Information on Biothreat Pathogens, Agents & Syndromes
Below are various fact sheets that will help clarify distinctions between biological and chemical threats, as well as provide more detail on biothreat characteristics, patterns, and associated risks.
- CDC Bioterrorism Agents. Centers for Disease Control and Prevention. The prominently cited list for Category A, B, and C bioterrorism agents, with details regarding the various associated risks.
- Biological Attack Human Pathogens, Biotoxins, and Agricultural Threats Fact Sheet. U.S. Department of Homeland Security and the National Academies. A fact sheet from DHS and the National Academies that defines biological attacks, details how agents may be developed and disseminated, describes the impact and risks following the release of a pathogen, and describes practical measures to take in the case of an attack.
- Public Information on Biological & Chemical Threats. World Health Organization. Details on the incubation period, or the time between exposure to an agent and the manifestation of illness, modes of transmission, the progression of illness and treatment for each disease has been provided for the biological threats listed.
- Agent Fact Sheets. Johns Hopkins School of Public Health Center for Health Security. Fact sheets with in-depth background information on a variety of biological and chemical agents.
Relevant Papers & Studies
Entrants are not required to have a deep background in biothreats, biosurveillance, or biosecurity to compete. Below are some relevant studies and examples of similar work that may help orient newcomers to the problem space.
- 2007 HSPD-21 Public Health and Medical Preparedness. In this directive the White House formally defined biosurveillance as “the process of active data-gathering with appropriate analysis and interpretation of biosphere data that might relate to disease activity and threats to human or animal health— whether infectious, toxic, metabolic, or otherwise, and regardless of intentional or natural origin—in order to achieve early warning of health threats, early detection of health events, and overall situational awareness of disease activity.”
- 2012 National Strategy for Biosurveillance calls for the Federal Government, acting across all levels of government (including state, local, territorial, and tribal [SLTT]) and with private sector partners, to: (1) integrate capabilities, including combining human, animal, and plant health data in what is now termed a “One Health” approach; (2) build capacity, including development and use of point-of-care diagnostics; (3) foster innovation, including new detection and health information exchange approaches; and (4) strengthen partnerships domestically and internationally.
- Biosurveillance: A Review and Update. Advances in Preventative Medicine. This paper focuses on the ways by which we detect bioterrorism agents and the effectiveness of various systems, such as syndromic surveillance, laboratory surveillance, and environmental surveillance.
- DHS Real-Time Biothreat Awareness Apex Infographic. S. Department of Homeland Security. Infographic describes the Biothreat Real-Time BioThreat Awareness program (Note: Program no longer active), which aimed to provide timely information to multiple authorities, enabling a collaborative, confident, and effective response that ultimately minimizes the impacts of a biological incident.
- Early Work on “One Health” Biosurveillance. Tom Slezak. This presentation discusses details of the National Strategy for Biosurveillance, including various definitions of biosurveillance, the biggest problems this strategy aims to address, and specific issues that Mr. Slezak has observed.
- Global Capacity for Emerging Infectious Disease Detection, 1996–2014. This report evaluates global improvements in the timeliness of outbreak discovery and communication during 2010–2014 as a follow-up to a 2010 report.
- Investing in Transformational Ideas, Innovative People, and Actionable Technology Development for Chemical Biological Defense Solutions. Jason Paragas. This presentation discusses evidence of a growing bioterror threat, the global engagement required to address preparedness, and examines three key strategic thrusts: (1) Disease Surveillance, (2) Rapid Threat Detection, and (3) Point of Need Diagnostics.
- In-Q-Tel’s B.Next Article Repository and Reading List.
Relevant Lessons from Analogous Efforts
When looking at the results from analogous efforts in biosurveillance, as well as adjacent innovation efforts in other industries and problem spaces, entrants can glean valuable lessons about anomaly detection, creative uses of data, emergency response and more.
- Data Mining and Machine Learning in the Context of Disaster and Crisis Management. International Journal of Emergency Management. The advances in information technology have made unprecedented volumes of data available to disaster management decision makers, however, this has also led to new challenges in effective management of large volumes of data. This paper explores the application of machine learning and data mining techniques to support the decision-making process for disaster and crisis management.
