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HomeNewsEmerging COVID variants can now be identified within hours. Here's how

Emerging COVID variants can now be identified within hours. Here’s how


With the scare of new COVID variants emerging, a group of scientists has developed a new rapid test kit that can only determine whether you are infected but can also detect which variant you are infected with. CoVarScan, which was developed last year is as accurate as other methods of diagnosing COVID-19 and can successfully detect all current variants of COVID-19.

“Using this test, we can determine very quickly what variants are in the community and if a new variant is emerging,” said Jeffrey SoRelle, Assistant Professor of Pathology and senior author of the study. “It also has implications for individual patients when we’re dealing with variants that respond differently to treatments.”

For the study, CoVarScan has been tested on more than 4,000 patient samples collected at UT Southwestern.

To determine which variant of COVID-19 a patient has, scientists typically must use whole-genome sequencing, which is time-consuming and expensive, relying on sophisticated equipment and analysis to spell out the entire RNA sequence contained in the viruses. Scientists pointed out, in that sense CoVarScan can play a game-changing role. 

How accurate are CoVarScan tests?

Compared to whole-genome sequencing, CoVarScan had 96% sensitivity and 99% specificity. It identified and differentiated Delta, Mu, Lambda, and Omicron variants of COVID-19, including the BA.2 version of Omicron, once known as “stealth Omicron” because it did not show up on some tests designed to detect only the Omicron strain.

“A common critique of this kind of test is that it requires constant adjustment for new variants, but CoVarScan has not needed any adjustment in more than a year; it is still performing very well,” said Dr. SoRelle. “In the future, if we did need to adjust it, we could easily add as many as 20 or 30 additional hotspots to the test.”

How CoVarScan was developed?

In early 2021, Dr. SoRelle and his colleagues at UT Southwestern wanted to track how well current tests were detecting emerging variants of SARS-CoV-2. But they realized that sequencing a lot of specimens would not be timely or cost-effective, so they designed their own test, working in the McDermott Center Next Generation Sequencing Core, part of the Eugene McDermott Center for Human Growth and Development directed by Helen Hobbs, M.D., Professor of Internal Medicine and Molecular Genetics.

CoVarScan hones in on eight regions of SARS-CoV-2 that commonly differ between viral variants. It detects small mutations – where the sequence of RNA building blocks varies – and measures the length of repetitive genetic regions that tend to grow and shrink as the virus evolves. The method relies on polymerase chain reaction (PCR) – a technique common in most pathology labs – to copy and measure the RNA at these eight sites of interest.

 



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