Microbiology: Viruses Flashcards Preview

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Flashcards in Microbiology: Viruses Deck (38):

Viral characteristics

-Nucleoproteinic entities, oblligate intracellular parasites, replicate directly from their genetic material
-Viral genomes can be ss or ds RNA or DNA, can be linear or circular, can be one or sever pieces, can be plus or minus sense (plus= same polarity as mRNA)
-All viruses contain nucleic acids and proteins, some contain lipid envelope + carbs on outside (proteins+genome compose capsid+core)
-Proteins can be structural (capsid) or nonstructural (nzs)
-Viruses can be helical (form a tubular shell for genome) or cubic (of icosahedron; 20 equilateral triangular faces, and 12 vertices)


Cubic viruses

-Composed of an icosahedron
-Contains 20 equilateral triangle faces, with 12 vertices
-Capsomers may be pentamers or hexamers. Each pentamer is at the vertices, so there are always 12 pentamers



-Transmitted by blood sucking arthropod insects
-Many cause encephalitis


Life cycle of positive stranded RNA viruses

-Absorption: virus proteins binds to specific receptors on the cell surface. Different cell types will display different levels of the receptor and thus the virus will infect different tissue differently
-Penetration and uncoating: Facilitated by receptor-mediated endocytosis of the virus. Once in endosome the viral proteins and their receptors interact to form a pore to extrude the viral genome
-Eclipse: disappearance of viral infectivity early in infection (viral genome inside cell but no progeny made yet). Genetic material sensitive to nucleases at this stage. For poliovirus, the RNA is confined to the cytoplasm
-Maturation and release: Production and assembly of new viruses, which are released when the cell disintegrates (since cell is not left intact, there is no cellular membrane to use as envelope. Thus +stranded RNA viruses are generally naked)


Poliovirus replication

-Polio genome contains coding for 4 proteins: inhibitors of cellular RNA/protein synthesis, viral RNA polymerase, structural proteins (capsid), protease needed for assembly/maturation
-The viral polymerase and cellular inhibitors are made immediately after uncoating, using cellular ribosomes and viral genome, and before genome replication can commence
-Viral genome replication: begins with parental (+sense) RNA, which is replicated to a template (-sense) strand. When these two complete stands are together, it is called replicative form (RF, has no loose +sense tails)
-The -sense strands are then used to make many copies of new +sense viruses. Many copies are made at once from a single -sense strand, giving the appearance of dsRNA w/ single stranded tails (of +sense strands). This is intermediate form (IF)
-All of this replication is done w/ viral RNA-RNA polymerase. Only +sense strands are incorporated into new viruses (many more +strands made than -strands)


+RNA virus polyprotein

-The viral genome encodes a single protein (one initiation site) called a polyprotein which contains a protease
-Protease cleaves itself to become activated, then cleaves the polyprotein into the final protein products
-Since there is one initiation site and multiple genes transcribed from it, the RNA is polycistronic


Assembly process of poliovirus

-First there are VP proteins (VP1,3,0) that form the protomer (one of each VP proteins makes a protomer)
-5 protomers combine to make a pentamer
-12 pentamers combine to make a procapsid
-To make a mature capsid, there must be viral RNA progeny and the cleavage of VP0 to VP2 and VP4. This cleavage makes the capsid infectious
-Cellular participation is needed for assembly


Influenza virus structure

-Contains 2 envelope proteins: HA (hemagglutinin) and NA (neuraminidase)
-HA binds to the cellular receptors and Abs, facilitating absorption and penetration. NA cleaves the cellular receptor (N-acetylneuraminic acid) to allow virus progeny to escape the cell
-Contains matrix (M) protein for structural function (anchors the envelope proteins)
-Contains 8 independent helical nucleocapsid (NC). Each NC has its own (and different) RNA segments needed for replication. Each NC is surrounded by a nucleocapsid protein (NP)
-Each NC contains its own RNA polymerase to initiate primary transcription early on in infection
-All -RNA viruses have helical capsids and are enveloped