- Effectiveness of National Biosurveillance Systems: BioWatch and the Public Health System: Interim Report. Institute of Medicine and National Research Council of the National Academies. This paper evaluates the effectiveness of DHS’s BioWatch program, under which DHS has deployed air samplers, primarily in outdoor locations, in more than 30 major cities with the aim of early detection and characterization of aerosolized biological threats.
- Event-based Internet Biosurveillance: Relation to Epidemiological Observation. Emerging Themes in Epidemiology. This paper examines the reliability of internet biosurveillance and evaluates disease-specific alert criteria against epidemiological data by reviewing and comparing WHO epidemiological data and Argus biosurveillance system data (Note: Project Argus is no longer active) for the H1N1 2009 pandemic.
- How AI Will Change the Way We Make Decisions. Harvard Business Review. This article explores the example of credit card fraud detection in order to examine the roles of prediction and judgement in decision-making, and how AI predictive algorithms and human judgement can work together.
- One Year Later–Implementing the Biosurveillance Requirements of the 9/11 Act: Testimony from Principle Investigator Wilson. Committee on Homeland Security. Wilson led the team on Project Argus. Speaking on the challenges Project Argus faced: “Despite our best efforts, there were operational restrictions which prevented Argus from reaching its full potential. Most importantly, we were unable to analyze domestic data, leaving a tremendous blind spot in the system. In addition, we were unable to work with international partners in order to validate our findings. We were also unable to share vital information with the global health community. These restrictions were mission crippling.”
- System Set Up After SARS Epidemic Was Slow to Alert Global Authorities. Washington Post. This article looks at the delay between disease outbreak and official alerts, by examining the chain of events in Mexico’s swine flu outbreak (2009), alongside the development of WHO’s pandemic response system and the revised International Health Regulations.
Below are a range of city data hubs, public data repositories and digital epidemiology tools designed to serve as starting points. Please note that not all of these data resources are updated in a timely or consistent and sustainable manner. There are many publicly available data sources and entrants are encouraged to continue to exploring beyond this list in search of the best data to support real-time detection.
City Data Hubs
- Analyze Boston. Includes data related to: geospatial, city services, permitting, environment, finance, public safety, economy, and transportation.
- City of Boston City Score. Example of an open data resource that correlates data sets for various city-level insights.
- Atlanta Regional Commission. Includes data related to: boundaries, community facilities, demographics, education, employment, environment, health and transportation.
- Chicago Data Portal. Includes data related to: buildings, community, education, environment, events, health and human services, parks and recreation, public safety, sanitation, service requests and transportation. Many of these datasets are updated at least once a day, and many of them updated several times a day
- City of New Orleans Open Data. Includes data related to: city administration, demographics, economy and workforce, environment, geographic base layers, health, education, social services, housing, land use, blight, parks, parkways, public safety and preparedness, transportation and infrastructure.
- City of Palo Alto Open Data Portal. Includes data related to: 3-1-1, city services, sustainability, city infrastructure, parks & open space, and emergency preparedness.
- City of Providence Open Data Portal. Includes data related to: economy, neighborhoods, public safety and reference, CodeRED Emergency Communications, open meetings, open budget and open checkbook.
- City of Seattle Open Data Portal. Includes data related to: city businesses, community organizations, neighborhoods and initiatives, education, finance, land base (with GIS layers), permitting, public safety, and transportation.
- Civic Apps for Greater Portland. An inter-jurisdictional repository of local public data, organized in chronological order.
- DataSF. Includes data related to: economy and community, city management, transportation, public safety, health and social services, geographic locations and boundaries, energy and environment, housing and buildings, and city infrastructure.
- Los Angeles GeoHub. Platform for exploring, visualizing and downloading location-based Open Data. Includes data related to: business, boundaries, health, infrastructure, planning, recreation and parks, safety, schools, and transportation.
- NYC Open Data. Includes data on: business, city government, education, environment, health, housing, public safety, recreation, social services, and transportation.
- Official City of Austin Open Data Portal. Includes data related to: transportation, health, neighborhoods, public safety, capital projects, open performance portal, city council, and finance.
- Open Baltimore. Includes data related to: city government, city services, housing, crime, finance, geography, health, neighborhoods, public safety, public works, and transportation.
- Open Colorado Data Catalog. A centralized resource for local governments and other organizations around Colorado to share open data. Includes data sets related to budget, crime, GIS, health, and transportation.
- Open Data Philly. Includes data related to: budget, economy, education, environment, food, health and human services, parks and recreation, planning, public safety, real estate, and transportation.
