11-11-09 Virus Structure and Classification 1. Explain how vaccines induce immunity.

Vaccines operate by inducing both humoral and cell-mediated immunity: 1. eliciting a humoral response: vaccines induce the production of virus-specific neutralizing antibodies. Neutralizing antibodies work to inactivate viral infectivity by binding to epitopes. 2. eliciting a cell-bound response: vaccines mount an immune response against infected cells that present major histocompatibility antigen from the host. In other words, both viral antigen and host histocompatibility antigen must be presented together for cellbound immunity to be generated from a vaccine. 2. List types of viral vaccines. Whole virus vaccines, which are either killed (via chemical inactivation) or live attenuated. Examples of live attenuated whole virus vaccines: MMR, chicken pox, influena, rubella, smallpox, Sabin polio, yellow fever, rotavirus Examples of killed whole virus vaccines: Salk polio, hepatitis B, hepatitis A, rabies, influenza Subunit vaccines, which contain viral surface protein (no internal protein or functional genetic material). Subunit vaccines are genetically engineered, produced in cell culture, and then purified. Examples of subunit vaccines: hepatitis B, genital papilloma 3. Describe what a virus is and the basic structures of virus particles. The following characteristics define the virus: They are nucleoproteonic entities They are obligatory intracellular parasites They are potentially pathogenic They have a genome that is either DNA or RNA, but never both. Can be single-stranded or double-stranded, linear or circular, be made of one or several pieces, (+) or (-) strand They replicate directly from their genetic material Size is not a defining criterion for viruses. Keep in mind that bacteria are pretty darn small themselves, and some viruses are larger than the smallest bacteria. Moreover, since viruses require cellular hosts for growth, they are not ancestral forms o cells, but rather derived from subcellular elements that have evolved infectiousness and genetic independence. 4. Describe the structure and the building subunits of an icosahedron. There are two types of proteins in viruses. Virion proteins are structural proteins, while nonvirion proteins are nonstructural (they are usually enzymes).

There are two concepts to virion structure: subunit composition and self-assembly Virion proteins form a shell around nucleic acid known as a capsid. The capsid is composed of protein subunits that function as building blocks for the shell. Subunit composition is necessary because 1. in order to form a complete viral shell, the protein would have to be very large and cannot be synthesized without debilitating defects. 2. Moreover, the virus would have to contain much more genetic material to construct a single giant protein. The protein subunits also have the ability to self-assemble without using any ATP. More complex viruses, however, may require some energy-dependent enzymatic intervention in addition to self-assembly. There are two geometric types of capsids: helical symmetry and cubic symmetry Helical symmetry consists of protein subunits assembling in a rotational pattern around the axis of symmertry and translation along that axis. Consequently, the protein forms a tubular shell for nucleic acid within. Cubic symmetry forms the basic icosahedron geometry, which consists of 20 equilateral triangles, 12 corners, and 60 equivalent protein subunits. The icosahedron is only found in very basic viruses. Most have a capsid that exceeds 60 quasi-equivalent subunits that resemble the icosahedral structure known as the icosadeltahedron. Subunits cluster into capsomers that are either pentamers (5 subunits) or hexamers (6 subunits). The number of capsomers is determined by the formula: C = (T-1)x10 +12 where T=number of subtriangles=triangulation number. Note that (T-1)x10 is the number of hexamers, while 12 is the number of pentamers (which is constant in an icosadeltahedron). Naked viruses only have the aforementioned helical, icosahedral, or icosadelaltahedral capsid. Enveloped viruses have, in addition to a capsid, a membranous envelope that is derived from cell membrane (its a lipid bilayer). The envelope membrane is studded with glycoproteins. A nonglycosylated protein lining called the matrix lines the interior surface of the envelope. The matrix connects the capsid to the envelope. 5. Explain the two viral classification systems. Horne-Lwoff-Tournier (HLT) classification system is based on structural criteria. More specifically, viruses are classified based on three criteria: RNA vs DNA Helical vs cubic symmetry of capsid Naked vs enveloped This generates eight large viral classes. Baltimore classification system is based on virus replicative strategy. Replicative mechanisms can be categorized as follows: dsDNAmRNA ssDNAdsDNAmRNA dsRNAmRNA ss(+)RNAss(-)RNAmRNA

ss(-)RNAmRNA ss(+)RNAss(-)DNAdsDNAmRNA ds/ssDNAdsDNAmRNA

6. Describe the different virological assays. ELISA: most commonly used! 1. Antibodies specific for viral antigen are coated on the microtiter plate 2. Blood sample from patient is added onto the plate 3. Incubate to allow for antibody capture of the antigens 4. Wash plate, then add second virus-specific antibody that has a bound enzyme (usually horseradish peroxidase) Electron microscopy: direct visualization of viral particles Hemagluttination: coat protein of certain viruses causes aggregation of rbcs Assay for viral enzymes: can assay reverse transcriptase for retroviruses PCR: use oligonucleotide primers specific for viral DNA or RNA Plaque assay: use for lytic bacteria, where cells on agar that are infected with virus die, forming empty areas known as plaque forming units (PKUs)