Cambridge, Massachusetts, U.S., September 23, 2026
Flagship Pioneering has secured a first-of-its-kind contract worth up to $47 million over five years under the ONTARGET program—Operationalizing Novel Technologies for Advanced Rapid Generation of Effective Medical Countermeasures—to advance biotechnology platforms designed to address evolving biological threats. The agreement establishes a framework through which technologies from Flagship’s ecosystem can be evaluated for their potential to accelerate the discovery and development of next-generation medical countermeasures (MCMs). Rather than focusing on one predetermined product, the program will assess multiple platform technologies spanning translational science, drug development, platform engineering, enabling technologies and artificial intelligence/machine learning. Initial projects will involve Flagship-founded Apriori Bio and Prologue Medicines, while additional programs may be introduced during the five-year agreement. The contract will be administered through Flagship Health Security Corporation, a new Flagship subsidiary created to facilitate government partnerships.
ONTARGET Targets Next-Generation Medical Countermeasures
The ONTARGET program is designed to identify and mature promising biotechnology platforms that could improve preparedness against emerging, adaptive and engineered biological threats. The program focuses on several technology areas, including broad-spectrum medical countermeasures, precision delivery technologies, toxin-neutralizing platforms, immune enhancement, disruption of viral pathways and AI/ML-enabled countermeasure discovery. Flagship’s ecosystem includes more than 40 companies and provides access to a broad range of scientific technologies rather than a single drug-development platform. This portfolio-based structure is intended to allow promising technologies to be evaluated and advanced as biological threats and medical countermeasure requirements evolve. The program is managed by the Joint Science and Technology Office within the Chemical and Biological Defense Program, with the goal of accelerating development timelines and improving the performance of medical countermeasures. The initial funding will support proof-of-concept research, while further projects may be selected throughout the contract period depending on their potential applications.
Apriori Bio Uses AI to Anticipate Viral Evolution
One of the first projects will involve Apriori Bio and its Octavia™ platform, a biology-enabled artificial intelligence technology designed to support development of variant-resilient medical countermeasures. Octavia is intended to analyze how viruses may evolve and identify approaches capable of maintaining protection as new variants emerge. Under the program, Apriori Bio will use the platform to generate one or more stable, cross-protective candidates. By anticipating viral evolution rather than responding only after a new variant becomes established, the technology could potentially shorten development timelines and improve preparedness for rapidly changing biological threats. The approach reflects a broader trend across biotechnology in which AI and machine learning are being integrated into therapeutic and vaccine discovery to analyze complex biological datasets and prioritize candidates more efficiently. The ONTARGET project will provide proof-of-concept funding to evaluate whether Apriori’s platform can contribute to faster and more adaptable medical countermeasure development.
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Prologue Medicines Advances Immune-Modulating Technologies
The second initial project involves Prologue Medicines, which will apply its DELVE platform to discover biological functions capable of modulating and enhancing human immune responses. DELVE uses advanced AI approaches to analyze millions of viral proteins and identify evolutionarily optimized functions that could potentially be applied to medical countermeasure development. The program aims to identify technologies that could strengthen immune resilience and enable rapidly adaptable countermeasures against a broad range of emerging and engineered threats. Together, the Apriori Bio and Prologue Medicines projects demonstrate two complementary strategies: anticipating viral evolution and identifying biological mechanisms that could improve immune protection.
The agreement also creates an opportunity for additional technologies from Flagship’s ecosystem to enter the ONTARGET program during the five-year contract period. Flagship has created and developed biotechnology companies spanning therapeutics, genetic medicine, artificial intelligence and platform-based drug discovery, providing a broad technology base that could potentially contribute to medical countermeasure research. However, the current projects remain at the proof-of-concept and development stage, and the contract itself does not demonstrate that resulting candidates will ultimately prove safe, effective or receive regulatory approval. For the biopharmaceutical sector, the program highlights growing interest in combining AI-enabled drug discovery, immunology, antiviral research and biotechnology platforms to improve preparedness against rapidly evolving biological threats. The initial Apriori Bio and Prologue Medicines programs will help determine whether these technologies can generate promising candidates for further development, while future projects could broaden the range of approaches evaluated under the ONTARGET framework.
Source: Flagship Pioneering press release
