Groups team up to track variants

By Nora Eckert

Forum News Service

ROCHESTER, Minn. — As Mayo Clinic physicians care for patients in the COVID-19 intensive care unit in Rochester, they’re far better equipped to battle the virus now than in the early days of the pandemic.

But there’s one key piece of information they often do not know: if the patient is infected with a COVID-19 variant.

“Mayo Clinic, like many other institutions, does not routinely test for variants,” said Mayo spokesperson Ginger Plumbo, adding that there are exceptions depending on the patient and guidance from the Minnesota Department of Health.

VARIANT TESTING, 9A

While being infected with a variant doesn’t typically change a patient’s care, it’s vital to understand how these mutated viruses spread and affect people who are vaccinated or unvaccinated. Their prevalence is undeniable. The delta variant has been declared the most prominent strain of COVID-19 in Minnesota and in the nation.

So, who tests for that? And how can health agencies know what the most prominent strain is when most positive samples go unsequenced?

The answer lies in between several connected organizations that do the time-consuming and expensive work of hunting down variants.

SLEUTHING OUT A VARIANT

Reviewing the list of COVID-19 variants feels more like a Greek lesson than a science one.

Alpha, beta and gamma infect many corners of the world and have driven different waves of the pandemic. Now, delta has risen as the dominant strain in the state and nation since it first sickened people in India last winter. It threatens higher rates of transmission and has brought mask mandates back to many areas of public life.

All of this has been caused by a few minuscule differences in the virus’ genetic code. As a virus replicates, these “errors” creep into its sequence. Enter: variants.

“In a perfect world, every time that virus replicated, it would replicate the exact same. But it doesn’t,” said Sara Vetter, who manages the infectious disease laboratory at the Minnesota Department of Health. “The more (a variant) is different, we know it’s gone through more and more rounds of replication and probably spreading to people, and is more distant to the original.”

Determining the presence of a variant takes much more time and money than running a test to see if someone is positive for COVID-19.

A PCR test — the most common form of a COVID-19 test — looks for specific targets in the organism, key clues that indicate the presence of the virus.

“So it’s a yes or no answer. It’s there or not,” Vetter said.

If conducting a PCR test is like watching a movie trailer, genetic sequencing for variants is like watching the three-hour extended cut. Once it’s clear that COVID-19 is present in someone’s system, machines read the genetic material from the positive sample to determine what infinitesimal differences could indicate the presence of a variant.

“It’s actually determining each nucleic acid at every spot over the entire genome, which is about 35,000 bases,” Vetter said.

It’s a time-consuming process which can take upwards of a week. Once the sample is transported from a clinic to the appropriate lab, it’s prepped and sits in the sequencing machine for about two days. After its genetic material is read, supercomputers analyze the results, determining if any genetic variations exist and if a variant is present.

The process can cost between $100 to several hundreds of dollars per sample, said Dr. Bobbi Pritt, the chair of the Division of Microbiology within the Mayo Clinic department of laboratory medicine and pathology.

HOW VARIANT DATA IS COLLECTED

The state Department of Health aims to sequence 25 percent to 30 percent of positive COVID-19 specimens. The chosen group of positive tests comes from a random sampling across the state. Federal and state health officials pay special attention to gathering samples from a variety of communities in an effort to accurately represent the spread of the virus and any variants. They also prioritize sequencing samples from patients who are hospitalized.

The delta variant has been detected in 90 percent of specimens sequenced since June 20, according to data from the state Department of Health.

Several different groups are involved in the effort to collect and sequence samples. One is the U.S. Centers for Disease Control and Prevention, which gathers random samples from clinics around the state and pays commercial laboratories to sequence them. These results are then sent back to the state Department of Health to report.

The Department of Health also sequences samples at its lab, partnering with the University of Minnesota’s genomic center, which serves as a “backstop” to run sequencing when the Department of Health lab is at capacity.

Mayo Clinic, too, sequences a segment of positive tests in its clinical lab — about 100 to 200 tests each week, Pritt said. Infrequently, this sequencing is conducted to inform patient care.

As of Aug. 2, there were 21 patients in Mayo’s COVID-19 intensive care unit. According to spokesperson Heather Carlson Kehren, that number has since “risen significantly,” but she said Mayo would not provide updated data because the number of patients is “constantly fluctuating.”

There is a larger Mayo Clinic lab focused on studying how COVID-19 has changed in the state since the start of the pandemic. There, researchers are sequencing 22,0000 samples. They’re about one-third of the way through that reserve.

Mayo also collects specimens from around the state and sends them to the Department of Health for sequencing.

With all sources combined, around 700 genomic sequencing tests were completed the week of Aug. 1, according to Health Department data. That was a stark increase from the average of 250 tests per week during the previous six weeks.

As the delta variant surges, 13,110 people tested positive for COVID-19 in Minnesota in the first two weeks of August. That’s more than all of the positive tests in July combined.

This means tracking variants is even more vital, said Vetter.

“The purpose of why we’re monitoring is twofold. One is that we have the general situational knowledge of what’s circulating,” she said. “But the other is outbreak tracking. We do have a side system to have people reach out to laboratories and get specimens if we need them to track an outbreak.”

While some of the dynamics surrounding the variant remain mysterious, there are tools that remain productive in preventing illness: washing hands, wearing masks and getting vaccinated.

As cases surge around the country, there is debate around how effective current vaccines are when they come head-to-head with the wily delta variant.

Dr. John O’Horo, a Mayo Clinic infectious disease expert, says the evidence shows vaccination is still a formidable barrier against the virus, as well as a means to hinder the development of more variants.

“At this point in time, the real thing to take away from this is that vaccines are a way to prevent complications, to reduce the susceptibility of communities and individuals to these variants,” O’Horo said. “The effectiveness of the vaccines depends heavily on what you’re looking at. The existing vaccines remain highly effective against hospitalizations and death.”