Long processing time to blame for slow COVID-19 variant identification

LITTLE ROCK — For health officials to find out what strain of COVID-19 is on a test isn’t a quick and easy process, involving a trip to Minnesota and the need for enough genetic material to sequence, according to Arkansas Department of Health Medical Director for Immunizations Dr. Jennifer Dillaha.

First, the test has to be sent to the Department of Health, and it has to be a PCR (polymerase chain reaction) test, used to detect genetic material from a particular organism, “to get sequenced,” Dillaha said.

“We can’t sequence antigen tests,” also known as rapid diagnostic tests that detect different proteins on the surface of the coronavirus, she said.

The PCR test “specimen is sent to Little Rock for the local health unit and then we run them on our PCR machines, and if it is a positive test, then we send the specimen to the public health lab in Minnesota and they sequence it for us,” Dillaha said.

“The PCR test by itself won’t tell you what the sequence is. You have to have a certain amount of genetic material from the test to be able to do the sequencing, so we don’t send ever single last one of them. We send the ones that meet the criteria for having enough genetic material.”

The turnaround time for the PCR tests as far as getting results varies, according to Dillaha, depending on if the courier is on time and where the Minnesota lab is with running the tests when they arrive. She said it generally takes a couple of weeks to get the results back from the sequencing and that includes transit time and how long it takes to process the specimen and report back to the health department.

Turnaround time for PCR test results once they arrive at the Minnesota lab right now is 24 hours, according to Department of Health public information officer Danyelle McNeill.

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Department of Health: Omicron might not peak for couple of weeks

LITTLE ROCK — The Arkansas Department of Health will be assessing this week to determine when the omicron variant will peak in the state.

“It has started to peak in some states that were hit with omicron before us so that gives us a general idea,” Dr. Jennifer Dillaha said. “We are thinking we might not peak for a couple of weeks.”

What comes after that with COVID-19 is unknown.

Dillaha said she is not aware right now of any other new variant or variants on the horizon.

“Of course, we sequence all of the samples, so if there is a new variant that shows up, we will know it,” she said. “We are not just looking for omicron.

When you do the sequence, it could be a different one.” However, she said that it takes a while to get the results and now there are a couple of weeks behind.

She said, though, for something like omicron, just showing that it is present basically is sufficient.

“We don’t have to show how many cases there are.

We just have to know what is circulating,” Dillaha said. “You have to keep in mind that results are from samples from two weeks ago or more.”

The best thing Arkansans can do both for protection against omicron and whatever comes next is get vaccinated or get a booster if they’ve been vaccinated, Dillaha said.

“Last week, we ran the numbers for cases, hospitalizations and deaths since Dec. 1,” she said. Those who are not fully vaccinated made up 63 percent of the cases. Those “fully vaccinated but not boosted” accounted for 34.7 percent.

“And then the people who are fully vaccinated and boosted for cases since Dec. 1 are 2.3 percent, so getting a boost dose is really important.”

The percentage was even higher concerning hospitalizations for those not fully vaccinated, she said, at 70 percent since Dec. 1. Those

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fully vaccinated but not boosted made up 28 percent and those fully vaccinated and boosted were 2 percent.

“For the deaths, it was 78 percent for people who were not fully vaccinated, 20.5 percent for those who were fully vaccinated but not boosted and 1.5 percent for people who were fully vaccinated and boosted,” Dillaha said.

According to Department of Health numbers, 53.8 percent of Arkansas 12 and up were fully immunized as of Wednesday morning and 13.1 percent are partially vaccinated. The number who have received a third dose was 494,122.

In White County, 40.8 percent of those 5 and over had been fully immunized and 6.5 percent was partially immunized.

“I would like to see a higher percentage of people getting boosted,” Dillaha said. “I think that would really help people avoid infection and stay out of the hospital.”

Even though the omicron variant is believed by health officials to cause less-severe disease on average, COVID-19 deaths in the U.S. are climbing and modelers forecast 50,000 to 300,000 more Americans could die by the time the wave subsides in mid-March because of how transmissible it has been.

Dillaha said there also are a couple of concerns that health officials are seeing with children, including “an increased incidence of new diagnosis of diabetes after kids have had COVID.”

“That’s been reported in the medical literature, plus we have good evidence that getting vaccinated is protective against getting MISC, which is the multiinflammatory

children,” she said. “So those two things can have serious health consequences for children, so we are strongly encouraging parents to get their children vaccinated.

“We do not yet know the long-term effects of getting infected with the omicron variant, but we know that the virus can have serious long term consequences so we can avoid the infection that is important, especially right now when we have very few treatment options available to us due to the scarcity of treatment resources.”

She said the best treatment right now is monoclonal antibodies, but they are in short supply since “Sotrovimab is the one monoclonal antibody that works against omicron, and, of course, we’re having this huge nationwide surge.”

Dillaha explained that monoclonal antibodies are a pharmaceutical product and the health department has the job of distributing them around the state to locations that are using them. “So our state gets a certain allocation of the monoclonal antibody that works and then we distribute it around, so you know it’s just a drop in the bucket in terms of what we need.”

With the limited supply, she said the monoclonal antibody treatment is “given to people who are immuno-compromised and not expected to mount an immune response if they get infected or not expected to mount an immune response to a vaccine.”

She said the reason only Sotromivab works against omicron is “because omicron has so many more sequences in mutations” than delta, “changes in the genetic sequence, which changes the protein structure.”

“The monoclonal antibodies attach to certain protein structures on the virus, so if that protein structure has changed, that antibody might not stick to it,” Dillaha said.

She said while the idea with the monoclonal antibodies is to use them to keep those infected out of the hospital, “sometimes that’s not enough and some people may end up in the hospital and some of them may die.” She said she has not seen statistics on the number of patients who have died after receiving monoclonal antibodies, but she hasn’t heard of anyone dying because of them.

In addition to the monoclonal antibodies treatment, Dillaha said there are two oral medications that are being used for treatment.

“The one that is preferred is Paxlovid, and it also is in short supply,” she said. “It is an anti-viral medication, an oral one, and then there’s Molnupiravir, and it’s more available. It doesn’t work as well as Paxlovid, but there are more doses available.”

Dillaha also recommends because it is flu season that those who have received the COVID-19 vaccine, or are going to get it, also receive the flu vaccine.

She said so far the state has seen more of a normal flu season, but “what you have to keep in mind is flu cases are not reportable. We don’t collect data on so many people are diagnosed with flu. We do collect data on how many people are in the hospital with the flu and how many people die from the flu.”

“The way we kind of keep a feel on how much flu is out there is that we have health-care providers that – not all of them, but some of them – have agreed to submit data to us that gives us an estimate of flu,” Dillaha said. “We are increasing and we likely will continue to increase. We usually peak in about January or February, so we encourage people to go ahead and get their flu vaccine if they haven’t already, and you can get a COVID vaccine and a flu vaccine on the same visit.”