How the CDC plans to track the mutating coronavirus

Changes to the SARS-CoV-2 genome can be difficult to identify and track.
SARS-CoV-2 strain under a microscope

Having more sequenced samples of SARS-CoV-2 will help epidemiologists and others in the public health field better understand the profile of different strains of SARS-CoV-2, and track their spread. NIAID

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An initiative spearheaded by the Centers for Disease Control’s Office of Advanced Molecular Detection (OAMD) seeks to bring the SARS-CoV-2 sequencing work of private and academic labs into the public sphere. They hope this will help to coordinate cross-country efforts to better understand the virus’s genome and all its current and potential future mutations.

Known as the SARS-CoV-2 Sequencing for Public Health Emergency Response, Epidemiology and Surveillance (SPHERES), the consortium of about 50 laboratories represent the majority of the United States’s almost 4000 genome submissions to GISAID, an international repository of viral data that provides open access to the genomes while preserving the intellectual property rights of sequencers. Going forward, they hope to submit many more sequenced viral whole genomes, including various strains of the novel virus, to GISAID and a variety of other open data repositories of this information, says Duncan MacCannell, chief science officer at the OAMD.

“By submitting to multiple repositories we make sure the data is as broadly available as possible,” he says. The OAMD—whose job it is to help everyone from local jurisdictions to larger branches of the CDC use cutting-edge sequencing technology in their work—wanted to coordinate a united American response.

“We started the consortium by reaching out to a lot of public health labs and… talking about what their needs were,” he says. As they started reaching out, though, the OAMD realized that a number of academic and private sector labs wanted to contribute sequenced genome data to the public fight to understand SARS-CoV-2 virus, he say. Rather than having all those labs working on their own, it made sense to bring them all into a coordinated effort.

In the short term, having more sequenced samples of SARS-CoV-2 will help epidemiologists and others in the public health field better understand the profile of different strains of SARS-CoV-2, and track their spread. Because SARS-CoV-2 mutates slowly compared to many other viruses, MacCannell says, it can be difficult to track its spread. More data will help.

This is all possible because genetic sequencing has taken huge strides in the past few decades. It used to be extremely time-consuming and expensive to do what’s known as whole-genome sequencing, which produces the most robust data for epidemiologists to use. Today, thanks to years of incremental improvements and a few big advances, it’s much faster and simpler. That’s good news for epidemiologists and people trying to figure out how to successfully treat COVID-19, the disease caused by SARS-CoV-2.

In the longer term, having this understanding of how different strains of SARS-CoV-2 are spread around the country might help researchers figure out which strategies meant to slow the infection’s spread are most effective.

It might also help us plan for future waves of the virus. “I think understanding the natural variation that can occur in the virus and being able to actually monitor that for emerging important trends is also going to be incredibly important,” he says.

This kind of work is done for a number of other disease-causing microbes, but the sheer scale of the COVID-19 pandemic requires a much larger response. The SARS-CoV-2 SPHERES is coordinating their work with other countries’ labs as well, and hopefully, the whole result will enable the international public health genomics community to get a much better picture of this chaos-causing virus.