PROVO, Utah – Health officials at first weren’t certain how to investigate the first known case in Utah of the more-infectious “U.K.” coronavirus variant, according to emails among federal, state and county agencies.
But that initial uncertainty may reflect the deficits of a nationwide disease surveillance system that relies too heavily on state and private labs to detect changes in infectious diseases, one Utah doctor said last week.
“Our state of knowledge about variants arising in the United States and how they’re spreading is, I hate to say this, pretty patchy and spotty,” Dr. Sankar Swaminathan, an infectious diseases specialist for the University of Utah, said in a news conference Thursday.
“We don’t have really a coordinated, integrated national system for high-level detection, proactively, of variation genetically. … For that reason I would say that we really have a very, to be honest, inadequate knowledge.”
Summit County announced Monday that a third Utahn — a woman there between the ages of 20 and 44 — had contracted the variant. The second case, in Utah County, was announced by state officials last week.
Without a national genomic surveillance system, Swaminathan said, it’s impossible to know how readily the U.K. variant has been spreading in Utah and in other states since the first Utah patient with the variant was confirmed in mid-January.
The 28-year-old Salt Lake County man first tested positive for the coronavirus on Dec. 31, when he was feeling ill, according to emails obtained by the Brown Institute for Media Innovation’s Documenting COVID-19 project and provided to The Salt Lake Tribune.
On Jan. 14, county health officials received word that the man’s test sample was one that had undergone genetic sequencing by the Utah Public Health Laboratory as part of its surveillance for variants of the virus — and he had contracted the so-called “U.K. variant.”
The man already had been identified as a possible contact by another person who had tested positive for the coronavirus at the end of December, the emails state. But it was two days after the man’s case was confirmed, on Jan. 16, that a county epidemiologist wrote that she had interviewed the man and the patient who likely infected him.
Neither had traveled recently, she reported, and the source patient didn’t know where he was exposed to the virus.
In the meantime, health officials announced the case to the public the day after it was identified — but they appeared to be uncertain how to proceed. County health officials weren’t sure whether it would be possible to learn whether the patient who exposed the man also had the variant, or whether the contact tracing should be handled differently for patients with the variant.
“Is there a specific type of investigation form that needs to be completed for variant case[s]?” one county epidemiologist wrote.
“Do we need to do more thorough investigation?” wrote Dr. Dagmar Vitek, director of the medical division of the county health department. “Collect PCR [a genetic COVID-19 test] on him and contacts, sequence, look at all his contacts?”
A scientist at the Utah Public Health Laboratory warned that the variant could be confirmed in the source patient only if he was still shedding the virus, more than two weeks after he was diagnosed; his original diagnosis was in an antigen test, with a sample that couldn’t be used for genome sequencing.
“There had been previous discussion on handling variant cases to quickly identify any travel and identify a potential source,” Nicholas Rupp, spokesman for the Salt Lake County Health Department, wrote Monday, when asked about the released emails.
County officials decided that for variant cases of COVID-19, they would go back to thorough contact tracing, where investigators follow up individually with each contact, Rupp said. For most COVID-19 cases, county investigators have moved to a “shared responsibility model,” where tracers ask the patients themselves to alert some of the people they may have had contact with.
The U.S. Centers for Disease Control and Prevention asked for details of the man’s case the day after the variant was identified, emails show. But the CDC didn’t ask for the sample to conduct its own whole genomic sequencing until Jan. 20.
It’s not clear what, if any, information the CDC’s sequencing produces over the Utah Public Health Lab’s sequencing. State health officials could not immediately be reached for comment.
The U.K. variant, dubbed B117, is substantially more contagious than the strain that has previously dominated the United States — but it’s not yet known whether it’s more likely to cause serious illness.
“There’s not a lot of evidence for that yet, but there is that concern in some of the strains that have been less characterized. And we just really don’t know how much of an issue that is,” Dr. Swamainathan said.
As of Thursday, the Utah Public Health Lab had identified only two cases of the U.K. variant, state epidemiologist Angela Dunn said in a news conference. “But keep in mind, we’re only sequencing 10 percent of all of our positives,” Dr. Dunn said.
That is “a lot compared nationally to other states,” she said. “But we’re still not able to sequence every single person who becomes positive. So the fact that we found two means that it’s here. It’s already community-spread. And so that means we have to be extra cautious when it comes to taking prevention measures.”
The more the virus spreads, the more likely it is to develop damaging mutations, Swamainathan said.
“It’s not necessarily that these things are coming in from abroad,” he said. “With the levels of transmission that we have here, we’re going to have our own homegrown variants arising as well.”