The Omicron variant is putting America’s coronavirus sequencing efforts to the test

By Jacqueline Howard, CNN

Rows of scientists sit before racks of coronavirus samples inside a laboratory in Henderson, North Carolina, wearing face masks and scrubs. All hours of the day and night, they transfer the samples from tubes to processing plates, searching for answers about the virus behind these Covid-19 cases.

From confirming a positive Covid-19 sample to prepping the DNA and then sequencing it, the process takes two to three days in the lab, said Lauren Moon, sequencing manager for MAKO Medical’s Next Generation Sequencing Lab in North Carolina.

Work like this is happening in labs around the United States as the country races to learn more about the newly identified Omicron variant.

“Knowledge is power in this, and the more that we know about something the more equipped we are to fight it. The more effective our vaccines are going to be and the more informed the public is, they can take appropriate safety measures,” Moon told CNN’s Dianne Gallagher.

“We want to sequence as much as possible,” Moon said. This lab has not yet detected Omicron variant positive tests, but cases are starting to emerge in several states.

These discoveries are no surprise. They’re the moments genetic detectives have been preparing for — and the reason the US has been ramping up its sequencing abilities.

As the coronavirus pandemic unfolded, other countries were able to identify changes to the virus sooner and take action quicker. Early this year, Biden administration officials acknowledged the country was “not where we want to be” on genetic sequencing of coronavirus variants, and then made major investments to improve it.

After South African scientists announced last week they had detected a previously unknown coronavirus variant, US officials acknowledged it was likely here already. They just had to sequence enough coronavirus samples to find it.

For now, almost all US Covid-19 cases are driven by the highly transmissible Delta variant, but on Wednesday, the first US Omicron case was identified in California. Then came another in Minnesota, then Colorado, more in New York City and in Hawaii. More are expected.

“We are now sequencing approximately 80,000 samples per week — about one in every seven PCR positive cases,” CDC Director Dr. Rochelle Walensky told a White House coronavirus briefing Tuesday.

There are a lot of unanswered questions around Omicron: Is it more transmissible? Can it cause more severe disease? Does it evade protection from vaccination or previous infection?

The answers start in the lab.

Sequencing many more specimens than a year ago

Genomic sequencing involves examining and decoding the genetic material of a virus to identify how it has changed over time. These changes occur as mutations.

Kelly Wroblewski, director of infectious disease at the Association of Public Health Laboratories, said in a written statement to CNN that sequencing can take just a couple days, but for many, it’s longer.

“We generally say about a week,” Wroblewski said.

It’s not as simple as a Covid-19 test with a swab. Only samples that are sent into laboratories for diagnostic testing can be sequenced to look for the genetic evidence to tell which variant of virus has infected someone.

The types of tests — diagnostic and sequencing — are done separately. Polymerase chain reaction or PCR testing makes the process easier. Quick antigen tests are not used to detect variants, nor are tests people take on their own at home.

Earlier this year, in January, an international database showed the United States ranked 61st in how quickly virus samples were collected from patients, analyzed and then posted online — taking about 85 days. Countries with far fewer resources, including Bangladesh, Sri Lanka and Suriname, processed samples more quickly than the United States.

As of November 24, based on data from the global science initiative GISAID, the United States appears to have moved up the list to rank 21st when it comes to the speed of collecting samples, sequencing and reporting results, taking a median of about 28 days.

An analysis of GISAID data by the Broad Institute of MIT and Harvard also ranked the United States 21st in terms of how many sequences are performed per 1,000 Covid-19 cases, as of November 24.

“Back in January, the numbers were quite low. It was really I think under half a percent in terms of the Covid infections that were prevalent were getting sequenced,” said Dr. Ingrid Katz, associate faculty director of the Harvard Global Health Institute and an associate professor at Harvard Medical School.

“The UK, for example, was sequencing around that time around 5%. Denmark was around 12%. Australia, they were doing like 60% of their detected viruses were getting sequenced,” Katz said. “So, now we’re in a better place, I would say, in turn, just because the federal government has infused more cash.”

