Are we doing enough to detect the next pandemic?

An overview of biosurveillance in the UK and the recent collaboration between ONT and the UK government to establish the world's first real-time, pathogen-agnostic biosurveillance system

Imagine if we treated pandemics like fires. We don’t wait for a house to catch fire before taking action—we invest heavily in prevention. Fire safety systems and firefighting teams exist because individuals can’t protect themselves from fires alone. What if we applied the same proactive approach to stopping disease outbreaks¹?

That’s the idea behind biosurveillance: a system designed to detect and contain infections before they grow into national or global crises. This isn’t just wishful thinking—visionaries like Bill Gates are already championing pandemic prevention systems akin to firefighting². For example, G.E.R.M. (Global Emergency Response and Mobilization) would be a dedicated team ready to spring into action during outbreaks, much like firefighters respond to emergencies.

While the global capacity to detect, track, and analyze infectious diseases has improved dramatically over the past few decades, the COVID-19 pandemic laid bare a harsh truth: our systems are still woefully inadequate at stopping the rapid spread of a novel pathogen. The result? Unimaginable loss and disruption on a global scale.

In this post, I’ll unpack the concept of biosurveillance in simple terms. Then, drawing on my own experiences interning at Oxford Nanopore Technologies (ONT) and living in the UK, I’ll share exciting details about a new biosurveillance system being rolled out in the UK—a collaboration between ONT and the UK government that could mark a turning point in how we manage infectious disease threats.

Why should this matter to you? Because better biosurveillance means fewer pandemics. It means:

• no lockdowns

• not being separated from your family

• a lower risk of societal collapse

In short, it means spotting and stopping outbreaks while they’re still small, localized clusters, rather than letting them escalate into global catastrophes. While international collaboration to prevent patient zero will always be critical, robust biosurveillance is the next best line of defense—and one that could save millions of lives. Don’t you want to be informed on this?

The need for biosurveillance

What is biosurveillance and why does it matter?

Biosurveillance is the systematic collection and analysis of data to detect and monitor the spread of pathogens. These pathogens can emerge from a variety of sources—zoonotic spillover, bioterrorism by individuals or states, or accidental releases from labs³. By leveraging diverse health data sources, such as clinical reports, wastewater samples, and genomic sequencing, biosurveillance allows us to respond swiftly to outbreaks and stop them from turning into pandemics.

Image description: a table of types of pathogen biosurveillance⁴.

The stakes couldn’t be higher. Responding to pandemics often requires vast healthcare mobilizations, international coordination, and travel restrictions—approaches that are not only disruptive but also extraordinarily resource-intensive and costly. In contrast, addressing smaller, localized outbreaks is far more manageable. Targeted interventions like quarantines, vaccination campaigns, and containment measures can stop a crisis before it starts.

History offers striking examples of both successes and failures in biosurveillance (or lack thereof). In 2004, a lab accident involving the SARS virus was quickly identified and contained, sparing the world a larger outbreak. Conversely, delays in early detection, such as during the COVID-19 pandemic, allowed the virus to spread unchecked, leading to devastating mortality rates, societal disruption, and catastrophic economic losses. The lesson is clear: swift detection and response can mean the difference between a contained outbreak and a global emergency.

Unfortunately, many countries remain unprepared. Their biosurveillance systems lack the capacity to deliver timely early warnings, leaving them vulnerable to surges caused by either known pathogens or entirely novel ones. Current systems often detect outbreaks only after they’ve gained a foothold—days, weeks, or even months after the initial cases emerge—giving diseases ample time to spread.

The challenge of effective biosurveillance systems

It’s not enough to simply have a biosurveillance system; it must be well-designed, robust, and adaptable. Programs like the U.S. BioWatch⁵ demonstrate the potential and limitations of existing systems. Launched in 2003, BioWatch continuously monitors air samples in U.S. cities to detect bioterrorism threats, such as anthrax or smallpox. While it has succeeded in its narrow mission, it was completely unequipped to detect the emergence of COVID-19.

This shortfall has not gone unnoticed. During a 2022 US Senate hearing, Senator Rob Portman asked a pointed question: “Why didn’t we detect COVID-19? Why did it take us so long?” He reflected on how it felt like the virus had already spread for months by the time it was identified. This delay illustrates a critical gap in current biosurveillance systems—the need for a broader and more flexible approach.

