MICRO 221 Virology

(+) RNA Protein Synthesis

-uses IRES - internal ribosome entry site - tells ribosome where to start translation in the middle of the mRNA -ORF - open reading frame that codes for the long polyprotein -once polyprotein is translated, 2A and 3C components have protease activity and direct the cleavage of the polyprotein to generate smaller polypeptides that have different designations (structural vs. non-structural=protease,replicase,transcriptase) -multiple cleavages take place

Varicella Zoster Vaccines

-vaccine for shingles=19,400pfus -vaccine for chicken pox=1350pfus -people get shingles later in life because the number of antibodies (decline in memory T cells) against the virus decreases over time and then body doesn't have a good/fast immune response when re-infected

ss(+)RNA Virus Replication

1. (+) RNA acts as mRNA to make polyprotein 2. Polyprotein cleaves via self-directed polyprotein cleavage into Non-structural, and Structural proteins. 3. Non-structural proteins (transcriptase) allow (+) RNA to make (-) RNA 4. Non-structural proteins (replicase) facilitate (-) RNA to (+) RNA (which can make more polyprotein) 5. Structural proteins assemble with (+) RNA to make progeny virus.

HIV: Chronic/Persistent Infection

Identification: -lymphadenopathy, opportunistic infections, rare cancers -depletion of CD4+T cells in peripheral blood -HIV-1 and HIV-2(slower declind in CD4+T cells, longer asymptotic period, lower mortality rates) -virions are always being produced

Viral Oncogene and Cancer

at least part of viral genome is expressed in transformed cell

Early genes

code for proteins that are required for genome replication and expression of late genes

Late Genes

code for viral structural proteins (proteins needed to make new capsids)

Uncoating at the nuclear membrane + example

endocytosis --> lysis of endosome --> docking onto nuclear membrane (uncoating on cytoplasmic side and nucleic acid enters nucleus) -No envelope and no way of fusing, so virus lyses to release nucleic acid ex. adenovirus

Mechanism of Nuclear-Replicating Virus: Herpesvirus

envelope fusion, docking at nuclear pore and uncoating on cytoplasmic side, insertion of nucleic acid into nucleus -tegument protein (VP16) also enters nucleus

Early proteins

enzymes necessary for replication of genome

Cap Snatching

ex. Influenza virus -(-) viral RNA recognizes and aligns with host pre-mRNA using -viral proteins facilitate endonucleolytic cleavage of host mRNA at the 5' cap and put it on the (-)RNA -viral genome uses the cap as a primer for transcription

Uncoating at plasma membrane + example

fusion (penetration) --> uncoating (ribonucleoprotein is released into cytoplasm upon fusion of the virus) ex. HIV

Apoptosis inhibited

tumour suppressor genes normally stop cells with other damaged genes from reproducing and encourages apoptosis - this function is inhibited I think?

Cytopathic Effects (CPE) of Virus Infection

-altered shape of host cell - rounding -inhibition of host DNA, RNA, protein synthesis - cytolytic viruses -damage to cell lysosomes, release of digestive enzymes - cell lysis -alteration of plasma membranes, susceptible to immune system, syncytia -cytotoxic effect of accumulating virus proteins -->cytoplasmic or nuclear inclusions -->size&location of inclusions may be virus-specific -inhibition of apoptosis -transformation of host cell into malignant (cancer) cell

Herpesvirus Capsid Assembly

-assembly of large, complex protein shells can require chaperones for accurate assembly = scaffolding proteins

Hepatitis B Virus

-can be a filament or sphere particle -I think nucleic acid is not associated with this?

Virulence

-capacity of a virus, compared to other closely related viruses, to produce disease in host -depends on viral factors: -->dose of virus, route of entry, tissue tropism, genetic changes -depends on host factors: -->age, immune status, species of host, nutritional state

Assembly of Icosahedral Capsids

-capsid assembles around virus genome OR -genome is "fed" into preformed capsids - "head fulls"

Herd Immunity

-chains of infection are likely to be disrupted when large numbers of a population are immune or less susceptible to the disease -the greater the proportion of individuals who are resistant, the smaller the probability that a susceptible individual will come into contact with an infectious individual, reducing threat of virus spread

