UAB lab tracking variants of COVID-19, finding UK strain is dominant in state

Updated: Apr. 20, 2021 at 11:39 AM CDT
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BIRMINGHAM, Ala. (WBRC) – Variants of COVID-19 account for half of all infections in the country, according to the White House, and soon, Alabama will get $3.5 million to expand testing for these mutations.

READ: US setting up $1.7 Billion national network to track virus variants

There are currently eight labs in Alabama, including the Fungal Reference Lab at the University of Alabama at Birmingham (UAB), decoding COVID DNA. The process is called viral genome sequencing.

“Primary samples are coming from patients in the hospital that test positive for COVID PCR or by COVID antigen tests. And so, a subset of these samples, not every single one, but a subset are being subjected to this novel method called viral genome sequencing,” explained Dr. Sixto Leal, Jr., MD, PhD, Department of Pathology, UAB.

“That information is being relayed to the Alabama Department of Public Health (ADPH) to be able to track variants of significance to public health and isolating quarantined individuals that are affected by these variants to mitigate their spread.”

As of April 12, there have been 188 confirmed cases of variants in Alabama, according to data from the Centers for Disease Control and Prevention (CDC). The CDC will now only provide variant data from states with more than 300 specimens. Alabama has not yet tested that many samples.

“We’ve been working very closely with the Alabama Department of Public Health to establish a statewide network of laboratories that are capable of sequencing. The plans are still in place. Right now, we are the main laboratory that is preforming viral genome sequencing,” explained Leal.

UAB began testing for variants in late January and has been averaging 24 samples per week.

“As soon as we started sequencing clinical samples, we reached out to UAB Infection Prevention, and infection prevention at other institutions as well to let them know to send us samples for viral genome sequencing, particularly from certain patients more likely to harbor variants strains of public health significance. So, these are individuals with particularly severe or atypical presentations of SARS-CoV-2. They’re more likely to harbor variants of the virus. Also, individuals who have been immunized that subsequently test positive for SARS-CoV-2. Those individuals are more likely than others to harbor variants strains that are able to evade the immune response,” said Leal.

Leal said UAB’s lab will soon test 100 specimens per week and will expand its targeted sequencing approach to include more random samples.

“To get a really good non-biased sense of each number of variant strain circulating in our area.”

Leal said the UK variant is the dominant strain in Alabama right now.

“When we identified the UK variant, we estimated that incidence based on what we had sequenced about 2 percent. Now, well about a couple weeks ago, it was 40 percent. Based on our most recent sequencing run, it’s probably more like 60 percent of the UK variant in the state,” said Leal.

The New York variant has also been identified in UAB’s lab, said Leal, and the more contagious South African variant has been found once.

“The South African variant, what we know about it, is it has a particular mutation that does make so that antibodies are less likely to prevent infection with this variant,” said Leal.

He added, “The main concern is individuals who have been vaccinated and subsequently come down with infection, those individuals may have been exposed to a new variant of the virus that is able to cause infection to those who have been immunized. That’s really the main reason to look at all the variants that are out there, that are circulating, so if we can identify any of the South African variant like we did… we want that not to spread throughout the population. So, if we can sequence and identify individuals with the South African variant and target our contact tracing efforts to prevent spread of the South African variant, we can stop the spread throughout our population and prevent another surge from potentially occurring.”

The Alabama Department of Public Health is still evaluating how it will spend the $3.5 million to expand testing, but Dr. Karen Landers said ADPH Bureau of Clinical Laboratories, “expects to develop its own capacity for genomic sequencing.”

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