Genetics of Viruses 🛁 (tbc)

Describe the structure of HIV in terms of the genome, surface proteins and enzymes within the capsid

Host range: Human immune cells such as CD4 helper T cells, macrophages, dendritic cells and brain cells.

Genome: Two copies of linear single-stranded (+) RNA.

Surface proteins:

1. gp120: attachment of virus to the host cell.

2. gp41: facilitate entry of virus into the host cell.

Enzymes:

1. Reverse transcriptase.

2. HIV integrase.

3. HIV protease.

Outline the reproductive cycle of HIV

Attachment and entry into host cell

1. gp120 glycoprotein on the viral envelope recognise and bind to CD4 receptor protein on the cell surface membrane of human immune cells.

2. Upon binding, the viral envelope fuses with the host cell's cell surface membrane, facilitated by gp41 glycoproteins.

3. The nucleocapsid is released directly into the host cell's cytoplasm.

4. In the cytoplasm, the nucleocapsid breaks down, releasing the viral enzymes and RNA genome.

Replication of viral genome

1. In the cytoplasm, the two copies of single-stranded (+) RNA act as templates for synthesis of two complementary linear single-stranded DNA.

2. The two complementary linear single-stranded DNA act as templates for synthesis of double-stranded DNA.

3. The newly synthesised double-stranded DNA enters the nucleus.

4. HIV integrase integrates the viral DNA into host cell's DNA to form a provirus.

5. The provirus remains transcriptionally inactive during the clinical latency stage for many years.

6. The viral DNA is transcribed to form single-stranded (+) RNA using host cell's RNA polymerase.

7. These single-stranded (+) RNA exit the nucleus and enter the cytoplasm to become the viral genome of new virus particles.

Synthesis of viral proteins

1. In the cytoplasm, single-stranded (+) RNA is translated to form an inactive polyprotein using host cell's ribosomes.

2. HIV protease catalyses the hydrolysis of the inactive polyprotein into individual functional proteins required for viral assembly and activity.

Self assembly of viral components to form new virus particles

1. Viral proteins surround the single- stranded (+) RNA.

Release of new virus particles

1. gp120 and gp41 glycoproteins are transported from the GA and incorporated into host cell's cell surface membrane.

2. New virus particles bud off from the host cell as host cell's cell surface membrane surrounds the viral RNA and proteins.

3. The viral envelope is derived from host cell's cell surface membrane with gp120 and gp41 glycoproteins incorporated.

4. New virus particles can now infect other human immune cells and the reproductive cycle continues.

Describe the structure of influenza in terms of the genome, surface proteins and enzymes within the capsid

Host range: Human respiratory epithelial cells

Genome: Eight segments of linear single-stranded (-) RNA.

Surface proteins:

1. Haemagglutinin: attachment of virus to the host cell.

2. Neuraminidase: cleaves sialic acid receptors to facilitate release of newly formed virus particles from the host cell.

Describe the structure of influenza in terms of the genome, surface proteins and enzymes within the capsid

Attachment and entry into host cell

1. Haemagglutinin glycoproteins on the viral envelope recognise and bind to specific sialic acid receptor on the cell surface membrane of respiratory epithelial cells.

2. Upon binding, the entire virus is taken into the host cell via endocytosis, forming an endocytic vesicle.

3. In the cytoplasm, acidification of the endocytic vesicle leads to uncoating of the viral (-) RNA.

4. The viral envelope and endocytic vesicle membrane fuses, releasing the viral (-) RNA which migrates to the nucleus.

Replication of viral genome

1. In the nucleus, single-stranded (-) RNA act as templates for synthesis of complementary single-stranded (+) RNA, catalysed by RNA-dependent RNA polymerase.

2. These complementary single-stranded (+) RNA act as templates for replication of single-stranded viral (-) RNA genome.

3. These single-stranded viral (-) RNA exit the nucleus and enter the cytoplasm.

Synthesis of viral proteins

1. The complementary single-stranded (+) RNA exit the nucleus and enter the cytoplasm.

2. These complementary single-stranded (+) RNA are translated to form viral proteins using host cell's ribosomes.

3. Viral proteins such as viral enzymes and capsids are synthesised by free ribosomes.

4. Viral proteins such as haemagglutinin and neuraminidase are synthesised by ribosomes bound to the rER and transported to the GA.

Self assembly of viral components to form new virus particles

1. Viral proteins surround the viral genome and enzymes.

Release of new virus particles

1. Haemagglutinin and neuraminidase are transported from the GA and incoporated into the host cell's cell surface membrane.

