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Creating a Blueprint for the Future: Lessons Learned From Public Health Laboratories in the COVID-19 Response

Toney, Denise PhD, HCLD; Pentella, Michael PhD, MS, D(ABMM); Blank, Eric DrPH; Becker, Scott MS

Author Information
Journal of Public Health Management and Practice: January/February 2021 - Volume 27 - Issue - p S101-S105
doi: 10.1097/PHH.0000000000001285
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Abstract

Public health laboratories have played a crucial role in the COVID-19 response since the Centers for Disease Control and Prevention (CDC) diagnosed the first case1 in the United States on January 20, 2020. In the months that followed, federal, state, and local public health laboratories worked almost nonstop to meet an unparalleled demand for SARS-CoV-2 testing. At the time of this writing, the demand was still growing.

As leaders in the public health laboratory community, we have examined the initial laboratory COVID-19 response to identify what has worked, evaluated problems, and considered next steps and adjustments needed to strengthen responses to future crises. This article presents our findings and recommendations.

It should be noted that public health laboratories, like other spheres of public health, remain chronically underfunded. Years of budget cuts and inconsistent federal and state resources have led to staffing shortages, high turnover, supply chain deficiencies, closures, and lack of high-throughput equipment with modern robotics. Funding issues ultimately compromise the ability of public health laboratories to keep pace with the demands of any crisis. This article explores the public health laboratory response with the understanding that adequate funding is essential for any real and sustained progress.

This article includes observations from leadership at the Association of Public Health Laboratories (APHL) based on member feedback via weekly surveys. It is also based on interviews with the directors of the Iowa State Hygienic Laboratory and the Virginia Division of Consolidated Laboratory Services. Virginia and Iowa represent the spectrum of APHL laboratories throughout the United States: As a sizable laboratory serving a large, diverse population, Virginia aligns with the experiences of public health laboratories in hot spots such as New York, California, and Florida. Iowa serves a smaller, more rural population as is typical of much of the Midwest.

Public Health Laboratories: An Overview

Public health laboratories focus on diseases and the health status of population groups. They perform limited diagnostic testing, reference testing, and disease surveillance. They also provide emergency response support, perform applied research, and offer training for laboratory personnel in other laboratories. Equipped with sophisticated instrumentation and staffed by highly trained scientists, these institutions deliver services that may be unavailable or cost-prohibitive elsewhere.2

Collectively, public health laboratories form the backbone of a national laboratory network on alert 24/7 to respond to novel strains of disease, natural disasters, chemical spills, foodborne outbreaks, and other health emergencies. They collaborate closely in these efforts with the CDC and the US Food and Drug Administration (FDA) within the Department of Health and Human Services (HHS), as well as other federal agencies, including the US Environmental Protection Agency, Federal Bureau of Investigation, and Department of Homeland Security.

Public health laboratories also partner with various international health entities to prevent and control global health threats. For example, state public health laboratories participate in the Global Influenza Surveillance Network, which monitors circulating strains of influenza to identify which ones to include in the annual flu vaccine.

A central public health laboratory that performs laboratory services for the jurisdiction is present in every state, territory, and the District of Columbia. Many states also have local public health laboratories, which range in size from large metropolitan laboratories to smaller facilities that serve a region or community. Some public health laboratories specialize in one area of practice such as environmental health, food safety, or agriculture, performing complex testing and surveillance.

Within the public health laboratory infrastructure, trained laboratory staff generate timely, accurate data related primarily to diagnostic testing, disease surveillance, and reference testing. They share a sense of mission to serve the public good and traditionally operate at the vanguard of a response to an emerging infectious disease agent, taking action to commence disease detection and manage initial laboratory services until clinical and commercial laboratories assume the workload. However, during COVID-19, public health laboratories have remained heavily involved and have increased their output to help compensate for early testing problems and meet the unceasing demand for faster, accurate testing across the country.

Four Categories for Evaluation

While scenarios, resources, and challenges differ across jurisdictions, we identified opportunities for evaluation and improvement in 4 key categories: testing surges, supplies, staffing, and regulations.

Testing surges

Challenges

Effective containment of any pathogen demands rapid, accurate test results. Regrettably, mistakes and delays occurred early in the US testing process. These are already well-documented3–5 elsewhere, but in short, initial COVID-19 tests developed by the CDC in February 2020 proved unreliable during validation at public health laboratories—underscoring the importance of validation protocols. Specifically, a technical problem6 (most likely a contamination issue) with the testing reagents showed false-positives where the virus was clearly absent, effectively invalidating any results.