Acute Infection

-completion of all stages of viral replication and cell death followed by clearing of the virus by the host immune system -rapid production of virus followed by rapid resolution and clearing of infection by host -ex. Influenza A Virus -many symptoms of acute infection (eg. fever, malaise, aches, nausea) due to robust host immune response - ex. interferon response

RNA Virus - Influenza Packaging

-concerted assembly: structural units of protective coat only form in association with genomic nucleic acid -NP (nucleoprotein) associates with viral RNA while RNA is being synthesized to form ribonucleoprotein (RNP). -NEP mediates export - export via vesicular transport of golgi, ensures RNA gets to cell surface -RNPs can serve as templates for replication, transcription, or bind MI for packaging/budding

HPV and Cancer

-discovered HPV DNA in cancer cells -HPV infects epithelial cells in cervical mucos membrane -HPV-DNA integrates into cellular genome when causing cancer

Immunopathology

-disease caused by virus infection not caused by virus but by host immune response to virus -majority of virus infections are silent

Activation of Interferon

-dsRNA=major trigger - so most RNA viruses are very good at triggering interferon response -endosomal dsRNA detectors or cytoplasmic dsRNA detector produce signal to transcribe and translate interferon - IFNa/b -IFNa/b binds to IFNAR receptor on another cell to signal an ISRE(interferon stimulated response element) which causes translation of proteins involved in establishing anti-viral state

Segmented (-) RNA Virus

-each segment encodes a single protein (monocistronic mRNAs) -can lead to antigenic drift ex. Orthomyxoviridae

Consequences of Latent Infections

-ex. Herpes virus -different sub-families of Herpesviridae can establish latent infections in different cell types -latency: virus genome persists in nucleus of infected neuron but only small subset of genes is expressed -reactivation: triggers repliation and shedding of infectious virus, often with characteristic disease -lifelong infections

DNA tumour viruses

-ex. SV40 -viral gene (T antigen) with no cell homolog that functions in virus replication by controlling viral anc cellular DNA transcription and replication -inactivation of "tumour-suppressor" genes

Chronic/Persistent/Latent Infection

-failure to clear virus infection leads to a reservoir of infection - delay of overt disease/pathogenesis -Chronic/persistent=constant low level virus production - slow release of virus without cell death -Latent=no detection of virus until reactivated - no viremia until activation but virus is present within cell -ex. Hepatitis B virus, HPV (chronic), Human Herpes Virus 1 (latent) -can eventually lead to cancer -->activation of host proto-oncogene (human) or insertion of oncogene (animals)=transformation event

Syncytia

-fusion of cells resulting in multinuclear cell mass

Oncogene

-gene which is a potential effector or component in the conversion of a normal cell to a cancerous cell

Gene Expression of (+) ssRNA viruses: Exception?

-genome acts as mRNA, can be translated directly by cellular ribosomes EXCEPTION: retroviruses

Gene Expression of Retroviruses:

-genome is (+) diploid RNA -circuitous system to make viral mRNA -replicate genome through DNA intermediate via reverse transcription with viral Reverse Transcriptase (animal cells don't have this enzyme) into a double stranded DNA -dsDNA transports to nucleus and integrates into host genome by Viral Integrase -Integrated DNA (provirus) serves as a template for the synthesis of viral mRNAs using host RNA Polymerase II -host RNA pol II also synthesizes genome length (+) RNAS (new genomes) using the provirus as template

Bacteriophage P22 Assembly Pathway

-genome is 41.7kbp but P22 packages DNA until capacity of capsid at 43.5kbp = headful DNA packaging -termination of packaging by cleavage of concatemeric DNA by gp2/gp3 terminase initiated when chromosome is at a defined packaging density sensed by portal proteins (gpI) NOT by initiated by sequence -tail assembly constructed by sequential addition of multiple copies of four gene products (gp4, gp10, gp26, gp9) to vertex occupied by poral ring only after all DNA is packaged

Ambisense RNA Viruses

-genomic RNA regions of both (+) and (-) sense -genome (-) RNA gives one subgenomic mRNA -antigenome (+) complement RNA gives a different subgenomic mRNA -5' end of each segment is (+) -(3' end of each segment is (-)

Packaging of Herpesvirus DNA

-genomic concatemers (multiples of entire genome linked end-to-end) -individual genomes must be packaged -HSV-I packaging signals: pac1 and pac2 lie within long terminal repeats between genomes -->required for recognition of viral DNA and cleavage of genomes

