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Scientists hunting for new variants amidst omicron surge

Genomic Sequencing
Posted at 12:04 PM, Jan 06, 2022
and last updated 2022-01-06 14:04:20-05

CHICAGO — The record-shattering COVID surge has proven new variants like omicron can quickly throw the public health response off balance. It’s why scientists around the world are digging deep into the molecular structure of COVID-19 to stay ahead of what could come next.

Scientists inside a level 2 bio-safety laboratory at Rush University Medical Center in Chicago are hunting for coronavirus variants.

“It's really critical that we understand which variants are present now, which ones are starting to emerge,” said Dr. Mary Hayden, the Director of the Division of Infectious Diseases at Rush’s Regional Innovative Public Health Laboratory (RIPHL).

Over the last year, genomics sequence testing labs like this have been popping up all around the U.S. and the world. Tens of thousands of COVID specimens are tested each day.

“Every time a patient is infected, you're getting so many new viral particles and each one of those is an opportunity for a mutation that could change the activity of the virus,” said Stefan Green, director of the Genomics and Microbiome Core Facility.

It’s why scientists are studying the virus’ genetic code.

“It's basically a long string of letters,” explained Hannah Barbian, a co-investigator and genomic virologist with RIPHL.

That chain of letters can reveal whether any changes or mutations have taken place. That can help determine whether the virus is becoming more dangerous or transmissible or potentially vaccine-resistant.

“That's why omicron was so concerning and also just the sheer number of mutations there were so many compared to what we had seen before,” said Barbian.

It was a genomic sequencing lab in South Africa that first spotted the omicron variant, identifying the more than 30 mutations on its spike protein.

“Making that information widely available to the world as quickly as they had, it gave the rest of us a little bit of an advantage to look out for this and to and to prepare,” said Hayden.

The CDC’s Nowcast modeling data shows just how quickly a new variant like omicron can emerge and spread.

On Nov. 24, the World Health Organization received reports of the new variant from South African scientists. The first case in the U.S. was confirmed a week later. By Jan. 1, it had eclipsed the delta variant in the U.S., making up 95 percent of new cases.

“There were a lot of predictions from very smart people who I respect greatly, who thought that delta was so efficient at transmission that we weren't going to see a big jump in mutation anymore in COVID that we'd see like minor alterations in delta,” said Hayden. “And clearly, that's not the case.”

In April, the Biden Administration pledged $1.7 billion to fight variants by scaling up genome sequencing work around the country.

The National SARS-CoV-2 Strain Surveillance Program, as it’s known, is essentially a genetic dragnet to catch the next potentially concerning variant.

“We need these global centers like ours because we don't know where the next novel strain will develop,” said Green.

There are about 68 state and local public health laboratories sequencing 15 to 20,0000 randomly selected coronavirus specimens each week – quadrupling the sampling that was being conducted just over a year ago.

“I think it's going to be really critical to sort of give the world a heads up that something new is coming in. And, you know, it's worth keeping a close eye on,” said Barbian.

Public health experts say investing in a global network of sequencing labs like this will not only help scientists stay ahead of new COVID variants but future pandemics as well.