Threat Agnostic Epidemiology and Surveillance in US Public Health Agencies: Future Potential and Needs

Introduction

As the frontline of the US public health system, applied epidemiologists at state, tribal, local, and territorial health agencies play a critical role in biodefense and ensuring the nation's health security by collecting, analyzing, interpreting, and disseminating data to minimize the impacts on the population's health during infectious disease outbreaks and human-induced or severe weather events. Epidemiology, biodefense, and health security more broadly are inextricably linked, as evidenced through public health emergencies including the HIV/AIDS epidemic, the 2009 H1N1 influenza pandemic, the 2014-2016 West Africa Ebola outbreak, and more recently the COVID-19 pandemic and mpox outbreak.

The National Biodefense Strategy describes a need for increased epidemiologic surveillance and laboratory capacities, including trained staff, updated and modernized surveillance systems, and interoperability between systems within the larger health security and national security enterprise. ¹ Preparing for the next large-scale outbreak or pandemic response necessarily involves improving detection and response capacity for currently unrecognized pathogens using threat agnostic approaches. There are many new promising scientific technologies and methods that will enhance threat agnostic capability; however, for these approaches to be implemented in public health practice, investments in the applied epidemiology workforce, training, and public health data systems are needed. In this commentary, we review key areas of epidemiology and surveillance practice, data modernization, and workforce capacity in US public health agencies related to threat agnostic approaches and we highlight areas of need and recommendations to support epidemiology within the health security enterprise.

Epidemiology and Surveillance Practice

Applied epidemiologists are at the epicenter of efforts to monitor and assess the public's health. Their toolbox includes a variety of methods for threat agnostic surveillance, including syndromic surveillance, electronic laboratory and case reporting, and wastewater surveillance. The existing public health data infrastructure and community partnerships allow epidemiologists to quickly identify emerging threats, collect and interpret data to inform actions, and relay information to colleagues nationwide to protect the public's health. Inclusion and engagement of applied epidemiologists and their tools are essential for threat agonistic surveillance and detection.

At its core, expansion of threat agnostic detection and characterization approaches to public health surveillance in the United States will rely on investment in diagnostics and ensuring access to testing. Current patient testing and public health surveillance systems rely on pathogen-specific diagnostic tests that require the patient to physically enter the healthcare setting to provide a specimen for testing. This traditional testing pathway presents many impediments to a threat agnostic approach to public health surveillance, especially for populations with healthcare access disparities (eg, uninsured, racial and ethnic minorities, persons with disabilities, those in rural areas or with transportation barriers). ² Each step along the traditional testing pathway introduces opportunity for missed detection; for example, if the patient delays presentation for testing, the provider does not perform testing, the optimal specimen and test type for the pathogen present is not collected, or positive results are not reported to a public health agency for surveillance and investigation. New approaches that intercede at key points in this testing pathway are needed to improve the timeliness and likelihood of detecting a potential public health threat.

The COVID-19 pandemic provided an opportunity to implement new approaches to patient testing and public health surveillance that may have future applications to threat agnostic detection. Diagnostic preparedness, the need for rapid access to diagnostics during a pandemic, has been a recognized priority for pandemic planning prior to COVID-19. ³ While the importance of rapid access to diagnostics is widely acknowledged, assays to detect SARS-CoV-2 virus were one of the earliest limited resources within the COVID-19 response, which highlighted the urgent need for continued global investment and planning in diagnostic preparedness for early detection of known or unknown pathogens (ie, “pathogen x”). Once SARS-CoV-2 assays were available, mass testing sites and home tests helped reduce barriers to testing, especially in underserved communities, and may be a promising practice for future outbreak response.^4-6 While home testing increased access and positive predictive values of tests were high, interpretation of negative results remained a concern. ⁷ Another limitation of home testing was the lack of reporting to public health agencies due to testing occurring outside of the healthcare setting, and therefore the results were not incorporated into situational awareness and response activities. Home testing may hold promise for future threat agnostic surveillance approaches, though additional research and creative solutions are needed to address challenges around communication, test performance, and public health reporting mechanisms, especially for high-consequence threats.