Biosurveillance in the UK

Before giving an overview of the state of biosurveillance in the UK, I want to rewind back to January 2020 and talk through how the UK government responded to the new pandemic ravaging the world⁶. All of the failures from that response pushed the country towards taking biosurveillance much more seriously and hopefully give some context to all the new developments in biosecurity in the country.

The COVID-19 Pandemic in the UK

When the virus emerged in early 2020, the UK government faced the dual task of preventing the National Health Service (NHS) from becoming overwhelmed while addressing the economic fallout. Notice how I’m not talking about reducing mortality rates - indeed, that was not the intention during much of the outbreak, much to the chagrin of the general public. The national pandemic response included three national lockdowns, tiered regional restrictions based on infection rates, and strict social distancing measures like mandatory quarantines and localized lockdowns. Support programs such as furlough payments, business loans, and incentives like the "Eat Out to Help Out" scheme were introduced to alleviate economic strain. The successful rollout of vaccines in early 2021 placed the UK among the first countries to offer widespread access, helping to reduce hospitalizations and deaths.

Then critical flaws in the UK’s response emerged. Lockdowns and restrictions had not been swiftly implemented, leading to a prolonged spread of the virus. Confusing and inconsistent public health messaging weakened public compliance. The “Track and Trace” system, intended to monitor outbreaks, was inefficient and costly. Additionally, travel restrictions were imposed too late, allowing the virus to spread through international arrivals at the country’s highly connected airports. Early detection could have enabled quicker action and improved outcomes.. The lukewarm response to the pandemic happened partially because, for a long time, it genuinely seemed like the UK had been spared from COVID-19 thanks to poor biosurveillance capabilities. This awful experience highlighted the urgent need for better biosurveillance systems to prevent future pandemics.

The state of biosurveillance in the UK

In recent years, the UK has developed a fairly robust biosurveillance system. Key legislation, such as the Animal Health Act and the Public Health (Control of Disease) Act, underpins this effort. Agencies like the UK Health Security Agency (UKHSA), DEFRA, and the Animal and Plant Health Agency (APHA) oversee its implementation. These initiatives are guided by the 2023 UK Biological Security Strategy7, which prioritizes preparedness and rapid response to emerging threats. A key component of this strategy is the National Biosurveillance Network (NBN), led by UKHSA8. This unifies data from multiple health sectors under the One Health approach9, which acknowledges the interconnected nature of human, animal, and environmental health to better identify and manage outbreaks. The UK also collaborates internationally on initiatives like the 100 Days Mission10, which aims to ensure vaccines and treatments are available within 100 days of detecting a new infectious disease.

Image description: a timeline showing the (sadly) real response to the COVID-19 pandemic versus an imagined response using the 100 Days Mission approach

There were already some biosurveillance strategies in place in the UK before the NBN. These included:

• Disease monitoring programmes run by APHA to track zoonotic diseases in livestock

• DEFRA’s Plant Health Risk Register to detect invasive species

• Environmental surveillance programs like the Countryside Survey to assess ecosystem health and invasive species threats.

You may notice these do not target pandemic-causing pathogens, which we somehow only realized was a problem during the COVID-19 pandemic when the UKHSA started using genomic sequencing and wastewater monitoring to keep track of cases. So, to reiterate, until the UK Biological Security Strategy was proposed in 2023, the UK didn’t really have a biosurveillance strategy in place to detect and prevent pandemics.

We are making strides, though. The second development phase of the NBN - called ALPHA Phase 2⁷ - is already running and will end in March 2025. It will trial the government’s response to Tick Borne Encephalitis (TBE), which is a disease on the rise in the UK due to factors like climate change. TBE does not pose a significant security threat, which makes it ideal for developing the target operating model for future One Health biosurveillance and data sharing.

The most significant bottleneck for a full, swift implementation is probably underfunding. For example, the Animal and Plant Health Agency's headquarters in Weybridge, a key site for managing animal disease outbreaks, require significant redevelopment, with £2.8 billion needed to address critical infrastructure failures. While the previous government committed £1.2 billion, full funding has yet to be secured, a delay highlighted by Dr Neil Hudson MP, a veterinary surgeon and biosecurity advocate, who emphasized that “biosecurity is national security”⁸.

Something you might be asking yourself is: how much of an impact did the lack of a biosurveillance system have during the COVID-19 pandemic in the UK? I will be honest and say that I’m not comfortable giving a quantitative answer - I haven’t read research addressing this exact question. Public Health England acknowledged that it “cannot exclude the possibility that COVID-19 was in the UK in December or early January” based on data gathered through a COVID-19 symptom-tracking app developed at KCL⁹. This suggests that from early January 2020 onwards there were potentially many, many more cases of COVID-19 in the UK than the 2 officially reported on January 29th 2020. So even though the UK’s late and lukewarm response is to blame for much of the disasters unleashed by COVID-19, by that point our first lines of defence probably had already been breached.

