1. Summary of virus introduction Two critical experiments that resulted in the discovery of virus –Infectious –Filterable agent Universal existence: Human, animals, plants and bacteria all can be infected by virus Submicroscopic, non-free living organism(dependent on live cells) DNA or RNA as genome, proteins as viral replication enzymes and protective coat, in some cases with lipids and carbohydrates (for enveloped virus), no organelles, no machinery for protein synthesis and metabolic activity Don’t grow or divide, assembly of individual components (DNA or RNA and proteins)

2. Taxonomy of virus

3. Classification of viruses Classical virus classification scheme --- type of nucleic acid (DNA or RNA) --- capsid symmetry (icosahedral or helical) --- presence or absence of envelop --- size of virus particles Recent classification scheme (ICVT) --- Genomes Baltimore classification --- based on the pathways viruses used to make mRNA and replicate

4. Origin of family names

5. Virus genome DNA viruses: --- Almost all DNA viruses infecting animals have dsDNA --- Exceptions are Parvoviridae (parvoviruses and adeno-associated virus) and Circoviridae (TT virus related hepatitis) which have ssDNA RNA viruses: --- Almost all RNA viruses have ss RNA --- Exceptions are Reoviridae (Reovirus, ds RNA) --- Positive strand (+): same polarity as mRNA (Picornaviridae) --- Negative strand (-): opposite polarity as mRNA all have helical capsid some have segmented genome (Orthomyxoviridae) --- Ambisense RNA genome: both (+) and (-) single strand RNA (Bunyaviridae and Arenaviridae)

6. Virus structure and assembly Virion: infectious, complete virus particle: RNA or DNA, proteins, enveloped viruses have carbohydrates and lipids Capsid: composed of repeating protein subunits (protomers) --- protect viral genome from extracellular nucleases --- impart structural symmetry to virion (icosahedral or helical) --- essential for the infectivity of virion --- in naked (non-enveloped) virus, the capsid serves as the attachment protein that bind to host cell receptor --- antigenic and provoke host immune response --- most viruses have one capsid, an exception is Reoviridae that has two capsid layers Nucleocapsid: composed of capsid and nucleic acid

7. Poliovirus (naked, unenveloped)Rhabdoviridae (rabies virus. Enveloped)

8. Enveloped virus Envelopes are acquired as nucleocapsids bud through cellular membranes. These portion of cellular membranes are modified by virus and contains the viral glycoproteins, not cellular proteins, and these viral glycoproteins appear as spikes on the surface of the virus particle Envelopes lack rigidity and therefore usually appear heterogenous in shape and size on electron microscope. Generally, enveloped viruses are spherical, but exceptions are bullet-shaped rhabdovirus, brick-shaped pox virus. Functions of spikes (glycoproteins) -- binding sites for cell surface receptors -- major antigenic determinants -- mediates virus fusion with cellular membranes

9. Human Immunodeficiency Virus

10. Pox virus

11. Types of capsid Icosahedral (isometric) capsid --- a solid shape containing 12 vertices, 20 triagular faces and 30 edges arranged around the surface of a sphere (soccer ball) --- example: adenovirus Knob (protomer) fiber Capsomer (3 protomers)

12. Types of capsid (cont’) Adenovirus: The rules of rotational symmetry are referred to as 2-3-5 symmetry

13. Icosahedral shaped viruses

14. Types of capsid (cont’) Helical capsid --- capsid is made up of a spiral or helix of protein subunits (protomers) --- example: Tobacco mosaic virus (TMV, naked or non-enveloped) Protomer (16.3) 18 nm 2 nm

15. Why virus needs to be assembled? Protection barrier: nucleic acids (DNA or RNA) are very sensitive to the nucleases or mechanical shearing and chemical modifications such as by ultraviolet light (UV) from the sun light. Essential for viral infectivity: in order for viruses to reproduce themselves in the cells, they need proteins on the surface of virus to bind to the cell receptors to initiate infection, in some cases, deliver the genome into the cells

16. Assembly Locations

17. Reovirus Herpesvirus Assembly factory

18. Protein transportation pathways inside the cell

19. Nuclear localization signals (NLS)

20. And how to assemble? Several RNA viruses undergo self-assembly as a helical nucleocapsid --- TMV: Heinz fraenkel-Conrat and R.C. Williams in 1957 The symmetry structure is held together by protein-protein, protein- nucleic acid, and protein-lipid interactions (hydrophobic and electrostatic) Because of symmetry, the structure is in free-energy state and stable and therefore the favored structure of the components Virus start to assemble spontaneously when there are accumulated viral components

21. Assembly of poliovirus

22. Assembly of bacteriophage T4

23. Assemble of tailed phage

24. Mechanism of packaging genome  Direct contact of genome with nucleocapsid or capsid proteins: small viruses such as picornaviruses contain specific proteins that interact with RNA.  Specialized viral encoded nucleic acid binding proteins: these proteins, called ribonucleoproteins, nucleoproteins or core proteins, contain a nucleic acid binding motif in the sequence, or recognize a specific packaging signal sequence in RNA or DNA. These proteins are highly basic which react with negatively charged nucleic acids.  Packaging by cellular proteins: unique to papovaviruses, so the small viral genome doesn’t need to devote its limited genome to packaging.