One surveillance approach that circumvents barriers associated with patient specimen collection altogether is wastewater surveillance. The detection of SARS-CoV-2 in wastewater made it possible to implement surveillance strategies to monitor COVID-19 community transmission, showing utility for outbreak recognition and early detection of emerging variants.^8,9 While SARS-CoV-2 was an initial focus area for wastewater surveillance in US public health agencies, recent detections of polio, influenza, and mpox viruses have raised important questions and highlighted critical challenges associated with wastewater surveillance for epidemiologists.^10-12 Wastewater surveillance holds promise for pathogen agnostic threat detection using metagenomic sequencing, a method used to detect any potential pathogen in a sample. However, wastewater surveillance is an emerging area of science and public health practice with considerations and challenges that need to be further explored and addressed. These include technical challenges (eg, lack of standard protocols, metagenomic method development to detect low concentrations of a novel pathogen in wastewater given the expected high levels of normal gastrointestinal microbes) and challenges related to interpretation and communication of results; defining appropriate use cases for wastewater surveillance and associated benefits and limitations; and addressing legal, ethical, and regulatory issues.

Like wastewater surveillance, genomic surveillance capabilities in US public health agencies grew substantially during the COVID-19 pandemic, driven by significant federal investments in funding for epidemiology and laboratory genomic sequencing activities. ¹³ Genomic surveillance has been critical to monitoring the emergence of SARS-CoV-2 variants, predicting surges in activity prior to their occurrence, and informing public health decisionmaking (eg, vaccine development and recommendations).^8,14 Genomic sequencing has been a critical tool for public health investigation across a range of pathogens, although the resources for such testing are limited and generally applied to specific pathogens and/or scenarios. Metagenomics has tremendous potential for both public health and clinical application and could be revolutionary for detecting novel pathogens and investigating outbreaks of unknown etiology. However, as an emerging field, there are limitations (eg, cost, expertise, resources to support it) and challenges to address around interpretation and communication of results, public health reporting, and legal, ethical, and regulatory issues.^15,16 Implementation of metagenomics in public health practice would require investments in workforce training and public health data systems.

The laboratory detection of pathogens is critical, but it must be paired with epidemiological information (eg, information about the person affected) for complete understanding of a health threat. As such, these novel and innovative laboratory surveillance data streams need to be effectively integrated at the patient level with epidemiological data, which requires continued investment in data systems and data linkage as well as trained epidemiology personnel to collect and analyze information and conduct investigations. Epidemiology data systems must be continuously maintained and improved over time to support health outcomes surveillance across the spectrum of illness, from early onset of symptoms (eg, outpatient and emergency department visits) to clinical diagnosis (eg, case-based surveillance) and severe outcomes (eg, hospitalizations, deaths). These data can be integrated, visualized, and made available for public health decisionmaking to implement control measures and prevent illness. They can also be effectively used to model the impact of potential interventions and to forecast the trajectory of outbreaks and epidemics. ¹⁷ Continued innovation to advance these disease surveillance approaches should be pursued and can be applied to future threat agnostic detection systems.

Data Modernization

The COVID-19 pandemic challenged assumptions and reemphasized prepandemic reflections on the critical need to improve the public health data infrastructure. Strategically advancing technology for public health surveillance across the entire system is essential to strengthening the nation's biodefense capacity and enhancing its health security infrastructure to prepare for future threats. Each expanded and innovative detection approach has the potential to generate massive amounts of data and new core data sources. For a coordinated response to emerging threats, newly generated data must not reside in silos; modernizing public health infrastructure for interoperability in data exchange will be an ongoing key principle to ensure the impact of leveraging data for action is realized. Data reported to public health authorities must fully adhere to national standards and implementation guides, and data quality and completeness must improve to render these sources sufficient and valuable for analysis and action.

