New test for COVID-19

A new type of test for COVID-19

An article published in the New England Journal of Medicine today highlights some promising advances in finding new ways to quickly test for COVID-19, as well as 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) as the basis for most gene editing that happens today.

Genetic markers

CRISPR does not itself have a particularly imaginative acronym. It stands for “clustered regularly interspaced short palindromic repeats”, which means a lot more to geneticists than most lay people. It is, however, starting to be used by medical professionals to detect the presence of viral or bacterial pathogens in the body.

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

Detecting the pathogens

Starting with a far more imaginatively named SHERLOCK process (specific high-sensitivity enzymatic reporter unlocking), which is an established way of testing for pathogens, 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 essentially increases the presence of a virus in a testing sample, to levels at which it can be tested. The amplified sample is then followed by CRISPR-mediated nucleic acid detection, which confirms the presence or absence of a particular virus in the sample.

The existing SHERLOCK process is, however, more complicated than existing point-of-care testing (the PCR swabs we’re all becoming increasingly familiar with). 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 sensitivity (accuracy) as existing PCR swab tests, although little data has been provided so far to support that claim.

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

To simplify the RNA extraction process and boost the sensitivity of the test, 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.

Further steps were taken to reduce the duration of sample extraction to just 15 minutes, with significantly reduced ‘hands on’ steps for the team processing the samples. The test has been called STOPCovid.V2.

Positive results

When compared to the Centers for Disease Control and Prevention (CDC) standard two-step test (the PCR swab test), the concentration of the sample using magnetic beads yielded a sample which contained 600 times the amount of detectable viral DNA than the standard PCR swab test. As a result, the test can apparently detect the presence of the virus at substantially lower levels than existing tests.

That, in turn, suggests it the new test may be able to reduce the number of ‘false negatives’ that the existing PCR swab tests are prone to deliver. One in five (20%) of PCR swab tests give a false negative result (source).

Although 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 also 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%, which 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.