new COVID DNA test

New test for COVID-19

A new type of test

An article published in the New England Journal of Medicine today highlights a promising new COVID test. It also has some of the best acronyms seen in healthcare for quite some time.

CRISPR gene editing technology is fairly well-known. By exploiting a family of DNA sequences, which play a key role in anti-viral defences in some types of bacteria, scientists use one particular variant of the genetic sequences (CRISPR-CAS9) to edit genes.

Genetic markers

CRISPR does not itself have a particularly imaginative acronym. It stands for “clustered regularly interspaced short palindromic repeats”. That means a lot more to geneticists than most lay people. Yet it is being used more and more to detect the presence of viral or bacterial pathogens in the body.

Now experts from Massachusetts Institute of Technology, Harvard and the University of Washington have found a way of testing for COVID-19 using gene markers,. It uses minimal equipment and delivers seemingly accurate results in less than an hour.

Detecting the pathogens

The team started with a far more imaginatively named SHERLOCK process (specific high-sensitivity enzymatic reporter unlocking). That’s an established way of testing for pathogens, but the teams have simplified the process even further.

SHERLOCK currently uses a two-step process to find pathogens. First the target (the virus) is amplified in a testing sample. That process itself can be difficult, but it increases the presence of a virus in a sample to levels at which it can be tested. The amplified sample is then followed by CRISPR-mediated nucleic acid detection. That step confirms the presence or absence of a particular virus.

The existing SHERLOCK process is more complicated than existing point-of-care testing (the PCR swabs we now know so well). Because it relies upon an RNA extraction step (isolating genetic material from the sample) and multiple liquid-handling stages, the risk of cross-contamination of samples is significantly increased when compared to existing tests.

“One pot” technology

Now using SHERLOCK as the starting point, the team have developed a new test called STOP (SHERLOCK testing in one pot). It seems to have similar accuracy as existing PCR swab tests, although not much data has been provided so far to support the claim.

The team say they have created a streamlined approach to extracting viral RNA using isothermal amplification. The test is subjected to a single source of heating to trigger amplification of the viral material. That’s in in contrast to the PCR test approach which requires a series of alternating temperature steps.

To simplify the RNA extraction process, the team developed a purification step using magnetic beads. Adding magnetic beads to the sample concentrated SARS-CoV-2 genes from a swab test into one reaction mixture. It also boosted the sensitivity of the test.

Further steps were taken to reduce the duration of sample extraction to just 15 minutes. There are also far less ‘hands on’ steps for the team processing the samples. The test has been called STOPCovid.V2.

Positive results

The test has been compared to the Centers for Disease Control and Prevention (CDC) standard two-step test (the PCR swab test). Magnetic beads being added yielded a sample containing 600 times the amount of detectable viral DNA. The test can apparently detect the presence of the virus at substantially lower levels than existing tests.

That suggests the new test may be able to reduce the number of ‘false negatives’ that existing tests are prone to deliver. One in five PCR swab tests give a false negative result (source).

Sadly only 202 samples were tested with the new approach, which is not a huge number in terms of medical trials. They were directly compared with established and proven negative and positive samples. The tests were run in a ‘blind’ trial, which means the testing team did not know which sample was which.

The study found that the STOPCovid.V2 test had a sensitivity (true positive) of 93.1% and a specificity (true negative) of 98.5%. That compares very well with current PCR swab test results. Positive samples were detected in between 15 and 45 minutes, which also compares well with existing PCR tests.

The team suggest that the simplified STOPCovid.V2 test is well suited to low-complexity clinical laboratories. The game is definitely afoot in the search for better COVID tests.

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