Replication of -RNA viruses

-After receptor mediated endocytosis by HA binding to N-AcNA, lysosome fuses w/ endosome to acidify it. This causes conformational change and eventually fusion of the viral envelope w/ the endosome membrane. This allows the viral genome to enter the cell
-Unlike +RNA viruses which can use their own genome for translation upon entering the cell, -RNA viruses must undergo primary transcription to create +RNA to use for translation
-Since there are 8 NCs, each one must be transcribed on its own into mRNA. Each one of the RNAs encodes a single protein, thus they are all monocistronic (unlike +RNA viruses which are all polycistronic)
-The mRNA of the virus is not a complete copy of the -RNA template since the mRNA ends 15-20 bases from the 5' end of the template
-The -RNA is transcribed to +RNA by the viral polymerase, which is transcribed again to the -RNA viral progenies (many of these are made)
-Progenies + proteins are packaged together to form mature viruses (they all mature independently), and are released constitutively by budding off from the cell surface (taking the envelope w/ them), without killing the cell


Genetic reassortment of the influenza genome

-Since influenza has an independently replicated, segmented genome the progenies will often become mixed (when a single cell is infected w/ two or more viruses) and result in genetic reassortment


Antigenic drift

-Antigenic drift is a slow process during which the influenza virus is changing the antigens on its surface (HA protein)
-This happens via point mutations in the HA gene (usually in 4 distinct areas in the "head" region of the molecule)
-Causes Abs that were once very good at neutralizing the virus to no longer be as effective
-The reason we get yearly flu shots


Antigenic shift and flu pandemics

-Appearance of new subtypes of influenza causes flu pandemics
-Only influenza A can cause antigenic shift due to the large number of animals that influenza A infects
-Genetic reassortment within a cell infected w/ human and animal subtypes leads to antigenic shift
-Changes the HA and NA molecules on envelope surface (novel proteins) which could only have come from genetic reassortment
-New subtypes appear every 10 years



-Frequent cause of acute upper respiratory tract (URT) infections (often in IC'd patients)
-Naked icosahedral virus w/ dsDNA and proteins


Life cycle I of adenovirus

-Absorption takes place in 2 stages: first there is binding of fiber protein on virus surface to a variety of cell receptors (including MHC and CAR), then penton base binds to integrins and allows internalization via RME (receptor mediated endocytosis)
-This is followed by rupture of endosome by acidification and breakdown of viral coat (uncoating)
-DNA is injected into nucleus through nuclear pores (DNA must reach nucleus for progeny to be made)


Life cycle II of adenovirus

-3 distinct phases: intermediate-early, early and late gene expression
-intermediate-early genes are regulatory growth factors required for subsequent phases and promotion of virus survival and proliferation
-early genes are the proteins required for DNA replication: DNA polymerase, precursor terminal protein (pTP) and DBP (single strand DNA binding protein)
-late genes encode structural proteins


Life cycle III of adenovirus

-DNA replication, occurs in nucleus
-Viral genome is coated w/ DBP, followed by binding of NF (I&III, host proteins) to origin of replication
-pTP and DNA polymerase are recruited, followed by a covalent link btwn deoxycytidine triphosphate (dCTP) and a serene reside in pTP. This acts as the primer for the synthesis of nascent DNA
-After DNA replication, most of the expressed genes are late genes


Life cycle IV of adenovirus

-Viral assembly begins in cytoplasm when monomers form into hexon and penton capsomers
-Empty immature capsids are assembled in the nucleus where the core is formed from genomic DNA and core proteins
-Virus particles accumulate in nucleus and ultimately cause cell death


Pathogenesis of adenovirus

-Spreads by aerosol, close contact, fecal-oral contact. Establishes pharyngeal infection
-Infects mucoepithelial cells of respiratory tract (most common), GI tract and cornea
-Requires humoral and cellular immunity to limit virus growth, mostly affects children and military



-Smallest eukaryotic virus, non-enveloped icosahedral w/ ssDNA
-Contains material for proteins required for DNA replication (non-structural, or NS) and capsid proteins (CAP, structural)


Life cycle of parvovirus

-Proteins on capsid bind to erythrocyte P antigen to initiate absorption and entry
-Replication occurs in nucleus, initiated by formation of hairpins (due to palindromic sequences) at ends of viral genome
-The intermediate dsDNA functions as template for gene expression
-Replication is highly dependent on cellular functions (uses NS1 to prevent genome degradation)
-Replication requires that the cell passes through S-phase (when the replication machinery is present) for replication to occur
-Released by nuclear and cytoplasmic rupture


