To stem the pandemic, the U.S. needs a national Covid-19 genomic sequencing effort

More than a year into the pandemic, the United States is at yet another critical inflection point. The number of Covid-19 cases remains high and is on the rise in more than half of states.

And though vaccination rates are climbing here, topping 4 million shots on April 3 alone, we are in a race between vaccinations and the proliferation of viral variants, which continue to spread and may be even more dangerous than the coronavirus that triggered the pandemic. The country must drastically improve genomic surveillance of Covid-19 cases, which is not happening often enough.

Viruses mutate as they multiply and spread. Genomic sequencing is an advanced test that determines the precise genetic information a virus carries. It can highlight variant strains that may spread faster, evade vaccines, or make people sicker by being less responsive to existing treatments.

Because genomic sequencing is a complicated test that requires samples from individuals who have fairly high viral loads, it cannot be used as a routine surveillance tool. Yet once it identifies worrisome variants in a region, routine laboratory tests can be created to track these variants in individuals with low viral loads who may not even know they have been infected, helping prevent further infections.

Since December 2020, the U.S. has sequenced about 0.3% of individuals testing positive for Covid-19, with wide variation between states. The United Kingdom has consistently been sequencing 10% or more. The low and inconsistent rate of sequencing means that the U.S. lacks robust data on how viral variants affect the population. This puts us at risk for missing new variant mutations that could crop up at any time, in any part of the country, with potentially devastating effects.

We are participants on a Covid-19 Testing Advisory Panel organized by Premier, Inc., a national health care improvement company. Made up of experts from the company’s member health systems around the country, the panel surfaces issues that require remediation in the nation’s response to the pandemic. The panel recently examined the issue of genomic sequencing and developed a set of five recommendations that will greatly improve the nation’s ability to track and stay ahead of the variants.

First, the federal government needs to create standard criteria that trigger genomic sequencing of a sample. For example, if a vaccinated individual develops symptoms of a Covid-19-like infection, their test samples should be sequenced, as it could indicate a new variant slipping through the protection offered by vaccines. Similarly, a patient exhibiting new, previously unidentified complications as a result of a Covid-19-like infection should also be sequenced.

Second, successful identification and subsequent genomic sequencing requires a consistent surveillance protocol for testing patients based on standardized national criteria for sample selection determined by viral load levels; patient characteristics such as symptoms and disease progression; demographic distribution; travel patterns; and community exposures. A standardized approach for determining what constitutes variants of concern and giving those variants understandable names also should be established.

This unifying strategy would improve consistency of sampling and help identify new variants faster. National standards for migrating findings of genomic sequencing into the faster routine testing strategies would also help create a consistent approach to identify clusters of infection.

Third, the federal government needs a better approach to organize and financially support the nation’s genomic sequencing network. While progress has been made with increased funding for genomic sequencing, most states and the federal government are exclusively contracting with large, commercial labs to perform sequencing. This means that samples must be sent out and results can often take two to three weeks to come back. This approach is a recipe for delays that could mean the difference between containment and outbreak.

Instead, the government should broaden and better organize the lab network to include hospitals, academic medical centers, and regional testing laboratories that have the ability and capacity to perform these tests in their communities. Broadening the lab network will help ensure that regionally based testing can produce more timely results, empowering immediate and effective public health action.

Fourth, genomic sequencing depends on the continued availability of Covid-19-positive test samples. Covid-19 testing rates have fallen in the U.S. in part because fewer people are sick or exposed to infected people. But it’s also because tests are still inaccessible to many Americans. To feed the sequencing pipeline and understand the movements of the virus during vaccine rollouts, the country still needs to be performing routine diagnostic testing at full capacity.

Fifth, we need to integrate genomic sequencing into local care delivery. To date, sequencing has been a public health and research activity; the latter data emanating from individual academic institutions and large-scale research consortiums. Although research results are shared with public health authorities, genomic sequencing is not currently an approved clinical test for medical diagnosis, and costs for doing it are not covered by insurance. University and research labs are repurposing other research funds, and drawing on intra-institutional funds, to do the sequencing.

Rigorous efforts to link viral genomic data with patient outcomes will help determine whether knowing the variant status of a patient’s Covid-19 infection should guide medical treatment decisions. For instance, if a variant outbreak is identified, it may be necessary to implement isolation protocols to prevent that variant from spreading. But this can only happen when providers are given timely information about the presence of variants among their patients.

For the Covid-19 pandemic to stay on a downward trend, the U.S. must optimize a national viral sequencing network that is scalable and based on regional capabilities for sequencing and public health intervention. Without such efforts, Covid-19 infections could again move through communities without adequate public health knowledge of what is happening, and why. This places society at great risk of going back to square one in the battle against this pandemic.

The U.S. has fought too long and too hard to allow that to happen.

James Crawford is a pathologist and senior vice president of laboratory services at Northwell Health. Jonathan Slotkin is a neurosurgeon, professor of neurosurgery, and associate chief medical informatics officer at Geisinger; and chief medical officer of Contigo Health, a Premier, Inc. company. Meg Wyatt is senior director of diagnostics services for Premier, Inc.