Course Notes - Virology

• Viruses are Obligate Intracellular Parasites - this means that they must replicate inside of a living cell and act as a parasite by using the resources of the cell to replicate their own DNA/RNA and make more viral particles. This also means that they are very dependent on the cell and most viruses use many cellular enzymes (like RNA polymerase, DNA polymerase and mRNA splicing enzymes) and other cellular components (like ribosomes and membranes) for their own purposes.

• A minimal virus consists of a genome containing EITHER RNA or DNA and a protein shell, called a capsid, to protect the genome. Some viruses also have a membrane which surrounds the capsid, called an envelope. Embedded in the envelope are proteins with sugars attached, called glycoproteins (glyco = "sweet"). The entire viral package including genome, capsid, and envelope is called a virion. This is the form the virus takes when it is outside of a living host cell and traveling in the environment between cells.
  
  Each of the virion components has a role to play. The genome contains the genetic code to make a new virus. The capsid protects the fragile genome from damage in the environment (like drying out or from sunlight). The envelope is an optional feature that helps some kinds of viruses enter its host cell more efficiently. The glycoproteins act like address tags and target the virus to a specific host or cell type that it prefers. If a particular kind of virus doesn't use an envelope, than the capsid proteins serve that function instead.
  
  Most viruses have a preferred host cell. For a hepatitis virus it is a liver cell, for a rhinovirus (rhino = "nose"), which is the major cause of the common head cold, then it is the upper respiratory tract (nose and chest), and for HIV it is the CD4+ T cell.

• All viruses have several steps they must accomplish in order to replicate their genomes and make new viral particles. These steps are:

1. Entry – some portion of the virus’s external structure (a membrane glycoprotein in the envelope or a part of the capsid) binds to some cellular protein receptor. This then initiates an entry event by which the virus either fuses with the outside of the cell membrane or is taken up by the cell. One inside the cell, the virus must uncoat and release its genome either into the cytoplasm or into the nucleus of the cell.

2. Protein Production – transcription and/or translation of the viral genome leads to the production of viral proteins. These proteins include any enzymes necessary to replicate the viral genome and the structural proteins required to make a new virion.

3. Genome Replication – the viral genome is copied, either by cellular enzymes or more commonly, by viral enzymes.

4. Packaging and Exit – once the new viral proteins and genomes are produced, they are assembled into new virions which then exit the cell by budding from the cellular membrane or bursting out of the cell.

• Even though these are the basic steps that all viruses MUST accomplish, each type of virus has its own unique and complicated way of carrying out these steps.
  
  
• HIV is particularly unique in that it is a RETROVIRUS. This means that it enters the cell with its genome as a piece of RNA which is then converted to DNA via a viral enzyme called REVERSE TRANSCRIPTASE.
  
  
• To enter a CD4+ T-cell, the gp120 protein on the outside of the viral envelope binds to the CD4 receptor on the outside of the cellular membrane. This causes a change in the shape of the two proteins and allows the gp120 to also bind to the CCR5 or CXCR4 co-receptor. This thne induces a region of the gp120 protein to be inserted into the cell’s membrane and allows the viral envelope to fuse with the cellular membrane which then dumps the internal contents of the virion into the cytoplasm of the cell.


• Once the viral RNA genome is inside the cell, the reverse transcriptase converts the RNA genome into a piece of double-stranded DNA. This piece of DNA is then inserted into the cell’s genome via a viral enzyme called INTEGRASE. The DNA copy of the viral genome inserted into the cell’s genome is called the PROVIRUS.


• The ends of the genome contain special region of DNA, called the LONG TERMINAL REPEAT (LTR). This region contains a promoter which directs the cellular RNA polymerase to transcribe the provirus into more pieces of RNA. The HIV tat protein helps encourage the cellular RNA polymerase to transcribe the HIV provirus. This is how HIV tricks the cell into making more copies of its genome. In addition, some of the RNA pieces made by the cell are actually viral mRNAs and can be translated to make the viral proteins.


• After the cell has transcribed the integrated provirus to make lots of RNA copies of the HIV genome and lots of viral proteins, HIV assembles them all into new virions. The viral proteins and genomes are initially assembled into an immature virion, which buds out of the cell, taking some of the cellular membrane containing gp120 along with it. This initially assembled virion is not mature, which means that it is not capable of entering a new cell. Inside the virion the PROTEASE enzyme cleaves some of the viral proteins into smaller pieces. This converts the immature virion into a mature virion, which can go off and infect new cells. Then the whole process starts all over again!!