Additional Material

Question 1

Bacteriophage

Answer 1

• Viruses that infect bacteria
• Humans have harnessed this to utilize as treatment for bacterial infections
• Still primarily experiment, used as a last resort
• Ubiquitous and diverse
• Can have RNA or DNA genomes
• 2 Life cycles
  
  • Lytic life cycle
    
    • Harnessed for medical therapy
    • Burst open the bacterial cell as part of the viral replication process, kills the bacterium in the process
    • 1) Attach and inject viral genome into the cell
    • 2) Degradation of host genome
    • 3) Replication of viral genome and synthesis of viral proteins
    • 4) Assembly and release
    • 5) New bacteriophage viruses go infect other bacteria
  • Lysogenic
    
    • Can spread antibiotic resistance of virulence mechanisms across bacteria
    • Integration into the host genome, slow production of viral products as the bacteria itself divides. In response to stressors, the phage may shift into the lytic cycle and recapture its DNA. In this process, it may scoop up bits of extra DNA or the incorrect DNA. This error prone mechanism can allow phage to pick up antibiotic resistance genes or virulence mechanisms that the phage may then be able to spread to different bacteria. This is an important bit of information we hope you’ll take away for our class – bacteriophage can kill bacteria but they can also help make them more resistant and stronger.

Question 2

Bacteriophage Therapy

Answer 2

Several disadvantages: Limited supply, not FDA approved, can cause severe immune response, could spread antibiotic resistance, may not be effective at killing the bacteria.

1. One disadvantage is that bacteria have evolved to be quite effective at developing resistance against phage infection.
2. A second disadvantage is that due the lysis of bacteria and the release of large amounts of antigens, phage therapy can result in an exaggerated immune response, potentially making patients even sicker and could even result in death.

In a unique case, it saved the life of Tom Patterson who had contracted Acinetobacter baumanii

Question 3

Review - DNA Viruses

Answer 3

Question 4

Review - HIV

Answer 4

Question 5

Review - RNA Viruses

Answer 5

Question 6

Coronaviruses

Answer 6

• Large group os +ssRNA viruses
• 10-35% cause the common cold
• Others include
  
  • SARS CoV >>> SARS
  • MERS CoV >>> MERS
  • SARS CoV-2 >>> COVID-19

Question 7

Coronavirus Structure

Answer 7

• The viral envelope consists of a lipid bilayer where 3 proteins are anchored:
  
  • Spike (S) glycoprotein
    
    • Attach the virus to receptor molecules on host cells
    • Activate fusion of the virion membrane with host cell membrane
    • Transmissibility and infectivity is controlled by the S protein
    • The cell receptor for SARS CoV and SARS CoV2 is angiotensin converting enzyme II (ACE2)
  • Membrane (M)glycoprotein
    
    • Binds to the nucleocapsid
  • Envelope (E) protein
    
    • Important for virus assembly and release
  • Nucleocapsid (N) protein
    
    • Found associated with RNA genome (protection?)
    • Plays a role in RNA replication and transcription

Question 8

COVID-19 Pandemic Timeline

Answer 8

• 12/31/2019 - China reports a cluster of pneumonia cases associated with a fish market in Wuhan
• 1/7/2020 – China confirms this is a novel coronavirus
• 1/20/2020 – first case in the US is reported
• 2/3/2020 – China publishes viral genome
• 3/11/2020 – WHO declares a pandemic

Question 9

Spectrum of COVID-19 Symptoms

Answer 9

• Asymptomatic or presymptomatic infection
  
  • Testing positive without symptoms
• Mild illness
  
  • Patient has symptoms consistent with infection (fever, cough, sore throat, malaise, etc) without shortness of breath, abnormal chest imaging
• Moderate illness
  
  • Evidence of lower respiratory disease and an oxygen saturation > 94% on room air
• Severe illness
  
  • Evidence of all of the above + an oxygen saturation < 94% on room air, a ratio of arterial partial pressure of O2 to fraction of inspired oxygen (P:F ratio) < 300
• Critical illness
  
  • Individuals who have respiratory failure, septic shock, and or multi-organ dysfunction

Question 10

COVID-19 Outpatient Treatment

Answer 10

• Preferred Therapies (listed in order of preference):
  
  • Paxlovid – inhibits viral replication (ritonavir helps inhibit nirmatelvir’s metabolism so it lasts longer in the body)
  • Remdesivir – nucleoside analogue
• Alternative Therapies:
  
  • Bebtelovimab – mAb attacks the spike protein
  • Molnupiravir - Small molecule ribonucleoside that encourages RNA polymerase to incorporate errors
  • Baracitinib – reduces IL-6 production by inhibiting JAK pathway

Recommends against continuing the use of Remdesivir, Dexamethasone, and Baricitinib after hospital discharge.

