Why the Department of Defense Should Invest in Biosurveillance

Building integrated, layered, and pathogen-agnostic detection systems
October 14th 2022


This brief recommends the Department of Defense (DoD) prioritize early warning of any biological incident in the FY24 defense budget and beyond. In particular, the DoD should deploy general purpose infrastructure for detection, characterization, and attribution of any potential pathogen in priority regions, on capabilities such as aircraft carriers, and in the homeland. DoD will benefit from two key developments: improved sequencing (the capability to identify pathogens by looking at their genetic material) and IT infrastructure to quickly analyze and communicate bioincident information to key decision-makers. The Department must also integrate incoming signals from the intelligence community into its early warning system.

Three specific recommendations include: Defense Health Agency (DHA) and Health Affairs (HA) developing an integrated data collection and analysis program that prioritizes high-information signals from new, advanced detection approaches; DHA acquiring sequencers at increasing scale for deployment at key locations, and implementing early warning capabilities for any pathogen over the next five years. 

As a result of these changes, the Department will improve its early warning of bioincidents by weeks to months at a favorable cost-benefit ratio. The cost of this system will be approximately $5m/site, including acquisitions, operating costs and 2-4 FTEs (full-time employees).


The Department of Defense faces a new threat landscape that includes increased risk of the development and use of advanced biological weapons that are engineered to complicate detection, attribution, and treatment. Currently, the Department lacks the detection capabilities for biological weapons needed to address the new threat landscape. In response to these increasing biological threats, the DoD is conducting its first ever Biodefense Posture Review. 

This brief will focus on improvements to bioweapon early warning, which will enable the DoD to respond quickly to biological incidents. The Department must detect and identify any pathogen, including those that are novel or engineered to avoid detection. A biosurveillance system that addresses the new threat landscape must be pathogen-agnostic, able to detect and characterize any biological incident without prior knowledge or selection.

We assess the public-health oriented approaches the Department has historically relied upon, and recommend they integrate improved early warning capabilities given technological breakthroughs over the last decade. While the Department’s existing approach focuses heavily on syndromic surveillance, new technology enables aggressive testing for pathogens before symptoms arise and should be deployed to complement and modernize existing efforts. Our recommendations focus on the need to invest in core infrastructure and layered capabilities that will enable the DoD to rapidly detect, identify, attribute, and characterize any pathogen, regardless of adversarial engineering efforts or non-deliberate outbreaks of novel pathogens.

We recommend that the DoD establish general-purpose detection infrastructure in key locations and effectively integrate outputs into a data collection platform to enable rapid decision making. Outputs from these detection layers can prompt decision-makers to act against deliberate biological incidents of high-consequence for the joint force, regardless of their origin. 

Current Biosurveillance Detection

Layer 1: Syndromic Surveillance — Watch for Disease

  • Syndromic surveillance was developed more than twenty years ago as a nascent form of pathogen-agnostic detection. While the term lacks a clear definition, the most common approach is for emergency-care facilities to report their chief complaints (CC) or medical histories of patients through an electronic system. An example is the Electronic Surveillance System for the Early Notification of Community-based Epidemics (ESSENCE), which is commonly used by the DoD and the Centers for Disease Control and Prevention (CDC). 
  • This detection approach relies on rapid onset of serious symptoms during a bioincident. During the COVID-19 pandemic, syndromic surveillance failed to contain the outbreak as many COVID-19 cases were asymptomatic or weakly symptomatic. Many early cases of COVID-19 were not detected, stalling and complicating early warning. The Department cannot solely rely upon this layer, especially given the ease with which adversaries could engineer around it simply by choosing pathogens with common or delayed symptoms.
  • This type of surveillance is further limited as it does not identify the pathogen responsible for the outbreak, inhibiting appropriate responses and delaying detection. It also does not aid in attribution or characterization. 
  • While syndromic surveillance will likely continue to be one layer of relatively pathogen-agnostic detection, it must be complemented with other modern detection layers.

Layers for the DoD to Fund and Deploy in FY24 

Layer 2: Multiplexed Environmental Detection at Scale — Test for more pathogens

  • Multiplexed diagnostics refer to diagnostic tests that can test for multiple pathogens at once from a single sample. For example, a platform based on gene-editing technology, mCARMEN, has targeted or multiplex capabilities for approximately 21 pathogens.
  • These platforms can conduct tests at large scale, are as accurate as PCR-based tests, and are much cheaper. The DoD can easily update and deploy these reconfigurable tests based on incoming intelligence on potential biological-weapons agents or targets. 
  • Occasionally, the DoD uses multiplexed panels to test individuals and the environment for biological-weapons agents. Operationalizing multiplexed detection more widely now will serve as a fine-grained, scalable approach to pathogen detection that can complement other detection layers.

