Actions the US must take today to detect, contain, and slow the spread of new highly transmissible COVID-19 variants

It shouldn’t be like this. Nearly one year after the WHO declared the COVID-19 to be a global pandemic, the US shouldn’t be this far behind so many other countries when it comes to testing for an infectious disease outbreak. The US is home to many of the world’s leading clinical laboratories, test manufacturers, and most prominent thought leaders. We should be leading the global fight against this coronavirus and laying the groundwork to ensure we are better prepared for the next outbreak. Instead, the US now ranks 38^th out of 130 countries reporting whole-genome sequencing data for COVID-19 as of late January. We are left relying on the surveillance efforts from other countries. As a medical director of the Clinical Laboratory at the Medical University of South Carolina, it’s all very frustrating but there are steps we can take today to fix these issues.

Last week, CDC Director Dr. Rochelle Walensky detailed how a number of public health, academic and commercial lab partners have recently put the US on track to sequence at least 7,000 samples weekly. While this is a good start, she recognizes that more resources and capacity are needed to increase our country's sequencing surveillance and outbreak analytics capacity at the levels demanded by this crisis. We must do more, and we must move quickly.

Over the past few weeks, US health officials have confirmed more than 470 local cases of the highly transmissible coronavirus variants that were first identified in the UK, South Africa, and Brazil. In fact, the first two cases of the B.1.351 variant from South Africa in the US have now been confirmed in my home state of South Carolina, the P.1 variant from Brazil was confirmed in Minnesota, and now hundreds of cases of the B.1.1.7 variant from the UK have been confirmed across the country. All three of these variants, which have evolved independently, are believed to be up to 50% more contagious than earlier forms of the virus, according to the CDC.

All viruses naturally mutate over time, and we have been expecting that SARS-COV-2 would as well. Unfortunately, the virus will continue to mutate, with an increasing likelihood that mutated strains will spread widely in the US and abroad. In the US, our limited ability to detect, sequence, and track the epidemiology of the coronavirus has almost eliminated any chance of minimizing community spread and hampered our ability to understand, contain, and eventually prevent more infections.

But why is that the case? How is it even possible for the US to be so far behind countries like the UK, South Africa, and Brazil with the sequencing and epidemiological testing? And more importantly, how do we fix it?

To help put these numbers in perspective, scientists estimate that a country needs to sequence at least 5% of its coronavirus cases to detect a new variant that represents up to 1% of the total cases in that country. Given cases over the past seven days, 5% would amount to roughly 52,000 sequences a week. At the end of January, the US had only sequenced about 0.32% of its total cases, according to a Washington Post analysis. By comparison, the UK had sequenced almost 6% of the country’s 3.7 million cases. The US must do better. We must improve these numbers immediately if we want to stop or even slow the spread of these new mutations.

As the Chair of the recently formed AMP COVID Response (ACR) Steering Committee, I am committed to working with my colleagues to solve these glaring problems. The ACR Steering Committee is a centralized body tasked with coordinating and communicating AMP’s continued efforts to guide diagnostic testing for the current COVID-19 pandemic and future emerging outbreaks.

The solution lies in our ability to work together to overcome a number of ongoing challenges.

• Collaboration – First and foremost, we must strengthen the relationships and communication between the public health and clinical laboratories across the country. We must recognize the slightly different but very complementary roles that both groups should ultimately play in pandemic response. For example, most clinical laboratories have the technology infrastructure and expertise in place to scale sequencing efforts, while public health laboratories do not. The federal government – either CDC or HHS – could help with all of the coordination. We must work together and there should be a clear plan that outlines roles and responsibilities.

If this pandemic has taught us anything, it’s that more coordination and transparency are needed across the board. We must create the infrastructure and procedures needed to receive, process, and share real-time data on a national scale. Then we must work together to improve the integration and implementation of this data. If we can identify these variants earlier, we can provide the country with a warning and chance to act before they start to spread.

To help facilitate a more coordinated response, we should consider identifying a number of highly qualified clinical laboratories across the country that could be designated as official public health laboratories whenever a national public health emergency is declared. This formal designation would automatically trigger additional funding, resources, and flow of information needed to scale testing capabilities and accelerate the overall response.

• Resources - Laboratories across the country have been on the frontlines of this pandemic since the initial days of the outbreak, doing their best to keep up with the ever-increasing demand for diagnostic and epidemiological testing despite multiple supply chain and personnel shortages. Whether through the Defense Production Act or other means, we must make sure they have access to the resources they need for timely testing. This means increased transparency, communication, and real-time transmission of information to understand resource availability and reagent and supply quantities. The need for testing supplies designed for acute care, surveillance, high-throughput, and other clinical needs should be monitored widely to provide immediate feedback to support data-driven supply allocations.

We must also leverage existing capacities and capabilities more effectively, or we risk even greater staff burnout, shortages, and associated concerns. We need to look to increase workforce support and access to career development, training, and ongoing educational programs to prepare the next generation of laboratory professionals for future public health emergencies.

• Funding - And last but not least, we need to make sure there is sufficient funding for all of these epidemiological studies. Biden administration officials said the president’s $1.9 trillion proposed spending plan also includes much-needed funding for genetic sequencing. While this is a good start, we’ll need more if we want to reach the 5% threshold of sequencing more than 50,000 samples per week. We must incentivize laboratories to conduct these studies and upload data to the GISAID database as soon as possible.

Timely diagnostic and epidemiological testing are foundational to an effective response to any emerging infectious disease. The good news is that we can start fixing these issues today. The recent steps taken by the CDC are a good start. But we have more work to do.

One positive outcome of this awful pandemic has been the unified commitment to improving our national response from the broad laboratory community, as well as healthcare providers and policy makers. AMP members will continue to communicate our membership’s deep expertise as part of our efforts to inform the Biden administration, guide healthcare providers, and educate the public. If we can work together to strengthen our collaborations, ensure access to resources, and provide adequate funding, we will be in a much better position to respond to not only this current pandemic but all future outbreaks.

Frederick S. Nolte, PhD

Chair of the AMP COVID Response Steering Committee

Professor and Vice-Chair for Laboratory Medicine in the Department of Pathology and Laboratory Medicine, and Medical Director of Clinical Laboratories and the Molecular Pathology Laboratory at the Medical University of South Carolina