COVID-19 variants: New test detects which strain is in your skewer

Scientists at Harvard University and MIT have developed a new test that Determine which variant of COVID-19 you have, uses 3D printed components and costs only $ 2 (approx. 1.44) per device.

Details of the diagnostic device and templates for 3D printing were published online. The team behind the test says they wanted to create something simple that, for example, “could be built by a doctor in Zimbabwe and 3D printed in their facilities”. It runs on batteries and gives results in an hour.

The test can successfully identify the alpha, beta, and gamma variants in a patient’s saliva, and the researchers say they are developing the device to detect the delta variant.

Should new varieties emerge, the team could run a specific test for the variety in just two weeks. The likelihood of this happening, according to experts, depends on the number of people who become infected. The more countries relax restrictions, the more likely it is that more people will become infected. This means the virus is more likely to change in ways that affect COVID-19 disease, creating a new breed of concern.

All four co-authors of the study spoke with us BBC Science Focus to explain everything you need to know about the new COVID-19 variant test.

How does the spit test of the COVID-19 variant work?

The test uses the scissors from the scientists’ molecular toolbox: CRISPR technology.

“CRISPR is part of the bacterial immune system that evolved to recognize and cut DNA,” explains Dr. Xiao Tan, one of the four lead authors of the study. “It’s a way for bacteria to defend themselves. What we have done is to co-opt this to see things that we are interested in. “

Unlike some CRISPR technologies, the scissors used in the spit test are not just one-cut wonders. Called SHERLOCK – which stands for “Specific Highly Sensitive Enzymatic Reporter Unlock” – it can actually detect the presence of COVID-19.

The researchers collaborated Dr. Jim Collins, one of the co-founders of SHERLOCK technology to develop their device. When SHERLOCK finds a particular spike protein that is specific for the variant in question, it activates an enzyme which then generates the fluorescent light that indicates the test is positive, said Devora Najjar, Co-first author. “So only if the CRISPR the [COVID-19 virus] it will start releasing the fluorescence. If not, you will not get any fluorescence. “

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The test is easy to carry out and no training is required, the researchers said. First, spit into the sample preparation chamber. Turn on the heat and wait about three to six minutes for the saliva to spread over the filter.

Then pick up the filter and move it into the reaction chamber column. Press down to add the skewer to three small pipettes, each containing SHERLOCK technology, which is specific for different variants.

An hour later you will either see a fluorescent light – bad news – or no light at all. An accompanying smartphone app can also read out the result.

The spit test uses minimal instruments, which is why researchers have named it miSHERLOCK. Compared to home PCR testing, the miSHERLOCK device is simpler and cheaper, say the researchers.

“I’m not sure how this works in the UK, but in the United States it costs $ 120 to send samples like the FDA-approved,” Tan said.

A device costs around $ 15 for the miSHERLOCK test. “But if you reuse some of the components, you can actually cut that down to maybe $ 6,” Tan explained. “Then we calculated what it would cost a commercial vendor, and you could probably cut this thing down to $ 2-3 per test.

“These are all the components you need to give you an answer immediately without having to wait 72 hours for the shipping process.”

Can the spit test detect the delta variant?

In research published in Scientific advances the team tested the device against the alpha, beta, and gamma variants. They say they are now working on targeting the Delta variant.

“When we started this project a few months ago, we were looking for varieties that were no longer the top varieties of interest,” said Najjar. “It speaks for the rapidly changing nature of the pandemic and that we need to create systems that are just as agile as the virus.”

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The tubes in the reaction chamber are called assays and can be customized to target a very small, specific piece of genetic code.

“You can imagine the device almost like a miniature coffee machine with different coffee pods. Aside from the fact that we designed each capsule and assay to contain these CRISPR enzymes, each specific to the gene we are looking for, ”explains Dr. Rose Lee, another study lead author and an infectious disease specialist at Boston Children’s Hospital.

The team is currently developing a “pod” that can detect the COVID gene in general and others that detect specific genes for the spike proteins of COVID variants.

Each assay takes about two weeks to create – every time a new variant DNA is identified, the team could create a new “dish” 14 days later.

Why do we need to know which variant a person has?

Because the virus has mutated, it has become more contagious, and other variants could prove more deadly.

“Knowing which variant you have could be of significant importance as it changes the way we think about therapies that we could use for the patient, such as treatment with antibodies,” said Lee.

In the case of Delta, a recently published study found that the strain was resistant to neutralization by multiple types of antibodies, and that a single dose of the Pfizer or AstraZeneca coronavirus vaccine had “barely noticeable inhibitory effects on the Delta variant,” even though two doses neutralized the virus.

It also helps countries keep track of the currently worrying variants in a population.

“Variant tracking is usually done by sequencing very few samples and then extrapolating from there to get an idea of ​​the entire population,” explains Dr. Helena de Puig, Co-first author.

While the miSHERLOCK device does not perform sequencing, ie cannot recognize a previously unknown strain, it provides data with which the distribution of known variants can be followed.

When can people in the UK buy the spit test?

This research now needs to be mass-produced and approved by agencies like the FDA before it can be mass-marketed. The team has stressed that their lab is unable to sell the devices and obtain FDA approval.

“Typically, to commercialize an assay, you need both manufacturability and FDA approval,” said de Puig. “We would be happy if this scientific work was applied in the clinics, and if there are production facilities that they would like to develop, we would be very, very happy to help them.”

The team hopes this can be used around the world to help people cope with the spread of COVID-19.

“It’s very easy for us to make the components, the only thing that needs to be changed, the small part that targets a specific tip of the variant,” Tan said.

“In fact, [the device] doesn’t even have to limit itself to COVID. There are many other infectious diseases that have virus particles in saliva that this could also be used for. We didn’t necessarily test them, but there’s no reason why it wouldn’t work. “

About our experts

Dr. Helena de Puig is a postdoctoral fellow building molecular diagnostic devices at the Wyss Institute for Biologically Inspired Engineering at Harvard University.

Dr. Rose A Lee works at Boston Children’s Hospital, where she works as a pediatric assistant in the Infectious Disease Department.

Devora Najjar is a research associate at the Massachusetts Institute of Technology (MIT) with a focus on bioengineering, participatory environmental monitoring and education.

Dr. Xiao Tan is Clinical Fellow at Wyss Institute and Lecturer in Medicine in Gastroenterology at Massachusetts General Hospital.