Identifying and Tracking SARS-CoV-2 Variants ¡ª A Challenge and an Opportunity

List of authors.
  • Scott J. Becker, M.S.,
  • Jill Taylor, Ph.D.,
  • and Joshua M. Sharfstein, M.D.


The emergence of worrisome variants of the SARS-CoV-2 virus has exposed the limited scale of surveillance efforts in the United States. More than 30 other countries conduct more sequencing of viral isolates than the United States does, thereby permitting greater understanding of the potential threat associated with various variants.1 To address this challenge, the Biden administration is planning to spend $1.75 billion included in the March 2021 American Rescue Plan on strengthening and expanding activities related to genomic sequencing, analytics, and disease surveillance and the workforce in these areas.2 This funding provides an opportunity to work toward establishing a more coherent and organized public health response system.

Public health surveillance encompasses the interactive system of public health agencies at various levels (including federal, state, and local) working with health care providers and the public to detect, report, and prevent illness and death.3 These activities depend on the availability of accurate and timely data that can be analyzed using modern epidemiologic methods.4 In the United States, public health surveillance and data systems are poorly funded, however, and they exist in silos. To avoid simply supporting the development of new silos for sequencing SARS-CoV-2 isolates, we believe the administration could pursue several approaches to building stronger surveillance infrastructure for the future.

First, to solve the current problem related to Covid-19 surveillance and tracking of variants, the federal government could build on the country¡¯s existing network of 130 state and local public health laboratories to expand capacity in the multiple areas required to support genomic surveillance. These laboratories already use next-generation sequencing to monitor seasonal influenza, identify pathogens associated with foodborne disease outbreaks, and track antimicrobial resistance, among other applications.

In recent years, state and local laboratories have been constrained by budget cuts and personnel attrition. Ensuring that a strong genomic-sequencing effort is maintained over the long term in every public health laboratory would promote a much-needed rebuilding process. Funds are needed not only to build instrument and information-technology infrastructure and enable electronic data acquisition and transfer but also to support academic and professional training programs in expanding the workforce by building a pipeline of students with appropriate laboratory, data analytic, and epidemiologic skills.

Having fully resourced and highly capable state and local laboratories operating in the high-complexity, wet-bench mode and performing low-complexity testing in nontraditional sites using point-of-care devices would result in a more resilient national surveillance system. It would enable the development of skills and resources that could be applied to a range of pathogens beyond SARS-CoV-2. If such a system had been in place in late 2019, some of the testing difficulties that the United States experienced early in the Covid-19 pandemic might have been avoided.5

Second, the newly designated funding could be used to build and support a national, publicly accessible database of viral sequences. A substantial amount of Covid-19 laboratory data has remained locked within single institutions or has been submitted to restricted databases. When each institution pursues its own research mission in isolation, the ability to identify larger, important trends is compromised. To counter this phenomenon, the government could require all laboratories ¡ª both public and private ¡ª that receive federal funding to immediately share sequencing information and associated metadata with a national, publicly accessible database, modeled in part on the system at the National Institutes of Health¡¯s National Center for Biotechnology Information. It will be important to ensure that the database-submission process is simple, efficient, and straightforward. Whenever possible, submissions should be linked to metadata with clinical information about patients, an approach similar to that used by the United Kingdom¡¯s Covid-19 surveillance program.

Data that are stored in this warehouse and stripped of individually identifiable patient information should be accessible to government and academic researchers. The Centers for Disease Control and Prevention (CDC) could create a governance structure to oversee the use of these data ¡ª one that considers issues such as patient privacy and intellectual property. Whether the warehouse is established at the CDC or elsewhere in coordination with the CDC and other federal agencies, the database¡¯s initial guiding principle should be to promote broad use to address Covid-19. The information collected in the database will be invaluable for the development of new metagenomic-analysis tools; for research on pathogen properties, including virulence, host range, and the potential for drug resistance; and most important, for the development of new therapeutics.

Third, the new funds could support the establishment of a national public health data network. The United States has too many stand-alone, disconnected surveillance networks that require their own data-collection systems and data-transfer pathways. It makes little sense to have separate workflows and information systems for each pathogen or public health problem.

Genomic-sequencing funds could be tapped to develop a new, flexible infrastructure that could ultimately support broad pathogen surveillance and data modernization for genomic sequencing for many infectious diseases. Eventually, such an effort might require a less-siloed organizational structure at the CDC. The agency could establish a training program to provide education on using these data, with training available at the state and local levels to boost investigational capacity.

Finally, funding for addressing SARS-CoV-2 variants could go toward fostering a new model of collaboration between public health and academic medicine. Public health agencies must monitor and respond to the urgent challenges facing populations; academic researchers excel at making discoveries that advance knowledge and capabilities. Too often, these worlds are isolated, thereby limiting opportunities for implementing research findings that could have practical applications for improving health.

To avoid a similar fate for genomic-sequencing efforts, the Department of Health and Human Services (HHS) could create a funding mechanism that requires state and local public health laboratories and their parent agencies to establish formal partnerships with academic medical centers. The model would align academia¡¯s role in developing new technical methods and data-analysis tools with public health¡¯s role in implementing these tools in the field. In addition to supporting the development of a pipeline for students interested in public health careers, this approach could become a model for further collaboration between academic medicine and public health.

Guiding near-term Covid-19 initiatives using these strategies won¡¯t be easy. The current scattered approach to public health surveillance reflects our health care system¡¯s disorganization, the chronic underfunding of public health, and the inconsistent engagement of academic medicine in these efforts. Fixing these problems will require strong federal leadership, starting with an empowered team at HHS that can set conditions for spending the funds included in the American Rescue Plan to bring about important changes. Success will pay dividends not only during the Covid-19 pandemic but also for other major health threats. It will lead to more effective ways of tracking and controlling seasonal influenza and other respiratory diseases, antibiotic resistance, and the emergence of new pathogens.

Covid-19 has caused hardship and loss for millions of Americans, and the emergence and spread of viral variants raise concerns that our global battle with the pandemic is far from over. Even as these variants expose the weaknesses in our laboratory infrastructure, new investments create the potential for designing a stronger public health system for the future. Funding designated for increasing our understanding of SARS-CoV-2 variants could be used in ways that would help guide the current pandemic response and yield benefits for years to come.

Funding and Disclosures

Disclosure forms provided by the authors are available at

This article was published on June 9, 2021, at

Author Affiliations

From the Association of Public Health Laboratories, Silver Spring (S.J.B., J.T.), and the Johns Hopkins Bloomberg School of Public Health, Baltimore (J.M.S.) ¡ª both in Maryland.

Supplementary Material

References (5)

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