In January 2021, Dr. Reynolds “Ren” Salerno, director of the Division of Laboratory Systems (DLS) at the US Centers for Disease Control and Prevention (CDC), joined us for a Q&A. One year later – and two years into the COVID-19 pandemic – we had more questions for Dr. Salerno and invited him to join us again.
Q1: COVID-19 continues to be our biggest public health challenge. How have the nation’s laboratories stepped up this past year to support the response?
From a systems standpoint, public health laboratories are now using many more high-throughput diagnostic systems and doing more genomic sequencing than ever before. Just finding the physical space to house these systems is a challenge, but then there’s the process for standing those systems up, validating them, performing quality control, and training their staff to use them effectively and appropriately—all under the pressure and strain of being at the center of the response to the pandemic. It’s an enormous amount of work and the way public health laboratories rise to the occasion never ceases to amaze me.
COVID-19 itself has been a roller coaster. We witnessed the emergence of the Delta variant in summer 2021, then things seemed like they were more under control in the fall, but then Omicron hit us hard at the end of the year. Going from high speed to low speed and then to maximum speed creates both organizational and operational challenges. These emerging variants created surges in the demand for testing and strained laboratories and testing sites across the country. Laboratory professionals have had to remain nimble to keep up not only with the new variants but also with the changing testing, reporting, and surveillance guidance, which shifts as the science evolves and we learn more.
There are also staffing challenges – the response relies on a huge volume of laboratory staff who have different backgrounds and levels of experience. Laboratory staff are under pressure to withstand and endure surges in testing and sequencing, and that can mean long hours and grueling, repetitive work. The pace of work can feel unsustainable. I continue to be in awe of laboratory professionals’ dedication to their work, to the COVID-19 response, and to public health.
Q2: Given the emergence of variants such as Delta and the more recent Omicron variant, how would you characterize the capacity of COVID-19 genomic surveillance in the United States and globally?
Our robust national genomic surveillance system collects data from three primary sources: the National SARS-CoV-2 Strain Surveillance (NS3) program, CDC-sponsored sequencing performed in commercial and academic laboratories, and metadata-tagged sequences generated by laboratories that were sampled as part of baseline surveillance. Collectively, the data generated through these three mechanisms empower us to identify emerging variants that may have implications for diagnostics, therapeutics, or vaccines authorized for use in the United States or that impact the transmissibility of SARS-CoV-2 or the severity of COVID-19. The U.S. genomic surveillance system is powered to detect a variant circulating at 0.1% with very high confidence.
Through NS3, CDC requests approximately 750 total specimens per week from all jurisdictions for sequencing at CDC and further characterization of representative viruses. This regular collection of specimens from across the United States supports variant laboratory characterization efforts, which provide important data to inform public health decision-making. Because hundreds of thousands of tests and specimens are flowing into testing laboratories, getting a national picture of the changes in the circulating patterns of variants is a massive undertaking. It requires a strong partnership between state and local public health laboratories and federal partners.
Since the beginning of the pandemic, public health departments have received $430 million to strengthen their next-generation sequencing and bioinformatics capacities. CDC has funded 29 contracts, many of which are to universities, through the broad agency announcements (BAAs) – and the agency is planning another round of BAAs to distribute additional funding. BAA awardees will work closely with state and local public health agencies to conduct genomic surveillance research.
CDC is also developing a Pathogen Genomics Centers of Excellence network to improve the connections between academia and public health, address both short- and long-term challenges, and implement scalable solutions to strengthen surveillance for SARS-CoV-2 and future pathogens of public health concern.
Globally, we need to continue our work to strengthen genomic sequencing capacity and ensure countries have the capability to utilize sequence data in a way that supports their national and sub-national public health goals in addition to contributing to global genomic surveillance for SARS-CoV-2 and other infectious diseases. Genomic surveillance improves health security for all of us.
Q3: In addition to supporting the COVID-19 response, what other Division of Laboratory Systems (DLS) accomplishments have you been most proud of this past year? What are the biggest priorities for 2022?
DLS deployed a record number of its staff to support response efforts last year, and I’m so grateful for the folks in our division who stepped up to help us make headway on some of our other the high-priority activities and initiatives. Improving CDC’s training and guidance on biorisk management has been a passion of mine since I came to CDC six years ago. In 2021, we published Biological Risk Management: General Considerations for Laboratories to support the work of laboratory professionals and individuals who perform point-of-care testing; we also released a new Introduction to Laboratory Risk Management eLearning course. Our work with APHL on the Next-Generation Sequencing (NGS) Quality Initiative has been incredibly important for the laboratory community and remains a high priority for DLS. We launched CDC OneLab, which endeavors to bridge, train, and sustain a capacity-building community among public health and clinical laboratory professionals to support rapid, large-scale responses to public health emergencies. The new OneLab network has already grown very fast and has already helped CDC provide specific guidance on SARS-CoV-2 specimen submission criteria. We also celebrated the launch of Lab TrainingVR: Personal Protective Equipment (PPE) Edition, which uses virtual reality technology to simulate the process of selecting the appropriate PPE and properly donning and doffing it. In my opinion, our VR training courses are setting a new standard for laboratory training.