DNA Viruses Target Cellular Tumour Suppressor Genes

-human tumour suppressor protein p53: -major role in cell cycle - guardian of genome -cell cycle arrest and apoptosis induced when DNA is damaged -pRB -negative regulator of cell proliferation - constrains the proliferation-promoting activity of E2F (transcription factors) to stop tumour growth -transiently inactivated as cells progress through cell cycle in normal cells -this control mechanism is disrupted in tumour cells

Virus Transformed Cells = Tools for Cancer Studies

-oncogenesis=multi-step process -each step has independent, irreversible genetic change leading to deregulation of cell growth, change in morphological, biochemical, or growth parameters of cell (SEE NOTES FOR LIST) -virus doesn't actually want to cause cancer - non-productive infection

Virus Multiplicity of Effects

-one disease/symptom can be caused by more than one type of virus ex. hepatitis (inflammation of liver) caused by: -picornavirus (Hep A virus) (+)ssRNA genome -flavivirus (Hep C) (+)ssRNA -satellite (Hep Delta) (-)ssRNA -hepevirus (Hep E) (+)ssRNA -hepadnavirus (Hep B) dsDNA -a particular virus can cause more than one type of disease because of latency ex. human herpes virus 4 causes: -Burkitt's lymphoma, nasopharyngeal cancer, B cell lymphomas, infectious mononucleosis

Scaffolding proteins

-participate in capside or nucleocapsid construction but are absent from mature virions -ex. Herpes virus

Helical Virus Packagin

-position of the RNA within capsid is determined directly by its binding to the proteins of the shell -ie RNA may be a specific length, and the helix proteins are being built to match RNA length -Bullet-shaped Vesicular Stomatitis virus: uses the same proteins to form its structure and package the RNA - RNA ends up sandwiched in between proteins - very well packaged

Course of HIV Infection

-primary infection=sudden decline in CD4+T cells and sudden increase in HIV RNA -clinical latency=CD4+ levels recover slightly and HIV RNA declines slightly - can remain in see-saw battle between CD4+ levels and HIV RNA levels for years -constitutional symptoms, and opportunistic diseases appear -eventually CD4+ cells deplete completely and HIV RNA sky rockets, DEATH

Human Immunodeficiency Virus Proteins and Receptors

-protease, integrase, reverse transcriptase packaged inside virion -gp120 receptor on outer surface for adsorption -host cell has CD4 receptor and Co-receptor on cell surface for adsorption

Early Gene Expression

-recognizable mRNA coding for early proteins must be presented by the virus in the cytoplasm -allows cascade of ordered gene expression, temporally regulated

Intracellular Assembly and Maturation

-relies on lysis of cell for egress -ex. Picornaviridae, Reoviridae, Polyomaviridae, Parvoviridae, Adenoviridae

Double Stranded DNA Virus Genome Replication (2 groups)

-replication exclusively nuclear - replication is dependent on cellular factors (uses host replication machinery) -ex. Baculoviridae, Papillomaviridae, Adenoviridae, Herpesviridae -2 or 3 cycles of transcription (immediate early, early, late cascade) OR -replication occurs in cytoplasm (Poxviruses) - these viruses have evolved all necessary factors for replication of their genomes so are largely independent of cellular machinary -ex. Poxviridae

Single Stranded DNA Virus Genome Replication

-replication occurs in nucleus, involving formation of a dsDNA replicative intermediate to serve as template for synthesis of ss genomic DNA -only single stranded DNA is packaged but it can be either (+) or (-) sense (depending on virus?) -ex. Parvoviridae

RNA Reverse Transcribing Viruses

-retroviruses/retroviridae -monopartite diploid genome -genomic RNAs (+sense) act as templates for RNA-dependent DNA polymerase (reverse transcriptase) producing a dsDNA genomic copy -->the genome is (+) sense RNA but cannot code for protein, needs to be converted to DNA first -dsDNA copy integrates into host genome as provirus and serves as template for viral mRNA synthesis and genomic (+)RNA synthesis -ex. HIV and Human T-lymphotropic virus Type I (HTLV1)

Small vs Large ssRNA Viruses:

-size of virus related to size of genome: Poliovirus - small genome, small size (22-30nm) Coronavirus - large genome, large size 120-160nm Dengue virus - 50nm

