1. What is a virus? Size – small (nm) Electron microscope
Do not absorb visible light (but UV)
Chemical composition
DNA or RNA
Coat protein (capsid)
Lipoprotein (lipid envelope)

2. Virus genome Small dsDNA, ssDNA, dsRNA or ssRNA
Linear, circular, segmented (more than one molecule, each holding a different gene or genes)
Code for between 1 and 300 proteins

3. Coat protein (capsid) 50 -90% of virus particle
Identical protein subunits called capsomeres
Functions
Protects virus genome ( from enzymatic attack and mechanical breakage)
Attachment, vector transmission and movement from cell to cell

4. Envelope Lipid bilayer external to the capsid
Contains virus - coded proteins – glycoproteins
Glycoproteins involved in host-cell attachment and penetration into host
Envelope sensitive to lipid solvents (ether, chloroform) which inactivate infectivity

5. Morphology 3) Enveloped – icosahedral or helical
Pleomorphic (varying shapes because lipid envelope not rigid structure)
4) complex types – separate shapes and symmetry, e.g. bacteriophages

6. Viral shapes

7. Enveloped viruses

8. Complex viruses

9. Bacterial viruses - bacteriophages

10. Virus replication 1. attachment/ adsorption to susceptible cell
2. Entry
3. Uncoating – release of nucleic acid
4. Replication and viral protein production
Early proteins:control next phase of replicative cycle (genome replication and late protein production)
Late proteins: usually structural proteins
5 Assembly and release

12. Detection of plant viruses
Why we need assays
Qualitative & quantitative
Qualitative
Detect virus in infected tissue
Identify it
Disease diagnosis
Symptoms are normally not reliable for diagnosis

13. Detection of plant viruses
Biological assay – tell us about viral infectivity or identity of virus by use of indicator hosts
Indicator hosts
Should have consistent, characteristic and clear symptoms of the virus
Useful for mechanically or vector transmissible viruses
Absence of symptoms does not always indicate non-infection. So we back inoculate to the plant where the virus was originally isolated

14. Types of assays Difficult in bioassays
Presence of inhibitors interfere with infection and thus reduce accuracy
Depend on the extend of virus aggregation – (buffer, pH – cause particles to disintegrate or aggregate)
Sap properties
Longevity in vitro
Dilution end point
Thermal inactivation point

15. Physical properties
Density – depends on the % of NA. the higher the NA, the greater the density. Measured in sucrose solution
Sedimentation rate – depends on the size, shape and density
Measure the distance of sedimentation and relate to centrifugation
UV absorption – measure at 260nm (NA), 280nm (proteins)

16. Electron microscopy
Microscopic – looking at changes that occur within the tissues of virus infected plants
Cytological and histological changes only visible in the light or electron microscope
Also have virus-induced structures in the infected cells – inclusion bodies – characteristic of infection by specific viruses
Pinwheel inclusions – characteristics of infection by potyviruses

17. Microscopic Changes in the cell Mitochondria Chloroplasts
Cause breakdown of the nucleus as the virus multiplies
Accumulation of virus particle in the nucleus and cytoplasm appearing as scattered particles or crystalline arrays
Fibrillar (fibre-like) rings
Mitochondria
Aggregations of the mitochondria
Abnormal membrane systems developing within mitochondria
Chloroplasts
Changes that result in structural and biochemical degeneration
Changes in colour – chlorosis as chlorophyll is lost
Chloroplasts become fragmented or grouped into abnormal clumps within the cell wall
Presence of large vessicles

18. Macroscopic changes as a result of virus infections
Symptoms caused by viruses

19. Virus induced structures
Inclusion bodies – most common in the cytoplasm (may occur in nucleus)
Crystalline structures
Formed by both isometric and rod shaped viruses
Occur after accumulation of virus particles in large numbers within the cell
These inclusions may be fibrous or crystalline
Ability to form crystals depends on the properties of the virus itself not on the concentration of the virus in tissue
Eg. TYMV – cystallizes in vitro after purification but not in tissue even when present in high concentration

20. Virus induced structure
Pinwheel inclusion
Induced by potyviruses and are diagnostic of the group
Made of protein which is different from that of a virus
Production coded for by the virus
Cylindrical – appearing as scrolls, laminated plates or pinwheels when viewed in cross-section
Originate and develop in association with the plasma membrane of host at sites lying over the plasmodesmata

