What is one requirement (describes their location) in regards to viral replication
Do viruses contain a genome of DNA or RNA
They can contain one or the other
What are naked infectious RNAs. These RNAs do not code for proteins. What are they commonly pathogenic against?
What are infectious proteins with no genome. In abnormal conformation they can induce other molecules of normal proteins to adopt altered conformation. Seen in diseases such as Creutzfeld-Jakob, Kuru, and Mad Cow Disease
What are the four components of a typical virus?
Genome: RNA or DNA that carries viral information
Capsid: Protein shell surrounding genome
Envelope: Lipid bilayer surrounding capsid (naked viruses don't have an envelope)
Surface proteins: viral proteins in envelope that function in viral entry into cells
Viral genome can range from double stranded to single stranded RNA/DNA
RNA viral genomes can be what two things? It describes whether they are one unit or more than one. What are humans' genome
Segmented (contain multiple nucleic acids) or non segmented (contain a single nucleic acid molecule)
Are most viral genomes haploid or diploid? What is an example of a diploid one?
What is the phase of viral replication in which there are specific interactions between the viral exterior (capsid or envelope glycoproteins) and receptors on the cell surface
Attachment (neutralizing antibodies often block viral entry by binding the virus and interfering with attachment)
Where are the three places where uncoating can occur?
Viral gene expression is a two step process employing what two steps
Transcription and translation
Nuclear DNA viruses (adenoviruses) use the cellular transcription machinery, but cytoplasmic DNA viruses (poxviruses) and all RNA viruses (except retroviruses and hepatitis delta virus) use viral RNA polymerases. Translation always employs cellular machinery because ribosomes are too complex for a virus to encode
What do viruses have that allows for gene expression even though they don't have the 5' cap since they weren't made in the nucleus.
IRES: internal ribosomal entry sites (permit ribosome binding to the mRNA independent of the 5' cap
What do viruses use so that their small genomes are able to encode more then one protein
Frameshifting (slipping of the ribosome from one reading frame to another to access the downstream gene)
Viruses often have mechanisms of reducing translation of the cellular mRNAs (host shut-off)
Free (shutoff mechanisms include inactivation of the cap-recognition complex by viruses that do not employ capped messages, inhibition of cellular transcription and degradation of cellular mRNAs)
What is the large structure of viral proteins that is then cleaved by cellular and/or viral proteases to make mature proteins
Where do DNA viruses usually replicate? RNA?
Cytoplasm (all RNA viruses encode their own nucleic acid polymerase except hepatitis delta)
What are the two pathways of viral capsid assembly and which viruses use which
Nucleation: The capsid form around the genome (hepatitis B/HIV)
Packing: An empty capsid forms and is then filled with the genome (herpesvirus)
Assembly of the capsid and envelope can occur separately (as seen in what virus) or concurrently (as seen in what virus)
Separate: hepatitis B
What are the three pathways in which a virus can be released from a cell
1. Lyse the cell (lethal to the cell)
2. Bud off from the plasma membrane
3. Enter the Golgi/ER and be secreted
What is the difference in cellular division and viral division?
Cells divide by fission, therefore this is a linear process. Viruses replicate by de novo synthesis thus there isn't continuous logarithmic growth for cells
What is the period called on a graph of infectious viruses/cell/hour in which it is the time between infection of a cell and the appearance of new viruses
Eclipse period (wouldn't detect any viruses in this period because it has all been taken apart)
What is it called on a infectious viruses/cell/hours graph in which a sudden appearance of new infectious virus as progeny viruses are assembled
(Burst size is the average number of new viruses produced in a single round of replication: typically around 50-1000 new per cell)
Name the three different types of viral infections and describe each one and give an example of a virus that causes this type of infection
Lytic infection: accumulation of viruses in the cell followed by death and rupture of the cell; adenovirus
Persistent Chronic infection: a persistent infection in which the cell is always producing progeny viruses; hep B and C
Persistent Latent infection: persistent infection in which the cell is not always producing progeny viruses.
Viral genomes can be altered in what two ways?
Mutations (cause a change in nucleic acid sequence; base substitutions; deletions; insertions)
Recombinations (genetic information swapping between two related viruses that have infected the same cell; either molecular recombination in which sequences are exchanged along a single nucleic acid chain; or by reassortment in which segments of many viral genomes are exchanged similar to how are cells pick one of the gametes to be passed on)
What are changes to viral genomes that have no biological effect because they do not alter the protein coding sequence or the regulatory function of non-coding regions
What are changes to the viral genome that kill the virus
What are mutations to the viral genome that improve the fitness of the virus relative to the environmental conditions it faces
What are mutations that make the virus insensitive to an environmental pressure
What are changes to the viral genome that are resistance mutations that allow a virus to evade neutralization by antibodies or T-cell responses
Do RNA viruses or DNA viruses have a higher mutation rate? Give two reasons why?
1. DNA polyermases have 3' to 5' exonuclease proofreading activity
2. There are cellular DNA repair mechanisms not RNA though
What are three factors governing accumulation of mutations in the viral population?
1. Mutation rate
2. Replication rate
3. Selective pressures (negative selective pressures can reduce mutations, positive selective pressures increase mutations)
What is the quasi species nature of RNA viruses mean?
basically that they are a cluster of closely related genomic sequences (the advantage to quasi species replication is that it allows the virus to rapidly evade the immune system or other selective pressures such as antiviral drugs, antibodies, or CTL cells by variation in the viral target sequence)
Most of the viral population contains a very high number of defective viral particle that are non-infectious (>99%)
Name five viral factors governing the spread and maintenance of viruses in a population
2. Pathology (viruses that produce progeny before the onset of disease)
3. Secondary attack rate (the proportion of individuals who are exposed to an infected individual and get infected)
4. Immune variance (reinfecting a previously infected host; actively messes with the immune system)
5. Animal reservoirs (increases persistence by providing alternate source of susceptible hosts)
Name the five host factors governing the spread and maintenance of viruses in the population
1. Population density
2. Social factors
3. Medical care
4. Public health initiatives
5. Herd immunity: proportion of population that is resistant to a virus
What is the most widely used technique to test for viruses in which the physician detects amounts and type of antivirus antibodies
Serology (usually an ELISA assay) (PCR is also a widely used one)
What is the test for detecting viruses in which the viral genome is detected
PCR (DNA viruses require PCR, RNA viruses require RT-PCR) (one limitation is that it is so sensitive that it can be prone to false positives, must be careful with the chain of custody)