Leverage COVID-19 experiences
to shape future responses

COVID-19 and Beyond:
Readiness for the Unexpected

In 2019, the national laboratory network known as PulseNet switched its foodborne disease surveillance efforts from pulsed-field gel electrophoresis to a new gold standard of whole genome sequencing (WGS). The change pushed public health laboratories across the country to acquire instrumentation and reagents and train staff in WGS laboratory procedures, data analysis and reporting.

Fast forward less than a year and that infrastructure, knowledge and bioinformatics capacity became the basis for COVID-19 testing and tracking efforts in the public health laboratories.

“Because PulseNet and the public health laboratories had already adopted WGS, they were able to much more easily and quickly implement COVID-19 testing,” said Shari Shea, MHS, MT(ASCP), APHL’s director of Food Safety. “That preparation and experience in foodborne illness testing helped the COVID-19 response be successful from the laboratory perspective.”

Being ready to respond to the unexpected is a hallmark of public health. And even as public health laboratories have soldiered through nearly two years of pandemic-related reprioritizing, adaptations and round-the-clock work, APHL and its members have been continuing to lay groundwork for public health laboratories to be ready to move beyond the COVID-19 response and tackle the next challenges.

The same WGS technology behind COVID-19 testing has positioned public health laboratories to play an important role in the US Food and Drug Administration’s New Era of Smarter Food Safety initiative. “One of the tenets of the New Era blueprint is technology that will make our food safer, and whole genome sequencing is a big part of that,” Shea said. Last summer, she and William Wolfgang, PhD, of the Wadsworth Center in New York were expert guests on a podcast with deputy FDA commissioner Frank Yiannis discussing how public health laboratories use WGS and the GenomeTrakr network for foodborne illness outbreak detection and response.

APHL is also supporting public health and environmental laboratories that are joining CDC’s National Wastewater Surveillance System, created in 2020 to monitor COVID-19 spread in communities. As funding became available late last summer and early fall, participating laboratories started building their systems, setting up instrumentation and establishing new collaborations, such as with municipal water treatment plants and academic institutions, for sample collection and testing.

“It’s been a very quick rollout and it’s rather impressive what they’ve been able to do already. We are working with our community of practice and CDC to finalize some guidance for laboratories,” said Julianne Nassif, MS, APHL’s director of Environmental Health. “That surveillance is being used to detect SARS-CoV-2 now, but we anticipate laboratories will expand the use of that tool for other pathogens in the future.” As of January 2022, there are 35 states, four cities and two territories that are funded for wastewater surveillance.

Of course, other public health needs haven’t stopped during the pandemic, and APHL is continuing to provide training and technical assistance to advance non-COVID-19-related efforts. In 2021, APHL staff arranged an intensive, multiday online training in high-resolution mass spectrometry for laboratories in the Laboratory Response Network for Chemical Threats. And after some pandemic-related delays, opioid biosurveillance programs are now underway in a handful of states to acquire and test clinical samples for natural and synthetic opioids, data that will help identify what substances are circulating in specific communities and inform local public health practices.

APHL also provided guidance on technical implementation of CDC’s lowered reference level for childhood lead exposure, which, in late October 2020, dropped to 3.5 mg/dL. “Contamination is a real issue at that level,” Nassif said. “We have some very experienced members in lead testing who provided testimony to the Lead Exposure Prevention Advisory Council, and we’re drafting specifics for laboratories to ensure they’re able to reliably measure at that level.”

Laboratorians can also now access a competency-based laboratory curriculum framework in food safety through APHL’s newly launched online learning portal, which provides a central location to access trainings and courses, track progress, earn continuing education credits and work toward relevant certification. The first five courses, aimed at entry-level laboratory professionals, cover general requirements such as laboratory ethics, biosafety, communication and other basics.

“These are things any laboratory professional needs to know when you walk into a public health laboratory, regardless of which department you’re going to work in,” Shea said. “The framework helps put in one place everything you need to know to succeed throughout your career, from entry level to management.”