CFG’s Response to the EU’s Medical Countermeasure Strategy

Introduction

Investing in biosecurity – A layered defensive strategy

The COVID-19 pandemic exposed the enormous human and economic costs of being unprepared for biological threats – over 25 million excess deaths and trillions in economic losses globally. Research shows that endemic diseases alone cost the European economy between €6-14 billion annually.^[1] 

The threat landscape in biosecurity is getting increasingly complex.  Climate disruption pushes wildlife and people into tighter contact, increasing the risk of new zoonotic outbreaks. In addition, the number of maximum‑containment laboratories has quintupled since 2000, raising the odds of an accidental release^[2]. The democratisation of synthetic biology is also lowering the barriers for malicious actors to produce harmful genetic material.^[3] 

Experts now estimate a 50% chance of a pandemic causing over 25 million deaths by 2050.^[4] 

By investing in and utilising the complementary technologies outlined in this response- more extensively covered in CFG’s upcoming project Strategic Innovation for European Security – the EU can build a robust, layered defence that will help protect present and future generations from biological threats.

In this context our proposal addresses two critical dimensions of the EU’s medical countermeasure strategy: early detection of pathogens through metagenomic sequencing and rapid response capabilities via secure biofoundries. 

We believe these elements are essential components of a comprehensive biosecurity architecture that complement pathogen-agnostic containment measures. The early detection provides a critical time advantage needed for effective countermeasure deployment before we reach epidemic proportion. Meanwhile, the biofoundries present instrumental tools to achieve optimal response to pathogen threats.

Altogether, these capabilities may establish a functional detection-to-deployment pipeline that addresses key vulnerabilities exposed during recent public health emergencies.

Our proposal addresses complementary aspects of medical countermeasure strategy that we think remain underdeveloped in the current EU planning. The detection and manufacturing elements of biosecurity create a comprehensive arsenal alongside containment technologies.

First, it aligns with HERA’s ongoing priority to improve detection capabilities. Second, our biofoundry network proposal aligns with broader concerns about strategic autonomy in the production of vaccines and other medical interventions. By addressing both of these aspects, our proposal offers a strategic approach to reduce critical vulnerabilities while building on European technological sovereignty in key domains.

Our recommendations complement the responses from Pour Demain, Blueprint Biosecurity and RAND Europe to this consultation. Our colleagues elegantly emphasised the instrumental role of pathogen agnostic transmission suppressing technologies like elastomeric half-mask respirators and air-decontamination tools. The complementary nature of our recommendations with those of other stakeholders will hopefully give policymakers a comprehensive framework spanning the full spectrum of pandemic countermeasures.

1. Our recommendations

A. Scale up metagenomic sequencing capabilities for advanced biointelligence

What it is
Metagenomic sequencing decodes all genetic material present in a biological sample, without prior knowledge of what is there. Unlike traditional methods, which only detect viruses that we already know to look for, metagenomic sequencing is “pathogen-agnostic” and can discover novel pathogens or mutations which other methods might miss.^[5] 

Why it matters
Conventional methods of biointelligence like Polymerase Chain Reaction (PCR) tests can only look for pathogens we already suspect are present in a sample, creating blindspots.^[6] Novel and “stealthy” pathogens – that are able to circulate undetected for long periods of time due to long incubation periods – are therefore not reliably detected by existing biointelligence systems.^[7] 

Metagenomic sequencing reads every fragment of DNA or RNA in a sample taken from environmental sources like air, soil, or wastewater, or clinical samples taken from patients. That matters because the next crisis may come from an unfamiliar virus or from a stealth variant that incubates quietly before exploding. Metagenomic sequencing addresses this capability gap.

Whereas metagenomic sequencing was previously prohibitively expensive to be utilised at scale, it has become radically cheaper in recent years. The most up-to-date cost models suggest that running ten sentinel wastewater biointelligence sites would cost only around €10 million annually, whilst substantially improving our ability to detect novel and stealthy pathogens.^[8] 

The EU has already taken steps to improve its biointelligence, with the HERA-funded EU4Health programme partnering with the U.S. company Ginkgo Bioworks to develop and integrate metagenomic sequencing in EU hospitals and healthcare facilities.^[9] Whereas this is an important investment, the EU should look for  more EU-based providers for strategically important technologies, especially under the presently volatile geopolitical environment.

Building upon this development, the EU can fund initiatives to make metagenomic sequencing a routine part of environmental and clinical biointelligence programmes like the European Wastewater Surveillance Dashboard^[10] and the GLOWACON consortium,^[11]  further bolstering pandemic preparedness across the EU.^[12] Doing so through partnerships where EU companies are represented and facilitating technology transfers to internalise critical metagenomic sequencing technologies within the EU biotech system will be important to expand the EU’s capabilities within this critical domain.

B. Secure biofoundries for faster vaccines and medical countermeasures

What are they
Biofoundries are highly automated facilities equipped with robotics, AI‑driven design software and advanced DNA‑synthesis platforms that can accelerate vaccine R&D innovation cycles and shorten the time from pathogen identification to mass‑produced medical countermeasures.^[13]

Why they matter
Respiratory pandemics, antimicrobial-resistant bacteria, and engineered biothreats all demand new medical countermeasures to be discovered, tested, and produced at unprecedented speeds. Although the COVID-19 vaccine was the fastest vaccine development in history,^[14][15] it still took a total of 458 days before one billion people had been vaccinated globally – at which point 29 million had been vaccinated in the EU, covering just about 6.5% of the total EU population.^[16]

Modelling by the Lancet suggests that more than eight million lives could have been saved globally if a vaccine had been ready within 100 days of COVID being fully sequenced.^[17] Accordingly, being able to reliably develop and produce novel vaccines within 100-days is now a widely endorsed goal.^[18] However, existing capabilities for vaccine development are insufficient to reach this target.

Biofoundries can supply the infrastructure required to improve our vaccine response time in line with the 100-days mission. Because they are able to screen thousands of vaccine constructs in parallel, they can compress the design–build–test–learning cycle from months to days.^[19] They can then export validated recipes to localised manufacturing sites – reducing the need to physically transport vaccines under strictly controlled temperatures across long distances.^[20] 

However, as compared with geopolitical peers, the EU and its Member States have underinvested in biomanufacturing in recent years. Between 2016 and 2022, the US stood for 64.16% of global investment in the sector, followed by China with 20.23%. EU Member States collectively accounted for only 9.36%,^[21] and has a comparatively fragmented biomanufacturing and venture capital ecosystem. “Bold measures” are therefore required in order to secure the future competitiveness of European biomanufacturing and improve production and development timelines for medical countermeasures in Europe.^[22] 

In order to improve its biomanufacturing infrastructure in a safe and effective manner, the EU can:

• Allocate internationally competitive multi-year funding commitments to:
  • Build new biofoundries within the EU.
  • Equip existing biofoundries with next-generation robotics and software tools.
  • Train and employ the highly skilled workers required to operate advanced biofoundries.

• Enact EU-wide “Know Your Customer” (KYC) regulations. Mandate uniform KYC-standards across all European biofoundries and providers of synthetic DNA to ensure that potentially dangerous DNA does not end up in the hands of malicious actors.
• Create a Trusted Partner scheme. Certify biofoundries that meet strict security and quality criteria, unlocking preferential access to public contracts and financing.
• Articulate pre-agreed surge contracts. Establish protocols and partnerships with EU-biofoundries and regional biomanufacturing facilities to coordinate on emergency vaccine research and production in order to minimise regulatory hurdles and enhance cooperation between facilities in future crises.

Endnotes