Viruses: intimate parasites Are viruses alive? Not made of cells, in violation of Cell Theory Do not grow (but self assemble) Do not metabolize (but steal energy) Cannot reproduce w/o a host cell (but other organisms may require another species in order to reproduce) Can evolve over time Some can respond to environmental stimuli Have a complex, organized structure

If not cells, then what? Viruses are particles Some components are essential A genetic material with the blueprint for making more Could be: ds DNA, ss DNA, ss RNA, ds RNA Space is limited, so genes are few A covering to protect the genetic material Capsid, made of one or more proteins Capsid + nucleic acid: nucleocapsid Viruses are obligate intracellular parasites

Viruses may have other parts Envelope: piece of organelle membrane or cell membrane covering capsid Virus is formed by budding, pushes through membrane taking a piece. Viral envelope usually contains viral proteins. Envelope makes virus susceptible to some disinfectants Spikes (peplomers) extend from envelope Used for attachment, escape Accessory enzymes Reverse transcriptase, RNA RNA enzymes

Viral size and shape Viruses range from 20 nm to 300 nm Ribosomes are about 30 nm The smallest known bacteria are about 200 nm Viral shapes: helical, polyhedral, and complex http://www.glencoe.com/qe/images/b136/q4323/ch18_0_a.jpg; www.blc.arizona.edu/.../ Figures/Icos_Virus.GIF; http://www.foresight.org/Updates/Update48/Images/T4Schematic.jpg

Examples of virus shapes Ebola Adenovirus http://www-cgi.cnn.com/HEALTH/9604/16/nfm/ebola.levine/ebola.reston.large.jpg; http://www.virology.net/Big_Virology/EM/Adeno-FD.jpg

Specificity A recurring theme in biology: Enzymes, membrane receptors, antibodies, etc. Viruses are limited to certain types of host cells Species barriers: rabies not specific, but most are Tissue type: rabies specific to nerve, salivary tissue Cell type: HIV infection mostly restricted to Helper T cells, a kind of lymphocyte. Different characteristics of host cells involved Attachment to cell surface often a major point Every type of organism has a virus that infects it?

Viruses across kingdoms A densovirus newly isolated from the smoky-brown cockroachPeriplaneta fuliginosa Acanthamoeba castellanii Promotion of In Vitro Survival and Transmission of Coxsackie B3 Viruses The causal organism is the Tulip Breaking Virus (TBV). The pathogen is a potyvirus and is divided into two strains, Genome characterization of Botrytis virus F, a flexuous rod-shaped mycovirus

Classification Microbes problematic, viruses especially so. No sexual reproduction, no asexual reproduction, just “assembly”. No clear evolutionary relationships Classification scheme (from David Baltimore) First, by nucleic acid type, e.g. ds DNA, + sense RNA Next, structural characteristics (presence of envelope, capsid shape), type of organism infected, etc.

Life cycle of a virus Manner of infection and reproduction depends on whether host is prokaryotic or eukaryotic. Life cycle here outlined is general: ADSORPTION: following contact, molecules on surface of virus bind to particular molecules on host cell. PENETRATION: the nucleic acid must get access to the machinery of the cell to replicate. http://www.tthhivclinic.com/Fig_20.gif

Life cycle continued SYNTHESIS/REPLICATION: once inside the nucleic acid issues orders leading to Replication of the nucleic acid Transcription (usually) and translation, producing the necessary capsid proteins. ASSEMBLY: a spontaneous process Capsid proteins and nucleic acid combine to make virion. Cheap but highly inefficient process. RELEASE: successful parasite must spread to others Virus causes lysis of cell or pushes through cell membrane. Virions may acquire an envelope.

Bacteriophage: lytic vs. lysogenic Most bacteriophages multiply then lyse the host cell This life cycle is called a lytic cycle Others are “temperate”, enter a lysogenic cycle. Lysogeny is an effective way to multiply the viral DNA Viral DNA inserts into the bacterial chromosome Now called a “prophage” Bacterial replication also replicates viral DNA Prophage may bring new genes for use by bacterium Damage to bacterial DNA (e.g. UV) prompts virus to begin lytic cycle; DNA excises, virus multiplies.

