Public Health Laboratories During the COVID-19 Pandemic: Challenges, Solutions & Lessons Learned

Public health laboratories need to have a voice in outbreak response planning, and past challenges must inform future efforts to effectively address emerging health threats in the United States.

There are over 130 public health laboratories in the United States. Every day, highly trained scientists at these laboratories detect and monitor health threats in conjunction with federal and international agencies, helping to keep you safe from all kinds of hazards such as environmental and natural disasters, foodborne illnesses, or even the next pandemic.

By now, nearly three years into the COVID-19 pandemic, it is well recognized that the US experienced significant testing challenges in its initial response. Early in the pandemic, and even now, testing is crucial for identifying new cases and halting further transmission, yet early efforts to expand testing capacities were hampered by quality assurance issues with an early diagnostic as well as limited testing capacity and massive backlogs leading to constrained testing availability and lengthy delays for patients and healthcare providers awaiting test results.

As researchers with the Outbreak Observatory, a project dedicated to conducting operational research during outbreak responses to inform efforts for future public health crises, we wanted to have a better understanding of what went wrong for public health laboratories during the COVID-19 pandemic so that laboratorians could be better prepared during the next crisis. To inform this analysis, we partnered with the Association of Public Health Laboratories, a nongovernmental organization dedicated to representing, empowering, and advocating for public health laboratories. Together, we analyzed the challenges that public health laboratories encountered from the beginning of the pandemic into early 2021 as well as how public health laboratories prevented, solved or otherwise addressed those challenges, culminating in lessons learned for future responders.

Our Findings

We conducted interviews with 68 leaders and staff from 28 local and state public health laboratories across 27 states. While it was apparent that the challenges facing public health laboratories evolved significantly over the course of the pandemic, these were the most prominent themes from our analysis:

  • National planning and guidance were in short supply but uncertainty was not. Public health laboratories reported they did not feel well-positioned to engage in short-term decision-making or long-term strategy development. This was in part due to federal agencies’ tendency to provide limited, confusing, and constantly changing guidance. The unprecedented and ever-evolving nature of the pandemic left laboratorians uncertain regarding what testing capacity was necessary for the response and nervous to overspend before the emergency became apparent.
  • Government leadership at times exacerbated laboratories’ challenges. We heard a handful of inspiring stories of governors or other jurisdictional leaders advocating on behalf of their laboratorians and fighting to secure the supplies, equipment, and financial resources desperately needed for response efforts. However, we also heard stories of jurisdictional leaders withholding needed funding, changing testing strategy without input from laboratory staff or even entering into contracts without input from the public health laboratory. At the federal level, public health laboratories noted that restrictions on usable COVID-19 diagnostics led to rampant supply chain difficulties that constrained testing capacity and fed into testing delays. Even when government agencies facilitated supply shipments, public health laboratories were sometimes left worse off, such as in one instance when a laboratory received hundreds of moldy vials from a federal supplier.
  • Fast adaptation, collaboration, and creativity was necessary to alleviate some issues. In the face of these struggles, some public health laboratories found a way via partnerships and innovation. Diversification of suppliers and platforms and in-house production of certain supplies helped to mediate the effects of the supply chain crisis. Armies of volunteers and temporary staff from private laboratories with suspended operations, former staff members, and even the National Guard helped with staffing shortages. Finding ways to automate certain practices or switching to higher throughput processes helped to boost testing capacity without requiring additional space and staff. However, these solutions still relied on access to expertise, partnerships, or additional resources, which were luxuries that not all public health laboratories had access to during the pandemic.
  • Recurring issues from pre-pandemic times don’t go away – they grow considerably. Inconsistent funding to maintain capacity, difficulty competing for talent with private industry, trouble retaining staff, and poor physical and technological infrastructure are not new issues, but they were major obstacles for COVID-19 testing efforts. In order to better prepare for the next crisis, we need to resolve these longstanding difficulties.

If policymakers, public health laboratories, and other partners ensure that future preparedness and response planning addresses these shortcomings before the next crisis, public health laboratories will be better able to execute testing and protect the United States from health threats. If not, the next outbreak response will be hampered by the same challenges.

Want to learn more? Read our published manuscript here:


Christina Potter, MSPH, is a Senior Analyst at the Center for Health Security and a Research Associate in the Department of Environmental Health and Engineering at the Johns Hopkins Bloomberg School of Public Health. Her research interests include analysis of outbreak preparedness and response, health systems strengthening, and health security. 

Jennifer B. Nuzzo, DrPH, is a Professor of Epidemiology and Inaugural Director of the Pandemic Center at Brown University School of Public Health. Her work focuses on health security, public health preparedness and response, and health systems resilience. She founded the Outbreak Observatory, which conducts operational research to improve outbreak preparedness and response.