- Open Data Houston. Includes data on: geographic boundaries, planning, public works and engineering, permitting, public health and safety, administration, neighborhood services, finance, environmental, property, flood hazards, and parking.
Public Data Repositories
- ArcGIS Hub Open Data search function run by ESRI, that pulls from approx. 77,000 data sets across the U.S.
- CDC Wonder. Wonder online databases utilize a rich ad-hoc query system for the analysis of public health data. Reports and other query systems are also available.
- Data.gov. The home of the U.S. Government’s open data.
- Open Government lists of resources by State and City.
- Data USA. A tool created by Deloitte, Datawheel, and a professor from MIT Media Lab. Data USA is the most comprehensive website and visualization engine of public US Government data, and through advanced data analytics and visualization, it tells stories about places in America, industries, education and skills. This is a good example of using open data to develop insights across the country.
- Enigma Public Data. A broad collection of public data, with curated collections by Enigma, across companies, governments, organizations, the U.S, and Universities.
- Google Public Data Explorer. A Google search function for public data.
- National Health and Nutrition Examination Survey (NHANES) database. A program of studies designed to assess the health and nutritional status of adults and children in the United States, combining interviews and physical examinations.
- Open Database Resource List for the Open Science Prize.
Digital Epidemiology & Health Information Tools
- CDC Epi Info™. A public domain suite of interoperable software tools that provide for easy data entry form and database construction, a customized data entry experience, and data analyses with epidemiologic statistics, maps, and graphs for public health professionals who may lack an information technology background. Epi Info™ is used for outbreak investigations; for developing small to mid-sized disease surveillance systems; as analysis, visualization, and reporting (AVR) components of larger systems; and in the continuing education in the science of epidemiology and public health analytic methods at schools of public health around the world.
- HealthMap. An established global leader in utilizing online informal sources for disease outbreak monitoring and real-time surveillance of emerging public health threats. The freely available Web site ‘healthmap.org’ and mobile app ‘Outbreaks Near Me’ deliver real-time intelligence on a broad range of emerging infectious diseases for a diverse audience including libraries, local health departments, governments, and international travelers.
- NextStrain. An open-source project to harness the scientific and public health potential of pathogen genome data. We provide a continually-updated view of publicly available data with powerful analytics and visualizations showing pathogen evolution and epidemic spread. Our goal is to aid epidemiological understanding and improve outbreak response (Winner of the Open Science Prize in 2017).
- OIE World Animal Health Information System (WAHIS). An internet-based system that processes data on animal diseases in real-time and informs the international community via an early warning system. Access to this secure site is only available to authorized users, namely the Delegates of World Organisation for Animal Health (OIE) Member Countries and their authorized representatives, who use WAHIS to notify the OIE of relevant animal disease information.
- Open Epi: Open Source Epidemiologic Statistics for Public Health. Free and open source software for epidemiologic statistics. The programs can be run in the browsers of many iPhone and Android cellphones.
- Wildlife Health Information Sharing Partnership – event reporting system (WHISPers). A Wildlife Health Information Sharing Partnership event reporting system with current and historic information on wildlife morbidity or mortality events in North America. Events typically involve five or more sick or dead wild animals observed in the same general location and time period. This information is collected opportunistically and provided here by multiple State, Federal, and other agencies to enhance collective understanding of disease in wildlife populations.
Existing Analogous Systems & Tools
Entrants can look to analogous systems and tools for inspiration, as well as for examples of systems that a solution may ultimately complement.
- BioWatch: DHS’s original response to the Amerithrax crisis. Deployed in more than 30 metropolitan areas, BioWatch uses air sampling equipment and program stations to collect samples over a 24-hour collection period. The samples are then taken to a lab for analysis to detect aerosolized biological threat agents of concern. Current manpower and the need to remotely test the samples does not allow for a shorter collection period. The complete process, therefore, can take anywhere between 12 and 36 hours, may allow for a pathogen to be widely spread before it is detected, and may hinder situational awareness and efforts at interdiction.
- Ongoing Challenges and Future Considerations for DHS Biosurveillance Efforts. S. Government Accountability Office (GAO). GAO reports on the progress and challenges with two of DHS’s biosurveillance efforts—the National Biosurveillance Integration Center (NBIC) and the BioWatch program.
