Rapid COVID-19 Test Identifies SARS-CoV-2 Variants in Hours

A number of COVID-19 tests currently exist, although they generally detect either a fragment of SARS-CoV-2 genetic material or small molecules found on the surface of the virus, and do not provide information to identify the variant. In addition, many researchers worry that these tests are not accurate in detecting some variants - or may miss future strains. 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. Now, scientists can tell which variant has infected a COVID-19 patient in just a few hours– a critical task that can potentially influence treatment decisions but takes days or weeks at most medical centers.

Last year, a team of pathologists at The University of Texas Southwestern Medical Center (UTSW, Dallas, TX, USA) had developed CoVarScan, a rapid COVID-19 test that detects the signatures of eight hotspots on the SARS-CoV-2 virus. Now, after testing CoVarScan on more than 4,000 patient samples, the team has reported that the test is as accurate as other methods used to diagnose COVID-19 and can successfully differentiate between all current variants of SARS-CoV-2. The testing results have helped public health leaders track the spread of COVID-19 in North Texas and make policy decisions based on the prevalence of variants. Doctors have also used the results to choose monoclonal antibodies that are more effective against certain strains infecting critically ill COVID-19 patients.

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. To test how well CoVarScan works, the team ran the test on more than 4,000 COVID-19-positive nasal swab samples from patients both with and without symptoms. The tests were validated with the gold-standard whole genome sequencing, and the results were used by doctors to choose treatments in some critically ill COVID-19 patients.

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. The team plans to continue developing CoVarScan as a commercial test and has a pending patent application based on this work.

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

“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,” added 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.”

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