Question 11

COVID-19 - Hospitalized Patients

Answer 11

• Remdesivir – nucleoside analogue
• Tocilizumab – anti-IL-6 antibody (may help reduce cytokine storm seen in severe covid)

Question 12

COVID-19 Prevention

Answer 12

Question 13

Prions

Answer 13

• There is a cell surface protein called a prion protein that exists on the cell surface within all of us.
• Prions are non-living infectious agents that are misfolded proteins that induce protein misfolding in prion proteins that can induce disease over time.
• The exact mechanism of this prior protein is not well understood. If this prion protein is exposed to a misfolded version of itself it is possible for that misfolded protein to cause conformational change in a normal protein such that the normal protein changes shape to the misfolded form. These misfolded proteins build up and form aggregates. They cause disease through a few mechanisms: causing damage through generation of misfolded protein sheets and through lack of the normal protein function and through gain of toxic activity.
• Cross-Species
  
  • Scrapie - sheep
  • Chronic wasting disease – deer
  • Bovine spongiform encephalopathy - cattle (aka: Mad Cow Disease)
  • Creutzfeldt-Jakob disease – humans

Question 14

Human Prion Disease

Answer 14

• Creutzfeldt-Jakob Disease
  
  • Characterized by dementia, behavioral abnormalities, and deficits in higher order thinking such as speech. Myoclonus is also seen.
  • Can be sporadic (a disease that occurs infrequently or irregularly) or genetic
• Variant Creutzfeldt-Jakob Disease
  
  • Specifically refers to people who consumed infected meat products from cows with mad cow disease and acquired the illness this way
• Gerstmann-Straussler-Scheinker syndrome
  
  • A genetic prion disease characterized by cerebellar degeneration with or without parkinson-like features; age of onset usually mid 40s, can occur with dementia as well. Characterized by clumsiness, incoordination, and gait ataxia
• Fatal familial insomnia
  
  • Originally described in families of Italian descent, has now been described across different populations. Characterized by neuronal loss most prominent in the thalamus. The disease is characterized by sleep disturbances, loss of normal sleep wake cycle, neuropsychiatric symptoms such as inattention, impaired concentration, and hallucinations. Dementia is rare. Onset is usually mid-50s
• Kuru
  
  • Endemic to Papua New Guinea and believed to be transmitted person to person in this society through ritualistic cannibalistic practices. The incubation time from consuming infected meat has been as long as 50 years. Presentation is first marked by tremors, ataxia, and postural instability. The name “kuru” means ”trembling”. It is later followed by a sedentary stage, where movement is difficult, tremors are common in this stage. Dementia is seen in the late stages of the disease.

Question 15

Human Prion Disease - Treatments (or lackthereof)

Answer 15

All prion diseases have no treatments currently available and are universally fatal, usually within 6-18 months of diagnosis.

Question 16

Prion Propagation

Answer 16

Not fully understood, but two models exist:

Heterodimer model

• A single misfolded protein convinces another single protein to misfold
• Limitations: doesn’t explain rarity of spontaneously occurring misfolded prions

Fibril model

• Strands of misfolded proteins exist together, normal proteins connect to the end of the string of misfolded protein and becomes misfolded itself
• Limitations: doesn’t account for exponential growth of misfolded prion protein seen in the disease process

Question 17

Prion Disease - Transmission

Answer 17

• Acquired
  
  • Through exposure to infected material
  • Infected material is most commonly the brain, spinal cord, retina, and olfactory bulb. Less common is CSF.
  • If you acquire it then you need to ingest it (into mouth, eye, etc)
• Familial
  
  • Genetic
    
    • Tend to be autosomal dominant w/ incomplete penetrance (so only need one parent but even if you have the mutation it doesn’t mean you will get the disease)
• Sporadic
  
  • Random chance (Most common)

Question 18

Prion Disease - Decontamination

Answer 18

• Prions are incredibly resistant to denaturing due to their structure, due to this it is difficult to decontaminate potentially exposed equipment or products
• Resistant to proteases, heat, ionizing radiation, and formaldehyde
• 100% bleach or sodium hydroxide used to decontaminate surfaces

Question 19

Prion Disease - Diagnosis

Answer 19

• Limited diagnostics
• Brain biopsy and tissue diagnosis
• Can test CSF for specific protein markers for CJD (14-3-3). Not particularly sensitive or specific for CJD but if it’s positive it might lead you to the diagnosis.
• Brain MRI characteristic findings (Most common)
• Clinical findings (Most common)