Microbiology 4- Viral properties Flashcards
Compare the size of viruses with bacteria
Viruses are smaller than bacteria and can be passed through a filter.
Which human virus was the first to be described
The first human virus to be described was Yellow Fever Virus. In 1901 Colonel Walter Reed of the US Army was intensely researching this disease because it caused havoc during the building of the Panama canal. There was a clear link with mosquitoes. Reed injected filtered serum from a patient into nonimmune individuals and reproduced the disease, thus fulfilling Koch’s postulates
Describe Koch’s postulates
The microorganism must be found in large numbers in all diseased animals, but not in healthy ones.
The organism must be isolated from a diseased animal and grown outside the body in a pure culture.
When the isolated microorganism is injected into other healthy animals, it must produce the same disease.
The suspected microorganism must be recovered from the experimental hosts, isolated, compared to the first microorganism, and found to be identical.
Define a virus
Viruses are infectious OBLIGATE intracellular PARASITES.
List some of the properties of viruses
They are energy-less, they float around until they come into contact with an appropriate cell
A virus has a genome that comprises DNA or RNA- never both.
Structural simplicity: Virus particles are structurally simple. They have highly repetitive units that are so regular they can be crystallized. TMV was crystaliized in 1932. This achievement fed the debate as to whether viruses were alive or not. Their capacity to form crystals made them seem more like an inorganic substance.
They are basic life forms composed of a protein coat, called a capsid, that surrounds genetic material. Viruses do not have organelles or ribosomes. Certain viruses are further enclosed by an external lipid bilayer membrane that surrounds the capsid and may contain glycoproteins. Some viruses also carry structural proteins and enzymes inside their capsid.
Within an appropriate cell, the viral genome is replicated and directs the synthesis, by cellular systems, of more viral components and genomes.
The components effect the transport of replicated viral genomes through the environment to new host cells.
How do we detect viruses now
Unethical to detect viruses by seeing whether they reproduce disease in healthy individuals. We use molecular methods, such as electron microscopy, to detect viruses and compare with health individuals/
Explain the symmetry of viruses
Viruses are symmetrical, they can multiple copies of the same protein arranged similarly.
What is meant by tegument
All the viral proteins carried in a virus
What are the 4 levels of viral morphology
Nucleic acid: DNA or RNA Ds vs ss Single or segmented pieces of nucleic acid Positive or negative stranded RNA Complexity of genome
Capsid:
Icosahedral
Helical
Envelope:
Naked
Enveloped
Size:
Diameter of the helical capsid viruses
The number of capsomers in icosahedral capsids.
Describe icosahedral symmetry capsids
Take 1 or more polypeptide chains and organise them into a globular protein subunit. This will be the building block of our structure and is called a capsomere. Place the capsomers into an equilateral triangle and place 20 triangles together to form an icosahedron. Package the genome inside the icosahedral capsid.
Describe helical symmetry capsids
In helical symmetry the protein capsomers are bound to RNA (always RNA because only RNA viruses have helical symmetry) and coiled into a helical nucleoprotein capsid. Most of these assume a helical shape except for the rhabdoviruses (rabies) which assume a bullet-shaped capsid.
Describe how a virus obtains an envelope
Viruses acquire this membrane by budding through the host cell nuclear or cytoplasmic membrane and tearing off a piece of the membrane as they leave.
Explain the difference between naked and enveloped viruses
Viruses that do not have membranes are referred to as naked viruses. Those with membranes are referred to as enveloped.
List some naked viruses
Symmetrical protein capsid Adenovirus Picornavirus Calicivirus Non-enveloped
List some enveloped viruses
Enveloped
Lipid envelope derived from host membrane
Pleiomorphic: measles virus
Typical shape: Ebola virus
Combination of capsid
and envelope
Herpes virus
Describe how viruses have been named previously
Virus names are random. Viruses have been historically named after:
associated disease, e.g. poliovirus, rabies,
type of disease e.g. murine leukemia,
place in the body where isolated, e.g. rhinovirus
geographical location where first found e.g. Sendai, Coxsackie,
person who discovered it e.g. Epstein Barr,
way imagined to be spread e.g. dengue means evil spirit, influenza means influence of bad air
Describe the Baltimore classification system
Commonly used nowadays is the Baltimore Classification system which places viruses into groups depending on the pathway they use to make their genomes into mRNAs.