Historically, public health agencies have not had the resources to maintain critical upgrades or acquisitions of new software platforms for their data systems and resources, which have consequently remained technologically behind.^18,19 While the federal government has provided short-term boluses of funding in response to the COVID-19 pandemic, total funds distributed in reaction to public health events fall short of what is needed for daily operations, let alone future responses. Continued and sustained investments in public health data infrastructure remain necessary.

Successes achieved during the COVID-19 pandemic included public health agencies managing the exponential increase in incoming laboratory results from nontraditional partners acting as testing sites. Public health and clinical healthcare collaborated to implement automated reporting methods, such as expansion of electronic laboratory reporting, standardized-state flat-file formats, conversion tools to translate alternate forms into electronic laboratory reporting standards, and intermediary tools and federal reporting technology platforms (eg, SimpleReport, the Association of Public Health Laboratories' Informatics Messaging Services). This forward-thinking joint implementation of modern technology has allowed public health agencies nationwide to adapt to meet pandemic-related reporting requirements and be better positioned for future responses to health threats.

Critical standards governing data elements and exchange mechanisms have not kept pace with technological advancement and ongoing revisions are needed to support end-to-end interoperability for threat agnostic detection and response. Collaborative ongoing development and full adoption of standards across clinical healthcare, public health, and private industry could specifically target barriers to data exchange. Although emerging infectious diseases pose challenges to anticipating essential data elements, best practices in epidemiology can be used to identify a set of predetermined data elements for early situational awareness in the public health response to an emerging threat. Collaboration is underway across the public health ecosystem to establish these standard core data elements to reduce response time and improve data-driven decisionmaking in the early phases of a response. Further necessary efforts include wide adoption of standardized data elements and reporting methods between clinical healthcare and public health, and targeted increases in completeness and quality of key data. Joint initiatives across clinical healthcare and federal public health organizations are underway, including the United States Core Data for Interoperability (USCDI)/USDCI+, Trusted Exchange Framework and Common Agreement, Qualified Health Information Network(s), and Fast Healthcare Interoperability Resources, with intent to scope connectedness and usability for public health surveillance. These joint efforts should continue to be funded and supported, incorporating real-world testing and early consultation with applied public health professionals to vet use cases and applicability.

Federal funding related to the Data Modernization Initiative equipped jurisdictions to complete assessments and develop strategic plans, which has laid the groundwork for targeted improvement to address the variation in jurisdictional landscapes while simultaneously coordinating national targets. Public health agencies at the state and local levels have also leveraged this funding to begin necessary technical projects to modernize systems and data infrastructure. ²⁰ Intentional, proactive investment in the public health ecosystem—including supporting public health agencies with sustainable, flexible funding that allows for innovation to address data modernization—is essential to the nation's health and national security to prepare for future public health threats.

Workforce Development and Capacity Building

Ensuring capacity for threat agnostic epidemiology, surveillance, and modernized data systems in US public health agencies requires a robust and well-trained public health workforce. The Council of State and Territorial Epidemiologists (CSTE) has enumerated and described the applied epidemiology workforce since 2001 through the Epidemiology Capacity Assessment. The most recent assessment was conducted in 2021 amid the COVID-19 pandemic. Most state health departments reported substantial to full capacity to monitor the health status of their communities (76%) and to investigate health problems and hazards (88%). ²¹ From 2017 to 2021, the number of applied epidemiologists working in state health departments increased 23% from 3,370 to 4,135. However, CSTE estimates that an additional 8,000 applied epidemiologists are needed to fill positions across all state, tribal, local, and territorial health departments. ²² Among the epidemiologist positions reported in the 2021 Epidemiology Capacity Assessment, over 60% supported infectious disease (1,498) or COVID-19 (978) activities, 5.9% (198) focused on informatics and 3.8% (127) on preparedness, and only 0.1% (5) supported genomic activities. ²¹ These data highlight significant gaps in noninfectious disease program areas and raise concern for the nations' all-hazard epidemiologic preparedness and response capacity.

