New AI Tool to Simplify a Test That Works Best for Hepatitis and COVID-19

As a result of AI-fueled enhancements, going beyond COVID-19 and pregnancy, the world could eventually come to depend on at-home tests for several diseases.

New AI Tool to Simplify a Test That Works Best for Hepatitis and COVID-19

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Researchers from the University of Florida have made use of artificial intelligence tools to facilitate a test that works well for both hepatitis C and SARS-CoV-2, the virus that causes COVID-19.

The streamlined test occurs in one small test tube in just a matter of a few minutes. Having additional refinement, it could also arrive at doctor’s offices soon and, one day, turn out to be available as home tests that are as simple as a pregnancy test.

We are trying to build a home-based test that is as reliable as a lab-based test. Our objective is to develop a simple test that eliminates the need for expensive equipment and provides results in just 10 to 20 minutes.

Piyush Jain, Study Lead Researcher and Professor, Chemical Engineering, University of Florida

For these goals to be accomplished, Jain’s group is innovating a system called one-pot reaction since the complete test happens in just one small test tube.

These tests, based on a technology called RT-LAMP, have the potential to amplify a small part of a virus’s genome and produce a visible signal when the virus has been detected. Reading these tests could be as simple as looking for a blue color or making use of a small device that can detect a change in the test tube.

The FDA has accepted some at-home, one-pot tests for COVID-19 as a part of the emergency use authorization. However, they have a comparatively high false positive rate, meaning that they are not as trustworthy as they could be.

We are combining another technology called CRISPR to determine the difference between a false positive and a true positive.

Piyush Jain, Study Lead Researcher and Professor, Chemical Engineering, University of Florida

As far as the biotech world is concerned, CRISPR has become recognized for its potential to drive quick genetic engineering enhancements.

Jain’s group depends on the CRISPR system’s potential to home in on specific genetic sequences. Just if the sequence for, say, the hepatitis virus is present will the test show a positive outcome?

The only issue? The RT-LAMP technology requires a temperature that goes to 150 °F, while CRISPR works best at 100°. That difference makes tests highly complex needing two separate reactions—too difficult for at-home use. Jain’s team has been attempting to bridge this gap by coming up with a CRISPR system that has the potential to resist higher temperatures.

From a heat-loving species of bacteria, scientists recently found a CRISPR enzyme that thrives at 140°. In their latest work performed, Jain’s group shifted to AI tools to examine this enzyme and find how they could make it survive at 150 °.

The AI programs proposed a few dozen alterations to the enzyme, which Jain’s group tested in the laboratory. Ultimately, they discovered four changes to the enzyme that allowed it to work at 150°.

It’s very challenging for any human to do this kind of analysis on an enzyme. We didn’t have to spend years; we could make these improvements in months. With everything working at the same temperature, now we are able to combine everything in a true one-pot reaction we call SPLENDID.

Piyush Jain, Study Lead Researcher and Professor, Chemical Engineering, University of Florida

The SPLENDID test was verified by the research group on clinical samples from patients with COVID-19 or hepatitis C. The test was almost 97% precise for SARS-CoV-2 and 95% accurate for the highly prevalent version of the hepatitis C virus discovered around the world.

Jain states that, even though the method did not work well against all other less predominant versions of the hepatitis C virus, direct changes to the test must rapidly enhance its precision.

The study was reported in the Cell Reports Medicine journal on May 8th, 2023.

The study was financially supported by the National Institute of Allergy and Infectious Diseases at the National Institutes of Health in the belief of developing easy tests for viruses like hepatitis C so they could be determined and treated early when treatments work best.

Currently, Jain’s group will work to refine the test, enhance its potential to differentiate between hepatitis C strains and confirm it in hospital settings in hopes of offering one day at-home tests also one day.

Journal Reference

Nguyen, L. T., et al. (2023) Engineering highly thermostable Cas12b via de novo structural analyses for one-pot detection of nucleic acids. Cell Reports Medicine. doi.org/10.1016/j.xcrm.2023.101037.

Source: https://www.ufl.edu/

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