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)

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

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

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

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

Viral shapes

Enveloped viruses

Complex viruses

Bacterial viruses - bacteriophages

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

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

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

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

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)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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)

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

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.