken eggs for culturing influenza A viruses
• Culturing of arboviruses using mice or mosquito cell lines

Viruses and Cancer

• Causes of cancer: alteration of parts of cell genome, caused by chemical mutagens, radiation and viruses.
• Neoplastic transformation: normal cells undergoing changes to become tumor cells, induced by, e.g., integration of viral DNA into the host cell's DNA.  Transformed cells (tumor cells) don't exhibit contact inhibition and divide indefinitely.
• "Oncogenic" viruses: viruses capable of inducing tumors in animals.
• DNA tumor viruses include, e.g., EB virus (causing nasopharyngeal carcinoma), HBV (causing 80% of liver cancer), and HPV (human papillomaviruses, causing sexually transmitted cervical cancer)
• RNA tumor viruses: e.g. retroviruses HTLV-1 and HTLV-2, causing T-cell leukemia
• Oncogene:
• In DNA tumor viruses, oncogene refer to genes encoding viral replication proteins, which cause uncontrolled division of host cells
• In RNA tumor viruses, "proto-oncogenes" are normal human genes.  When proto-oncogenes mutate, e.g., due to viral integration, their tumor-suppression functions are altered, causing uncontrolled cell division.

Latent viral infection

• Latent viral infections: virus remains in the host cell for long periods of time without active multiplication or producing infection, e.g., herpes simplex virus, which produce cold sores only when induced (e.g. by fever); chickenpox virus, which cause shingles in 10-20% of carriers. Latency is usually a result of host immune suppression, not viral dormancy.