New Covid-19 test can identify all variants

Researchers at the University of Texas (UT) Southwest have created a rapid Covid-19 test that can identify different variants of the coronavirus in as little as four hours.

The researchers hope doctors will be able to use their test, called CoVarScan, to tailor Covid-19 treatments to patients based on which variant they have.

CoVarScan could also be used to track variants that appear in different communities, and even identify new ones.

“It’s been such a pleasure and, really, an honor to be able to use this skill set, what we have, and build something that has public health utility,” said Andrew Clark, assistant professor of pathology at UT Southwestern and study author.

The research was published in the journal clinical chemistry recently.

Looking for a specific variant of the SARS-CoV-2 virus is a little different from a typical rapid test.

Dr. Jeff SoRelle, an assistant professor of pathology at UT Southwestern, said a normal rapid Covid-19 test is a bit like walking into a library and asking if they have a specific book.

You get a “yes” or “no” answer.

Looking for variations is like reading specific paragraphs in two similar books to determine whether the books are in their second or third edition.

Between edits, words may be added, deleted, or completely changed.

Finding out which edition of SARS-CoV-2 someone has is usually done through a process called “whole genome sequencing”, where scientists look at the entire viral sequence – or read the entire book – to determine where the differences lie.

This process can be expensive and take one to four weeks to produce results.

CoVarScan works by instead examining just eight regions, or hotspots, of the SARS-CoV-2 genetic sequence.

Each variant is a little different at these hotspots.

Dr. SoRelle’s team can analyze each of the regions to identify a unique mutation pattern specific to each variant.

They also used CoVarScan to identify different Omicron subvariants.

“They create unique signatures, or fingerprints, of mutations,” Dr. SoRelle said. “We can really tell the difference between each of them.”

To make sure CoVarScan was doing it right, the team analyzed just under 4,000 Covid-19 positive nasal swab samples throughout the test. They checked the results of CoVarScan against the results of whole genome sequencing.

Dr. SoRelle and his team found that CoVarScan was very good at correctly identifying variants.

What makes CoVarScan unique is its ability not only to detect existing variants, but also to detect new variants that have yet to develop.

The team began this research in January 2021, before the Delta and Omicron variants existed.

Once they know the genetic sequence of a new variant, CoVarScan can search for the unique fingerprint of the variant’s mutations with existing ones.

“We wouldn’t necessarily need to change what we’re doing in testing,” he said. “It is enough to change what we are looking for.

Padmapriya Banada, a research assistant professor at Rutgers University who was not involved in the study, said CoVarScan’s ability to detect future variants as well as current variants is critically important.

However, a challenge in making CoVarScan more widespread is that it identifies hotspots using scientific equipment that all labs might not have.

She said more work would be needed to implement CoVarScan in places like schools or doctors’ offices that might not have such technical equipment.

“It requires some technical expertise,” Banada said. “But given what it offers, it probably overcomes those limitations.”

CoVarScan is already provided to anyone who tests positive for Covid-19 at UT Southwestern Medical Center, and Dr. SoRelle is working with Dallas County to see if CoVarScan can help hospitals track the most common variants in their area. – TNS

About Hector Hedgepeth

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