Pathogenesis of parvovirus

-Spread by respiration and oral secretion
-It first undergoes limited replication in the cells of the URT
-Then it spreads to bone marrow by viremia, where it infects erythroid precursor cells and establishes lytic infection
-Causes a biphasic disease: in the first phase erythrocyte production is halted (related to viremia). Produces flu symptoms, then Abs control viremia and leads to resolution
-Second phase is immune-related: complexes of virons and Abs cause rash and arthralgia
-Called fifth disease, characterized by "slapped cheek syndrome" rash, with lacy macroppapular rash on trunk and limbs
-Usually present in children, can cause hemolytic anemia as complication
-Can pass through placenta and infect fetus (infects rapidly dividing cells most)


Herpes viruses

-Large enveloped dsDNA universal viruses
-3 subfamilies: alpha (HSV, VZV), beta (cytomegalovirus CMV, human herpes virus 6/7 HHV6/7), gamma (EBV)
-Contains tegument: a protein-filled region btwn the envelope and capsid
-Has an icosahedral capsid around DNA and protein core
-All herpes virus genomes have inverted repeats that can lead to viral DNA circularization
-Sizes of herpes viruses genomes can vary greatly


Life cycle of herpes virus

-Absorption is mediated by envelope glycoproteins binding to different receptors on different cells
-Binding of receptors results in direct fusion of the envelope w/ the cell membrane and release of capsid into cytoplasm where it migrates to and enters the nucleus via pore
-Upon entry, tegument proteins are released into cytoplasm and migrate to nucleus where they facilitate viral replication and gene expression
-Genome once in the nucleus is circularized, viral genes are transcribed by cellular RNA polymerase and are regulated by viral and host TFs
-Also displays 3 phases (intermediate early, early, late) of gene transcription
-DNA replication is carried out by viral DNA polymerase, w/ multiple potential origins of replication
-First replication is bi-directional, then switches to rolling circle. Replicaiton leads to high MW DNA concatemers
-Assembly: concatemers are cleaved and packaged in their capsids in the nucleus. Capsids move to cytoplasm where they are surrounded by tegument
-The complex buds off from the cell membrane carrying the glycoproteins on the envelope



-Herpes virus can enter latent stage allowing it to escape immune system
-Possible réservoirs of the virus are: DRG (HSV and VZV), B cells (EBV, HHV8), T cells and macrophages (CMV)
-During latent infection, viral DNA is maintained as an episome (not integrated) w/ limited expression of specific virus genes (latency associated transcripts, LAT) that are required to maintain latency
-Reactivation can be caused by: UV light, suppression of immune system (fever, trauma, pneumonia), stress


Pathogenesis of HSV (herpes simplex) 1 and 2

-Primary cause of oral herpes (cold sores) and genital herpes
-Infect epithelial cells of mucous membranes, or can enter through wounds
-Initial infection causes reddened area that blisters and crusts over (blister and fluid filled w/ virus)
-Virus travels up the nerve and establishes latency in DRG
-When reactivated it travels back down nerve cell to initial site of infection
-Complications include: encephalitis, neonatal herpes, keratitis (in eye)


Varicella Zoster virus (VZV)

-Causes chicken pox (varicella) in children and shingles (zoster) in adults when it is reactivated
-Goes latent in DRGs
-Infects epithelial cells of respiratory mucous membranes
-Spread through contact or respiratory route
-Virus spreads from lungs to lymphocytes, monocytes, to skin
-Rash occurs on face, scalp, trunk, and arms/legs
-Complications: CNS infection (blindess/paralysis), can be transmitted to fetus


Epstein Barr virus (EBV)

-Cause of infectious mononucleosis
-Infects epithelial cells of mucous membranes in throat and B cells
-Viral replication occurs in mucous membranes and is shed in saliva, taken up by B cells
-Infection of B cells results in swollen lymph nodes (due to heterophile, or non-specific, Ab formation). Virus remains latent in B cells
-EBV associated w/ types of cancer (lymphoma, nasopharyngeal, leukemia)


Cytomegalovirus (CMV)

-Usually asymptomatic or mild infections
-Infects epithelial cells, monocytes and lymphocytes
-Initial infection of the URT, then carried by lymphocytes and monocytes to spleen and lymph nodes, and finally to epithelial cells of salivary gland, kidneys, testes, cervix
-Virus shed in saliva, urine, vagina and semen
-Transmitted sexually and from mother to fetus, through breastfeeding, blood transfusions, transplants
-Causes B cell proliferation w/o heterophile Ab production
-Can be latent in lymphocytes, kidney, heart
-Complications: in neonates, IC'd, CNS infection. Affects many organs