Slow Virus Diseases

-slow development of symptoms -ex. Measles virus - brain turns to mush -prions

Virus Role in Cancer

-some viruses act as carcinogens - expression of a viral oncogene (v-onc) -DNA tumour viruses -retroviruses -certain adenoviruses reveal oncogenic potential only in experimental conditions

Concerted Assembly

-structural units of protective coat only form in association with genomic nucleic acid -RNA virus - Influenza

Non-segmented (-) RNA Virus

-sub-genomic mRNAs are synthesized from the single, long (-) sense RNA

Mechanism of Nuclear-Replicating Virus: influenza virus

Uncoating within endosome (in cytoplasm), then nucleic acid enters nucleus

Egress of Naked Capsids

-no envelope -lysis -apoptosis of host

Why must DNA viruses that replicate in the cytoplasm (Poxviruses) encode their own DNA-dependent RNA polymerases?

Host eukaryotic cells do not have enzymes to transcribe viral DNA in the cytoplasm

(-) strands are coded by:

(+) strands

(+) strands are coded by:

(-) strands

Assembly of Helical Nucleocapsids

(RNA viruses) -viral genomic RNA is generally coated with nucleocapsid protein during its synthesis

Cellular oncogene

(c-onc) -cell proto-oncogene which has been activated in tumour cells OR -normal cell gene which can be altered to become an active oncogene

Why must viruses code for their own RNA-dependent RNA polymerases?

Host eukaryotic cells don't have enzymes to synthesize mRNA from a viral RNA genome

Consequences of Non-Lytic Infections

-non-lytic pathway in non-permissive cells (incomplete virus cycle) can lead to cell transformation (non-regulated growth) -discovery of viral and cellular oncogenes via study of retroviruses

(+) ssRNA Viruses

-(+) RNA genome serves as mRNA -ex. Picornaviridae (polio, rhinovirus) -purified genome is infectious -replicate in cytoplasm -synthesize large polyprotein, which is cleaved to produced final protein products ex. Poliovirus

(-)ssRNA Virus Replication

-(-) RNA virus must use virion enzyme RDRP to make (+) mRNA -mRNA is translated to proteins -transcriptase protein transcribe (-)RNA into full length (+)RNA (mRNA) that is capable of being transcribed to protein -replicase protein makes (-)RNA again out of the (+)RNA that was made by transcription -structural viral proteins used in assembly of new (-)RNA into virions -transcriptase/replicase=RNA-dependent RNA polymerase ex. Influenza virus (Orthomyxoviridae)

ss(-)RNA Viruses

-(-) strand RNA genome can be template for transcription (of shorter mRNAs) via transcriptase and for replication (of full length RNA) via replicase -ex. Orthomyxoviridae (influenza virus), paramyxoviridae, Rhabdoviridae -uses its own transcriptase to make mRNA - has no proofreading function - high mutation rate - antigenic drift -(-) strand genome alone is not infectious -segmented genomes can lead to antigenic drift (orthomyxoviridae (flu)) -viral mRNAs are gene unit length, code for single polypeptides

Assembly and Egress Resulting in Two Virion Phenotypes

-Baculoviridae - intranuclear assembly results in two phenotypes -Budded Virus (BV): used for systemic infection -->transport through nuclear membrane, acquiring envelope during budding through cytoplasmic membrane -Occlusion Derived Virus (ODV): used for horizontal infection of other hosts, extremely stable in environment -->envelopment of intranuclear virus, then occlusion into protein crystal -->humans are safe from this because ODV needs an alkaline gut and human gut is low pH

Hepadnaviridae

-DNA transcribed to mRNA, translated to protein -but also: DNA to RNA -RNA reverse transcribed to make new DNA (with Reverse Transcriptase)

DNA Reverse Transcribing Viruses

-Hepadnaviridae -ex. Hepatitis B virus (the only example of this virus type) -gaps in circular partially dsDNA genome are repaired and the genome is then converted to a closed circular molecule by a DNA polymerase packaged in the virion -mRNAs for proteins and full-length RNA template for genomic DNA synthesis using virally encoded reverse transcriptase are transcribed

VZV (Varicell Zoster Virus-Chicken Pox/Shingles) Infection

-Primary Infection=Chicken pox -Reactivation Infection=Shingles (herpes zoster virus) later in life 1. day 0 infection via conjunctiva and upper RT 2. replication in primary lymph nodes 3. day 4-6 viremia and replication in liver, spleen,etc 4. day 14 secondary viremia and infection of skin and rash appearance - infection of sensory ganglia and establishment of latent infection 5. reactivation: infection of skin and rash again, travel to CNS

