For the past two decades, the Boise lab of Interpath Laboratory has helped doctors, nurse practitioners and hospitals diagnose and treat patients. With the recent arrival of SARS-CoV-2 variants, the lab took on a different task: helping Idaho epidemiologists look for variants. “We feel really fortunate that we’ve been involved in this process,” said Judy Kennedy, Interpath’s marketing director.
Just as vaccines were rolling out, scientists broke some news: They had discovered slightly tweaked versions of the coronavirus that causes COVID-19.
These variants seemed to spread more easily. They seemed to make people sicker. And some of them had changed in subtle ways that seemed to make it harder for antibodies to attack.
First, there was B.1.1.7 — a variant that scientists discovered in the United Kingdom. Then, fast and furious came more variants, found in places where COVID-19 was bouncing between enough people that it had plenty of opportunities to adapt.
Almost all of these “variants of concern” have officially arrived in Idaho. Laboratories had confirmed at least 95 cases of Idahoans infected with one of the variants, as of Friday.
The head of the U.S. Centers for Disease Control and Prevention warned the public and government officials last week to keep their guard up against COVID-19, to avoid a fourth surge in cases as the pandemic continues.
“We have so much to look forward to, so much promise and potential of where we are and so much reason for hope,” CDC Director Dr. Rochelle Walensky said, according to news reports. “But right now, I’m scared.”
A local epidemiologist and infectious disease specialist says he’s concerned, too. But he holds optimism that COVID-19 vaccines will be able to save lives and prevent hospitalizations.
“So far, we think previous infection and vaccination will give you some protection against the variants in this stage, of a variable amount,” said Dr. Sky Blue of Sawtooth Epidemiology & Infectious Diseases. “We don’t have anything that is just a complete escape (from the protection of vaccines).”
And even if people get infected with the variants, antibodies from vaccination “still may be enough to protect you from having serious disease,” he said. “Those are some of the known unknowns that we’re still waiting to get data on.”
What we know, and don’t know, about the COVID-19 variants in Idaho
The Idaho Department of Health and Welfare works with laboratories around the state and country to check for “variants of concern” in Idaho. The fastest growing groups appear to be the B.1.427/429 and B.1.1.7 variants.
The B.1.427/429 emerged in California and is believed to be 20% more transmissible and capable of slipping past some antibodies. The B.1.1.7 — 50% more transmissible — is rapidly overtaking the original “wild” coronavirus and is responsible for a recent surge in coronavirus cases in other parts of the U.S.
The only way to find out whether a person is infected with a new variant, or one of the original COVID-19 viruses, is “genomic sequencing.” There’s a limited number of laboratories in Idaho and in the U.S. capable of sequencing viruses.
The CDC launched a nationwide program this year to monitor for new variants and strains. State officials say they send nine samples per week to that program, which sequences about 18,000 samples per week from across the country.
“We are working to increase the number of Idaho labs that can perform this sequencing,” Christopher Ball, Idaho Bureau of Laboratories director, said in an email to the Idaho Capital Sun last week. “We’ve applied for federal funding to help develop a new testing line at the University of Idaho Genomics Resource Center to provide additional capacity in northern Idaho, and we’re supporting the Boise VA Medical Center as they bring their sequencing program online.”
The Idaho Bureau of Laboratories in Boise is one of the labs doing sequencing, but its capacity is limited.
There’s another limiting factor, too: reality.
A few things have to go right for a laboratory to even be able to sequence the virus. First, a person has to be tested for COVID-19 while they are infected. Second, the test has to pick up plenty of the genetic material from the person’s respiratory system. Third, the fragile genetic material has to stay fresh and intact while it’s packaged up and sent to the lab.
Then, it can take upwards of two weeks for Idaho health officials to get the results and find out whether a COVID-19 variant was detected. (The results aren’t used to flag individual patients; they are used to monitor whether a variant is circulating in a community.)
Idaho health officials said last week there were 100 cases of Idahoans infected with COVID-19 after being fully vaccinated. Half of them experienced no symptoms, and most of the others felt like they had a cold, allergies or the flu, officials said. Hospitalizations were rare among these early “breakthrough” infections, according to Idaho officials.
Among those cases, only 16 patients’ samples were sequenced as of Thursday, Deputy State Epidemiologist Kathryn Turner said in an email to the Idaho Capital Sun. Of those, three — or 19% of the samples — turned out to be a variant that has public health officials worried. Idaho is still waiting for results from two of the 16 samples.
Doctors sound the alarm about variants in Idaho
Health care providers in two different parts of the state are warning that variants seem to be spreading rapidly in Idaho.
Physicians from East Idaho, one of the worst U.S. hot spots last month, told the Post Register they believed variants were part of the reason their hospitals were filling up again. They noted that few samples had been sequenced for variants in the region.
