As mutated versions of the novel coronavirus pop up across the U.S. — including at least one that is more contagious — researchers in Washington say surveillance in the state is falling short of what’s needed to quickly spot new variants.
While Washington is doing better than many other states, only about 1.7% of viral genomes has been sequenced since the start of the pandemic. In December — when the new variants began to explode across the U.K. and other countries — more than 70,000 people in Washington tested positive, and fewer than half a percent of those cases have been sequenced so far.
Public health, academic and industry scientists who are preparing a recommendation for the incoming Biden administration say an effective program would sequence viral genomes from at least 5% of positive cases, looking for mutations that could make the virus more transmissible, more virulent or resistant to vaccines, said Lea Starita, a research assistant professor of genome sciences at the University of Washington and Brotman Baty Institute.
It’s likely at least one of the variants is already in the state and just hasn’t been detected yet due to the low level of sequencing, she added. That means health officials are largely flying blind at a time when new forms of the virus could be spreading silently.
“With anything like this, you want to be able to put out the fire before it gets too big,” Starita said. “If you can’t see the fires starting, you might be in big trouble.”
A more infectious variant that arose in the U.K. is now the dominant virus there and probably accounts for the country’s steep rise in cases, scientists say. Though it spreads more easily, it does not appear to cause more severe illness, and recent tests found it remains vulnerable to the Pfizer-BioNTec COVID-19 vaccine.
The U.K. variant has been detected in several U.S. states, including California, Florida and New York. Another potentially worrisome variant now circulating widely in South Africa has not yet been detected in the U.S., nor has a third variant from Brazil.
Researchers in Ohio this week also reported the discovery of two distinct variants that appear to have emerged in the U.S. and may be spreading more rapidly than the original viral type.
The U.K. variant was detected soon after it emerged because public health labs there sequence about 7.4 percent of all positive cases, 25 times the U.S. rate.
The main reason for the slow pace of sequencing in Washington and across the country is that there’s no national strategy or dedicated funding, researchers say.
Viral sequencing in Washington is conducted by two academic groups. The UW Medicine Virology Lab aims to sequence 100 to 200 genomes a week out of the thousands of samples sent to the lab for diagnostic testing, said computational biologist Pavitra Roychoudhury.
Researchers at the Brotman Baty Institute are getting back online after shutting down for several weeks to switch to a cheaper, faster sequencing system, said Starita. They’re just starting to process December’s backlog and hope soon to crank out 100 genomes a day.
The group analyzes positive cases detected through SCAN, a surveillance network in King and Pierce counties, and samples provided by the Washington State Public Health Laboratory in Shoreline.
The sequences are shared in a national repository coordinated by scientists at the Fred Hutchison Cancer Research Center and other institutions.
Since most samples come from the Puget Sound area, that leaves big blind spots in other parts of the state, Starita said. That’s also the case nationally. North Dakota, which recently experienced the world’s highest infection rate, just submitted its first sequence to the repository, Starita said.
“That’s just appalling,” she said. “There’s very little sequencing outside of the main technology centers.”
The UW Virology group has to juggle sequencing with its more pressing mission of processing diagnostic tests, said assistant director Alex Greninger.
“We can’t prioritize sequencing above patient care,” Greninger said. “We don’t have special sources of funding that are earmarked for this.”
Genomes are sequenced in batches that take three to five days to run. Greninger estimates each individual genome costs at least $100 in staff time and supplies — with the latter sometimes still in short supply.
Roychoudhury and her colleagues recently found themselves scrambling to find enough freezer space for specimens. At times, they’ve had to stop sequencing when reagents also used for testing are running low.
A new CDC program is offering grants to boost sequencing and help fill in the gaps, and scientists hope the incoming Biden administration will make it a higher priority, Starita said.
While the U.K. sequences genomes at a higher rate than the U.S., British surveillance was also aided by serendipity: The country’s most common diagnostic test just happens to detect one of the key mutations. But that test is not widely used in the U.S., though it’s sometimes employed as an initial screen to prioritize samples for sequencing, Greninger said.
The variant that swamped the U.K. is likely to follow a similar trajectory in the U.S., said Trevor Bedford, a computational biologist at The Hutch. It appears to be about 50 percent more contagious, with each infected person passing the virus along to 15 percent of close contacts, compared to 10 percent for the original strain.
It’s still rare in the U.S., accounting for probably one infection in a thousand, Bedford said. He expects it will be detected in Washington any day now and is likely to become dominant in the state and nationwide by March.
That doesn’t bode well for winding down the pandemic, he added.
“I am worried that we’ll see a spring wave associated with the variant when just four weeks ago I was expecting Washington state and the U.S. to be getting things mostly under control by around March,” Bedford said in an email.
In an interview last week, Gov. Jay Inslee described the U.K. variant as extremely concerning and said it could necessitate even stricter control measures. “If it took hold in our state, even if we had the highest level of reduction of mobility that we had in the spring, we would still have to have additional intervention to bring the [transmission] level down,” he said.
Better surveillance could help guide and tailor the public health response, Starita said, possibly identifying hot spots early enough to snuff them out.
The new variants circulating now don’t represent the end of the evolutionary story for the novel coronavirus. It will keep evolving, looking for ways to dodge the human immune system, and the vaccines, Roychoudhury said.
Reducing the number of infections is one of the most effective ways to slow that process. “Every case is a new petri dish for the virus to evolve and change and have these mutations come up,” she said.
It’s likely to be several years before the virus morphs enough to render current vaccines impotent, said Jesse Bloom, a virologist at The Hutch who has been studying thousands of possible mutations. And tweaking vaccines is something pharmaceutical companies know how to do, he added.
But the emergence of new variants makes it even more important to take the precautions already known to slow the spread of the disease, Greninger stressed.
“These viruses do not leap tall buildings in a single bound,” he said. “They actually need your help. Masks make a difference. Washing your hands makes a difference. Reducing your interactions with other people make a difference.”