This year, DLS will focus on ramping up our work related to Electronic Test Orders and Results (ETOR) and expanding our biosafety capacity-building efforts for clinical laboratories. We’ll continue our work on the Extension for Community Healthcare Outcomes (ECHO) Project. The division is also leading the development of a National Quality Forum measure to ensure that healthcare institutions nationwide align with recommended quality and safety guidelines and establish a standard for a low rate of blood culture contamination. We’ll also be launching OneLab REACH – a targeted and customized learning management system that laboratory professionals can use to access COVID-19 relevant education and training resources. It should be another great year for our division.
Q4: We’ve seen significant investments by the administration and Congress in public health infrastructure this year. The American Rescue Plan and the infrastructure measure, for instance, included new funding to improve laboratory capacity and strengthen workforce. What does this mean for the public health response to COVID-19 and future health threats?
The COVID-19 response has presented the public health field with some unique challenges and opportunities. It’s important to reflect on what we’ve done thus far and ask ourselves some tough questions:
Have we built a sustainable genomic surveillance infrastructure that didn’t exist pre-COVID?
Have we diversified our testing infrastructure in a way that will make us more responsive to future public health emergencies?
Have we built a sustainable test result reporting infrastructure that gives us the kind of demographic data we need to understand what the national picture looks like early on in responses?
Do we have guardrails and systems in place to ensure that we provide access to testing for those who have been disproportionately affected by the pandemic?
Can we recruit more people into public health who will be committed to public health careers through the next crisis?
In terms of funding, we need to think long-term and invest accordingly. We need sustainable solutions and infrastructure to drive change. We clearly have a lot of work to do.
Q5: What have we learned from the COVID-19 response that can be applied to other areas of public health laboratory work?
Hopefully by now we all realize that laboratories are the pointy edge of the spear. We can no longer tolerate descriptions of public health laboratories as places that only conduct epidemiological analysis, surveillance, or research. And clinical laboratories are no longer exempt from public health practice. Clinical and public health laboratories are on the front lines – not behind the scenes – of the nation’s COVID-19 response. They’re the forces that often put themselves out there before anybody else can.
We’ve learned the importance of cultivating and maintaining relationships, especially the connections between clinical and public health laboratories, and collaborations between the public and private sectors. We’ve also been reminded yet again that there is an ongoing need for well-trained, highly qualified laboratory expertise, and that we need to continue improving data quality and electronic data exchange and reporting systems.
The authorization of such a wide variety and number of different tests for SARS-CoV-2 has demonstrated the importance of clearly communicated testing guidance and testing strategies. Developing, revising, and communicating testing guidance has required new partnerships and collaborations between laboratory experts and epidemiologists that did not really exist before the pandemic. Extending and deepening these partnerships, emphasizing information exchange rather than one-way data reporting, will definitely strengthen public health practice.
I’m not sure whether laboratory testing will ever go back to where it was before the pandemic. In many cases, testing is now happening outside the traditional “white lab coat” space. The expansion of point-of-care testing and the rise of self-testing—both for public health—demand that we consider how non-traditional testing settings could be relevant to other public health challenges. The starkest evolution is self-testing. Never before has self-testing been applied on such a massive scale to address a public health emergency. Self-testing empowers consumers to take public health action on their own—without necessarily involving the public health system. We must carefully monitor and evaluate the utility and value of the tremendous financial and technological investment in self-testing because it may change how we approach all public health testing in the future.
Reynolds M Salerno, PhD
Dr. Ren Salerno is the director of the Division of Laboratory Systems in the Center for Surveillance, Epidemiology, and Laboratory Services at the US Centers for Disease Control and Prevention (CDC). His division improves public health, patient outcomes, and health equity by advancing clinical and public health laboratory quality and safety, data and biorepository science, and workforce competency. He is the lead CDC official for the federal tri-agency Clinical Laboratory Improvement Amendments (CLIA) program, and the Designated Federal Official of the US Clinical Laboratory Improvement Advisory Committee (CLIAC). He is co-author of Laboratory Biosecurity Handbook (CRC Press, 2007), and co-editor of Laboratory Biorisk Management (CRC Press, 2015). He was the lead author for the International Organization for Standardization’s technical standard 35001 on laboratory biorisk management (ISO, 2019). Most recently, he served as the lead for CDC’s Expansion of Screening and Diagnostics Task Force for the COVID-19 Response.