We’ve failed to prevent patient zero, and someone, somewhere, has been infected by a novel pandemic-potential pathogen.

In the early stages of an outbreak, we may only be aware of mysterious ‘flu-like’ symptoms(<https://www.vox.com/science-and-health/2020/1/6/21051589/wuhan-china-outbreak>), or worse, few recognised symptoms at all(<https://en.wikipedia.org/wiki/Timeline_of_HIV/AIDS>). Our ability to identify the causative pathogen, track cases and respond quickly could be the difference between a small local outbreak and a global pandemic.

The goal for interventions discussed in this unit is to:
\- Identify pathogen
    \- Goal: identify when there is a pandemic-potential pathogen circulating in humans as early as possible.
\- Detect human cases
    \- Goal: determine the number and location of infected patients.
\- Contain outbreaks
    \- Goal: prevent all future infections.


By the end of the unit, you should be able to:
\- Identify and explain a range of interventions to detect and contain early infections.
\- Begin to evaluate the promise of these interventions against a range of factors, established in session 3.


Resources: Detecting and Containing Early Infections

Exercises: Detecting and Containing Early Infections

**Pick one of the five options** to dig deeper into. Resources for each can be found in the ‘optional resources’ section. Message your cohort Slack channel to let them know which option you will be covering:

**(Option 1) Clinical metagenomic sequencing**
Comprehensive analysis of microbial and host genetic material (DNA and RNA) in samples from patients in clinical settings.

**(Option 2) Environmental metagenomic sequencing**
Comprehensive analysis of genetic material (DNA and RNA) in samples from environmental settings (e.g. wastewater).

**(Option 3) Loop-mediated isothermal amplification (LAMP)**

**(Option 4) CRISPR-based diagnostic tools**

**(Option 5) Digital disease surveillance**
Techniques such as detecting disease outbreaks from search queries and social media posts, and digital contact tracing.

**For your chosen option, read the additional resources and prepare notes to present it to the rest of your cohort. You may be asked to present during your discussion session:**
​
- Explain the technology and its relevance to outbreak detection
- Which currently-existing, widespread technologies aim to fulfil a similar role to the technology you studied? In what ways is the technology you studied an upgrade over the existing technology, and to what extent do you think this would make a difference in the event of an outbreak?
- Consider how useful this technology would be (compared to existing alternatives), for diseases with different incubation periods. For example:
    - Pathogens like SARS-CoV-2 that display symptoms with a short incubation period (symptoms show ~1-10 days after infection)
    - Pathogens with long incubation periods and latent states (e.g. HIV and Tuberculosis)
- In which contexts might this technology be rendered ineffective?
- How well does this intervention score against the factors you established in the session 3 discussion?



Next generation detection deep-dive

Recalling and reflecting on previous learnings is an excellent way to deepen your understanding and help retain them in your memory.

**Pick one of last session’s deep-dives which you didn’t read about, but which one of your cohort presented about in the discussion session. **From memory, spend roughly 10 minutes trying to write up your understanding of the intervention using the following prompts:

- Explain the intervention and its relevance to outbreak prevention
- What are the strengths of this intervention and in which contexts might it be the most effective at preventing outbreaks? For those inventions focused on human-caused outbreak events, consider factors such as:
    - State vs non-State actors
    - Accidental vs deliberate release
- In which contexts might this intervention be rendered ineffective?
- How well does this intervention score against the factors you established in week 3 discussion (e.g. cost-effectiveness, technology readiness level etc.)?

As a reminder, the interventions covered were:

1. Prevention of zoonotic spillover
2. Oversight of enhanced pandemic potential pathogen (ePPP) research and dual-use research of concern (DURC)
3. The Biological Weapons Convention
4. Regulations on DNA synthesis
5. Bioengineering detection and attribution



[Optional] Reflection on interventions to prevent patient zero

Pandemics

How do we stop a local outbreak from becoming a global disaster?

Detecting and Containing Early Infections

How do we make pandemics a thing of the past?

Building a Pandemic-Proof World

How could new technologies both increase and reduce the risk of pandemics?

Pandemic Risk Over the Coming Decades

What does it take to prevent the first human infection?

Preventing Patient Zero

How can governments minimise harms when a pandemic spreads worldwide?

Governmental Response to a Global Pandemic

How could new innovations help us prepare for and prevent future pandemics?

Technologies to Strengthen Future Pandemic Response

Make high-stakes decisions in a simulated pandemic scenario.

Pandemics

Resources: Detecting and Containing Early Infections

Resources (35 mins)