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Virology test 1 lecture 5

front 1 replication of DNA viruses II	back 1 1/31
front 2 this lesson about rest of DS viruses: - normal DS DNA - DS DNA that go thru retroviral stage	back 2
front 3 double stranded DNA viruses	back 3 double stranded double stranded with RNA activity 3 families of DNA viruses are enveloped - herpes, Pox, hepadna viruses Pox viruses don’t need to replicate in nuclei - they are independent bc have machinery they need to replicate
front 4 class I: double stranded DNA	back 4 subdivided into 2 groups: replication is exclusively nuclear replication of these viruses is dependent on cellular factors replication occurs in cytoplasm these viruses evolved / acquired all factors for transc./replication of genomes and are largely independent of the cellular replication machinery

front 5 double stranded DNA virus replication	back 5 diverse/more complicated replication mechanisms than RNA viruses some require host pol, some encode their own replication factors dsDNA viruses make use of several mechanisms to replicate their genome bidirectional replication rolling circle mechanism strand displacement
front 6 DS DNA bidirectional replication (GO OVER THIS)	back 6 bidirectional replication 2 replication forks established at replication origin site + move directions opposite of each other
front 7 DS DNA rolling circle mechanism (GO OVER THIS)	back 7 produces linear strands while progressing in a loop around circular genome
front 8 DS DNA strand displacement (GO OVER THIS)	back 8 method where one strand is made from template strand, complimentary strand is made from prior synth. strand = dsDNA genome During strand displacement replication, only one strand is replicated at a time. This synthesis releases a single-stranded DNA, which in turn is copied into a double-stranded DNA.

front 9 DS DNA viruses transcription	back 9 3 step process to make mRNA transcription preinitiation complex binds to DNA upstream of site where transc. begins -> allows recruitment of host RNA polymerase (RNA pol can be from self or from host, depending on if the virus has its own things needed to replicate) use negative srand (non coding strand) as template for synth. mRNA strands RNA pol terminates transcription upon reaching stop signal
front 10 ds DNA cviruses	back 10 Ds DNA virus does 2 things with its genes - make mRNA -> translated in ribosomes of infected cell (NO viruses have their own ribosomes for translation) - replicates its ds genome – make copies
front 11 what ribosomes must ALWAYS be used for translation?	back 11 HOST CELL RIBOSOMES viruses NEVER have their own ribosomes
front 12 DS DNA viruses subdivided into 5 families	back 12 polyomaviridae papillomaviridae adenoviridae herpesviridae poxviridae infect mammals and us

front 13 polyomaviruses	back 13 small nonenveloped circular DS DNA widespread in nature latent in healthy hosts after primary infection illness occur in immunocompromised ppl Immunocompetent healthy host-> viruses may internalize + be latent - we are exposed to them - whether we get sick or not depends on our immune strength ex: human polyomaviruses BKV and JCV cause hemorrhagic cystitis and progressive multifocalleukoencephalopathy In ppl recipients of organs, they are subjected to immunosuppressed states, and these viruses can make them sick bc of lowered immune system ex: merkel cell polyomavirus may cause merkel cell carcinoma ex: SV40 can cause tumors, usually is latent though if healthy
front 14 papillomaviruses	back 14 small nonenveloped icosahedral circular DS DNA infect humans, cattle, dogs, rabbits, monkeys, and some more. ex: HPV (human papillomaviruses) infections are usually subclinical or can cause benign lesions but infections by high risk types can lead to cancer genome: early region code for transforming proteins that mediate oncogenic properties of the high risk HPVs (E6/E7 genes) late region encodes for major L1 capsid protein -> accounts for most of virion mass + mediates viral attachment (what vaccines are based on) noncoding long control region has regulatory elements for viral DNA repl./transc.
front 15 mechanism by which cellular transformation of E6/E7 genes of high risk HPV work?	back 15 E6 protein complexes with tumor suppressor protein P53 and targets it for destruction E7 complex w/ tumor suppressor protein (Rb) -> regulates expression of genes that activate cell cycle (normally p53 and Rb inhibit cellular proliferation) E6 protein made by HPV inhibits function of p53 E7 protein made by HPV inhibits function of Rb
front 16 in HPV infected cels, HPV oncoproteins lead to	back 16 continued cell proliferation without time for repair of DNA damage leads to genetic instability + accumulation of addl. cellular mutations + chromosomal changes -> thus infections with higher risk HPVs prepare ground for cellular genetic alterations that underlie cervical cancer HPV proteins lead to cont. cell proliferation

