Exercises: Viruses, viroids, and prions

Give three reasons why viruses are not considered living organisms according to classical criteria (cellular organization, metabolism, and reproduction) and one reason why the debate remains open.

Describe the basic structure of a virus (genome, capsid, and, in some, envelope) and explain the difference between a naked virus and an enveloped virus, with an example of each.

What are viroids and what are prions? State which organisms the former infect and give a human or animal disease caused by prions.

Describe the lytic cycle and the lysogenic cycle of a bacteriophage, indicating how they differ and what consequence it has for the bacterium when the phage enters latency.

Look at the structure of the virus in the image. a) Explain the function of structures 1, 2, and 4 during cell infection. b) Reason why structure 3 makes this type of virus particularly sensitive to soap and alcohol-based solutions. c) Is it possible to know from the image alone whether its genome is DNA or RNA? Justify your answer.

The 'One Health' approach views human, animal, and environmental health as a single interconnected system. Explain this using viral zoonoses: give two examples (rabies, avian influenza, or COVID-19) and reason how deforestation, intensive livestock farming, and the wildlife trade facilitate a virus jumping from an animal species to humans.

During an outbreak of a novel respiratory virus, a basic reproduction number $R_0 = 2.5$ is estimated.

1. a) Public health authorities consider two alternative scenarios: implementing non-pharmaceutical containment measures (masks and ventilation, which reduce the transmission probability per contact by $40\,\%$) or relying exclusively on a vaccine with an efficacy of $80\,\%$ administered to $60\,\%$ of the population. Quantitatively predict which of the two strategies will independently manage to halt the expansion of the outbreak (making the effective reproduction number $R_t$ less than $1$), justifying your calculations.
2. b) A public official states: "If we manage to vaccinate $50\,\%$ of the population with a $100\,\%$ effective vaccine, the virus will become extinct immediately because half of the population will no longer transmit it". Refute this statement quantitatively and biologically by calculating the resulting value of $R_t$ and describing what will happen in the short term to the epidemic curve.

In a laboratory, two emerging viruses that infect human lymphocytes are analysed: virus Alpha (with a double-stranded DNA genome of $150\text{ kb}$) and virus Beta (with a single-stranded RNA genome of $15\text{ kb}$). Viral particles are isolated from patients after six months of infection:

• In Alpha, the sequence of the attachment glycoprotein gene shows an average divergence of $0.001\,\%$ relative to the inoculated strain.

• In Beta, the divergence in the homologous protein is $4.2\,\%$, with a broad cloud of variants found within a single host.

1. a) Justify at the molecular and enzymatic level the cause of this huge disparity in the mutation rates observed between both viruses.
2. b) To combat both pathogens, a protein subunit vaccine based on a single variant of the attachment protein and an inhibitory drug targeting that protein are tested. Make a reasoned prediction of the medium-term effectiveness prognosis of these strategies in Alpha and in Beta.
3. c) What viral target or pharmacological strategy would you propose for virus Beta in order to reduce the likelihood of it developing resistant variants?

A research team is trying to determine the nature of the infectious agent causing a new spongiform encephalopathy. To do so, they subject samples of infectious brain tissue to different treatments before inoculating them into healthy laboratory mice:

• Treatment 1: Exhaustive digestion with DNases and RNases $\rightarrow$ $100\,\%$ of the mice fall ill.

• Treatment 2: Ultraviolet irradiation at lethal doses for nucleic acids $\rightarrow$ $100\,\%$ of the mice fall ill.

• Treatment 3: Autoclaving at $121\text{ }^\circ\text{C}$ for $20\text{ minutes}$ $\rightarrow$ $100\,\%$ of the mice fall ill.

• Treatment 4: Prolonged boiling in sodium hydroxide ($1\text{ M}$) or digestion with harsh proteases $\rightarrow$ No mice fall ill.

• Treatment 5: The intact infectious sample is inoculated into Knock-Out mice in which the $PRNP$ gene has been deleted (they do not express the normal cellular protein $\text{PrP}^\text{C}$) $\rightarrow$ No mice develop the disease or multiply the pathogen.

1. a) Interpret the results of treatments 1, 2, and 4: deduce the biochemical nature of the pathogen and justify why its discovery represented an apparent violation of the central dogma of molecular biology.
2. b) Explain at a structural level (secondary conformation and aggregation) why treatment 3 failed but treatment 4 managed to neutralize infectivity.
3. c) Deduce from treatment 5 the mechanism by which this pathogen manages to "replicate" in a healthy host and explain why mice without the $PRNP$ gene turn out to be immune.