Alpha, beta, gamma, delta and now omicron — the coronavirus variants are making their way through the Greek alphabet quickly and there is no sign of slowing. Unfortunately, the testing technology has not kept pace with this virus’s evolution, and today — just like two years ago — a positive result simply means you have the virus. It offers no information about the variant, which can influence how your immune system reacts or your body’s response to medicine.
But that could change. Scientists at Rutgers University announced that they have developed a new color-coded test that will deliver information about the variant along with regular PCR results. Their research shows it offers a much faster and more streamlined approach than the current technology. Current PCR tests can deliver a readout in about a day, but variant sequencing, which relies on deeper analysis at off-site labs, can take up to two weeks. Scientists hope these new tests will be able to identify variants in a broader swath of patients, which could improve public health surveillance and help make better treatment decisions.
“It’s exciting technology,“ said Suraj Saggar, chief of infectious disease at Holy Name Medical Center in Teaneck, New Jersey, who wasn’t involved with the research. “We are going to keep seeing mutations that will enable these variants to escape antivirals and monoclonal antibodies and this test will help doctors know which therapies to use.”
Most treatments on the market, such as antiviral pills, are still effective against the circulating strains, but new variants have knocked out some medicines. During the first part of this winter’s surge, omicron spawned a subvariant called BA.2, which spread faster and became more prevalent. One of the most frequently used monoclonal antibodies at the time, sotrovimab, was no longer effective against the new subvariant, studies showed. BA.2 had adapted and acquired too many mutations for the drug to neutralize the virus, leading the Food and Drug Administration to revise its emergency use authorization on sotrovimab to exclude regions of the country where BA.2 was prevalent.
But a COVID test that identifies variants can help doctors determine which patients could still benefit from drugs like sotrovimab, potentially saving lives.
The test, announced in early May in the Journal of Molecular Diagnostics, can be integrated into regular PCR testing done at a pharmacy or hospital lab. According to Sanjay Tyagi, co-developer and molecular biologist at Rutgers University, “the technology is more accessible because it's available to absolutely anybody who has a PCR machine.”
What makes this test different from the standard are color-coded probes or beacons that pick up the mutations in the virus's genetic code. Omicron has a unique combination of 60 mutations in its genetic code that make it different from the original virus. So far, Tyagi and his team made enough multicolor tags to detect nine of the most common mutations in omicron and the other variants. If the delta variant is present, the test sample will glow green, for example, and for omicron, it will glow red.
One limitation is that that test can only be used to detect known variants. It will not immediately find something new, right as a novel mutant spills from our cells. However, Tyagi says it can be adapted very quickly after scientists spot and classify an emerging variant of interest.
His team plans on adding new probes as needed for future mutations that arise. Adapting the test can be done in a week.
“The technique is really simple,” he said. “In one week you will have a working test for any new variant that might emerge.”
Roy Gulick, chief of the division of infectious diseases at Weill Medical College of Cornell University, agrees that the new test could be promising for treatment decisions, but he also sees a way to improve public health.
Right now, the need for specialized equipment and off-site testing mean that only a small fraction of infected people are tested for their variants. Both Gulick and Saggar said that their hospitals only do deep sequencing to find out a variant’s identity due to the added cost and time involved.
A California study puts the cost of variant sequencing at $33. Tyagi says the Rutgers test would cost abou the same as a current PCR test. Patients and insurance plans are typically charged about $100 for a PCR test, though the actual cost of the materials is much lower. One saliva-based PCR test, developed by Yale, takes $1 to $4 to make.
This lower price plus being able to check for variants right when people get swabbed — rather than waiting for the extra steps of sequencing — could greatly help doctors and public health officials keep tabs of the circulating strains.
But Gulick also worries that the tags would need to be updated often.
“We are gonna keep seeing mutations and additional variants,” Gulick said. “It's truly Darwinian evolution we are watching and so for the next wave you would need to change the test.”
Correction: A previous version of this story misspelled Suraj Saggar’s last name.
