Lecture 12: Viral Genetics and Evolution

*Hershey-Chase experiment

Confirmed that the viral nucleic acid genome (DNA) is the genetic code that infects bacteria

What enabled the Hershey-Chase experiment to draw its conclusion?

Radioactive labelling (of proteins and nucleic acid)

Life cycle of T4 bacteriophage

1. Adsorption and penetration of bacteria cell

2. Arrest of Host Gene Expression and production of phage-specific mRNA molecules (Synthesis of Early Proteins)

3. T4 DNA Replication

4. Continued replicatoin of T4 DNA; first appearance of coat proteins

5. Assembly of Coat Proteins around Phage DNA molecules. Synthesis of phage lysozyme begins

6. Lysis and Release

*T/F: Viral genomes must make mRNA that can be read by host ribozyme. Why is this important?

T

• Viruses do not encode their own ribozyme which are required for DNA replication

The Baltimore system

A classification system for viruses based on their type of genome and method of replication.

*What is the center of the Baltimore system’s classification technique?

mRNA positive-sense

*mRNA is always the (+/-) strand

+

*DNA of equivalent polarity is also the (+/-) strand

+

*T/F: RNA and DNA complements of (+) strands are negative (-) strands

T

*T/F: Not all (+) RNA is mRNA

True

*T/F: All (+) sense mRNA is used to translate protein

F

The seven classes of viral genomes

1. dsDNA

2. gapped dsDNA

3. ssDNA

4. dsRNA

5. ss (+) RNA

6. ss (-) RNA

7. ss (+) RNA with DNA intermediate

Viral DNA or RNA genomes are structurally diverse

• Linear

• Circular

• Segmented

• Gapped

• Single-stranded (+) strand

• Single-stranded (-) strand

• Single-stranded ambisense

• Double strand

T/F: Only viruses contain the pure RNA genome

T

Negative sense RNA is not infectious while positive sense RNA is. What is the reason?

Negative-sense RNA requires polarization (to positive-sense RNA) to be translated into protein

• Positive-sense RNA has the same polarity as mRNA which allow it to be directly translated by host ribosomes to make viral proteins.

*Viral genomes encode gene products and regulatory signals for:

• Replication of the viral genome

• Assembly and packaging of the genome

• Regulation and timing of the replication cycle

• Modulation of host defenses

• Spread to other cells and hosts

Viral genomes do not encode:

• tRNA

• Ribozyme

• Energy production or membrane bio

• Membrane biosynthesis

Note: All these materials are taken from the host

HPV16 viral replication mechanism

Rolling circle replication (to replicate genome)

Which viral genome evolves faster: RNA genome vs. DNA genome.

Viral RNA genome

**There is a new treatment developed against RNA viruses that target RNA dependent RNA polymerase (RDRP). Why may this treatment be safer than others?

Hosts have reverse transcriptase but not RDRP (which is used by RNA viruses to replicate)

• Targeting RDRP is good for us because we don’t have it → less toxicity risk

What genomes encode RNA dependent RNA polymerase?

RNA virus genomes

Retrovirus

A type of virus that replicates its RNA genome through reverse transcription into DNA.

Rotavirus

dsRNA genome and is infectious**

Dengue virus

ssRNA (+)

Influenza virus

ssRNA (-) ← not infectious

Adaption is..

dynamic, not fixed

• Ex. A viral protein can adapt (change) to the environment for better survival

Viral evolution

the constant change of a viral population in the face of selection pressures

What did the “Germ of an idea” prove?

• It debunked the theory that new viruses come from comets in space.

• It found that viruses from a reservoir in the stratosphere was spread to us by birds (airborne)

*Red Queen Theory - mechanisms of evolution

• As host populations grow and adapt, virus populations are selected to infect them

• Viruses can also select for hosts → evolution of host populations in response to virus

• Overall, evolution is dynamic and hosts and viruses are co-evolving

• If a host population cannot adapt to a lethal viral infection, the population may be exterminated

Modern virology: As host population grow and adapt, virus populations are [fill in blank] that can infect them.

selected

New “emerging” diseases, repetitive infection from influenza virus, and drug resistance in HIV show that…

The public is constantly confronted with the reality of viral evolution

*Four main driving forces of viral evolution

• Large number of progeny (allow for more mutations → high survival rate)

• Large number of mutants

• Quasi-species effects

• Selection

*Evolution is possible only when..

mutations occur in a population

• However, most mutations are destructive and only some are beneficial

T/F: Mutations are produced during copying of any nucleic acid molecule. In RNA viruses, RDRP is error prone, so mutants do not have it.

T

RNA viruses lack proofreading activity in RNA dependent RNA polymerase, resulting in..

high error frequencies in genome replication

T/F: DNA viral genome replication is not as error prone as RNA viruses

T

• DNA viruses have a proofreading mechanism during genome replication while RNA viruses do not

DNA viruses (properties)

• DNA viruses imitate hosts

• Genome replication is not as error-prone as RNA viruses → stability

• Proofreading mechanism

• Most DNA viruses generate less diversity, resulting in slower evolution that RNA viruses

The Quasispecies theory

The concept that viral populations exist as a diverse mixture of genetic variants.

• Theory is based on chemical kinetics

• Provides a mathematical framework in order to understand molecular evolution

Quasispecies effects

• Viral infections are initated by a population of particles, not a single virus

• The large number of progeny produces are complex products of selective forces inside the host

• The survivors that can co-reinfect a new host reflect the selective forces outside the host

The myth of consensus genome sequences

For a given RNA virus population, the genomes share consensus sequences, but the quasispecies are a mixture (not pure strains) of genetic variants and every genome is different from each other.

Survival of the fittest

A rare genome with a particular mutation may survive a selection event, and this mutation will be found in all progeny genomes

Survival of the survivors (Piggy pack)

Some unlinked (unselected) mutations get a free Pigger pack and survive selection events

• Ex. One virus that lacks a component (required for survival) receives that component from another virus → survival, and it looks like the infection is caused by a single virus but it is actually two viruses compensating each other

Mutations in viral polymerase that reduce the frequency of errors..

• Do NOT have a selective advantage when wild-type and anti-mutators are propagated together

• Lower rates are neither advantageous nor selected in nature

• Mutants often have less fitness

[High/ low] mutation rates are selected during virus evolution

High

• Mutations are good for viral populations to adapt to changing environments

T/F: Every virus has its own error threshold

T

Error theshold

Mutation is an advantage, but selection and survival balances genetic fidelity and mutation rate

• Exceed it: loss of infectivity

• Below it: Cannot generate enough mutations to survive selection

RNA viruses evolve [close / far] to their error threshold

close

DNA viruses evolve [close / far] to their error threshold

far

*Muller Ratchet theory - Genetic bottlenecks

Each round of error-prone replication works like a ratchet, “clicking” relentlessly as mutations accumulate at every replication cycle → allows the gear to move forward.

Offense selection

A mutation a virus causes the host antibody that is specific to that virus to be unable to bind to the virus (because of conformational change etc).

Defense selection

A mutation in a host antibody prevents it from binding its original virus.