A point-of-care COVID-19 test developed by researchers at the University of Illinois Urbana-Champaign can now detect and differentiate the alpha variant of the SARS-CoV-2 virus from previous strains in saliva samples.
The new test builds on the group’s past developments, which allowed samples to bypass the laboratory – first using nasopharyngeal inoculations, then with saliva samples. The point-of-care amplification and testing process, called LAMP, is more efficient than PCR because it does not require expensive thermal cycling machines. The researchers said the assay does not require RNA extraction and purification steps, similar to saliva tests in Illinois.
The results of the study, led by Rashid Bashir, a professor of biotechnology and dean of Grainger College of Engineering in Illinois, mechanical science and engineering professor Bill King and bioengineering professor Enrique Valera, are published in the journal Lab on a Chip.
“Our study shows that it is possible to test for variants of the same coronavirus strain in a single point-of-care test that takes 30 minutes using a portable handheld device,” Bashir said. “The new test is scalable to suit future pandemics, COVID-19 or otherwise, and can be used in home or other settings.”
The updated process utilizes a genetic phenomenon called S-gene target failure – which is present in the alpha variant but not in the early strains of the SARS-CoV-2 virus – to distinguish between the two alpha variants, the researchers said.
“The new omicron variant also exhibits S-gene target failure and could be tested for by adapting the approach developed in this study,” Valera said.
During the new testing process, specially selected genetic primers are placed on additively manufactured cartridges and dried before adding the patient samples. The selected primers are set against the S gene and are specific for detecting the target gene’s target failure against 69-70 deletion in the alpha variant, the study reports.
The study confirmed the device’s efficacy by testing 38 clinical saliva samples, including 20 positive alpha variant samples.
The researchers said they would like to refine their method of testing up to five different viruses, viral strains and variants in a single test, compatible with nasal inoculation and saliva media.
Co-authors of the paper were graduate students Jongwon Lim and Robert Stavins and Karen White and James Kumar of Carle Foundation Hospital.
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Intelligent components and environments at the University of Illinois Urbana-Champaign, the National Science Foundation, and the National Institutes of Health supported this study. Clinical trials were obtained from the Carle Foundation Hospital and the U. of I. COVID-19 detection study.
The authors are also affiliated with Electrical and Computer Engineering, Beckman Institute of Advanced Science and Technology, Carle Illinois College of Medicine, Holonyak Micro and Nanotechnology Lab, Cancer Center in Illinois, Materials Research Laboratory and Carl R. Woese Institute of Genomic Biology.