Laboratories in Washington state have identified more than 600 cases of COVID-19 caused by coronavirus variants that state and federal officials are tracking closely, according to a report released last week by the Washington Department of Health.
Through genomic sequencing, the state has identified 592 cases involving one of five “variants of concern,” which have characteristics that scientists believe could allow them to spread more easily, cause more harm or reduce the effectiveness of vaccination or treatment, according to the U.S. Centers for Disease Control and Prevention.
The state also documented 13 cases involving one of three “variants of interest,” which are under further investigation by researchers.
“All the variants of concern have arrived in Washington state and are rising in many parts of the state,” said Pavitra Roychoudhury, a computational biologist with UW Medicine. “I think this underscores the importance of doing genomic sequencing in a regular fashion. It’s preparing us for what might come through the population.”
The state has ramped up genomic sequencing of the novel coronavirus and is working with several labs to search for new variants and identify trends. If a more contagious or more deadly variant takes off, and the state’s vaccination campaign can’t head off its momentum, some researchers are concerned it could lead to a fourth wave of disease. Understanding which variants are dominant could drive policy decisions and reopening plans.
Sequencing helps officials know “how the virus is evolving and get out in front of it,” said Kelly Wroblewski, director of infectious disease for the Association of Public Health Laboratories. “You can adjust your public health messaging or public health interventions.”
The United States was behind countries like the United Kingdom, which identified late last year one of the first worrisome variants, in investing in genomic sequencing.
Over the last four months in the U.S., “we’ve closed the gap significantly,” Wroblewski said, adding that Washington is one of the states now “leading the way.”
Last month, more than 6% of coronavirus cases confirmed through molecular testing were sequenced, according to the state report.
The B. 1.1.7 variant, which was first identified in the U.K. and is believed by scientists to be about 50% more infectious, has made the largest splash nationally. It has grown steadily in prevalence since the beginning of the year, according to national data from the CDC. Earlier this month, it represented just under 10% of new U.S. cases.
In Washington state, while B.1.1.7 continues to spread and has been detected in 152 cases, it has not yet become dominant, said State Epidemiologist Dr. Scott Lindquist.
What has surprised Lindquist is the even more rapid proliferation of two variants that arose in California: B. 1.427 and B. 1.429. Both are considered concerning because they are more contagious and show some resistance to natural and vaccine-induced immunity.
So far, the two California variants have been detected in 422 cases in Washington.
In one of the research labs working with the state, 30% of all variants sequenced have been California varieties, Lindquist said.
Experts said it’s difficult to extrapolate from Washington’s data what proportion of all cases are due to variants because the data collection is not necessarily representative and the sample size is relatively small.
“It’s an easy thing to misinterpret and you have much better statistical power when you’re looking at that across the country nationally,” Wroblewski said.
New modeling from Dr. Joshua Schiffer and his colleagues at the Fred Hutchinson Cancer Research Center suggests that super spreader events will be key in allowing new variants to gain a toehold and then take over.
Their work, which has not yet been peer reviewed, found that most new variants die out quickly. But those that are disseminated early on to large numbers of people — as in the Skagit County choir practice that helped spread the virus in Washington and the Boston biotech conference in February 2020 that is partly blamed for the initial outbreak on the East Coast — are the ones that thrive.
It’s not clear yet whether that’s happening with variants in Washington, according to Lindquist. “I do believe super-spread events will be an issue,” he said. “We just have not seen enough genotyping results yet to see any clear results.”
That underscores the importance of masking and avoiding the types of situations that present the virus with an abundance of targets, Schiffer said.
“The public health message is more of the same. The really high-risk environments are crowded, indoor events. If we can avoid those and mask effectively, that is going to be key to prevent these variants from winning the race with the virus.”
The state is also keeping an eye on breakthrough cases, when someone tests positive for the novel coronavirus after completing their vaccination regimen.
Vaccines are not 100% effective, and some rare breakthrough cases are to be expected.
Samaritan Healthcare, in Moses Lake, reported two breakthrough cases earlier this month, according to Gretchen Youngren, a spokesperson for the organization.
Youngren said one fully vaccinated employee received routine testing following an outbreak among staffers who had yet to accept the vaccine. The employee, who was asymptomatic, tested positive also. Another employee received routine testing after reporting symptoms associated with allergies. Both took 10 days off for mandatory isolation but have returned to work.
Dr. Michael Kalnoski, of Atlas Genomics, a company that performs laboratory testing for King County, said his lab had returned five positive test results for people who had indicated to the county that they were fully vaccinated.
“After you get your second vaccine shot and you wait two weeks. It’s not your get-out-of-jail-free card and that you’re immune,” Kalnoski said.
At a briefing Thursday, Health Secretary Dr. Umair Shah said the state is analyzing possible breakthrough infections but is still vetting the circumstances to be sure the cases meet the CDC’s definition: COVID-19 that strikes people at least two weeks after they have been fully vaccinated.
Health officials plan to monitor for any evidence they are related to new variants that may be more resistant to immunity, Lindquist said.
“We’re working with every local health jurisdiction to identify any epidemiology that would point to things like: Is it more common with a certain vaccine, more common with a certain lot? Was it storage issues? Anything that would show us trends,” he said.