Bureaucratic hurdles then delayed efforts by other laboratories and organizations to develop alternate tests. Compelled by the urgency of the situation, the Association of Public Health Laboratories (APHL) sent a letter7 to the FDA commissioner seeking authorization for public health laboratories to develop their own tests for the detection of SARS-CoV-2. This drew attention to the issue, helped break the logjam, and unshackled laboratories eager to begin testing. Still, the virus rapidly spread across the country and maxed out the nation's testing capacity. In Iowa, where the previous H1N1 pandemic in 2009 called for approximately 10 000 tests, COVID-19 has already exceeded 250 000.

Laboratory directors took different approaches to address the surge. In Virginia, the director assigned managers to oversee each core function of the response. Daily manager meetings generated new approaches for streamlining the testing process, including specimen accessioning, prioritization, and results reporting.

In COVID-19 hot spots, overloaded laboratories routed their tests to others with greater capacity. APHL's online community and regional consortia facilitated this process by sharing capacity status along with other critical information. The commercial laboratory sector was also key in assisting with the off-load of excess volume from public health laboratories in the early days of the pandemic response, until they encountered supply issues (discussed in the next section) and other roadblocks related to global testing demand.

Recommendations

Opportunities do exist for public health laboratories to leverage technology and automation to manage future testing surges. The widespread adaptation and use of electronic test orders and results (ETOR) platforms, for example, allow laboratories to automatically exchange standardized test orders and associated results across different facilities, eliminating time-consuming, error-prone manual data entry. Laboratories across the country now use the APHL Informatics Messaging Services (AIMS) Platform, initially developed to maintain pandemic influenza surge capacity, to easily share vital test and report information.

Technology can also help determine who should seek out tests in the first place. On this front, APHL recently teamed with Apple, Google, and Microsoft to create an Exposure Notification System to alert participating residents of possible virus exposure and empower them to make testing decisions.8

Where possible, laboratories should incorporate high-throughput testing systems, which can double or even triple their current capacity. The first such system developed for COVID-19 processed up to 1000 tests in 24 hours, and new offerings have the potential to process up to 100 000 samples per day.9 Laboratories can further justify the substantial investment by incorporating high-throughput testing into noncrisis responsibilities, such as influenza, newborn screening, and sexually transmitted diseases.

Supplies

Challenges

By some estimation, COVID-19 tests comprise up to 30 different components, such as swabs, personal protective equipment (PPE), common transport media, reagents, and pipette tips, among others. Just one missing component renders testing impossible. For much of the COVID-19 response, public health laboratories found themselves dangerously low on many of these items. At the outset, test kits themselves were sparse, followed by extraction kits as testing ramped up into the spring and then consumables in the summer. These ongoing shortages resulted from historic global demand and the associated supply chain disruptions. During an outbreak, supply shortages result in testing delays.

Laboratories that fared best with supply stock reported having strong, ongoing relationships with vendors. As they did with testing surges, public health laboratories collaborated to share and redistribute testing supplies based on need. Laboratories also brought on multiple tests from different manufacturers to work around supply chain shortages and maintain some level of testing. Ultimately, the ability to share was limited since the virus spread across the entire country. Testing demand and supply trends data are shown for 18 weeks commencing April 13, 2020, in the Figure.

FIGURE
FIGURE:
Testing Demand and Supply Trends Commencing April 13, 2020Abbreviation: PHL, public health laboratory.

Recommendations

Greater transparency about supplies and vendors, as well as a nationally coordinated inventory system, could help alleviate shortages. Where cost and space permit, public health laboratories should also consider stockpiling supplies for future pandemics, especially swabs, PPE, and other essential nonperishable items. On the federal level, APHL recommends that the Strategic National Stockpile contain testing materials such as collection kits and viral transport media, at a minimum.

The limited shelf life of reagents makes them more challenging to stockpile. Mass production of reagents should begin as soon as an outbreak is detected anywhere in the world, with the assumption it will reach the United States within a short time.

Staffing

Challenges

In most jurisdictions, public health laboratory staff have worked extended hours and multiple shifts per day, often 7 days a week, to accommodate testing demand. While this has been necessary, overreliance on tired, stressed, overworked staff increases the risk of testing errors and burnout of essential personnel.