front 17 adenoviruses	back 17 medium sized nonenveloped (naked) icosahedral nucleocapsid isolated from human adenoids range of illnesses caused ex: mild resp. virus (common cold), conjunctivitis, deadly disease in ppl w/ weakened immune system genome linear, nonsegmented DS DNA (30-40 genes) heavily relies on host cell for survival/replication relies on cellular apparatus for transcription, but possesses various mechanisms that regulate viral gene expression ex: trans-acting transc. activators like E1A protein, post transc. regulation of expression, etc. infection of cells divided into 2 stages (early/late)
front 18 gene therapy - adenoviruses	back 18 adenoviruses - popular viral vector for gene therapy due to ability to affect replicating and non replicating cells code for proteins w/o integrating into host cell genome use as vehicle to administer targeted therapy in form of recombinant DNA/protein found to work in monogenic diseases + cancer Used as vector Adenoviruses big enough to accommodate transgenes Use to repair or internalize 1 particular gene that may be missing, mutated, etc. Used as vehicle to administer targeted therapy Oncolytic adenoviruses -> lyse the cells as cancer treatment
front 19 vaccines - adenoviruses	back 19 adenoviruses used to make viral vector COVID-19 vaccines Ad5 - vector to transport surface protein gene of SARS-CoV-2 goal is to genetically express the spike glycoprotein of covid Vaccines - some COVID 19 vaccines use adenoviruses as vectors to introduce spike Adenoviruses good for gene therapy + vaccines
front 20 herpesviruses	back 20 enveloped large DS linear DNA 3 groups alpha herpesviruses type 1 type 2 chickenpox virus short cycle, induce cytopathology, broad host range beta herpesviruses cytomegalovirus and human herpesvirus 6/7 long cycle, restricted host range y herpesviruses epstein barr virus and human herpesvirus 8 (kaposi sarcoma virus) very restricted host range all herpes virus can establish lifelong latent infection w/ specific tissues (characterized for each virus)

front 21 herpesvirus transc., gene replication, and capsid assembly occur in	back 21 host cell nucleus genes replicated in specific order immediate-early genes early genes late genes
front 22 immediate-early genes encode	back 22 regulatory proteins
front 23 early genes encode	back 23 enzymes for replicating viral DNA
front 24 late genes encode	back 24 structural proteins

front 25 how herpesvirus get out of cells and what happens in latent cells	back 25 virion progeny transported to cell membrane via golgi complex + host cells die as mature virions released in certain cell types, virus stays in lifelong latent state ex: latency of chicken pox (in nerves) -> CAN get shingles when older neurons, monocytes, lymphocytes latent viral genome may reactivate at any time
front 26 transmission of HSV 1 and 2	back 26 1 - oral 2 - genital
front 27 control of herpesvirus infection	back 27 prevention vaccine for chickenpox HSV 2 and cytomegalovirus only have passive immunity avoid contact when lesions are visible treatment acyclovir for hsv 1, 2, and chickenpox etc, see slide
front 28 herpesviruses (80 genes)	back 28 encode many enzymes of DNA metabolism + trans-acting factors that regulate temporal expression of virus gene, controlling phases of infection transcription of the large, complex genome is sequentially regulated in a cascade fashion Not as independent as poxvirus Encode enzymes involving DNA metabolism Expression is regulated Cytomegalovirus – related to microcephaly, Etc.

