L2 - VIRAL LIFE CYCLE

Question 1

Generalized steps in viral replication:

Answer 1

• infection and disassembly of the infectious virus particle (disassembly = virus releases its genome to the site of replication in the host cell)
• replication of the viral genome + synthesis of viral proteins by host cell machinery
• reassembly into progeny virus particles

Question 2

Timing & stages of viral lifecycle

Answer 2

• timing starts after the virus has crossed the membrane into host cell
  1. Eclipsed phase: no viral particle produced from the host cell at all because the virus is effectively taking over the host cell machinery and preparing the host cell to produce viral particles
  2. Maturation & release phase: host cell is exponentially producing viral particles
  3. Decay of viral progeny (since viral particles might not be able to survive well)
• There is a variation in life cycle and number of particles produced in a certain amount of time for different viruses
  o Ex. Bacteriophage – life cycle = much faster (slower in animal and plant viruses)

Question 3

1. Host cell attachment

Answer 3

• different viruses recognise & bind to different host cell receptor proteins (usually glycoproteins, glycolipids) on the host cell surface – initiate viral lifecycle inside host cell
• this determines which cells can be infected (determines the virus’ cell or tissue tropism)
• Most viruses will have 1 receptor, but some can have co-receptors (2 receptors)
  o Ex. HIV-1
• Mutations in virus receptors can allow switching between target cells
• Mutations in host cell receptor (ex. deletion in the CCR that results in lack of HIV binding site) can also cause protection against viral infection

Question 4

2. Host cell infection and disassembly

Answer 4

• a variety of mechanisms are used by different viruses to infect a host cell as a prelude to viral replication
• common themes are: (common goal: release of viral genome into the host cell)
  o fusion or
  o endocytosis uncoating (disassembly)
  o some also have endosome acidification

Envelope viruses: proteins on envelope binds to host cell receptor

Capsid viruses: proteins on capsid binds to host cell receptor

Question 5

HIV

Answer 5

binding of viral proteins to host cell receptor causes conformational change of the viral envelope, causing hydrophobic peptides to be plunged into the surface of the cell membrane. This allows the fusion of the viral membrane with the host membrane. The viral core then enters the host cell, releasing its RNA into the cytoplasm

Question 6

Influenza

Answer 6

binding to receptor on host cell surface does not trigger fusion (no conformational change upon binding), but triggers the cell to form an endosome that encapsulates the virus, drawing it inside the cell. Acidification of the endosome induces conformational change in the viral envelope, causing it to break down so uncoating can occur and the viral RNA is released into the host cell cytoplasm

Question 7

Polio

Answer 7

binding to receptor on host cell surface results in endosome formation. Either on the cell surface or in the endosome inside the host cell, the viral capsid then undergoes conformational change that produces a pore in the capsid and a pore in the endosome membrane which allows RNA extrusion into the cytoplasm.

Question 8

adenovirus

Answer 8

DNA viruses replicate in nucleus – binding to receptor on host cell surface results in endosome formation. Endosome membrane then breaks down to release viral core inside the host cell. Presence of nuclear localization signal on the capsid facilitates its docking to the nucleus where the viral DNA is released.

Question 9

3. Replication of the viral genome

Answer 9

• most DNA viruses replicate in the nucleus (except poxviruses)
• most RNA viruses replicate in the cytoplasm (except retroviruses, influenza)
• viral polypeptides often cleaved by host/ viral proteases – virus highly dependent on host cell for replication (mostly use host cell ribosome, RNA pol, but not DNA pol)

4 categories of viral replication:
* ssRNA +sense (ex. Polio)
* ssRNA -sense
* dsDNA
* retroviruses (+sense RNA virus)

Question 10

ssRNA +sense (ex. Polio)

Answer 10

o viral RNA can be directly translated by host ribosome to produce capsid & RNA dep RNA pol (diff from host cell RNA pol which the virus can’t use for replication because it is DNA dep RNA pol – reads DNA while viral genome is in RNA form)
o the produced RNA dep RNA pol synthesizes -sense RNA from the viral RNA
o RNA dep RNA pol then copies the -sense RNA again to synthesize a +sense RNA
o spontaneous assembly of +sense viral RNA & capsid

Question 11

ssRNA -sense

Answer 11

o -sense RNA can’t be translated directly by host ribosome, so -sense RNA viruses will have its own virion RNA dep RNA pol which is released into the host cell along with its genome to transcribe the -sense RNA into a +sense RNA
o +sense RNA translated to produce capsid and the virion RNA pol
o +sense RNA also continues to be transcribed by virion RNA pol into -sense RNA
o spontaneous assembly of -sense viral RNA, capsid, & virion RNA pol

Question 12

dsDNA

Answer 12

o gets into nucleus by nuclear localization signal
o undergoes transcription (inside nucleus) & translation (in cytoplasm) into capsid and DNA polymerase which both re-enter the nucleus
o the DNA pol can then perform replication of the viral DNA
 require its own virion DNA pol since many are needed for effective viral replication
 also require other host cell proteins for replication
o spontaneous assembly of the viral DNA and capsid inside the nucleus
o poxviruses – contain their own replication machinery and does not require host cell replication machinery at all, so replication can occur in the cytoplasm

Question 13

retroviruses (+sense RNA virus)

Answer 13

o contain 2 proteins present in virion particle & encoded in the genome
 reverse transcriptase: reverse transcribes viral RNA into DNA, so results in dsDNA from a ssRNA
 integrase: integrates viral DNA into the host cell genome (viral DNA is now called a now called a provirus - a virus genome that is integrated into the DNA of a host cell)
o the host is then responsible for every step of the viral lifecycle: replication of viral genome, and transcription, translation of the viral proteins
o spontaneous assembly of all the viral elements (genome + the 2 proteins)

Question 14

4. Virus assembly

Answer 14

• Non-envelope virus
• Envelope viruses

Question 15

Non-envelope virus

Answer 15

o capsid assembly generally occurs at the site of viral genome replication (often self-assembly with simultaneous binding of viral genome to the capsid protein due to the presence of packaging signal on viral mRNA that binds to certain motifs on capsid)
o once capsid protein & viral genome are formed and produced complete virion particle, they wait inside until host cell lyse due to a high amount of viral progeny, so they are then released

Question 16

Envelope viruses

Answer 16

o viruses with envelopes are assembled either on cell surface or in sub-cellular compartments. The viral envelope is derived from the host cell

o nucleocapsid (particle of capsid + viral genome) binds to internal side of the cell surface membrane at the region where envelope proteins are present (viral envelope proteins induced to produce by host cells upon infection and trafficked through ER onto the cell surface waiting for the nucleocapsid to be formed)
o matrix protein is responsible for binding of core to envelope proteins
o binding triggers fusion and budding through the cell membrane until the virus is released as a progeny variant

Question 17

Maturation step

Answer 17

• once the viral progeny are released, they will undergo a maturation stage (esp. RNA viruses) which will induce their infectivity (not infectious till mature)
• therefore, viruses will not mature until they have left the host cell – this prevents binding to the same host cell which is ineffective

Question 18

viruses that use surface budding + host cell lysis

Answer 18

• some viruses use both machinery (surface budding + host cell lysis)
  Ex. smallpox (pox viruses)
  o produced by virion machinery inside the host cell
  o has 2 diff morphological with hv diff # of membranes
   enveloped virion – released by budding from host cell. Has high infectivity so they are used to infect cells within the same host
   intracellular mature virion - released by lysis from host cell. Less infectivity but more stable outside the host cell so they are used to infect between different hosts