21. Virus induced structures
Tubular bodies
Proteinaceous inclusion body
Associated with infections by viruses of the nepo and comovirus group
Contain single rows of virus particles
Help in translocation of viruses between cells via plasmodesmata

22. Factors influencing symptom expression
Host – genetic composition – susceptible or has resistant genes
May modify the nature of symptoms produced
Age of host at the time of infection. Young plants more susceptible to virus infection(CELLS ARE QUIKLY REPLICATING).
Why? Virus depends on host for multiplication – transport of assimilates & metabolism slower in older leaves

23. Factors influencing symptom expression
Environmental factors
Temperature - high temp reduces virus symptoms
Eg CMV – slows virus replication
High temp – affect host ability to resist virus infection
Light
High light intensities produce “hard” plants – less susceptible to virus infection than plants grown under low intensities
High light intensities after inoculation reduce symptoms
Nutrition – nutrients that favour plant growth also favour host susceptibility eg nitrogen levels – succulent plant

24. Economic impact of viruses
Reduction in yield or quality of infected crop
Divide the crops into three classes
Perennials
Annuals
Vegetatively propagated plants
Outbreaks are often more serious eg trees why? Once infected will remain infected for life
Symptoms may vary from season to season
Severe infections - remove tree to prevent tree from spreading to other health trees
Losses – immediate, loss of income before the healthy replacement tree becomes productive
Costly in terms of the time and land invested in such crops eg. Tristeza virus on citrus and disease

25. Economic impact of viruses
Annual crops – e.g. vegs and cereals sown from seed
Virus infections may be serious resulting in complete crop loss within a particular season
Outbreaks vary from season to season
Vegetatively reproduced plants
Can be serious if propagules used are infected
Sometimes symptoms are relatively mild or the viruses may be latent in the infected cultivars
Performance of the crop is reduced every year by a relatively small amount

26. Factors affecting losses
Cultivar
Virus strain (some more virulent)
Vector (mode of transmission and persistence(feeding time required to transmit the virus))
Time of infection in terms of the plant growth stage
Nutritional state of crop
Weather
Presence of other parasites
Introduction of new varieties

27. Factors affecting losses
Paya ringspot in Taiwan
Viruses becoming important after spread into new areas – Citrus tristeza virus
Viruses becoming prevalent in periods of unusually favourable weather – Barley yellow dwarf virus
Cropping systems
Choice of crop /cultivar
Way the crop is grown (Agronomic practices) e.g overlapping of summer and winter crops
Genetically uniform crops and large scale cultivation – papaya ringspot in Taiwan
Short rotations and monocropping –grapevine fan-leaf virus

28. Transmission of viruses
Mechanical transmission – naturally rare and unimportant
Occurs with potato virus X, tobacco mosaic virus and cucumber mosaic virus
Widely used in bioassays
Virus enters through wounds
Use abrasive – carborundum or celite

29. Transmission of viruses
Seed transmission – more than 100 viruses transmitted in this manner
Virus comes from ovule of infected plants
Can also come from the pollen
Virus carried in integument of seed and infects seedling at germination
Pollen transmission – results in reduced fruit set
Can spread through fertilized flower and down into mother plant eg prunus necrotic ring spot virus

30. Transmission of viruses
Insects – most common & economically most important means
Most important vectors – aphids, leafhoppers, whiteflies and thrips
Insects sucking mouth parts – stylet borne viruses – nonpersistent transmission
Semi persistent transmission – virus acquired after feeding for a period ranging from minutes to several hours - Virus persists in vector for 1 – 4 days
Persistent viruses – accumulate in insect body
Circulative
Propagative viruses – transovarial (offspring aquires the virus from thre mother) and transtadial (virus retained after molting)

31. Transmission of viruses
20 plant viruses transmitted by one or more species of nematodes
Longidorus, Paralongidorus and Xiphinema – transmit several polyhedral-shaped virus (nepovirus) eg tobacco ring spot
Trichodorus and Patrichodorus transmit two rod shaped tobraviruses – tobacco rattle and pea early browing

32. Transmission of viruses
Fungus tramsmission
Plasmodiophoromycetes – Polymyxa and Spongospora
Chytridiomycete – Olpidium
Fungi transmit more than 30 plant viruses
Virus borne internally others carried externally on resting spores and zoospores. Virus released when the virus germinates.