That turning point came in April, many months before the emergence of Omicron, when the Biden administration announced plans to release $1.7 billion in funding to help the CDC and states more effectively track and combat coronavirus variants.

The identification of the first known Omicron cases in the United States and “the rapid turnaround in sequence analysis is an example of the importance of our investments this year to expand genomic sequencing across the country — and to build a system that is prepared to swiftly respond to new and emerging Covid variants,” Walensky said during a White House briefing Friday.

Currently, there are about 68 state and local public health laboratories sequencing for coronavirus variants as a “critical part” of the CDC’s national strain surveillance network, Scott Becker, the Association of Public Health Laboratories’ chief executive officer, told reporters during a virtual news briefing Tuesday.

These labs “are sequencing between 15,000 and 20,000 specimens per week. That number is four times greater than just a year ago,” Becker said.

“In November of 2021 alone, 190,000 specimens were sequenced by the entire public health system, which includes public health labs, CDC, and CDC-contracted labs. In addition, public health laboratories also submit a subset of those specimens to CDC for strain characterization, and more detailed lab studies,” Becker said in the briefing.

“Nationally between 5% and 10% of all diagnostic specimens are sequenced and come from public health laboratories, commercial laboratories, CDC-contract labs, academic labs, and other partners,” Becker said Tuesday. “Our system can detect variants down to 0.1% of circulating viruses.”

Still, that can vary from place to place. Lea Starita of the University of Washington wrote in an email to CNN that, “In some states, like Washington, we are sequencing up to 20% of all cases (that’s a lot).”

There’s also room for improvement, wrote Starita, research assistant professor in the department of genome sciences at the University of Washington and co-director of the Brotman Baty Advanced Technology Lab.

“I would like to see a concerted effort to require COVID-19 testing for incoming travelers where positive cases could be followed up with sequencing,” Starita wrote, adding that “being able to more easily link the sequencing data available in the US to health data would aid genomic epidemiology efforts.”

‘It’s just got to be part of our public health response moving forward’

In places like the United Kingdom, there is a more centralized system for data, Starita wrote.

“The UK prioritized sequencing from the beginning of the pandemic and had a huge head start. Furthermore, because of their nationalized health care system, the UK can tie their sequence data back to patient data very quickly to link variants to disease severity, drug treatments, vaccine status,” Starita wrote. “This is obviously a massive boon to epidemiology efforts and is extremely difficult in the US with its broken health care system and balkanized health data.”

In South Africa, where health authorities first alerted the world to the Omicron variant, the nation “has had a robust genomic epidemiology program” that began years before the coronavirus pandemic in order to track human immunodeficiency virus or HIV and tuberculosis, Starita wrote.

“The key to spotting new COVID-19 variants is having sufficient national coordination and a dedicated workforce,” Peter Thielen, a molecular biologist at the Johns Hopkins Applied Physics Laboratory, wrote in a separate email to CNN.

“The US has and continues to improve genomic surveillance capacity through partnerships that span academic, commercial, and government laboratories,” Thielen wrote. “In places such as the UK and South Africa, their surveillance capacity has allowed them to very quickly identify variants from within their borders, and this has enabled exceptionally rapid data dissemination. Once a variant is identified in one location, countries like the US can quickly mobilize to identify variant introduction within communities or as they enter into the country.”

Having such a centralized system to help connect variants with the impact they had on a Covid-19 patients’ outcome can also help scientists examine which mutations could be associated with more severe illness or transmissibility.

“When the virus is accumulating mutations, typically, it’s mutations that make the virus more fit that occur — mutations that allow the virus to persist. So, when we see a lot of mutations, we have to think that those mutations are making the virus more fit,” Stacia Wyman, a senior genomics scientist at the Innovative Genomics Institute of the University of California, Berkeley, told CNN.

Sequencing programs will remain important to track emerging pathogens around the world for years to come, said Katz of Harvard Medical School.

“It’s just got to be part of our public health response moving forward. It’s a good, important investment,” Katz told CNN. “I wish I could say that this is going to be the only global pandemic we’ll see in our lifetime, but unfortunately, I think that’s pretty unlikely.”

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CNN’s Dianne Gallagher and Maggie Fox contributed to this report.