It’s been nearly three weeks since Idaho health officials flagged five coronavirus samples as having possibly dangerous mutations, shipping them to national labs for more thorough screening because state labs can’t yet do that.
Still, the state doesn’t know for sure if more infectious or more deadly virus variants are here.
“All five of the samples were of insufficient quality to generate usable full genome sequences,” Idaho Department of Health and Welfare spokesman Zachary Clark told the Post Register in an email Thursday.
Clark said one sample had “limited coverage in the spike gene region of interest,” which is the protein the virus binds to human cells through, “and it was not” the U.K. variant.
That variant, formally called B.1.1.7, is estimated to be 50% more infectious and potentially more deadly. The Centers for Disease Control said Tuesday that it has been linked to at least 541 cases nationwide, including in Teton County, Wyoming, which borders Teton County, Idaho, a tourism-driven county that has added the highest rate of new cases by population statewide.
The Associated Press reported Thursday that the U.S. “fell behind in the race to detect dangerous coronavirus mutations. And it’s only now beginning to catch up.”
“The problem has not been a shortage of technology or expertise. Rather, scientists say, it’s an absence of national leadership and coordination, plus a lack of funding and supplies for overburdened laboratories trying to juggle diagnostic testing with the hunt for genetic changes,” the news wire service wrote.
The CDC publicly reports data on the presence in U.S. states of three coronavirus variants: B.1.1.7; the B.1.351 variant, first identified in South Africa, which is linked to three cases; and the P.1 variant, first identified in Brazil, which is linked to two cases.
Clark said “no further work is being done on these samples.” Because the samples were too poor to test, the state doesn’t have evidence yet to say that new coronavirus variants are or aren’t in Idaho. But, Clark said, “we should all behave as if they are.”
Clark said it’s “difficult to say” why the samples weren’t good enough to spot virus variants. He said all five samples were “stored for several weeks before sequencing was attempted,” and it’s “hard to predict” how many times samples will be thawed, frozen and handled. Environmental changes can degrade the quality of RNA within cells, making it more difficult to extract meaningful information out of them.
“State and national labs are very selective in identifying samples with higher viral loads because these samples have greater success rates for producing quality sequences and the appropriate depth of coverage needed to assemble a full genome sequence suitable for” analyzing variants, Clark said.
Clark said Idaho will continue sending coronavirus samples to the CDC and other national research labs. The state’s “highest priority” is to make the state able to generate “high quality” genetic sequencing data and conduct “bioinformatics analysis by the end of the month,” he said. State labs are developing guidance to collect virus samples throughout the state.
“Our hope is that this strain surveillance program will continue to grow in coming weeks,” Clark said.
The CDC estimates by March, most coronavirus cases in the U.S. will come from the new U.K. variant. The ease of more transmission could lead to more infections, hospitalizations and deaths.
Labs in the state cannot yet fully sequence samples itself, health department spokeswoman Niki Forbing-Orr previously told the Post Register, but they can flag samples that may contain the variant; the state health department hopes that its public health lab can begin sequencing “as soon as possible this year,” according to a Jan. 12 blog post.
“This virus is mutating, and it doesn’t care of it’s in Idaho or South Africa,” Ilhem Messaoudi, director of a virus research center at University of California, Irvine, told the Associated Press.