On parle de poursuivre les mesures sanitaire pour 2-3 ans même si un vaccin est développé
We better start learning ...some wording is good to know , no need to read all.
https://msu.edu/course/mmg/569/Introduction to Virology.htm
I: Definition and Characteristics of Viruses
A) Viruses have been defined as
sub-microscopic, obligate intracellular parasites. They can, however, be seen in the electron microscope. Because of their small size, they were originally distinguished as infectious agents that were "
filterable"; i.e., they pass through very small (0.2-0.4 micron) filters. This is a reasonably good definition, but there are some bacteria and mycoplasmas that it might also apply to since they are also very small and are obligate intracellular parasites. So, what else distinguished viruses from cells?
B) Viruses lack "metabolism", and they lack the necessary molecules to have such a metabolism, such as ribosomes, glycolytic enzymes, amino acids, ATP, etc.
C) Viruses have a limited amount of genetic material. In some cases, it is only enough to encode a small number (3-5) of proteins.
D) Viruses exhibit different patterns of growth, or proliferation, than cells. Cells grow by division, which gives rise to exponential growth (1>2>4>8, etc). This is true of bacterial, animal, and plant cells in culture. In contrast, viruses grow by infecting host cells, synthesizing new viral components inside these cells, and finally assembling new virus particles which are then released. In the case of lytic viruses (ones that lyse cells), this gives rise to a "
one step growth curve". In 1939, Ellis and Delbruck did an experiment showing this pattern of virus production for a bacteriophage. The pattern also holds true for many lytic animal viruses. In this experiment, viruses are added to cultured cells at t=0, and free infectious virus in the medium are measured at various times after infection. A typical one step growth experiment is shown below. It demonstrates several different stages in the infection cycle.
1)
Adsorption: During this period, virus attaches to and enters cells, and the titer of free virus in the medium may actually decline.
2)
Latent period : the time before new infectious virus appears in the medium.
3) After the latent period, free infectious virus appears very rapidly, but then plateaus out as all of the cells that were initially infected are killed. If more uninfected cells are present, (if the infection was done at a low
moi), a second round of replication can occur, giving rise to a second burst of virus.
4) If one assayed what was inside of the infected cells at various times, infectious virus would be detected inside of the cells before they were released. The time until these first
intracellular viruses appear is sometimes called the
eclipse period.
Some Common Terms in Virology:
PFU: Plaque Forming Unit, is the amount of virus required to form one plaque in a monolayer of susceptible cells. A
plaque is a "hole" in a monolayer of susceptible cells where the cells have been lysed by the virus. If a virus was 100% infectious, then the number of pfu in a sample would equal the number of virus particles. However, in reality, the pfu is usually considerably less than the number of virus particles judged by microscopy or other physical methods. You will see examples of plaques in the first laboratory. Plaque assays are often used to
titer viruses, i.e., to determine the number of
infectious units per ml.
MOI: Multiplicity of Infection, or the # of virus (usually in PFUs) per cell added to an infection.
II: Why Study Viruses?
A) Viruses are the cause of many diseases of animals, humans and plants.
B) Viruses are simple genetic systems that allow us to study basic biochemical mechanisms such as replication, transcription, mutation, etc. Some important scientific advances that were made using viruses were: the discovery of RNA splicing, the development of the first
in vitro DNA replication system, the first complete genome sequenced, etc.
C) Because they are obligate intracellular parasites, viruses use the host cell machinery to express their genes and replicate their genomes. They therefore tell us a great deal about the biochemistry and cell biology of mammalian cells. In many cases, viruses also disrupt important cellular processes, and therefore give insight into what happens when cell regulation is disrupted ( development of cancer, immune deficiencies, etc.).
D) Viruses are fascinating in their own right because they have evolved very unique, interesting and varied life cycles.
For additional Introductory Information on Viruses, see the
Introduction to Virology from Course 109.
III: Review of Animal Cell/Molecular Biology
Because viruses can only grow inside of cells and require host cell metabolism, it is important to understand how cells work in order to understand how viruses work. Following is a very brief review of some (but not all) aspects of cell and molecular biology that will be important to understand for this class.