“We’re No. 1 for cases in the United States,” Dr. Richard Nathan, an infectious disease specialist at an East Idaho hospital told the newspaper. “It would be nice to have some information about why.”
Elke Shaw-Tulloch, administrator of the Idaho Division of Public Health, said last week that health officials are “definitely keeping our eye on slight increases that we’re seeing in certain areas.”
One local health group has been monitoring its COVID-19 test results for one telltale sign of a variant — the dropoff of a certain gene.
Dr. David Peterman, CEO of Primary Health Medical Group, has been closely watching his clinics’ data and sharing it with the state.
The data, shared with the Idaho Capital Sun, show a steady increase during the month of March in the percent of positive COVID-19 tests with that trait — going as high as 30% to 70% of tests each day.
“We’re seeing a significant increase” in tests with that trait, said Gene Chapman, the Boise-based regional director of laboratory operations for Interpath Laboratory.
Interpath is one of the labs that processes the everyday COVID-19 tests that Idahoans get at local clinics. It’s been running tests for Primary Health for much of the pandemic.
And just by chance, the lab’s process for determining whether a patient does or doesn’t have COVID-19 relies on checking for certain traits in the patient’s test sample. As it happens, one of those traits is the “s-gene” — the gene that drops off in B.1.1.7 and other variants.
At the end of each day, Interpath sends off samples with that “s-gene” trait to the Idaho Bureau of Laboratories to be sequenced. IBL then determines what kind of variant it has on its hands — a harmless one or a “variant of concern.”
Interpath’s first Idaho sample went off for sequencing on Feb. 8. It took 14 days for another suspicious sample to come through. But in the past few weeks, that has ballooned. The Boise-based lab sent off 13 samples to be sequenced on Thursday alone.
“We’re seeing consistent s-gene drops every day now,” Chapman said. “Two or three one day, or maybe 10 the next day.”
It’s impossible to know for sure, based on that trait, whether those Idaho samples are harmless variants — since many genetic changes don’t really matter — or whether they’re among the few that spread faster, cause worse disease or evade immunity.
But experience with lab testing in surges elsewhere in the U.S. makes it seem likely that these are indeed a worrisome variant.
When a specialized lab ran tests from other surge locations, “a month into it, if it was a spike gene failure, it was nearly universally a B.1.1.7 (variant),” Blue said. “If you have those now, it likely is gonna be the (B.1.1.7).”
To Peterman, these numbers are a bright red flashing light: warning.
“In other states, particularly in Europe, when the percent (of B.1.1.7 variants in tests) arrives at 40% and stays there, that’s where it becomes extremely cumulative and becomes very rapid,” he said in an interview.
Peterman says Primary Health’s own data show that younger people aren’t signing up for vaccines as enthusiastically as older Idahoans did.
Vaccine hesitancy, among younger people who tend to seed viral outbreaks, is a recipe for a fourth surge, he says.
All Idahoans age 16 and older can now be vaccinated. (Want the vaccine? Use our guide to find appointments.)
What can Idahoans do to prevent a fourth surge?
Experts at local, state, national and global public health agencies all have the same advice.
The best way to keep outbreaks under control is to continue to follow COVID-19 guidelines. Wear a mask. Keep a distance. Avoid large gatherings. And get the vaccine; once Idahoans are fully vaccinated, they can relax somewhat on COVID-19 restrictions, the CDC says.
“As we work to offer vaccine to more Idahoans and learn more about how these variants behave, our best defense is to stay consistent with our health and safety measures,” Kimberly Link, communicable disease control manager with Central District Health, said in a news release in February. “We know that the choices we’ve made in the last year to wear a face covering, keep our distance from others, wash our hands frequently, and stay home when we’re sick will serve us well in helping to protect us from these potentially more severe variants.”
While there is some evidence that certain variants can shrug off antibodies from vaccines or prior infection, early data suggest that vaccines remain somewhat-to-very effective against the existing variants.
Slowing the spread remains important even with vaccines now being widely available. That’s because, every time the virus replicates itself, it can pick up new changes to its genetic material. When more people have protection from antibodies, some versions of the COVID-19 virus will stop being able to infect people. But every time someone spreads the coronavirus, it gives the virus another opportunity to mutate in a way that gets around those antibodies.
“Early on, when everybody was completely susceptible, the virus didn’t need to get any mutations to do damage,” Blue said. “Now, for a virus to continue to spread, evolutionarily, the playing field is different.”
Peterman notes that Idaho and the Treasure Valley seem to be taking a more cavalier approach to the pandemic.
“We should be wearing masks, distancing,” he said. “I get it, this is not what everyone wants, but …”
Some local schools are bringing students back into the classroom, he said, despite research and real-world experience that shows children spread the variants much easier than they did the original version of the coronavirus.
“It’s extremely worrisome,” Peterman said.
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