Human herpes virus

-Many types
-HHV6 causes exanthum subitum in young children
-HHV8 is associated w/ Kaposi's sarcoma



-Integrate their RNA genomes (2 copies) into host DNA as provirus (persists there permanently and passed onto daughter cells)
-Enveloped, RNA->DNA via reverse transcriptase
-Provirus directs synthesis of new viral mRNA (which is also new virus genome)
-Then buds from cell surface
-Viral proteins: Gag (structural; matrix, capsid), Pol (enzymes; protease, RT), Env (fusion; SU for receptor, TM for anchor)
-Regulatory elements: LTRs (long terminal repeats) produce viral transcript (5' LTR acts as promoter, 3' acts as polyA tail signal), and packaging signal


Classification of retroviruses

-Simple (alpha, beta, gamma, delta)
-Complex: Human T cell leukemia virus (HTLV1), lentivirus (HIV), spumaviruses
-All contain 8-10 KB genomes that code for viral proteins and act as regulatory regions
-Make at least 8 proteins but only have 1 promoter (1 primary transcript)
-Strategies: ribosomal frameshifting (bypass STOP), splicing (Env), precursor proteins cleaved by protease
-The types of enhancers present in 5'LTR determines which types of cells the virus can express in and infect (e.g. HIV LTR has binding sites for TFs active in T cells)


Life cycle of HIV- Entry

-Primary receptor is CD4, co-receptor is CCR5 or CXCR4
-Binding of SU to CD4 causes conformational change to expose co-receptor binding site in SU
-Binding to both CD4 and co-receptor causes exposure of fusion peptide, which promotes fusion of the cell and viral membranes
-Capsid is released into the cell


Life cycle of HIV- RT and integration

-Reverse transcriptase is primed by host tRNA binding to viral mRNA @ primer binding site (PBS). RT makes ssDNA copy
-Most of the viral genome is degraded by RT, second DNA strand is copied from a small piece of remaining RNA at "PPT" site
-Final result is dsDNA
-Integrase nz trims 2 bases off the ends of each DNA strand (causing sticky ends)
-Integrase then joins the viral DNA to the host DNA on one strand and host DNA repair nzs close the gaps on the other strand (provirus is completely integrated)
-Integration is random but favors active gene regions b/c HIV integrase recruits host factor LEDF to target active regions of chromatin


Life cycle of HIV- assembly, release, and maturation

-Gag, gag-pol proteins, and Env are targeted to membrane
-RNA is incorporated into irons b/c nucleocapsid (gag) recognizes the packing sequence in the RNA
-Virus buds off
-After release, viral protease is activated and cleaves polyproteins, viral core condenses and viron matures (becomes infectious)


Importance of HIV co-receptor

-Co-receptors are needed by the virus to infect cells, but aren't needed for normal functioning of the cells
-Those who are mutant or lack CCR5 are much more resistant to HIV
-Possible therapy target: making an HIV patient's T cells CCR5-


Current antiviral therapy options

-Fusion inhibitors (blocks conformational changes involved in fusion)
-CCR5 antagonists
-RT inhibitors (nucleotide analogs)
-Protease and integrase inhibitors


Oncogenesis by retroviruses

-3 mechanisms
-First is transforming retroviruses which carry an oncogene
-These viral oncogenes (v-onc) are cellular proto-oncogenes that were incorporated into the viral genome. Cause oncogenesis b/c they lost regions that modulated normal activity or were over-expressed
-Second is by insertional oncogenesis: retrovirus happens to integrate near a cellular proto-oncogene and the strong enhance of the LTR trans-activates expression of the cellular oncogene
-Third is by some viral proteins that can eventually transform cells into cancers
-These proteins usually cause dysregulation of growth in infected cells (such as tax protein in HTLV1)


Retroviral vectors as gene therapy

-Viral genomes coding for proteins are removed and placed w/ code for the missing protein (LTRs/packaging signals remain)
-Retroviral vectors lead to permanent persistence of transferred gene w/o viral infection
-Does lead to formation of infectious particles that infect other cells with the therapeutic gene
-Risk is insertional oncogenesis: can induce some cancers (i.e. leukemia; use weaker enhancers in LTRs)