Layer 3: Sentinel and Wastewater Detection — Test for all pathogens

  • Sentinel detection is an early warning system that tests high-risk individuals such as combatant commanders or front-line military personnel in key regions, using general purpose sequencing to detect both novel and known pathogens. 
  • Wastewater detection would apply a similar approach to testing wastewater in key military facilities. As during the COVID-19 pandemic, wastewater detection can accelerate the time from outbreak in a community to detection by multiple weeks. 
  • The only approach today that can detect all known pathogens identifies pathogens based on their genetic material. Deployed in key locations, these sequencers will serve as the most important infrastructure for early warning systems, enabling sentinel detection and wastewater detection now as well as detection approaches that are still maturing. Initial characterization to understand a novel pathogen and attribution of a pathogen’s origin can be conducted by sequencing its genetic material.


The Biodefense Posture Review and the Department’s budget process should prioritize integrated, layered, and agnostic detection systems as a major recommendation.

Specific steps for implementation:

  • The Biodefense Posture Review should include as a top-level recommendation to create integrated, layered, and agnostic detection systems for modern pathogen early warning against any biological threat, especially those that are novel and/or engineered to avoid detection from current DoD syndromic surveillance. 

The Defense Health Agency (DHA) should create layered biodefense capabilities and ensure that outputs from all biodefense layers are integrated into the Department’s data collection platforms. 

Specific steps for implementation:

  • Acquire commercial off-the-shelf capabilities for multiplexed detection at scale, in particular those that are gene-editing based are ready to be deployed. 
  • Acquire commercial capabilities to conduct pathogen-agnostic sequencing of individuals and multiplexed, targeted sequencing of wastewater. 
  • Hire and train personnel (2 FTEs/site) or use contractors to deploy reconfigurable, multiplexed tests at scale and in key locations.
  • Hire or train specialists (2 FTEs/site) or use contractors to perform next-generation metagenomic sequencing, work flows, and analysis of sequenced genomes. 
  • Work with the intelligence community to identify high-risk groups and shift the detection posture accordingly. This includes testing high-risk groups threatened with attack or reconfiguring detection methods to look for specific biological weapons or non-deliberate outbreaks of novel pathogens.
  • Develop SOPs for adjusting the biosurveillance posture as intelligence is received. As DHA creates an integrated data collection platform, it must ensure that high-information inputs, especially from multiplexed diagnostics, sentinel metagenomic sequencing, and wastewater testing are integrated as key inputs for detection of any biological incident. 

CBDP should invest in new layers that complement existing syndromic biosurveillance and commercially-available technology, especially capabilities that will develop the Department’s wastewater detection to detect any pathogen. 

Specific steps for implementation:

  • In FY2023 and FY2024 the CBDP should apply a portion of its recent funding increase to leverage private innovation and conduct challenges to detect any pathogen in wastewater.
  • The CBDP should research and develop additional pathogen-agnostic approaches, such as host-based detection, e.g., serological tests and wearables.
  • In case it is more feasible for internal reasons, CBDP should also explore acquiring and deploying pathogen-agnostic testing together with the Services and Combatant Commands. 
  • This brief recommends that DHA lead acquisition and operation of new detection capabilities. However, an additional option would be to pursue cost-sharing with other key biosurveillance actors in funding the roll out and scale up of these capabilities.

The DoD must plan for scaling up these new detection approaches in its medium-term funding plans, i.e., over the FYDP.

Specific steps for implementation:

  • In FY2024 DHA purchases multiplexed detection devices and sequencers and operationalizes testing of individuals and wastewater in INDOPACOM and EUCOM.
  • In FY2025 and beyond, DHA will fund and expand coverage of multiplexed and also pathogen-agnostic detection to eventually include the majority of U.S. military bases.


  • Early warning is a critical part of the “detect, respond, mitigate” pipeline for addressing biological incidents.
  • Integrated and layered detection are needed to support the Department’s approach of integrated deterrence. 
  • In the short term, DHA should purchase readily available technology to deploy multiplexed, rapidly reconfigurable diagnostics at scale, and establish the routine use of sentinel and wastewater sequencing to complement existing syndromic surveillance layers in key areas of operation by FY2024.
  • In the longer term, the DoD should foster innovation in pathogen-agnostic detection including for novel pathogens at scale through DoD research and development and partnerships with the private sector.
  • The Department should incorporate layered capabilities and systems in the other facets of the bioincident response, accelerating detection characterization, and attribution on the order of days to weeks.