Do you have a Covid variant case? Nobody will tell you

Coronavirus infections from variant strains are spreading rapidly in the United States, but there’s a big problem: Lab officials say they can’t tell patients or their doctors if someone has been infected with it. variant.

The federal rules about who can be notified of variant cases are so confusing that public health officials may just know the county where a case has arisen but cannot do the type of investigation and provide the notifications needed to slow the spread, Janet Hamilton said. , executive director of the Council of State and territorial epidemiologists.

“It could be associated with a person in a community setting at high risk or not, but without patient information we don’t know what we don’t know,” Hamilton said. The group has asked federal officials to break the rules. “Time is counted.”

The problem is that the tests in question for detecting the variants have not been approved as a diagnostic tool by either the Food and Drug Administration or under federal rules governing university laboratories – which means that the tests currently used for the genomic sequencing are also high. level lab research without communication with patients and their physicians.

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Amid limited testing to identify different strains, more than 1,900 cases of three key variants have been detected in 46 states, according to the Centers for Disease Control and Prevention. This is worrying given early reports that some could spread faster or turn out to be deadlier or that they could thwart existing treatments and vaccines.

Officials representing public health laboratories and epidemiologists have warned the federal government that limiting information on variants – in line with obscure regulations governing clinical laboratories – could hamper efforts to investigate pressing questions about them.

The Association of Public Health Laboratories and the Council of State and Territorial Epidemiologists jointly urged federal officials this month to “urgently” relax certain rules that apply to clinical laboratories.

Washington state officials detected the first case of the variant found in South Africa this week, but the infected person did not provide a correct phone number and could not be contacted about the result positive. Even though health officials are looking for the patient, “legally we can’t” tell them about the variant because the test is not yet federally approved, said Teresa McCallion, spokesperson for the health department. of the state, in an email.

“However, we are actively looking for what we can do,” she said.

Laboratory testing experts describe the situation as a 22-point trap: Scientists need enough case data to make sure their genome sequencing tests, which are used to detect variants, are accurate. But while waiting for the results to arrive and for further examination, the cases of variants are increasing.

The shift is in part reminiscent of the situation of a year ago. Amid regulatory missteps, approval of a Covid-19 diagnostic test has been delayed as the virus spread undetected.

The limitations also put laboratory professionals and epidemiologists at a standstill as public health officials attempt to trace contacts of people infected with more contagious strains, said Scott Becker, CEO of the Association of Public Health Laboratories. . “You want to be able to say [patients] a variant has been detected, ”he said.

Complying with laboratory rules “is not doable in the time frame demanded by a rapidly evolving virus and responsive public health system,” the organizations wrote.

Hamilton also said telling patients they have a new strain could be another tool to encourage cooperation – which is in decline – with efforts to trace and sample their contacts. She said the notifications could also further encourage patients to take advice to stay in isolation seriously.

“Can our investigations be better if we can disclose this information to the patient?” she said. “I think the answer is yes.”

Public health experts have predicted that the B.1.1.7 variant, first found in the UK, could be the predominant variant strain in the US by March.

As of Tuesday, the CDC had identified nearly 1,900 cases of variant B.1.1.7 in 45 states; 46 cases of B1351, which was first identified in South Africa, in 14 states; and five cases of variant P.1, initially detected in Brazil, in four states, CDC director Dr Rochelle Walensky told reporters on Wednesday.

A February 12 memo from North Carolina public health officials to clinicians said “the results of the sequencing will not be released to the vendor” because the genome sequencing at the CDC is performed for surveillance purposes and is not not an approved test under the Clinical Laboratory Improvement Amendments Program, or CLIA, which is overseen by the Centers for Medicare & Medicaid Services.

The subject was also discussed this week in Illinois. Telling patients they are positive for a variant coronavirus is “not currently permitted” because the test is not CLIA approved, said Judy Kauerauf, section chief of the Communicable Disease Control Program. Illinois Department of Public Health, according to a file obtained by the COVID -19 documenting project from Columbia University’s Brown Institute for Media Innovation.

The CDC has stepped up its genomic sequencing in recent weeks; Walensky said the agency was only driving him on 400 samples a week when she started as a director, up from more than 9,000 samples this week.

Patients and doctors in the dark

The Biden administration has committed nearly $ 200 million to expand the federal government’s genomic sequencing capacity in hopes of being able to test 25,000 samples per week.

“We will identify variants of Covid earlier and better target our efforts to stop the spread. We are quickly injecting targeted resources here because the timing is critical for these rapidly evolving variants, ”Carole Johnson, testing coordinator for President Joe Biden’s Covid-19 response team, said on a call with journalists this month.

Hospitals are getting high-level information about whether samples being sequenced have tested positive for the variants, said Dr Nick Gilpin, director of infection prevention at Beaumont Health in Mich., Where 210 cases of the variant B.1.1.7 have been detected. Yet patients and their doctors are not sure who has been infected.

“It’s relevant from a systems perspective,” Gilpin said. “If we have a bunch of B.1.1.7 in my backyard, it’s going to make me think a little differently about the way we do business.”

It’s the same in Washington state, McCallion said. Health officials may share general numbers, such as 14 out of 16 outbreak samples at a facility were identified as B.1.1.7 – but not who those 14 patients were.

There are arguments for and against notifying patients. On the one hand, being infected with a variant will not affect patient care, say public health officials and clinicians. And people who test positive would still be urged to take the same precautions when it comes to seclusion, wearing a mask, and washing their hands, regardless of the blood pressure they are wearing.

“There would be no difference in medical treatment if they had the variant,” said Mark Pandori, director of the Nevada Public Health Laboratory. However, he said, “in a public health emergency it is really important that doctors know this information.”

Pandori has estimated that only 10 or 20 labs in the United States are able to validate their variant lab tests. One is the laboratory at the University of Washington in Seattle.

Dr Alex Greninger, deputy director of clinical virology laboratories, who co-created one of the first tests to detect SARS-CoV-2, said his lab started validating the sequencing tests last fall .

Greninger said he plans to have a federally authorized test for whole-genome sequencing of Covid-19 in the coming weeks.

“So any issues you notice when notifying patients and using [the] the results will not be a problem, ”he said in an email.

San Diego-based Illumina and other companies have approved coronavirus testing machines that can also detect variants. However, since the additional sequencing capability has not been specifically approved by the FDA, the results can be shared with public health officials but not with patients and their physicians, Chief Medical Officer Dr Phil Febbo said. of Illumina.

He said Illumina hadn’t asked the FDA for further approval, but that it could if the variants started to cause greater concerns, such as escaping vaccine protection.

“I think that at present it is not necessary for individuals to know their strains,” he said.