What is the central dogma of the genome
DNA — RNA — Protein
Describe the differences in RNA viruses
Positive RNA- just like mRNA. On entering a host, its RNA can immediately be translated by host ribosomes into protein.
When negative stranded RNA viruses enter a cell, they are not able to begin translation immediately. They must first be transcribed into a positive strand. To do this, negative stranded RNA viruses must carry, in their capsid, an enzyme called RNA-dependent RNA polymerase, which will carry out transcription of the negative strand into the positive. Humans or mammals do not have RNA-dependent RNA polymerase.
List the exceptions to these RNA viruses
Retroviruses, of which HIV is a member, are unique because of their ability to incorporate into the human genome, using reverse transcriptase to convert ssRNA into dsDNA.
Reoviridae, including rotavirus, is unique as they are the only viruses with a dsRNA genome.
dsRNA is converted into mRNA.
Describe the differences in DNA viruses
Most DNA viruses have both a negative strand and positive strand. The negative strand is read, while the positive strand is ignored. Parvo-viruses are the exception and have a single-stranded positive DNA.
Give an example of a ssDNA virus
Parvovirus B19; fifth disease/Slap face
Give examples of dsDNA viruses
HSV1; cold sores, smallpox,
Papillomavirus; warts
Give examples of dsDNA viruses that use RT
Hepatitis B; hepatocellular carcinoma
Give examples of + ssRNA viruses that use RT
HIV; AIDS
Give examples of +RNA viruses
SARS, norovirus; winter vomitting disease, poliovirus; poliomyelitis, dengue virus; DHF,
Give examples of dsRNA
Rotavirus; diarrhoea
Give examples of - ssRNA viruses
Ebola, rabies, Lassa fever, Influenza, Measles, Mumps
Describe the consequences of viral genome type
RNA viruses and retroviruses use their own polymerase to replicate.
These lack proof reading capacity leading to high mutation rate.
RNA viral genomes are limited in size due to inherent instability to RNA vs DNA. The largest RNA viruses are coronaviruses genome size around 30kb. RNA viruses often use complex coding strategies to make more proteins than expected from a small RNA genome.
DNA viruses have genomes up to 100s kb. There is plenty of room for accessory genes that can modify the host immune response. These genes are often lost in passage in culture.
Segmented genomes allow an additional easy form of recombination known as reassortment, but also impose more difficult packaging strategies. Influenza has 8 different RNA segments, rotavirus has 11!
Why do viruses have a high mutation rate
Viruses have no proof-reading mechanisms- high mutation rate.
Beneficial when strong selection pressure is applied.
Does the disease that the virus causes have any association with the way it replicates
Disease virus causes has little association with the way it replicates, different viruses cause similar symptoms despite having different nucleic acids.
Describe the role of accessory genes
Contribute to pathogenicity- encode immune antagonists- allow viruses to evade the immune system.
Describe the 4 basic steps in viral reproduction
Adsorption and penetration
Uncoating of the virus- to allow nucleic acids and proteins to interfere with host cell
Synthesis and assembly of viral products (as well as inhibition of the host cell’s own DNA, RNA and protein synthesis).
Release of virions from host cell either by lysis or budding.
Describe how the virus enters the host cell
Attachment to the host cell by specific interaction between the virus attachment protein and a host cell receptor (a molecule on the surface of a host cell that has a completely different role but that the virus has evolved to use as its key for entry to the interior of the cell). Viral encoded protein is usually on the capsid or glycoprotein. Unlike the bacteriophage which injects its DNA, these viruses are completely internalised, capsid and nucleic acid. This internalisation occurs by endocytosis or by fusion of the virion envelope with the host cell membrane.
Describe the other steps in viral replication
Entry of the virus genome to the host cell and synthesis of viral mRNA (primary transcription).
Translation of viral mRNAs into viral proteins by host cell ribosomes in the cytoplasm.