A) Cell Structure: Animal cells are highly compartmentalized; they have a number of membrane-enclosed internal compartments that are physically separated from one another. Each of these compartments, or
organelles, carries out one or more special functions. Some of the important organelles and structures found in animal cells are described below.
i:
Nucleus: The nucleus contains the cell's genome, which is double stranded DNA organized into
chromosomes. The nucleus is therefore the site of cellular DNA replication and RNA transcription (except for that which occurs in mitochondria, which have their own genomes). All of the enzymes used for DNA replication, RNA transcription, and RNA processing are found in the nucleus. This is especially important for DNA viruses, which usually require access to these cellular enzymes to replicate/express their own viral genomes. The genomes of almost all DNA viruses therefore need to be transported to the nucleus in order to be replicated and transcribed. The nucleus is surrounded by a double membrane known as the
nuclear envelope. This envelope contains "
nuclear pores", which are the major site of transport of macromolecules between the nucleus and the cytoplasm (and vice-versa).
ii:
Endoplasmic Reticulum (ER): The ER is the site of synthesis of both secreted and membrane proteins, which are targeted there via "
signal peptides". The ER is also the site where the initial carbohydrate groups are added to glycoproteins. Viral
envelope proteins are synthesized in association with the ER.
iii:
Golgi Apparatus: After synthesis in association with the ER, secreted and membrane proteins are transported to the golgi for further glycosylation and maturation. Sorting of proteins also occurs in the golgi. After sorting, proteins are then transported to their final destination, such as secreted, plasma membrane, lysosome, etc.
iv:
Endosomes: Endosomes, or endocytic vesicles, are vesicles that "pinch off" of the plasma membrane and bring external molecules into the cell. They are an important path of entry of viruses into cells.
v:
Lysosomes: Lysosomes are the site of degradation of many macromolecules, including proteins, nucleic acids, carbohydrates, etc.
vi:
Cytoplasm (cytosol): The cytoplasm is the site of much of cellular metabolism, including synthesis of soluble proteins.
vii:
Plasma Membrane: The plasma membrane of animal cells (unlike bacterial or plant cells) is directly accessible to the external environment, and is the site of attachment and entry of viruses. It is composed of a lipid bilayer (glycolipids, phospholipids, etc) in which membrane proteins are embedded. The plasma membrane is impermeable to most macromolecules, including proteins. Viruses must therefore use specific mechanisms to cross this barrier.
B: Cellular Processes
i:
DNA Replication: DNA replication is the process by which a DNA molecule is copied into daughter molecules. For cellular genomes, this involves replicating double stranded DNA (linear in animal cells, circular in bacteria). Replication of cellular genomes is always
semi-conservative, which means that each daughter molecule contains one old and one new strand. Replication starts at specific sites on DNA that are known as
origins of replication, or origins. The enzymes that synthesize DNA are known as
DNA polymerases, and there are 3 of them in animal cell nuclei. They are known as pol
a, pol
b, and pol
d. Each plays a different role in replication and repair of DNA, which we don't have time to discuss. Pol
a and
d are the polymerases most involved in replication. All of the DNA polymerases share several properties which are important to understand.
- DNA polymerase always synthesizes in a
5'-3' direction (on the new strand)
- DNA polymerase has a "
proofreading" function that allows it to repair a misincorporated base, so that it can correct its mistakes. This makes it very accurate.
- DNA polymerase cannot initiate synthesis "de novo"; it can only extend an existing strand. This is because it needs a free 3'-OH group to extend. Therefore, some other enzyme is usually needed to initiate DNA replication. This is either a "primase" or, in many cases, an RNA polymerase.
DNA replication requires numerous proteins in addition to DNA polymerase and a priming enzyme. These include helicases, DNA binding proteins, ligases, etc, which we don't have time to discuss.
ii:
Transcription: Transcription is the process by which RNA is synthesized. In cells, the template for RNA synthesis is almost always DNA. The enzymes that carry out transcription are known as
RNA polymerases (DNA dependent RNA polymerases). In mammalian cells there are 3 different RNA polymerases that are used to transcribe different classes of RNA.
Pol I: ribosomal RNA
Pol II: mRNA
Pol III: 5s rRNA and tRNA and some viral RNAs
In addition to these polymerases, transcription requires a variety of other enzymes and transcription factors. Transcription begins near sequences known as
promoters, which are the sites on DNA where RNA polymerase binds. There are usually also sites for transcription factor binding nearby. Transcription always proceeds in a
5'- 3' direction on the newly synthesized strand.
iii:
RNA Processing: Most mRNA in mammalian cells is highly processed after it is synthesized. This processing involves 3 steps that are important to remember.
-
capping: Most mRNAs contain a 7-methyl-G at their 5' end. This is added post-transcriptionally in the nucleus.
-
polyadenylation: Most mRNAs contain a stretch of As (poly A) at their 3' end. The poly A is also added post-transcriptionally.
-
splicing: Most mRNAs are spliced in the nucleus. Splicing is the process by which introns are removed from a pre-mRNA.
iv: Translation: Translation is the process by which proteins are synthesized using an mRNA template. It occurs on free ribosomes in the cytoplasm, or on ribosomes bound to the ER membrane. Each codon (3 nt) in the mRNA directs the incorporation of 1 amino acid into the growing polypeptide chain.