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Virus Notes

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MICR 2420
Joseph Lam

VIRUSES  Viruses are more difficult to study than bacteria because they are smaller, you must use electron microscopy, obligate parasites require host for biochemical characterization and DNA replication, they need to find the right host and need to develop culture systems (ie. Cell lines), simple life forms have simpler cellular structures, need to culture that you have more to look at (to see cell envelope), requires very cold storage and liquid nitrogen. Advantages: leads to the molecular level and use of molecular tools, every time there is a study conducted there is a lot of genomic discoveries developed  Virions – virus particle, consists of an infective nucleic acid contained within a protective shell made of protein  Viroids – smaller than viruses, infectious agents, nucleic acid genome is the entire infectious particle, no protective capsid  Usually viruses have small genome containing DNA or RNA contained in a capsid composed of capsomeres, some viruses have evolved further and have specific genes that make proteins of an envelop  Enveloped viruses – consist of a protein capsid and tegument proteins enclosed within phospholipid membrane derived from the host cell, includes virus-specific proteins Icosahedral symmetry – present in viruses that package their genome in an icosahedral capsid with varying types of symmetry, polyhedral with 20 identical triangular faces and 12 corners ie. Papilomavirus is very uncomplicated because it has no envelope – just capsid  Baltimore classification: 7 categories, based on the composition of their DNA  Retrovirus – specific feature genome contains reverse transcriptase to transcribe RNA to DNA Bacteriophages:  Bacteriophages – viruses that infect bacteria, first viruses to be studied, T series infects E. coli, they need: host recognition and attachment to a cell that can support their reproductive strategy, genome entry from cell and gain access to machinery for gene expression, assembly of virions, and progeny virons must exit and find a new host cell to infect. genome of T4: dsDNA linear, encodes 250 proteins, circularly permuted T4 phage vron: o fairly complex protein production for a virus due to complex injection mechanism o dsDNA linear, circularly permutated with 3-6 bp terminal repeats o Tail fibers actually recognize receptor and allow tail to take contact with host (infects E.coli with LPS and porin OmpC o Circularly permutated – every phage head will hold same amount of DNA because if they are missing any they will not survive to next generation o All have same essential genest and set up so that replication always cuts at repeated terminal end causing terminal valancy  different order of gene sequence causes diversity within viruses resulting in lysogeny in bacteria  Plaque– viruses cannot be isolated as colonies (they disperse in suspension), a plaque (clear area) is formed when viruses form a single progenitor lyse their surrounding host cells in a viral plate culture  Plaque assay – for lytic bacteriophages, tests to see if the virus has lytic activity and to see how many viruses are in a sample. A diluted suspension of bacteriophages is mixed with bacterial cells in soft agar and the culture is then poured over a nutrient agar plate and the bacteria grow homogeneously as an opaque sheet (confluent growth) where no bacteriophages are present, where there are bacteriophages, it infects the cell, replicated and spreads progeny phages to adjacent cells killing them. The loss of cells results in a round clear area.  Plaques produced by lytic phages form clear plaques where lysogenic phages (temperate) make cloudy plaques containing lysogenized viable cells Temperate Phages  Temperate phages – can infect and lyse cells like a virulent phage but also has an alternative pathway to integrate its genome into that of the host cell o T4,T6,T2 are phages that have the ability to take on either lysogenic or lytic cycle  Lysogeny – integration of the phage genome into host genome as a prophage, a condition in which the phage genome is replicated along with that of the host cell as the host reproduces  Prophage – the integrated phage genome into the genome of the host – what you find in the host that belongs to the virus  Lysogens – bacterium host that contains the genetic material of a virus inside of it  Lytic cycle – when a phage particle injects its genome into a cell, it immediately reproduces as many progeny phage particles as possible, involves replicating the phage genome as well as expressing phage mRNA to make enzymes and capsid proteins, the host cell eventually lyses releasing the progeny phages  Lysis – a “burst”, after a phage inserts its DNA its genes are expressed by the host cell RNA polymerase and ribosomes, the phage genome is replicated and phage capsid proteins are produced, a gene from the phage genome expresses an enzyme that lyses the cell wall releasing the mature virions, number of particles released = burst size  PFU – plaque forming units, plaques can be counted and used to calculate the concentration of phage particles in a given suspension of liquid culture  Virus tire – lowest concentration of a virus that still infects cells  Cytopathic Effect (CPE) – cell lysis and clumping after virus infects tissues  First successful growth of a culture was in tissue, in tissue culture the time course of animal virus replication is usually much longer than that of bacteriophages, the burst size is much larger though Positive Single Stranded RNA Viruses of Animals  crossing eukaryotic membrane much easier for viruses than crossing bacterial membrane but interior structure usually more complex in order to use host gene expression system  Picornaviruses – pico=very small, 30nm in diameter, contain single stranded ssRNA and genome is also mRNA o Poliovirus – polio, crippling, icosahedral o Rhinovirus – common cold o Coronavirus – SARS : severe acute respiratory syndrome o Hepatitis A – hepatitis of liver o Foot and Mouth Disease virus – aphthovirus – affecting cattle  Coronavirus (+ssRNA – capped)  Virions enveloped, largest genome of all RNA viruses, club-shaped glycoprotein spikes thus a “crown”, important pathogens of mammals and birds, causes respiratory tract infections, replication occurs in the cytoplasm using the host cell machinery  SARS (severe acute respiratory syndrome) – o outbreak was 2002-3, 916 deaths worldwide, 37 countries infected, started in Hong Kong, may still be present in its natural host reservoirs and could return in the future, fatality is very low for young people but over 50% for seniors o acute disease that spreads very fast through humans (10% mortality rate) o flu-like symptoms and very high fever, antibiotics = ineffective (viral), patients must be quarantined Negative ssRNA Viruses of Animals  Rhabdoviruses and Orthomyxoviruses  Rhabdoviruses – (rhabado=rod) o Rabies (zoonotic, animal bites), vesicular stomatitis virus (VSV), potato yellow dwarf virus  Orthomyxoviruses – (myxo = mucus, interaction with mucous/mucous membranes) o enveloped (do not see capsid), respiratory, colonize in the mucous membrane and ingest as respiratory pathogens - droplet infections  Influenza – cilia movement impeded by cold weather causing seasonal virus  ortho vs. papmyxo (mumps, measles, parainfluenza) Influenza
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