- DHS National Biosurveillance Integration Center (NBIC). NBIC seeks to enable early warning and shared situational awareness of acute biological events in order to support better decisions and effective national responses, through rapid identification, characterization, localization, and tracking. NBIC has played a large role in developing various systems and tools for biosurveillance (e.g., NCB-Prepared).
- DoD DTRA Biosurveillance Ecosystem (BSVE). A rapidly emerging capability being developed by the DTRA Chemical and Biological Technologies Department to enable real-time biosurveillance for early warning and course of action analysis.
- Early Aberration Reporting System (EARS). EARS is a web-based, adaptable syndromic surveillance tool used by public health officials in the United States and abroad. This tool analyzes syndromic data from emergency departments, 9-1-1 calls, and physician offices. The analyzed data might include signs and symptoms such as abdominal pain, breathing difficulty, or back pain. EARS can also incorporate school and business absenteeism data and data from over-the-counter drug sales, and ambulance run data into its analysis. Identified deviations in current data are compared to a historical (five year) or nonhistorical (seven day) mean. The output includes tables, graphs, and maps that indicate geographic locations of aberrations. The EARS aberration detection measures appear sensitive enough to serve as an early warning system for bioterrorism events, though it appears to apply mostly to local-level warnings, rather than national-level warnings. (Online Journal of Issues in Nursing).
- Electronic Surveillance System for the Early Notification of Community-Based Epidemics (ESSENCE). ESSENCE was created to offer a disease surveillance tool that can be efficiently deployed on a stand-alone computer in diverse settings, and it monitors and provides alerts for rapid or unusual increases in the occurrence of infectious diseases and biological outbreaks. ESSENCE provides interactive reporting, structured analysis, ad hoc queries of disease syndromes, disease and injury categories, and reportable medical events, as well as detection and alerts based on International Classes of Diseases Version 10 codes, pharmacy prescriptions, radiology and laboratory test orders, and advanced text parsing of patient chief complaints.
- FirstWatch®. FirstWatch® Real-Time Early Warning System is a syndromic surveillance system that monitors 9-1-1 calls, law enforcement, fire, and emergency medical services data from computer aided dispatch (CAD), ProQA advanced telephone triage, and poison control center data for patterns that suggest a threat to public safety or health. It also can include hospital emergency department records, nurse-call triage information, hospital diversion data, and field data in the analysis of a potential threat. Users can customize the system’s real-time analysis to meet their region’s surveillance needs. In addition to alerts, output includes charts, graphs, and maps that indicate the distribution of suspicious events.
- National Syndromic Surveillance Program: BioSense Platform. The NSSP provides syndromic surveillance practitioners access to and use of the cloud-based BioSense Platform, a secure integrated electronic health information system with standardized analytic tools and processes. These tools enable users to rapidly collect, evaluate, share, and store syndromic surveillance data. By using the BioSense Platform, health officials can analyze syndromic data to improve their common awareness of health threats over time and across regional boundaries. ESSENCE (see above) is the platform’s primary syndromic surveillance tool (CDC).
- RAMBO (rapid-air monitoring particles against biological threats) project. The design of the final RAMBO system foresees the use of two miniaturized sensors: (1) Surface-enhanced Raman spectroscopy (SERS) provides an early warning of the presence of a bio-agent, and (2) Polymerase chain reaction (PCR), based upon the presence of bio-agent nucleic acid sequences, for the final confirmation of positive detection. The combination of SERS + PCR in a microfluidic cell enhances the reliability of the sensor detection.
The below information on various privacy policies may be helpful to entrants as they consider the types of privacy constraints their Stage 1 submissions may face.
- DHS Privacy Compliance. A summary of DHS’s privacy compliance process and documentation.
- HHS Health Information Privacy. Information on HIPAA access rights and more.
- HHS 45 CFR 46 Sub-Part A: Basic HHS Policy for Protection of Human Research Subjects. Details regulations on human research subjects, including data.
- DHS Handbook for Safeguarding Sensitive Personally Identifiable Information. Guidelines for how to identify and protect Sensitive Personally Identifiable Information (PII).
- Guide to Protecting the Confidentiality of Personally Identifiable Information (PII): Recommendations of the National Institute of Standards and Technology. Guidelines for a risk-based approach to protecting the confidentiality of PII.
Note: All links are provided for informational purposes only.