Viruses & Human Disease

Lecture 1,

Define: Viruses

Obligate intracellular parasite whose genomes replicate only in suitable host cells

What are the seven steps of virus replication?

1. Binding to cell receptor

2. Entry and uncoating

3. Early gene expression

4. Replication of viral genome

5. Late gene expression

6. Assembly of virions

7. Exit

Why do some viruses replicate in the cytoplasm vs the nucleus

DNA viruses typically replicate in the nucleus unless they make their DNA polymerase own.

RNA viruses typically replicate in the cytosol and encode for their own RNA polymerase.

What do viruses depend on the host cell for?

Ribosomes for protein synthesis, (some) DNA replication, and energy metabolism

Why do RNA viruses mutate more?

RNA viruses make more mistakes because they do not have a built-in mechanism for proofreading like DNA polymerase. Resulting in more mutation and the evolution of RNA viruses.

Define: Zoonosis

Transmission of viruses from animals to humans

How can a virus infect both humans and animals?

Virus undergoes genetic reassortment to cross the species barrier and infect both humans and animals. Can occur when two strains infect the same host cell.

Define: Bacteriophages

Viruses that infect bacteria.

What is the impact of having ancient viral sequences in the human genome?

This helped shaped mammalian evolution, it helps fuses cells of the placenta together, creating a barrier between the placenta and the womb..

Accounts for ~8% of our genome.

What is the approx. amount of bacteriophage particles in the worlds water? What is their role?

There is >10³⁰ bacteriophage particles in the worlds water. They infect and kill microbes (bacteria) in the water to prevent them from overwhelming the ecosystem.

What are some examples of how viruses can be used as a tool of discovery?

• Discovery of DNA as genetic material - bacteriophages

• Reverse transcription - retroviruses

• Oncogenes - retroviruses that cause cancer

• Introns - adenovirus

• mRNA Special Structures (5’ cap and 3’ poly-A tail) - pox virus

• Transcription factor and enhancer motifs - SV40

• Nuclear Localization of Protein - SV40

What are some early examples of viruses in history?

• Polio documented in Ancient Egypt

• Rabies documented in Ancient Mesopotamia

• Small Pox documented ~3,000 years ago

• Inoculation of Small Pox in India and China in the 11th century

Who and when was the first vaccine produced?

In 1796 Edward Jenner produced the first vaccine against smallpox. This was accomplished by infecting individuals with cowpox that gave individuals immunity against smallpox.

Define: cross protection

A phenomenon in which a pre-existing viral infection or vaccination prevents a secondary infection with the same or closely related virus

Who and how was the first attenuated viral vaccine produced?

Produced by Louis Pasteur in 1885. Pasteur passaged rabies virus in rabbit using spinal cord extracts. After serial passages, the preparations induced only mild disease (attenuated) yet produced effective immunity against rabies.

What is the Chamberland Filter? What did it prove?

.It is a porcelain water filter invented in 1884, with pores ~0.1 - 1 microns. This helped prove that there are filterable and non-filterable agents that both cause disease. It was known that there were filterable agents, such as fungi and bacteria, that cause disease. However, after filtering, there was still an agent that caused disease, something smaller, that we now know to be viruses.

What is the capsid?

Protein shell that surrounds/protects the viral genome during transmission from cell to cell

What is the viral envelope?

Host cell and virus derived lipid bilayer

What is the nucleocapsid?

Viral genome associated with its nucleocapsid/capsid protein. Term to describe the core structure found within an envelope

What is a virion?

A virus particle, an infectious structure.

What is the role of structural proteins?

They are present in mature virion, form protective shell, deliver genome into new host cells.

They should be easily disassembled during entry (metastable state- stable enough to survive outside the cell but unstable enough to uncoat in host)

Are virions symmetrical or asymmetrical?

Symmetrical

How many different proteins are needed to build capsids? Why is it so?

Only one viral protein can be used to construct an entire capsid. There are typically very few or even one viral protein due to genetic economy (want a simple/small genome) and efficient assembly.

Why are there non-covalent interactions between the viral protein subunits of the capsid?

So that the subunits can disassemble easily.

What are the three types of capsid symmetry?

Helical, icosahedral, complex

Define: Helical symmetry

Repeated protein subunits can interact along a common axis to form a helical/tubular structure. RNA is bound by capsid in a repeating fashion. Allows flexibility in nucleocapsid.

Define: Icosahedral symmetry

Closed, highly symmetrical structure composed of 20 triangular faces. Formation of a simple closed shell with 60 identical protein, simple icosahedral → T=1 : 60 capsid protein subunit. 60 x (T-value) = # of subunits.

Define: Complex capsid

Viruses with asymmetrical structures that do not fit simple helical or icosahedral symmetry. Ex: Adenovirus, Reovirus, Herpes, Retrovirus, Poxvirus.

When does genome packaging occur for icosahedral and helical capsids

For many icosahedral viruses, capsid self-assembly can occur prior to packaging of genome​.

For helical capsids, packaging occurs more simultaneously with replication of the genome​.

Define: Proteases`

Involved in virion maturation (processing of capsid proteins)

What are other components found in a virion?

Viral polymerase, integrase (if inserting into host genome), matrix proteins, proteases, matrix proteins, nucleases. Some viruses package host-derived molecules too (histones or tRNA)

What is the role of matrix proteins?

They connect the nucleocapsid to viral envelope

What is the typical viral genome size?

~1-2 kb but can be up to 300 kb

What to viruses encode in their genome?

Capsid proteins, polymerases, and immune evasion proteins.

What is the difference between positive and negative sense RNA?

Positive-sense RNA can act directly as messenger RNA (mRNA) to make proteins, while negative-sense RNA is complementary and must first be copied into a positive-sense strand before translation. If negative sense RNA the virus must bring RDRP to make mRNA.

What does the enzyme DDDP, “read” and “produce”?

Reads: DNA

Produces: DNA

What does the enzyme DDRP, “read” and “produce”?

Reads: DNA

Produces: RNA

What does the enzyme RDRP, “read” and “produce”?

Reads: RNA

Produces: RNA

What does the enzyme RT, “read” and “produce”?

Read: RNA

Produce: DNA

What must viruses with dsRNA bring with them?

They must bring RDRP to make mRNA since (+) RNA strand is trapped inside dsRNA and host ribosomes cannot access it.

What is ambisense RNA genome?

Genome that contains coding regions in both positive and negative-sense orientations.

What is the Baltimore classification system?

Framework that groups viruses into seven distinct classes based on their type of genetic material and how they generate messenger RNA (mRNA).

What are the seven groups of the Baltimore system?

• Class I (dsDNA): Double-stranded DNA viruses that use standard host transcription. Need DDRP.

• Class II (ssDNA): Single-stranded DNA viruses that synthesize a double-stranded intermediate before making mRNA. Need DDDP.

• Class III (dsRNA): Double-stranded RNA viruses that use their negative strand as a template to produce mRNA. Need RDRP.

• Class IV ((+)ssRNA): Positive-sense single-stranded RNA viruses where the genome directly acts as mRNA. Need RDRP.

• Class V ((-)ssRNA): Negative-sense single-stranded RNA viruses that must copy their genome into a positive-sense mRNA strand using viral enzymes. Need RDRP.

• Class VI (ssRNA-RT): Single-stranded RNA viruses that use reverse transcriptase to convert their RNA genome into a DNA intermediate before integration. Need RT and DDRP.

• Class VII (dsDNA-RT): Double-stranded DNA viruses that replicate through an RNA intermediate using reverse transcriptase. Need RT, DDDP, and DDRP.