2. viral replication

virus replication cycle

1. Attachment
2. Penetration
3. Uncoating
4. Transcription “mRNA production”
5. Translation
6. Genome Replication
7. Assembly
8. Release

1. attachment

binding of the virion to host cells 

• Glycoprotein spikes attach to receptor on host cell

• Must recognize and attach to trigger entry/penetration into the cell

Viral Attachment protein

Protein or glycoprotein that attaches to cellular receptor (ON VIRUS)

target of neutralizing antibodies → can block virus from attaching

Receptor 

Cellular target that virion binds

Usually specific protein or carbohydrate

Initiates entry by membrane fusion or receptor-mediated endocytosis

2. penetration

virus gains access to interior of the cell 

• Membrane fusion (only enveloped viruses)

• Receptor-mediated endocytosis (both types of viruses)

Membrane Fusion

at plasma membrane

ONLY in enveloped viruses

Can also fuse membranes in an endosome

Receptor-mediated endocytosis

virus is engulfed by a vesicle after binding to receptors on cell → brought into cell 

vesicle can break down by membrane fusion at the endosomal membrane

OR

by simply breaking down inside of  the cell

3. uncoating 

Release of the genome from the capsid

4. Transcription

synthesis of mRNA

viral genes (DNA or RNA) → mRNA

5. translation

mRNA → protein

6. replication

production of progeny copies of the virion nucleic acid (DNA/RNA)

7. assembly

production of new virion fron the newly synthesized components

8. release 

process when new virions leave the cell 

6 Basic Steps of Viral Replication

1. Attachment

2. Penetration (entry)

3. Uncoating

4. Synthesis.

a. Production of mRNA

b. Translation of mRNA into viral proteins (translation done by the cellular
ribosomes ONLY)

 c. Replication of the viral genome

5. Assembly

6.  Release

what type of cells do viruses replicate in?

it depends on the virus, they replicate in specific host cells

Tropism

Target cells that a virus is able to infect

cell has receptors for attachment and allow replication

Tropism for specific species: humans vs. all mammals (Papillomaviruses are highly species-specific)

Tropism for specific tissues: epithelial cells vs. neurons vs. white blood cells (HSV replicates in neurons and epithelium)

Permissive

a cell that can support virus replication

must have:

Proper surface receptors for the virus (Attachment)

Biosynthetic machinery to support the complete replicative cycle of the virus (Transcriptional factors, Posttranslational processing enzymes, etc.)

Nonpermissive cells

do not allow the replication of a particular strain of virus

may:

Lack a receptor, necessary enzyme pathway or transcriptional activator

Express an antiviral mechanism that inhibits replication

SARS-CoV-2 attachment protein + cellular receptor

Attachment protein: Spike

Cellular Receptor: Angiotensin Converting Enzyme II (ACE2)

One notable benchmark for measuring immunogenicity of a vaccine is the
production of ___________.

neutralizing antibodies (can protect from infection + disease if exposed) 

central dogma

DNA → RNA → Protein

some viruses do not adhere to this 

translation is done by ribosomes of the cell (NOT VIRAL, VIRUSES do not have ribosomes) 

What must happen in every productive viral infection?
(basic) 

1. Production of mRNA
2. Translation of viral proteins
3. Replication of viral genomes

What must happen in every productive viral infection?
(more specific) 

1. Viral mRNA must be made, regardless of the type of viral genomic nucleic acid

2. Virus must use cellular components and energy to synthesize proteins from mRNA
• Proteins for structure of new viruses, building blocks
• Polymerases, enzymes, evasion proteins, etc.

3. Must replicate its genomic nucleic acid to package in new virions
• All progeny virions must contain a copy of the nucleic acid genome to be infectious to a new cell

Baltimore Classification

Classification system on how viral genomes get to mRNA

Viral genomes must make mRNA that can be translated by host ribosomes
• mRNA is ribosome ready - plus (+) strand
• Complement is the negative (-) strand
• Many viruses, but only 7 known types of viral genomes

what _____ dependent ______ polymerase is always required for RNA replication? why? 

