A new mutation of covid-19 that shows increased transmissibility was recently detected in the Seattle metro area with a PCR (polymerase chain reaction) test. The variant, which first emerged in the United Kingdom and is spreading to other countries, was later confirmed with RNA sequencing by the University of Washington Department of Laboratory Medicine and Pathology as the UK coronavirus variant called B.1.1.7.
The B.1.1.7 variant, the first of its kind discovered in King County, was detected by Atlas Genomics, a high complexity, molecular diagnostics laboratory that serves the state of Washington through a number of high-volume public covid testing sites. Atlas Genomics, which employs the LigoLab LIS & RCM Operating Platform, detected the mutation using a three-target assay.
According to Atlas’ Medical Director, Michael H. Kalnoski, MD, the B.1.1.7 variant has a small deletion in its genome, which causes the S gene (responsible for making the Spike protein), one of the three assay targets, to not be detected by the covid PCR test. If the S gene “drops out” and the other two targets are positive, this may be indicative of the presence of the UK coronavirus variant.
Lab officials also said the ability to detect the UK variant with a PCR test was good news because that means patients and public health officials can be notified about the potential mutation in a matter of hours. Sequencing would still be required to confirm the suspected variant but obtaining PCR results expeditiously is helpful.
“Speed is critical when you’re dealing with a variant shown to be more contagious,” says Atlas Genomics General Manager Rob Rovig. “If our test can pick it up with PCR, then we’ll know well within 24 hours rather than having to wait a week or longer to get the variant confirmed through RNA sequencing.”
Atlas Genomics is one of dozens of laboratories across the country using TestDirectly, a web-based patient engagement portal developed by LigoLab, that improves turnaround times and connects the patient directly with the laboratory for test results. In this case with TestDirectly, the patient and public health officials were both automatically notified about the positive result in real-time which enabled the patient to immediately begin to quarantine and mitigate disease spread.
According to LigoLab CEO Suren Avunjian, TestDirectly was developed to remove potential delays in the laboratory and facilitate safe and streamlined covid-19 testing.
“With more testing and fast and accurate test results, we can identify the virus and its mutations, take action to contain its spread, and start making our way toward a more normal life,” says Avunjian.
TestDirectly eliminates paperwork and manual processes and enables patients to self-register, select a local collection facility, and book an appointment, all from the comfort of their computer or mobile device. The platform supports community and organizational testing, drive-through, walk-up, and on-site collection workflows, and covers the lifecycle of a case and a specimen, including laboratory processing, report delivery via email or SMS, and billing operations.