Oxford Nanopore Technologies (ONT) steps up to the challenge

ONT has recently partnered with the UK government, NHS England, Genomics England, and UK Biobank in a groundbreaking initiative to transform the country’s approach to biomedical research and pandemic preparedness. This initiative was officially announced on the 5th November 2024.

As someone who interned at ONT during the summer of 2024 as a software engineer, I’ve had firsthand experience with the company’s cutting-edge sequencing technology. So let me tell you all about it. ONT is a global leader in portable and scalable sequencing technologies. The company has developed devices like the MinION (which fits in the palm of your hand like a really fat USB stick) and GridION , which have been used across various applications, from pest biosecurity surveillance in Australia¹⁰, to creating vast genomic datasets like the world’s largest epigenetic dataset focusing on cancer, dementia, and complex diseases¹¹. ONT devices are used literally everywhere, even on the International Space Station¹²! The company’s innovative nanopore sequencing technology¹³ captures long-read genetic information, making it ideal for understanding disease transmission and resistance. This makes ONT a highly valuable partner in building scalable biosurveillance systems that can detect and respond to emerging health threats in real-time.

Image description: a MinION sequencer aboard the ISS

Image description: minION sequencing device being used in Guinea during the 2013-2016 Ebola outbreak.

Image credit: Tommy Trenchard / European Mobile Laboratories

This new collaboration will involve 30 NHS hospitals (out of ~1,140), where real-time sequencing will analyze patient samples from severe respiratory infections, providing diagnostic results within just six hours. This rapid turnaround time will drastically improve the UK’s biosecurity capabilities, helping clinicians match patients with the appropriate treatments more quickly AND respond appropriately in case an outbreak is flagged. The partnership is also part of the UK government’s broader 100 Days Mission¹⁴, which hopefully means other countries will follow suit very soon.

Why is this biosurveillance approach is not being scaled up even more? My guess is that one of the biggest hurdles is the high cost of the sequencing devices. ONT’s entry-level MinION sequencer costs £800, while more advanced machines like Illumina’s MiniSeq can go up to £50,000. Reducing the cost of sequencing devices is essential for biosurveillance, and until costs come down, scaling biosurveillance systems will be constrained¹⁵.

Prepared or playing catch-up?

The recent collaboration between ONT and the UK government is a positive step toward improving biosurveillance. However, it won’t be fully implemented for years. The first iteration of this biosurveillance system needs to be shown to be safe and robust enough to be scaled up across the country. Also, sequencing costs are still too damn high.

In the meantime, we’re vulnerable. Is biosecurity really being treated as national security?

1. In this article, Richard Williamson advocates for a comprehensive, proactive, and globally cooperative approach to pandemic prevention, likening it to fire-fighting strategies to minimize costs and save lives. I first came across this reading and concept during the Biosecurity Fundamentals course run by BlueDot Impact.

2. In this TED Talk, Bill Gates proposes a 3,000-strong GERM team to prevent pandemics by stopping outbreaks early.

3. This CSR report urges creating a global early warning system to detect and stop biological threats before they cause pandemics.

4. Table entries are taken from this CSR report and this forum post.

5. An official factsheet detailing facts and accomplishments of BioWatch, a US system designed to detect the presence of biological agents that have been intentionally released into the air.

6. Some amazing infographics detailing the UK response to the COVID-19 pandemic, such as events in chronological order with dates and statistics.

7. Official government details of ALPHA phase 2

8. Dr Neil Hudson’s address to parliament in 2024, in which he urges the UK government to safeguard national biosecurity

9. A Guardian article going over evidence that COVID-19 was present in the UK weeks before the first official cases were reported.

10. A fact sheet going over how ONT devices are being used in Australia to monitor the pest browsing ant, which is a national biosecurity threat.

11. You can read more about this collaboration with the UK BioBank here.

12. A Nature article reporting the use of ONT devices on the ISS.

13. This is an official video by ONT explaining how how nanopore technology works. I watched it myself when preparing to interview at ONT.

14. Learn more about the UK government’s vision here

15. This forum post (with an attached report) examines key technological and non-technological bottlenecks in biosurveillance systems, focusing on PCR, LAMP, and metagenomics sequencing to enhance pathogen detection and pandemic response.