Proto-oncogene

-normal cell genes, regulate various signal transduction cascades that control cell growth, proliferation and differentiation

Egress of Enveloped Viruses

-acquire envelope from budding -envelope from cell membrane: released into extracellular environment directly -envelope from ER or golgi: often secreted from infected cell (exocytosis or reverse endocytosis)

Late Gene Expression

-once regulatory proteins produced, can direct host to produce more virions

Cytolytic Viruses

-inhibition of host DNA, RNA, and protein synthesis

Interferon Mechanism to Produce "Anti-Viral" State

-interferon a/b and/or dsRNA (from any RNA virus) activates inactive PKR (interferon-stimulated protein/dsRNA-dependent protein kinase) to phosphorylate. -This activates PKR-P which phosphorylates and inactivates the eIF-2a-P enzyme which is required for initiation of translation. So translation is inhibited/shut down. -This causes the cell to die (apoptosis) BUT now the cell cannot support replication of a virus - sacrifices itself so that the virus cannot replicate

Gene Expression of (-) ssRNA viruses and double stranded RNA viruses:

-mRNA must be transcribed from (-) sense genome by viral RNA-dependent RNA polymerases NOTE: animal cells do not have this kind of enzyme, so it must be brought by the virus - MUST PACKAGE A VIRUS-ENCODED RNA-DEPENDENT RNA POLYMERASE INTO THE VIRION

Pathogenesis

-method by which viruses produce disease in host

Influenza Epidemics

-mostly affect elderly and young adults

dsRNA Viruses

-multipartite genome transcribed within partially open capsid by viral transcriptase packaged within the virion -ex. Reoviridae (ie. Rotavirus=double capsid, Orthoreovirus=oncolytic virus) - different species have different numbers of segments -large family of viruses -Respiratory Enteric Organ Virus -10-12 mRNAs ((+)stranded) leave capsid for: --translation (mostly monocistronic mRNAs) to yield viral proteins --one RNA assembles within a precursor particle where it serves as template for viral replicase (synthesis of the complementary strand) (the core associates with the mRNA molecules, where final process of replication occurs - so you have synthesis of a complimentary strand and end up with a new dsRNA genome)

Budding of Influenza Virus

-neuramidase and hemagglutinin in cell membrane as well as host cell proteins -capsid buds and ends up with only N. and H. proteins in its envelope -virion then matures outside cell

Orthomyxoviridae enzymes packaged within virion

-neuramidase spike on outside -polymerase on inside of virion

Retroviruses and Cancer

-viral homolog of normal cellular gene that has been activated (altered) so that it functions as tumour inducer -activation of proto-oncogene to oncogene can include: transduction, integration, point mutations, inserttions, gene amplification, translocation, protein-protein interactions

Intracellular Assembly, Maturation linked with Egress

-virions extrude or bud from cell surface -ex. all (-) RNA viruses: Rhabdoviridae, Paramyxoviridae, Orthomyxoviridae -ex. Some DNA viruses: Herpesviridae, Baculoviridae -ex. Retroviridae

Hepatitis B Virus Replication (DNA Revers Transcribing Virus)

-virus enters cell, nucleic acid enters nucleus -partial dsDNA circular genome is repaired in nucleus (by a polymerase - don't know if it's cellular or viral) -circular dsDNA now transcribed into genomic (+)RNA(unspliced) and mRNA -mRNA makes viral proteins (RT and core) -RT is used to make genomic DNA from the transcribed (+)RNA and core proteins aid in assembly of the virus -assembly involves budding of core+nucleic acid into endoplasmic reticulum, then vesicular transport to cell membrane

Virus-Host Interactions

-virus must be stable in environment to survive before encountering host -virus must gain entry to susceptible host and undergo replication -virus must overcome series of obstacles at each stage or level of infection to proceed to subsequent level -lab animals and cell cultures serve as model systems of pathogenesis

Inhibition of Host Interferon Signalling Pathway

-viruses have evolved proteins that interfere with the interferon response process so that virion replication can continue

Preventing Influenza Infection

-wash hands frequently -annual flu shot to build up number of strains you are immune to and to provide "herd immunity"