RNA, RNA bc host cells cannot convert RNA to RNa

+ sense (coding strand) RNA

genome functions as mRNA, proteins made immediately

positive → protein

- sense (non-coding strand) RNA

must make complementary + sense RNA first

polymerases that can be viral or cellular function

DNA dependent DNA/RNA polymerase

DNA dependent DNA Polymerase

Make DNA from DNA template

Often provided by host cell (Cellular DNA replication)

Some viruses encode their own (Parvo, Pox, Herpes)

DNA-dependent RNA Polymerase

Make RNA from DNA template (transcription)

Host cell: RNA Polymerase II (for mRNAs)

Poxvirus RNA Polymerase (extra-nuclear life cycle)

polymerases that are NEVER cellular function

RNA dependent DNA/RNA polymerase

RNA-dependent RNA Polymerase

Make RNA from RNA template

NOT a cellular function (ever), must be encoded by virus

RNA-dependent DNA Polymerase

Make DNA from RNA template

NOT a cellular function (ever) Must be encoded by virus

Reverse transcriptase (HIV, HBV)

polymerase overview pic

DNA virus replication + transcription polymerases used 

Replication of DNA genomes usually occurs in nucleus + uses DNA dep DNA polymerase (DNA genome → DNA genome)

transcription: uses DNA dependent RNA polymerase (DNA genome → protein) 

RNA virus replication

Must make and/or bring RNA-dependent RNA polymerase

Mutate faster than DNA viruses bc polymerase has no proofreading (1 million times more than DNA polymerase) 

which viruses evolve faster? DNA or RNA?

RNA bc they mutate faster

Plays a role in immune evasion and antiviral resistance

+sssRNA replication + translation

replication: +ssRNA → -ssRNA → +ssRNA uses RNA dep RNA polymerase

translation: +ssRNA = mRNA can become proteins 

-ssRNA replication + translation

1st step for both: RNA dep RNA poly to become +ssRNA

translation: once +ssRNA = mRNA → proteins

replication: RNA dep RNA poly → RNA (+ssRNA to -ssRNA)

Retrovirus

Retroviridae (HIV)

RNA genome – ssRNA (+) genome

Virion contains reverse-transcriptase (NEVER CELLULAR FUNCTION)

Generates a DNA copy from RNA template (RNA dep DNA polymerase)

DNA integrates into host-cell’s DNA

New RNA genomes are transcribed by host RNA polymerase II (DNA dep RNA polymerase) 

RNA → DNA → new RNA

Viral Replication Strategies: Retroviruses

1. +ssRNA → -ssDNA using RNA dependent DNA polymerase

transcription: DNA dep RNA polymerase (DNA → +ssRNA → translation)

replication: DNA → +ssRNA DNA dep RNA polymerase

Hepatitis B virus

Hepadnaviridae

Circular partially dsDNA genome

DNA is “repaired” by host-cell machinery

Long RNAs are transcribed (pre-genomic RNA,pgRNA)

New partially dsDNA genomes are reverse-transcribed from long RNAs

DNA → (using DNA dep RNA polymerase) RNA → (using RNA dep DNA polymerase) new DNA

SARS-CoV-2: Replication

Family: Coronaviridae

Genome: ssRNA (+), Enveloped

Polymerase: RNA dep RNA polymerase

high likelihood of mutations accumulating

Actual mutation rate is much lower than other RNA viruses like influenza due to exonuclease function of its polymerase

Variants

escape from antibody neutralization, escape from monoclonal antibody therapy, resistance to antivirals

Viral Replication: Release

1. Budding

2. Cell lysis

3. Exocytosis

1. Budding

capsid and proteins push out of cell membrane taking lipid bilayer with them

ONLY ENVELOPED

2. Cell lysis

cell bursts open releasing contents

non-enveloped virus, or enveloped (got membrane from organelle inside the cell)

3. Exocytosis
   

virus inside the cell has membrane that fuses with the lipid bilayer and gets released

(non-enveloped, enveloped - has two membranes before exocytosis)