Omicron raises stakes for quick Covid-19 sequencing for variant-specific treatment

The US still lags nations such as the UK in identifying new varieties of the coronavirus. PHOTO: REUTERS

WASHINGTON (BLOOMBERG) - The Omicron variant presents a new problem for doctors: Some drugs may work better than others, but knowing what to prescribe will hinge on quickly figuring out what variant of Covid-19 a person has in the first place.

Right now, doctors don't treat Covid-19 patients based on which mutation of the virus has infected them. Even when the information is available, doctors are rarely told which form of Covid-19 a person has. That may need to change as new drugs emerge and as the virus evolves into versions that can render existing drugs less effective.

Early data suggests some drugs may be better suited to attack Omicron than others. On Tuesday (Dec 14), Pfizer announced its promising antiviral pill worked against the new variant in lab tests. The opposite was true for biotech Adagio Therapeutics, which said its experimental antibody therapy didn't work as well against Omicron, sending its shares plunging.

It's early days in the fight against Omicron. Delta is estimated to make up 97 per cent of cases that are sequenced in the US. But Omicron has the potential to soon comprise a bigger share given how fast it's spreading in other countries. And if there is clear-cut evidence that certain drugs work better than others, that could make rapid variant identification key to battling the pandemic.

"If we end up in a place where there's a serious mix of Delta and Omicron in various parts of the country then it might require a rapid genome test to figure out which variant each patient has and which drugs to use," said outgoing National Institutes of Health Director Francis Collins in an interview. "We need to develop ways to do that without having to have a high-tech laboratory in every clinical facility."

That's far from being a reality now. Even after US President Joe Biden pledged some US$1.7 billion (S$2.3 billion) towards sequencing efforts, the country still lags nations such as the UK in identifying new varieties of the coronavirus.

Going from a Covid-19 swab to a reported mutation in the US can take anywhere from 10 days to three weeks, according to Ms Molly Polen, spokesman for the laboratory group the American Association for Clinical Chemistry.

That's too long to guide a patient's treatment, particularly for Pfizer and Merck's new pills which are designed to be given within days of a diagnosis. In addition, most sequencing labs don't have regulatory clearance to tell patients or doctors what mutation a given person has. Data from these facilities is normally used for public-health purposes, such as disease surveillance, rather than patient care.

Testing for variants

To help inform medical decisions faster, the NIH has turned to its Rapid Acceleration of Diagnostics initiative, a Shark Tank-like incubator, to develop a cheap variant detection test that could work within hours.

Through the RADx initiative, the NIH's bioengineering institute is working on a few tests that hone in on the distinct characteristics of different mutations. Such tests would save time for doctors, who wouldn't have to send out samples to speciality labs and wait for full genome sequencing that often takes a week or longer.

New approaches could be cheaper too, said Mr Bruce Tromberg, director of the National Institute of Biomedical Imaging and Bioengineering. RADx is working with academic partners such as Emory University and the University of Washington, as well as companies like Helix Opco and Thermo Fisher Scientific.

Mr Tromberg hopes the tests will be authorised in time to distinguish between Omicron and Delta, if that becomes necessary. They could cost as little as US$20, lower than the price of traditional sequencing operations.

Timing is everything

Speed is of the essence when it comes to treating Covid-19. Almost all of the drugs on the market and in development are most effective at preventing serious disease in high-risk patients if given within days of symptoms starting. That makes some experts wary of adding more diagnostic steps.

With the limited treatment options currently available for Covid-19 patients, being prompt is more important than being precise, said Dr Anu Osinusi, Gilead's vice-president of clinical research for hepatitis, respiratory and emerging viruses.

"That's going to make the biggest impact versus trying to tailor against different variants," she said.

Drugmakers are scrambling to figure out how their drugs work against Omicron. The most promising antiviral so far is Pfizer's pill Paxlovid. It prevented hospitalisation or death in almost 90 per cent of high-risk Covid-19 patients in a study that didn't focus on what mutation a person had. The drugmaker confirmed on Tuesday that the therapy remains effective against Omicron in lab tests.

Merck's experimental antiviral and Gilead Sciences' remdesivir appear likely to retain their power against Omicron because of the way that the drugs stop the virus from replicating. But preliminary lab data suggests monoclonal antibodies from Eli Lilly and Regeneron Pharmaceuticals may be less effective at treating the mutation.

Lilly expects to report more data on how well its treatment works against Omicron late this week or early next week, according to Dr Nicole Kallewaard, a virologist and research adviser to the company.

"The need for variant testing will be more critical for the choice of monoclonal antibody therapy," Dr Collins said, "because many of the existing monoclonals are predicted to have limited efficacy against Omicron."

Others wait, watch

There are many unknowns about Omicron that will take weeks to answer: how quickly it spreads, the severity of disease it causes or whether it will become the dominant mutation in the US. And drugmakers have yet to amass conclusive data on how effective their treatments are at quelling the disease caused by the variant.

Testing for variants like Omicron is "critically important from a public-health perspective", said Mr Richard Besser, Chief Executive Officer of the Robert Wood Johnson Foundation and a former acting director for the CDC. "But from an individual patient perspective, I don't think that's yet relevant."

That's left many labs capable of making high-speed Covid-19 variant tests waiting and watching. Scientists want to know if Omicron will change how drugs are used before pouring resources into developing new tests.

"If we received word today that it was of vital importance to do variant testing, it would probably take us two to three weeks to set up production to do it for everyone," said Mr Dwayne Breining, the executive director of Northwell Health Labs, the largest lab network in New York State. But until it's relevant to identify Omicron in order to decide which drugs to use, "insurers aren't going to be paying for it".

The NIH should still pursue rapid mutation tests, Robert Wood Johnson Foundation's Mr Besser said. Using treatments on patients who won't benefit only raises the possibility of breeding even more problematic variants. "It's a good thing we're thinking about this for Covid," he said.

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