MI07 - Viral Replication and Synthesis

What must occur in every successful viral infection?

• Viral mRNA must be produced.

• Proteins must be synthesized from mRNA using host ribosomes.

• The viral genome must be replicated to package into new virions.

• Progeny virions must contain a full copy of the genome to be infectious.

What are the 8 steps in the viral replication cycle?

1. Attachment

2. Penetration

3. Uncoating

4. Transcription (mRNA production)

5. Translation

6. Genome replication

7. Assembly

8. Release

What is transcription?

Making RNA from a DNA template.

What is translation?

Ribosomes reading mRNA (+ sense) to make proteins.

What is genome replication?

Copying the viral genome (DNA or RNA) for packaging into progeny virions.

What are the 7 Baltimore groups of viral genomes? (don’t need to memorize these)

• Group I: dsDNA (e.g., Herpesvirus)

• Group II: ssDNA (e.g., Parvovirus B19)

• Group III: dsRNA (e.g., Rotavirus)

• Group IV: ssRNA (+) (e.g., Coronaviruses, SARS-CoV-2)

• Group V: ssRNA (–) (e.g., Influenza, Rabies)

• Group VI: ssRNA (+) via DNA (Retroviruses, HIV)

• Group VII: dsDNA via RNA (Hepadnaviruses, Hepatitis B)

Which genome can be immediately translated as mRNA?

+ sense ssRNA genomes.

What is the difference between + sense and – sense RNA?

• + sense RNA = coding strand, ribosome-ready, can be translated directly.

• – sense RNA = non-coding strand, must first be copied into + sense RNA.

Why are RNA viruses more prone to mutations than DNA viruses?

Their RNA-dependent RNA polymerases lack proofreading activity.

What are the 4 types of polymerases used in viral replication?

• DNA-dependent DNA polymerase (DDDP) – DNA → DNA

• DNA-dependent RNA polymerase (DDRP) – DNA → RNA

• RNA-dependent RNA polymerase (RDRP) – RNA → RNA

• RNA-dependent DNA polymerase (RT) – RNA → DNA

Which polymerases can be cellular?

DDDP and DDRP.

Which polymerases are never cellular?

RDRP and reverse transcriptase (RT).

Which viruses must encode their own polymerase?

All RNA viruses (because cells cannot replicate RNA).

Which viruses must bring a pre-made polymerase in the virion?

– sense RNA viruses and dsRNA viruses (they need RDRP immediately).

Where do most DNA viruses replicate?

In the nucleus (exception: Poxviruses replicate in the cytoplasm).

• This is because the machinery for host DNA replication is in the nucleus

Where do most RNA viruses replicate?

In the cytoplasm (exception: Influenza replicates partly in the nucleus).

What is the mutation rate of RNA viruses compared to DNA viruses

About one million times higher (≈1 error per genome per replication/per 10,000 bp)

What family does SARS-CoV-2 belong to?

Coronaviridae.

What is its genome type?

Enveloped, + sense ssRNA.

How does SARS-CoV-2 replicate its genome?

• Genome serves directly as mRNA for protein synthesis.

• Viral RDRP makes a – sense RNA intermediate, which is used to make more + sense genomes.

How is SARS-CoV-2 released?

Exocytosis.

What type of genome does HIV have?

Enveloped, + sense ssRNA.

What enzyme is contained in HIV virions?

Reverse transcriptase (RNA-dependent DNA polymerase).

What is the replication pathway of HIV?

RNA genome → DNA copy by reverse transcriptase → integration into host DNA → transcription of new RNA genomes and mRNAs by host RNA polymerase II.

Why can retroviruses not be eliminated once integrated?

Their DNA integrates permanently into the host chromosome

What family does Hepatitis B virus belong to?

Hepadnaviridae.

What is the genome of HBV?

Circular, partially double-stranded DNA.

How does HBV replicate?

• Host cell machinery “repairs” the partial dsDNA.

• Viral transcription makes long pre-genomic RNA (pgRNA).

• Reverse transcriptase uses pgRNA as a template to make new partially dsDNA genomes.

Which viruses use reverse transcriptase (RdDp)?

Retroviruses (HIV) and Hepadnaviruses (Hepatitis B).

What is the central dogma of molecular biology?

DNA → RNA → Protein.

Do all viruses follow the central dogma?

No. Some, such as retroviruses (RNA → DNA) and Hepatitis B (DNA → RNA → DNA), reverse or modify it.

What is a property of all ssRNA (–) viruses?

They are all enveloped.

What is a property of ssRNA (+), non-enveloped viruses (e.g., poliovirus)?

They are resistant to drying and acidic pH.

What types of infections do DNA viruses often establish?

Persistent infections, such as latent or chronic infections (because they integrate in the host genome)

How does SARS-CoV-2 replication differ from other RNA viruses?

It has an exonuclease proofreading function, giving it a lower mutation rate than influenza or many other RNA viruses.

What are the 3 mechanisms of viral release?

• Budding (enveloped viruses acquire lipid bilayer from host membrane).

• Cell lysis (usually naked viruses, sometimes enveloped).

• Exocytosis (viruses in vesicles fuse with plasma membrane to release).