Laboratory directors also implemented new work protocols, such as alternating staff schedules for late night testing, and created equitable leave policies to improve morale and staff retention.

Simply adding new staff when a pandemic strikes is not a realistic option, as it requires time and effort to hire and train qualified personnel. Public health laboratories in Virginia and Iowa lessened the burden by temporarily reallocating staff from other departments with smaller or less-essential workloads. In Iowa, where the state public health laboratory is linked to the university system, the director recruited university researchers after its research laboratories suspended normal operations.

Few of these ad hoc tactics are sustainable. Personnel borrowed from other departments will eventually need to resume their core responsibilities, such as monitoring water quality or testing for foodborne pathogens. Public health laboratory directors will need to find ways to integrate COVID-19 testing into their daily routines.

Recommendations

COVID-19 has magnified the importance of strong, updated continuity of operations planning. Leaders must have plans in place for practically any disruption and the myriad effects—including staff overburdening and disaster-related absenteeism. The following are among the key questions to ask:

  • What disruptions have we experienced in the past, and which ones could we experience?
  • How will we maintain critical operations if our normal staffing plan is insufficient?
  • Who can we recruit to support our laboratory staff in performing critical tasks?

Diversified cross-training of staff during noncrisis periods can increase the ability of laboratory personnel to quickly assume new roles during an emergency. However, truly avoiding acute staff shortages requires a coordinated and sustained commitment to systemic change.

Federal leadership, relevant agencies, the public health community, and higher education institutions must increase their focus on developing the nation's pipeline of laboratory talent between crises. A truly comprehensive approach should include new training and educational programs, maintaining competitive salaries, increasing recruitment, and funding fellowship programs. Universities should consider forming a new field of study focused on laboratory systems development.

On a larger scale, the public health laboratory system would benefit from a national reserve force of skilled, qualified technicians ready to deploy during an outbreak. Partnerships with clinical, hospital, and academic laboratories could identify retirees willing to help with accessioning and similar support tasks while core staff perform tests.

Regulations and policy

Challenges

Oversight and regulatory practices have yielded mixed results so far in the pandemic. Early on, relaxed antibody test rules allowed several manufacturers to provide tests not validated to produce accurate results. This created serious problems as the pandemic spread and more people were tested.

The approval and widespread distribution of rapid antigen tests with guidance that conflicts with the FDA's authorization continue to raise issues for both public health surveillance and personal health care decisions. And currently, there is no regulatory approach to evaluate a test's performance after it receives FDA authorization.

The reporting of results to the HHS by any testing entity, as mandated under the federal CARES Act, has also proven challenging. Many point-of-care (POC) testing locations, including physician offices and schools, are not equipped with electronic reporting capabilities and must do all reporting manually.

Moreover, APHL and its public health partners remain dismayed by the degradation of public trust stemming from the perceived political influence on science-based approaches to managing the pandemic response. Furthermore, the number of federal agencies, including task forces, which were frequently given varying roles and responsibilities, made an orderly national response difficult, if not impossible.

On the positive side, all laboratories performing COVID-19 testing are licensed under the federal Clinical Laboratory Improvement Amendments (CLIA), which helps maintain acceptable standards of quality.

Recommendations

From a policy perspective, the HHS should consider establishing a new office focused on national laboratory policy, led by an undersecretary (or deputy assistant secretary) much like the role of the Undersecretary for Food Safety within the US Department of Agriculture. This office could coordinate and facilitate the laboratory system across the department and liaise with other federal agencies, the states, and the private sector to ensure an early, robust laboratory response across all laboratory sectors (public health, commercial, clinical, academic) in the future.

For a more effective testing strategy, the FDA should encourage a combined approach that includes both Emergency Use Authorization (EUA) tests and innovative new approaches while ensuring all tests adhere to uniform quality and performance standards. Ideally, the CDC, FDA, and other relevant federal partners would continue evaluating EUA tests postapproval. The FDA has issued more than 250 EUAs for SARS-CoV-2 tests to date, including real-time polymerase chain reaction tests, antibody or serological tests, and POC and rapid antigen tests. Ongoing evaluations will enable public health laboratories to advise their jurisdictions on the most appropriate tests for their situations.