Interferon

-when chicken cells exposed to inactivated virus they produce interferon substance to protect other cells from infection by life influenza virus -cells respond to IFN by establishing an "anti-viral" state within the cell

General dsDNA Virus Replication Cycle (ex. Herpes virus)

1. Adsorption, Penetration, Uncoating 2. In nucleus, circularization of genome and transcription of immediate-early genes through mRNA intermediate 3. immediate early/alpa-proteins (products of immediate early genes) enter nucleus and recognize genomic DNA to stimulate transcription of early genes 4. early/beta-proteins (products of early genes) enter nucleus to function in DNA replication, yielding concatemeric DNA (multiple copies of same DNA sequence linked in series) and late genes are also transcribed (genes evolve to create progeny DNA?) 5. late/gamma-proteins (products of late genes) enter nucleus to associate with DNA and participate in progeny virion assembly

Stages in Viral Replication

1. Entry into host 2. Primary replication (virus replication cycle) 3. Spread through host 4. Cell and Tissue tropism (cells/tissues respond to virus) 5. Host immune response 6. Secondary replication 7. Cell injury 8. Clearance/persistence

HSV-1 Infection

1. Mucosal epithelium=sit of primary infection 2. virus travels down axon to neuronal cell body 3. latency established in sensory ganglion (ex. trigeminal ganglion HSV-1) 4. reactivation from latency at a later time OR 4. Virus can travel down neuron to brainstem and cause encephalitis or infection elsewhere from original site of infection

5 Methods of virus modification of host systems + examples:

1. RNA splicing to compress more genetic info into genomes ex. Adeonviridae, Papillomaviridae 2. Modify host-cell transcription -cap snatching ex. Orthomyxoviridae 3. Modify host-cell translation -degradation of cap-binding complex to shut off host translation and use of IRES (internal ribosome entry site) ex. Picornaviridae 4. Stimulate host-cell macromolecular synthesis (S phase) ex. Polyomaviridae 5. Inhibit cell apoptosis ex. Baculoviridae

Three General Strategies for Uncoating

1. Uncoating at Plasma Membrane 2. Uncoating within Endosomes 3. Uncoating at the Nuclear Membrane

ssDNA Virus Replication Cycle

1. Virus DNA is (+) or (-) 2. Replication directed by template using cellular proteins: dsDNA to ssDNA 3. dsDNA transcribed to mRNA, mRNA translated to virus proteins 4. Virus proteins involved in re-formation of ssDNA in 2. (?) 5. ssDAN assembles into new (+) or (-) virus. 1. Hairpin Formation allowed by inverted terminal repeats of ssDNA 2. This creates a 3' end from the one hairpin which serves as primer for synthesis of a complementary strand. The replisome pushes through and "flattens" the hairpin at the 5' hairpin. 3. Nuclease nicks the parent strand just before the hairpin. 4. The nick provides a 3' primer for DNA synthesis. The replisome pushes through the hairpin to flatten it. 5. Two hairpins reform at one end (one daughter, one parent). 6. This provides a 3' primer for the one strand. Synthesis proceeds, displacing the other strand, which refolds to form genomic DNA. Result: genomic DNA and a dsDNA

Generalized Reoviridae Replication

1. dsRNA does not function as an mRNA so the initial step is to make mRNA (transcription) within core in cytoplasm -the (+)mRNAs are made by virally-coded RNA polymerase (from the virion), the mRNA is capped and methylated, and then extruded from the vertices of the capsid. 2. mRNAs are translated, and resulting viral proteins assemble to form an immature capsid. mRNAs are packaged into the immature capsid and are then copied within the capsid to form double stranded RNAs (It is not known how each capsid gets one of each of the 11 mRNAs) More mRNAs are now made by the newly formed immature capsids. 3. More proteins made and eventually immature capsids bud into lumen of ER (virus inclusion body) and acquire a transient envelope which is lost as they mature.

dsRNA Virus Replication

1. dsRNA in core particle makes a number of mRNAs using viral RDRP 2. most mRNAs translate viral proteins involved in the following steps 3. one mRNA is partially assembled into a new core 5. the partial-core-associated mRNA serves as template for viral replicase to synthesize a complimentary strand of RNA to form a full dsRNA genome 6. This subviral particle is fully packaged as a progeny virus