Epidemiologists are in a unique role to collect and interpret data to inform public health response and policymaking, yet ensuring mechanisms are in place prior to a response is essential. ²³ Epidemiologists should be familiar with the available data systems and community partners to collect and interpret data in a meaningful way for prioritizing public health intervention. The epidemiologists who collect and analyze surveillance system data and conduct investigations in response to threat detections require regular technical training to stay up-to-date on best practices and crosscutting skills to ensure a nimble epidemiology workforce that can readily adapt to the needs of future public health threats. The use of wastewater surveillance and genomic surveillance for COVID-19 generated useful data to inform response, but the epidemiology workforce had to both practice these novel methods and learn about them simultaneously. To promote readiness among the applied epidemiology workforce, ongoing professional development opportunities should focus on data science, cross-disciplinary collaboration (eg, solution-oriented collaboration across laboratory, epidemiology, and informatics staff), and emerging surveillance methodologies and practices.

The current role of the epidemiologist supporting public health activities is frequently restricted by grant requirements that negatively affect an agency's ability to respond to emerging and future unknown threats. Future funding models should be less restrictive and adopt a flexible epidemiologist model. ²⁴ The flexible epidemiologist can work across multiple diseases and topics and is essential for pandemic response and to address emerging threats. Recent experience with e-cigarette or vaping use-associated lung injury, Zika virus, and COVID-19 illustrates that effective public health response requires subject matter expertise and skills across topic areas (eg, injury and outbreak response, maternal and child health, environmental health) and relies on the entire trained workforce to support operations during an extended response. Additional trained staff can offer support for the primary staff lead and alleviate the burden of an extended response to minimize burnout.

States have relied heavily on federal partners to fund epidemiology activities and personnel. In 2021, 85% of epidemiology activities and 83% of epidemiology personnel were funded with federal dollars. ²¹ COVID-19 federal funds that supported pandemic response injected significant resources into public health but are not intended to be a permanent resource. ²⁵ The eventual fiscal cliff will leave funding for epidemiology vulnerable to cuts that will risk progress made. While the US Centers for Disease Control and Prevention (CDC) Public Health Infrastructure Grant (CDC-RFA-OE22-2203: Strengthening US Public Health Infrastructure, Workforce, and Data Systems Notice of Funding Opportunity) has emerged as a funding resource for current state and local health department modernization activities, the ongoing reliance on congressional appropriations and subsequent distribution by CDC on an annual basis adds challenge to planning projects with longevity. The lack of sustained funding and loss of current time-limited, supplemental funding risk delaying the modernization of the public health data system and inhibiting the hiring and retention of key staff who support daily operations. Ultimately, the work of data modernization will remain “under construction” until sufficient funding to support systems and skilled staff are consistently available, which impedes the US public health system's ability to effectively implement and leverage threat agnostic surveillance approaches in the future.

Conclusion

Epidemiologists play a key role in connecting the public's health to the nation's security by bringing subject matter expertise, technical skills, and nontraditional national security enterprise partners to the table. The 2021 Global Health Security Annual Report references achievements and impacts in multiple technical areas including zoonotic diseases, surveillance, emergency response operations, and emergency preparedness. ²⁶ Historic, recent, and future achievements in health security are contingent on robust, connected, and interoperable applied epidemiology and surveillance technologies, systems, personnel, and corresponding sustainable funding. Strategies aimed at developing and enhancing epidemiology and surveillance capacity in US public health agencies to support threat agnostic detection and response are urgently needed to ensure readiness for future public health threats (Box). Taking a threat agnostic approach to biodefense is to approach biodefense through the lens of applied epidemiology.