To expedite accurate reporting, APHL continues working with POC test providers to stand up electronic reporting systems. Going forward, consolidation may be most effective for some circumstances, including entire school systems providing reports for the schools they represent.

In terms of public health laboratory leadership, current requirements in many jurisdictions prevent qualified candidates from assuming senior roles because they lack an advanced life science degree. By allowing flexibility, such as permitting senior staff to substitute a combination of a doctoral degree in public health and laboratory experience for a life science degree, jurisdictions could increase the number of skilled leaders available during emergencies.

Conclusion

The COVID-19 pandemic is far from over, and other crises are sure to follow. To fulfill its mandate, the public health community must continuously learn from its experiences—good and bad—and explore all available options to improve speed, quality, and collaboration. This is especially vital in the face of perpetual budget and staffing shortfalls.

Sustainability is also paramount when considering modifications for the future. Short-term solutions must evolve into stable, lasting changes that maximize the ability of the nation's public health laboratories to safeguard their communities.

With appropriate evaluation and application, each lesson learned from the laboratory COVID-19 experience can form part of a broader blueprint that leads to better preparation and execution when the next crisis inevitably strikes.

Implications for Policy & Practice

  • Forming a nationally coordinated inventory system and a strategic national stockpile of testing materials.
  • Mass producing reagents and other necessary supplies at the first sign of a global outbreak.
  • Developing and sustaining a robust national pipeline of laboratory talent with an emphasis on improving training, salaries, recruitment, and funding for fellowship programs.
  • Establishing a national reserve force of skilled, qualified laboratory scientists.
  • Creating a new HHS office focused on national laboratory policy.
  • Pursuing a testing strategy that encourages innovative test development while holding all tests to the same high standards of quality and performance.
  • Allowing greater flexibility while maintaining high qualification standards in credential requirements for public health laboratory leadership.

References

1. Holshue ML, DeBolt C, Lindquist S, et al. First case of 2019 novel coronavirus in the United States. N Engl J Med. 2020;382:929–936. https://www.nejm.org/doi/full/10.1056/NEJMoa2001191. Accessed August 12, 2020.
2. Centers for Disease Control and Prevention. Public Health 101 Series: introduction to public health laboratories. https://www.cdc.gov/publichealth101/laboratories.html. Accessed August 16, 2020.
3. Shear MD, Goodnough A, Kaplan S, et al. The lost month: how a failure to test blinded the U.S. to Covid-19. The New York Times. https://www.nytimes.com/2020/03/28/us/testing-coronavirus-pandemic.html. Updated April 1, 2020. Accessed August 12, 2020.
4. Cohen J. The United States badly bungled coronavirus testing—but things may soon improve. Science. February 28, 2020. https://www.sciencemag.org/news/2020/02/united-states-badly-bungled-coronavirus-testing-things-may-soon-improve. Accessed August 12, 2020.
5. Arnold C. Why the U.S. coronavirus testing failures were inevitable. National Geographic. March 30, 2020. https://www.nationalgeographic.com/science/2020/03/why-united-states-coronavirus-testing-failures-were-inevitable. Accessed August 12, 2020.
6. Wilman D. CDC coronavirus test kits were likely contaminated, federal review confirms. Washington Post. June 20, 2020. https://www.washingtonpost.com/investigations/cdc-coronavirus-test-kits-were-likely-contaminated-federal-review-confirms/2020/06/20/1ceb4e16-b2ef-11ea-8f56-63f38c990077_story.html. Accessed August 7, 2020.
7. Baird RP. What went wrong with coronavirus testing in the U.S. The New Yorker. March 16, 2020. https://www.newyorker.com/news/news-desk/what-went-wrong-with-coronavirus-testing-in-the-us. Accessed August 7, 2020.
8. Association of Public Health Laboratories. Bringing COVID-19 exposure notification to the public health community. https://www.aphlblog.org/bringing-covid-19-exposure-notification-to-the-public-health-community. Published July 17, 2020. Accessed September 25, 2020.
9. National Institutes of Health. NIH delivering new COVID-19 testing technologies to meet U.S. demand. News release. https://www.nih.gov/news-events/news-releases/nih-delivering-new-covid-19-testing-technologies-meet-us-demand. Published July 31, 2020. Accessed August 10, 2020.
Keywords:

COVID-19; lessons learned; preparedness; public health laboratories; public health policies; testing

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