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Virology - Coggle Diagram

- - - - Glycoproteins
    - - Capsid
      - Genome
    - - HIV
      - Influenza
  - - - Capsid
        
        Surface proteins
      - Genome
    - - Adenovirus
      - Poliovirus
- - - - large dsDNA virus
        
        Polymerases
        
        DNA pol. and RNA pol. II (self-sufficient)
        
        Example
        
        Poxvirus
        
        Replication
        
        Cytoplasm
        
        DNA pol. only
        
        Example
        
        Herpesvirus
        
        Replication
        
        Nucleus
      - small dsDNA virus
        
        Polymerases
        
        No polymerases encoded
        
        Example
        
        Papillomavirus
        
        Replication
        
        Nucleus
    - - small ssDNA virus
        
        Polymerases
        
        No polymerases encoded (such
        viruses exist only as no
        polymerase encoding(
        
        Replication
        
        Nucleus
        
        Example
        
        Parvovirus
    - - Polymerases
        
        Must carry RdRP to produce mRNA
        
        And then use that RdRP again on mRNA to produce dsRNA (genome)
      - dsRNA quicky
        detected by innate
        immunity, so it has to be
        kept secured in a capsid
        
        And then of course it needs to stay inside the cytoplasm
    - - dsRNA intemediate made
        only during replication
        
        Example
        
        Poliovirus (remember Roosvelt)
        
        Picornavirus family
        
        mRNA has VpG protein instead of 5' cap
        
        Structure of genome
        
        Structural proteins (P1)
        
        1 more item...
        
        Non-structural proteins (P2/P3)
        
        3 more items...
        
        5' UTR
        
        1 more item...
        
        SARS-CoV-2
        
        Zika virus
        
        Flavivirus family
        
        Attachment and Entry
        
        Enveloped
        
        2 more items...
        
        Replication
        
        (+) sense RNA is transferred
        to replication complexes
        
        2 more items...
        
        Translation
        
        Have 5'-cap
        
        1 more item...
        
        NS2B/NS3 is the main protease,
        however, furin present in Golgi
        cleaves between pr and M
        
        1 more item...
        
        Virion budding
        
        After translation and proteolytic cleavage capsid (C) protein encapsulates (+) sense RNA and it buds into ER lumen acquiring prM and E proteins that were inserted in ER membrane before
        
        1 more item...
        
        Immune system modulation
        
        NS4A, NS4B and NS1
        
        2 more items...
        
        NS3
        
        1 more item...
        
        NS5 (RdRP)
        
        1 more item...
    - - Retrovirus e.g. HIV
      - Only (+) sense
    - - Replication
        
        dsRNA intemediate made only during replication
      - Transcription
        
        (-) sense to (+) sense RNA (mRNA) by RdRP
    - - Rarest
- - - - What molecules do viruses bind to?
        
        Two most important molecules
        
        Cell surface carbohydrate
        
        Examples
        
        Sialic Acid
        
        Influenza A
        
        2 more items...
        
        Heparan Sulfate
        
        Herpes Simplex
        Virus (HSV)
        
        2 more items...
        
        Transmembrane proteins
        (Integral membrane proteins)
        
        Responsible for functional
        binding that triggers entry
        or fusion mostly
        
        Example
        
        Poliovirus CD155
        
        1 more item...
      - How do viruses bind
        to these molecules?
        
        Rollind adhesion
        
        Low affinity and high avidity
        
        Functional binding
        
        High affinity binding that initiates entry
      - Concepts
        
        Rolling and scanning of cell surface is
        caused by low affinity and high avidity
        
        Influenza A is an exception
        
        It uses sialic acid for both rolling and
        functional binding (different form of sialic acid)
    - - Entry mechanisms
        
        Passive diffusion
        
        Small, non-polar molecules
        
        Transporter or channel
        mediated transpot
        
        Way smaller than viruses molecules transported
        
        Endocytosis
        
        Different endocytosis
        
        Phagocytosis
        
        Used by immune cells
        
        Macropinocytosis
        
        Used for cells
        taking up liquids
        
        Viruses trick cells into activating this
        uptake mechanism to get into cells
        
        1 more item...
        
        Receptor mediated endocytosis
        
        Clathrin-mediated
        
        Virus binds to a functional
        receptor (transmembrane)
        
        AP-2 recruited
        
        1 more item...
        
        Caveolin-mediated
        
        Rarely used so won't study
        
        Membrane fusion
        
        Enveloped viruses exploit this
        
        HIV
        
        gp41 interacts with CD4, then with CCR5 or CXCR4, then gp120 inserts into membrane and folds back on itself which brings membranes together and they fuse releasing HIV nucleocapsid into the cytoplasm (no need for endosomal escape)
        
        HSV
        
        Membrane fusion or endocytosis
        
        Injection
        
        Poliovirus injects
      - Endosomal escape
        
        Virus specific
        
        Adenovirus
        
        Acidifying endosome cause partial disassembly of capsid which releases protein VI which inserts itself into endosomal membrane and lyses it
        
        Influenza A
        
        Acidifying pH causes HA protein to change shape and insert itself into endosomal membrane. Then it folds back onto itself and causes membrane fusion. Simultaneously, M2 pump in influenza A envelope pumps protons in which cause M1 matrix disassembly and release of vRNPs to the cytoplasm
        
        This is often employed by enveloped viruses
        like HSV to fuse membranes with endosome
        
        HSV though can also enter
        through membrane fusion
        
        1 more item...
        
        Poliovirus
        
        Inject nucleic acid directly, no need for endosomal escape
        
        HSV
        
        If taken up by endocytosis
        
        Membrane fusion to escape endosomes
        
        If taken up by membrane fusion
        
        No need to escape endosomes
    - - Virus is in the cell and it has escaped endosome, this stage
        now explores how genetic material in the virus becomes
        available for transcription/translation
        
        HIV
        
        After escaping endosome, HIV starts reverse transcription where dsDNA is produced inside the capsid where it forms PIC (pre-integration complex) which is then important through the NPC to the nucleus where it is integrated and then transcribed into mRNA
        
        Influenza A
        
        vRNPs released to the cytoplasm and then they travel to the nucleus and are imported through NPCs
        
        Adenovirus
        
        Partially disassembled capsid travel and docks at NPC where it disassembles and genetic material is injected in the nucleus
        
        Poliovirus
        
        The simplest one. It just injects its nucleic acid
        
        HSV
        
        Start synthesising nucleic acid in the capsid which travels close to the nucleus, pore opens in the capsid and nucleic acid is delivered to nucleus via NPC