In this unit we imagine that we have failed to prevent the initial outbreak and someone, somewhere is infected with a potential pandemic pathogen.

They may have been infected through interactions with an animal, a laboratory accident, or a deliberate biological attack. They may not have symptoms, or even be aware that they have been exposed. The longer this goes undetected, the more chance there is for the disease to spread through the human population.

This unit covers three main elements of early pandemic detection:

**Detecting that there is a pandemic-potential pathogen circulating in the population.**

This is especially difficult when the pathogen is novel (we don’t know what we’re trying to detect) or if there is substantial asymptomatic or pre-symptomatic transmission (remember the [“stealth” scenario](https://www.gcsp.ch/sites/default/files/2024-12/securing-civilisation-against-catastrophic-pandemics-gp-31.pdf) from unit 1). One of the most promising technologies is metagenomic sequencing, reading all the DNA and RNA fragments in a sample and trying to work out what's in there.

**Characterising the pathogen.**

Once authorities have detected that there is a concerning outbreak, we must rush to gain situational awareness. What is the causative pathogen? How does it spread? What is the case definition? How many people are currently infected and where are they? Do we have any existing effective treatments?

**Detecting individual cases and taking actions to contain the spread.**

When case numbers are low, testing to identify infected individuals, contact tracing and quarantine can be effective. Vietnam employed this to great effect during the first year of COVID, although it required draconian enforcement and was much less effective against the more infectious omicron variant. Conventional wisdom is that containment is unlikely to be possible with highly transmissible [“wildfire” pandemic scenarios](https://www.gcsp.ch/sites/default/files/2024-12/securing-civilisation-against-catastrophic-pandemics-gp-31.pdf).


Detection overview

Detection deep-dive

Pick 1 of the following 3 topics to dive deeper into. We've given you some resources on the following pages as a starting point.

- **Option 1: Country-specific biosurveillance**
    - Map the current biosurveillance systems in a specific country and investigate how they could be improved
- **Option 2: Metagenomic sequencing technology roadmap**
    - Study the current state of metagenomic sequencing and what would be required to make it as ubiquitous as PCR
- **Option 3: Rapid individual testing**
    - Explore emerging technologies for detecting individual cases

You will bring the results of your research to share in your group discussion.


Pick a country. It could be the country you were born in, the one you're in right now, or any other one you choose.

**Using your own research and the resources below, try to answer the following 2 questions:**
1. If a novel virus started spreading in that country today, what is the process by which it would first be detected and characterised?
2. What would be the critical challenges to setting up national biosurveillance system like [the one described for the US](https://naobservatory.org/blog/biothreat_radar/) in the overview resources?

Try to be as specific as possible! If it helps, you could narrow down the outbreak to a specific state, county or city.


Option 1: Country-specific biosurveillance

This option gets quite technical! We recommend you only pick it if you've studied biosciences to at least undergraduate level.

Polymerase chain reaction (PCR) is the gold standard for clinical testing worldwide. But this only tests for the presence or absence of a specific DNA sequence that you know you're looking for.

Routine clinical metagenomic sequencing would allow us to detect novel pathogens, as well as emerging variants of known ones.

**In this deep dive, you goal is to understand (and be able to teach your cohort):**
- How the two main next generation sequencing technologies work
    - Sequencing by synthesis (SBS), used by Illumina
    - Nanopore sequencing, used by Oxford Nanopore
- The technological requirements for ubiquitous metagenomic sequencing


Option 2: Metagenomic sequencing technology roadmap

During COVID, we saw the widespread use of [rapid antigen tests](https://en.wikipedia.org/wiki/COVID-19_rapid_antigen_test) alongside PCR. While these were less sensitive than PCR, they were cheap to produce, easy to do and delivered results within 5-30 mins. We call these kinds of tests "point-of-person" diagnostics. PCR tests, on the other hand, had to be sent to a lab run by trained staff and only delivered results in days.

Rapid, accurate point-of-person diagnostics could be valuable for a few reasons:

**Disease diagnosis and pathogen early-detection in low-resource settings. **Say we have cheap rapid diagnostic that can [test for each of the 100 most common diseases at the same time](https://www.nature.com/articles/s41586-020-2279-8). Firstly, this would give us the ability to better diagnose and treat many of the most common diseases. Furthermore, if someone displays flu-like symptoms but tests negative for all the diseases on that test, then that sample could be sent to a central lab for metagenomic sequencing, allowing us to detect novel pathogens and variants.

**Identifying individual cases for targeted disease containment. **During the early days of the COVID pandemic, without widespread testing, public health systems relied on broad interventions like lockdowns and travel restrictions. In a world where we can quickly develop and deploy rapid tests for novel pathogens, we can be better informed about who exactly has the disease.

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Read the 'Triple Rapid Framework' blogpost below, then pick one of the diagnostic technologies. For the technology you pick, explain:
- Why it's 'better' than existing PCR or rapid antigen tests
- How it would need to be deployed to be useful early in a pandemic
- What are the key blockers to this deployment?



Option 3: Rapid individual testing

Biosecurity

Learn how metagenomic sequencing can detect novel pathogens, how to rapidly characterise emerging threats, and how swift containment can stop transmission before widespread outbreaks.

Detecting Early Infections

Building biodefences is both urgent and achievable: pandemics have killed millions, AI and synthetic biology are creating new threats, but a radically more pandemic-proof world is possible.

Building a Pandemic-Proof World

Examine upstream interventions that stop threats before they emerge: AI safeguards, DNA synthesis screening, the Biological Weapons Convention, lab biosafety standards, and governance of risky research.

Preventing Engineered Pandemics

Discover pathogen-agnostic defences deployable within hours: next-generation PPE, far-UVC air treatment, and biohardening strategies that protect people before we know what we're facing.

Non-Pharmaceutical Interventions

Explore how to accelerate vaccine development, and how broad-spectrum antivirals can treat multiple threats before pathogen-specific treatments exist.

Rapid Medical Countermeasures

Map the biosecurity landscape and identify where your specific skills can contribute: organisations hiring across policy and technology, concrete projects seeking talent, and pathways into the field.

Biosecurity

Detection overview

Resources (2 hrs 20 mins)