Influenza Virus Replication (-)ssRNA

1. endonuclease activity of PB1 protein cleaves cap and ~10 nucleotides from 5' end of host mRNA (cap snatching) - inhibits host translation 2. fragment used to prime viral mRNA synthesis by RDRP activity of PB1 - caps its own mRNA that goes to cytoplasm 3. viral mRNA translated - early products include more NP and PB1 proteins 4. RNA pol activity of PB1 synthesizes +ssRNA from genomic -ssRNA 5. RNA pol activity of PB1 synthesizes new copies of the genome using +ssRNA from 4. as templates. - some of the new genome segments serve as templates for more viral mRNA. 6. viral mRNA molecules transcribed from other genome segments encode structural proteins (HA and NA) that are translated by ER ribosomes and delivered to cell membrane. 7. Viral genome segments packaged as progeny virions and bud from host cell.

Retro virus replication

1. entry and loss of cell envelope 2. loss of viral capsid 3. reverse transcriptase makes a DNA strand complementary to RNA genome, and then another strand to make dsDNA 4. integration of dsDNA cope into host chromosome 5. transcription by host cell polymerase makes many mRNA copies that make viral proteins and copies of (+) RNA genome (full length RNA as opposed to the mRNA that has been spliced to make proteins) 6. mRNAs translated into envelope proteins, capsid proteins, and reverse transcriptase 7. (+)RNA and proteins assembled into virion at cell membrane and viral budding takes place 8. maturation of virus once budded out of host cell - protease is involved in maturation

Mechanism of Nuclear-Replicating Virus: Adenovirus

Docking at nuclear pore and uncoating on cytoplasmic side, insertion of nucleic acid into nucleus

Alternative ssRNA Virus Replication

Flavivirus (includes: yellow fever and dengue viruses) and Picornavirus: -(+) RNA genome (mRNA) replicated to (-) full length complement, then replicated to (+) strand genome (mRNA) again Alphaviruses: -(+) RNA genome (mRNA) replicated to (-) full length complement, then replicated to (+) strand genome (mRNA) again but ALSO mRNA synthesis form (-) complement to get subgenomic mRNA (smaller piece of mRNA)

Mechanisms of Virus-Induced Transformation

Integration Oncogene Uncontrolled Mitosis Apoptosis inhibited

Mechanism of Nuclear-Replicating Virus: Hepatitis B virus

penetrates via endocytosis, uncoating within endosome, capsid (protein + DNA) enters nucleus and possibly dissociates within nuclear pore

Mechanism of Nuclear-Replicating Virus: Poliovirus

May not need to penetrate cells at all to release RNA genome into cytoplasm -interaction with PVR (poliovirus receptor), endocytosis, then uncoating OR -interaction with PVR (poliovirus receptor), uncoating at cell membrane Nucleic acid = +RNA with VPg at 5' end

Define Uncoating

Ordered removal of capsid and/or release of nucleic acid. (Seperation of the viral nucleic acid from its protein coat)

Which DNA viruses do not make their mRNA like most other DNA viruses? How do they make mRNA?

Poxviruses (replicate in cell cytoplasm - where host pol II is not present) must encode their own viral RNA polymerase

How do DNA viruses make their mRNA?

Produce viral mRNA using the (-) strand of the DNA genome as template. NOTE: both strands can act as templates for transcription depending on the orientation/location of the gene. -Most viral DNA use host RNA polymerase II in the nucleus of the cell (where pol II is located)

Uncoating within endosome + example

penetration via endocytosis --> endosomal acifications --> virus is uncoated and ribonucleoprotein exits endosome ex. influenza virus

Mechanism of Nuclear-Replicating Virus: HIV

Uncoating in cytoplasm, then nucleic acid enters nucleus

Integration and Cancer

all or part of the viral genome usually persists in transformed cell genome

Mechanism of Nuclear-Replicating Virus: Porvovirus

penetrates via endocytosis (?), recycling of endosome, endosomal acidification (?), entire virus passes through a nuclear pore (it is small enough) - intact entry, then uncoating in nucleus -end up with uncoated virions(?)

Uncontrolled Mitosis and Cancer

mutated cell proto-oncogene (or expressed at abnormally high levels) converts a normal cell to a cancer cell

Transformation and Cancer

results from corruption of normal regulation of cell growth and differentiation -can be caused by any mutagen