2. New virus particles bud off from the host cell's cell surface membrane to form new enveloped virus particles.

3. The viral enveloped is derived from the host cell's cell surface membrane and incorporated haemagglutinin and neuraminidase.

4. The release of new virus particles is facilitated by neuraminidase, which cleaves sialic acid receptors.

5. Newly formed virus particles can now infect other respiratory epithelial cells and the reproductive cycle continues.

Describe the structure of lambda phage in terms of the genome, capsid shape and other features

Host range: Bacterium (Escherichia coli).

Genome: Single copy of linear double-stranded DNA.

Capsid shape: Icosahedral.

Other features:

1. Non-enveloped.

2. Attached to the protein capsid is a non-contractile tail which has one tail fibre at the tip.

Outline the reproductive cycle of lambda phage

Attachment and entry into host cell

1. The tail fibre of the lambda phage recognise and bind to specific receptor protein sites on the bacterial cell wall.

2. Upon binding, an enzyme lysozyme is released from the tail fibre, degrading the bacterial cell wall.

3. This allows lambda phage to inject its DNA into the bacterial host cytoplasm.

4. Within the host cell, the linear phage DNA circularises.

5. After which, the lambda phage can either replicate via the lytic cycle or lysogenic cycle.

Lysogenic cycle

1. The circular phage DNA integrates into a specific site on the bacterial host chromosome. When integrated, the phage DNA is known as a prophage.

2. One prophage gene codes for a protein which prevents transcription of most of the other prophage genes. Hence, the prophage is mostly silent within the bacterium.

3. Every time the bacterial host cell divides by binary fission, it replicates the prophage along with its own chromosome, passing on copies of the prophage to its daughter cells.

4. A single infected bacterial cell can quickly give rise to a large population of bacteria carrying the virus in prophage form. This mechanism enables the virus to propagate without killing the bacterial host cells.

Lytic cycle

1. Occasionally, the prophage in the bacterial host chromosome is triggered by environment signals such as radiation or chemicals to switch from the lysogenic cycle to the lytic cycle.

2. When this happens, the prophage is excised from the bacterial host chromosome and this initiates the lytic cycle.

Replication of viral genome

1. Phage DNA enters the bacterial host cytoplasm.

2. Phage DNA is transcribed to form phage RNA and translated to form phage enzymes.

3. Bacterial host DNA is degraded by one of the phage enzymes.

4. Other phage enzymes use host cell’s metabolic machinery such as DNA polymerase and DNA nucleotides to replicate phage DNA.

Synthesis of viral proteins

1. Phage DNA directs the host cell’s metabolic machinery such as RNA polymerase to transcribe phage DNA to form phage mRNA and translated to form phage proteins.

Self assembly of viral components to form new virus particles

1. Phage proteins self assemble to form phage heads, non-contractile tails and tail fibres.

2. Phage DNA is packaged inside capsids to form nucleocapsids.

Exit of new virus particles from the host cell

1. A phage enzyme damages the bacterial cell wall and cell surface membrane.

2. The bacterial cell swells and lyses due to the entry of water, releasing 100-200 new bacteriophages.

3. Newly formed bacteriophages can now infect other bacterial cells and the reproductive cycle continues.

Outline the process of antigenic drift

1. Antigenic drift is a mechanism for genetic variation in viruses that involves the accumulation of mutations within the genes that code for viral glycoprotein spikes.

2. Viruses often have high rates of mutations.

3. Spontaneous mutations are due to the lack of proofreading ability of RNA-dependent RNA polymerase and reverse transcriptase.

4. These mutations may result in conformation changes in the structure of viral glycoprotein spikes which act as surface antigens of the virus.

5. Hence, the host immune system is less able or unable to recognise slightly different viral surface antigens.

6. Different glycoprotein spikes may also allow viruses to bind more effectively to host cells.

7. Antigenic drift can bring about seasonal epidemics.

Outline the process of antigenic shift

1. Antigenic shift is a mechanism for genetic variation in viruses that involves genetic recombination of nucleic acid from different viruses to form a new subtype.

2. This happens when two or more genetically different strains of viruses co-infect the same cell.

3. The new virus particles may consist of randomly assembled RNA segments, resulting in new combinations of RNA segments.

4. This results in genetically different virus subtypes with significantly different combinations of glycoprotein spikes.

5. Antigenic shift can bring about major pandemics because the population is not immune to the new form of virus.