Measuring numbers of virions: the Plaque Assay Virus and host cells are mixed Bacteria cover in a Petri dish as a “lawn”, eukaryotic cells cover bottom of a dish. Multiplication of virus leads to release, spread to and destruction of nearby cells. Visible as holes, plaques, on bacterial lawn; eukaryotic cells in culture are first stained for easier view to see plaques. http://dept.kent.edu/biology/Courses/30171/imageQBT.JPG; news.bbc.co.uk/.../ _230333_cell_culture_300.jpg;

Growing viruses Obligate intracellular parasites: require a host cell!! Whole organism Animal models, human volunteers Ethically, humans require consent, safety, pay Eggs: aseptic incubator Various cells and membranes support growth of viruses Shell provides protection from bacterial contamination Used for large batches of viruses for vaccines Egg allergies a problem sometimes http://www.fao.org/ag/againfo/foto/egg-facts.gif

Growing viruses continued Organ/tissue/cell culture Minced tissue, separated into cells by enzyme treatment Grown in sterile plastic dish with nutrient solution Cells prepared this way grow until dish is covered, stop. Scrape up, use some to inoculate new culture Limited number of rounds of replication Transformed cells, with cancer properties, grow forever. Must be subcultured when dish bottom is covered Cell culture major reason for advances in virology

Viruses and disease Most of discomfort, some of damage, is due to host defense response to viral infection. Cytopathic effects: damage caused by viruses Cells change shape, change size (round up, swell) Cells become sticky (clump, fuse to form syncytia) Syncytia are giant, multinucleated cells Cells change internally (vacuoles, inclusions) Location, appearance of inclusions characteristic of certain viruses; comprised of viral parts or cell debris Cells die.

Other effects of viruses Transformation: cells become cancer-like Lose contact inhibition Continue to multiply In vivo, produce tumors Certain Herpes-type viruses, genital wart virus, etc. Some viruses cause birth defects = teratogenesis Damage to critical cells in fetus, failure to form parts Typically, virus is mild and able to cross placenta Rubella (German measles virus), CMV

NOT viruses Viroids: naked RNA Prions: infectious protein particles Cause of infectious disease in plants Prions: infectious protein particles Got Stanley Prusiner the Nobel Prize, but still controversial. Cause of Mad Cow Disease, Scrapie, Elk Wasting disease, Creutzfeldt-Jakob disease, Kuru, etc. Transmissible spongioform encephalopathies Misshapen protein causes normal protein to also fold incorrectly, increasing their numbers Replication without the presence of nucleic acid

Prions Normal cell protein Misfolded version: prion www.stanford.edu/.../2004anderson/index.html

Attack and defense Virus has ways of attacking Specific binding to host cell receptor Receptors involved in normal cell functions Virus may regulate cell division for its own replication Insertion of viral DNA into chromosome allows virus to hide from immune system Causes adjacent cells to fuse, allows cell to cell spread without leaving cell.

Defense by host Host has ways of defending Cell mediated immunity (T cells): infected cells killed. Antibodies intercept virions between cells, in fluids Interferon produces anti-viral state, prevents replication Natural killer cells act Using antibodies as tags Quickly before B &T cells ready

Pathogenic Viruses Name of virus what family it belongs to what disease it causes, organ system affected DNA or RNA? Route of transmission; reservoirs, vectors Viral virulence factors (selected viruses) Immunizations

A molecular biology lesson RNA mutates more readily than DNA Copying mistakes by the enzymes are not corrected Not double stranded, so no mismatches noticed that can be fixed. Many variants result Less chance of lasting immunity Harder to create vaccines

HIV: Human Immunodeficiency Virus Host range Main types of cells infected: T helper cells and dendritic cells (including macrophages, microglia) Have CD4 and CCR5 glycoproteins on surface Infection process RNA is copied into cDNA by reverse transcriptase cDNA inserts into host chromosome New RNA made Protein precursor made, then processed; assembly occurs Virions bud through cell membrane

HIV life cycle Binding to host cell Copying RNA into DNA by Rev Trans Integration into host DNA Transcription Translation Assembly and exit by budding www.aidsmeds.com/images/HIVLifeCycle1.gif

Disease process Chronic infection AIDS diagnosis: T cells continually made, continually destroyed Eventually, host loses AIDS diagnosis: Acquired Immuno Deficiency Syndrome CD4 cell count below 200/µl; opportunistic infections Examples of opportunistic “infections” Pneumocystis carinii pneumonia (PCP pneumonia) Kaposi’s sarcoma; Tuberculosis; several others

Prevention and Treatment Prevention is easy Practice monogamous sex, avoid shared needles HIV cannot be spread by casual contact, skeeters Drug treatment Nucleoside analogs such as AZT Protease inhibitors prevent processing of viral proteins Nifty animation at: http://www.hopkins-aids.edu/hiv_lifecycle/hivcycle_txt.html