Replication of the viral genome, usually by making a small number of complementary copies that are then themselves copied at high numbers into new genomes (asymmetric replication).
Assembly of the virus proteins into new virions, association and encapsidation of the new genomes.
Exit from the infected cells and dissemination to new hosts.
Describe the difference between late and early proteins
Early proteins are regulatory- required for DNA replication and for further transcription of late mRNA
Late proteins are structural- transcribed after viral DNA replication has begun and is transcribed from progeny DNA. The capsid structural proteins are synthesised from the late mRNA genome.
How do naked virions exit the cell
Cell lysis or exocytosis
How do enveloped virions exit the cell
Acquires its new clothing by budding through the Golgi apparatus, nuclear membrane, or cytoplasmic membrane. tearing off a piece of host bilayer as it exits.
What do +ssRNA need to be converted into before replication
-ssRNA to use as template strand, RNA dependent RNA polymerase is translated to do this.
What do -ssRNA need to be converted into before replication
+ssRNA using a pre-made viral RNA dependent RNA polymerase that is carried by the virion.
How are viruses visualised
Viruses are very small (10-500 nm diameter) and are visualized with the electron microscope.
Describe another method of detecting viruses
Cytopathic effect is usually a result of the virus lysing the cell.
This could be due to shut down of host protein synthesis or accumulation of viral proteins.
Lysed cells are stained black to show infected cells- plaques- hole in cell when cell dies- viruses form plaques in monolayers
Describe the plaque assay
Dilutions of virus can be assayed to find the end point at which they no longer produce such effects. This allows their quantification.
A specific example is the plaque assay in which foci of infection can be counted.
Describe syncytia
Viruses with surface proteins that can fuse at neutral pH often fuse cells together
How can we detect viruses that produce little effect on cells
Some viruses produce little visible change on the cells but can be detected using antibodies to their proteins that will be expressed during replication. Immune fluorescence or immunohistochemistry allow the antibody binding to be seen. Antibodies generated in the lab to unique virus proteins indicate which cells are infected
or where in the cell the virus proteins are located.
Describe some techniques for seeing viruses that do not use cell cultures
Techniques for ‘seeing’ viruses that do not use cell cultures include detection of the particles or the viral proteins, or the virally encoded nucleic acid.
Viruses that attach to red blood cells can be visualized using the haemagglutination assay.
Cells infected by viruses can be lysed and antibodies to viral antigens used in Western Blot or enzyme-linked immunosorbent assay (ELISA).
Nucleic acid detection is usually by the polymerase chain reaction (PCR)- process genome in different ways depending on how it replicates
Viruses can be manipulated in the laboratory in order to study them.
Detecting virus particles EM- expensive, not specific, HA
Detecting virus cytopathic effect in cultured cells (Virus isolation)
Detecting antibodies to virus (serology)- difficult in acute infections- response is too quick.
Describe how we can propagate viruses
We can passage viruses in the laboratory by providing permissive cells, often continuous lines of transformed cell cultures.
Viruses may accumulate mutations that adapt them to the ‘new’ host.
This can lead to attenuation and was the basis for generation of vaccines in the past.
For some viruses we have no permissive cell lines: norovirus ‘Winter Vomitting Disease’. And Hepatitis C virus remain difficult to study in the laboratory.
What is meant by continuous cell lines
Continuous cell lines are monocultures propagated indefinitely due to their transformation. They may grow as monolayers on a plastic support or in suspension.
What is meant by a primary cell culture
Primary cell cultures may include several different cell types and may retain aspects of the original tissue
Describe how we can manipulate viral genomes
Virus genomes are so small they can be synthesized.
When introduced into permissive cells they direct synthesis of all their component are new viruses are made de novo.
This allows reverse genetics, the creation of viruses at will with engineered mutations in their genomes.
New generation of vaccines- synthesis viral genome- remove genes that contribute to pathogenicity- but keep genes that allow their recognition and ability to replicate-basis behind live attenuated vaccines
Describe classical genetics of manipulating viral genomes
Classical genetic techniques involve growing the virus under different conditions, for example temperature or in the presence of a drug, that may induce changes in the genome and studying their effects.
