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Electric Crispr Chip Quickly Detects Covid-19 Virus

Crispr genome edits illustration

(NIH.gov)

9 Nov. 2020. An engineering lab developed a chip device that uses gene editing and an electric field to detect viruses responsible for Covid-19 infections. A team at Stanford University in California described the device last week in the Proceedings of the National Academy of Sciences.

Researchers in the microfluidics lab led by mechanical engineering professor Juan Santiago are seeking fast, reliable ways to detect in the SARS-CoV-2 virus responsible for Covid-19 infections. The RT-PCR test is the so-called gold standard diagnostic for SARS-CoV-2 coronaviruses. RT-PCR stands for reverse transcription – polymerase chain reaction, a type of genetic analysis, to detect in this case the viral RNA signature for SARS-CoV-2. That test, however, requires sending nasal and throat swab samples back to a remote lab for purification and analysis, often taking a day or more to return results.

Santiago’s lab studies microfluidic devices, also known as labs-on-a-chip, for detecting disease-causing organisms in human fluids, or food and water. One of the techniques employed by the lab is isotachophoresis, a process using an electric field to separate molecules with different electric-charge properties. For detecting SARS-CoV-2, the sample is put into a hand-held microfluidic device with fine channels and wells, submitted to an electric field that separates out and purifies RNA in the sample. The RNA is then reverse-transcripted to DNA and amplified with isothermal amplification that also traces the RNA chemistry to its DNA source.

The separated and amplified nucleic acids are then analyzed with a gene-editing technique called Crispr, short for clustered regularly interspaced short palindromic repeats. Crispr is a genome-editing process based on bacterial defense mechanisms that use RNA to identify and monitor precise locations in DNA. This technique uses Cas12, a more compact and efficient enzyme that seeks out the specific sequence for SARS-CoV-2. The Cas12 editing enzyme is linked to a fluorescing chemical, which if SARS-CoV-2 is found, emits a detectable signal when enzyme cuts the strand.

“Our chip is unique in that it uses electric fields to both purify nucleic acids from the sample and to speed up chemical reactions that let us know they are present,” says Santiago in a university statement.

The team tested their device with 64 nasopharyngeal swab samples — taken with long sticks extending through the nose to the back of the throat — from people divided evenly between those who tested positive for Covid-19 infections and healthy individuals. The results show readings from the lab’s microfluidic device agree with gold-standard RT-PCR tests 97 percent of the time. The researchers also say the chip device returns results in 30 to 40 minutes, and uses 100 times less reagents than conventional RT-PCR tests.

“Our test can identify an active infection relatively quickly and cheaply,” adds Stanford graduate student Ashwin Ramachandran, the paper’s first author. “It’s also not reliant on antibodies like many tests, which only indicates if someone has had the disease, and not whether they are currently infected and therefore contagious.”

Santiago is co-founder of Purigen Biosystems Inc. in Pleasanton, California, a company commercializing the lab’s isotachophoresis technology. The university says the lab is also working with Ford Motor Company to advance the technology into a marketable product.

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Hat tip: Fierce Biotech

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