front 29 herpesvirus gene expression	back 29
front 30 poxvirus	back 30 isolated from birds, insects, reptiles, marsupials, mammals complex enveloped virions large - visible by light microscopy ds DNA genomes terminal hairpins linking the 2 DNA strands -> single polynucleotide chain ex: variola virus (VARV) - cause smallpox (extinguished w/ vaccines). molluscum contagiosum and monkeypox most frequent in world 10 infect ppl zoonoses minor abrasions of skin encode all enzymes needed for RNA and post. transc. modification of mRNAs, and DNA synth. replicate in cytoplasm using only host ribosomes many enzymes packaged (all it needs) in virus particle -> so replication occur in cytoplasm under viral control Poxviruses - best known – variola virus – cause smallpox - extinguished w/ vaccines Large – large enough to see on light microscope DS DNA genome w/ terminal hairpins 10 poxviruses infect humans Poxviruses – zoonotic (from animals) Poxvirus outbreaks recently due to cessation of vaccines - bc they are very similar to each other
front 31 unlike other DNA viruses that rely on nucleus, poxviruses replicate entirely	back 31 in the cytoplasm of infected cells
front 32 poxviruses evade ___ well	back 32 innate / adaptive immune responses using proteins encoded by their large genome

front 33 poxvirus gene expression	back 33 by virus enzymes associated w/ core of particle + divided into 2 phases early genes 50% of poxvirus genome expressed before genome replication late genes expressed after genome replication in the cytoplasm but expression is dependent on virus-encoded rather than cellular transcription proteins
front 34 poxvirus replication cycle	back 34
front 35 additional effects of DNA viruses: on the cell cycle	back 35 p53 inhibitors SV40 large T (polyoma) adenoma E1A HPV E6 RB inhibitors SV40 large T (polyoma) Adeno E1B HPV E7 Addl effection of DNA viruses - tumor suppressors – breaks in cell cycle - viral proteins interact w/ inhibitors
front 36 viral effects on host cells	back 36 viruses can have one of several diff effects on their cellular hosts abortive infections cytolytic infections persistent infections

front 37 abortive infections	back 37 virus cannot go in cell (depends on receptor) if infect cell unable to receive virus -> abortive infection, does nothing to the cell may result when virus mistakenly infects a cell that does not permit viral replication (tropism)
front 38 cytolytic infections	back 38 lead to cell lysis and release of large numbers of virus
front 39 persistent infections	back 39 may be productive, latent, or transforming exit thru budding can be latent can be transforming - oncogenic, transforms the cell
front 40 coordinated replication of viral components	back 40 expression of viral regulatory proteins (immediate early genes) expression of viral genes involved in replication (early lytic genes) replication of viral genome expression of late lytic genes (capsid, envelope) assembly and egress

front 41 DS DNA with RNA intermediate hepadnaviridae	back 41 hepadnaviruses - group of DNA viruses infect hepatocytes + can cause liver injury and hepatocellular carcinoma (HCC) in mammals/birds Hep B (HBV) - cause acute/chronic Hep B, cirrhosis, and HCC in humans small enveloped partially DS DNA (3-3.4 Kb) replicated by reverse transcription of RNA intermediates use overlapping reading frames (ORF) to encode envelope nucleocapsid proteins polymerase w/ domains that having priming, reversetranscriptase, and RNAse H
front 42 what family of viruses is DS DNA with RNA intermediate?	back 42 hepadna viridae
front 43 genome:	back 43 small genomes of partially DS, partially SS circular DNA genome = 2 strands 1 longer (-) sense (purple) 1 shorter (+) strand of variable length (orange) 2 ends of long meet but not bonded together, and the shorter strand overlaps over the divide
front 44 replication	back 44 viral DS DNA convert to covalently closed circular DNA by viral polymerase (in nucleus) replication involve RNA intermediate 4 main reading frames encoded = virus has 4 genes that encode 7 proteins core capsid protein C viral polymerase P surface antigens (preS1, preS2, S, X, HBeAg)