In recent weeks, prescriptions for Pfizer’s blockbuster drug Paxlovid have skyrocketed. That’s good news for many COVID-19 patients, as the pill has been proven to reduce serious illness from SARS-CoV-2 infections. But a slew of new lab studies show that the coronavirus can mutate in ways that make it less susceptible to the drug, by far the most widely used of the two oral antiviral drugs approved in the United States to treat COVID-19. Researchers have found some of those mutations in variants already circulating in infected people, raising new concerns that doctors may soon lose one of their best therapies for fighting COVID-19.
Taken together, the studies show that “when you put pressure on the virus, it escapes,” said David Ho, a virologist at Columbia University who was one of the first to mutate drug resistance some 30 years ago. documented in HIV. Ho was not involved in the new studies, but is doing similar work on SARS-CoV-2. While the newly identified mutations aren’t widespread yet, Ho and many other scientists believe it’s only a matter of time. “Given the amount of infections out there, it’s going to come,” Ho says.
The resistance studies follow other recent concerns about Paxlovid, which in the United States remains limited to use in people with risk factors that make them more likely to develop severe COVID-19. Confirming anecdotal reports widely reported by the media, several studies have shown that a small percentage of infected people who receive the regular 5-day course feel better initially, but their symptoms return. And questions have grown about whether Paxlovid helps people who aren’t at high risk for serious illness — Pfizer stopped a large trial of the drug earlier this month in standard-risk COVID-19 patients because it didn’t offer statistically significant protection against death or hospitalization.
The U.S. Food and Drug Administration (FDA) granted emergency use approval for Paxlovid in December 2021. The drug consists of nirmatrelvir, the active antiviral drug, and ritonavir, a compound that slows the breakdown of nirmatrelvir in the body. Due to bottlenecks in the production of nirmatrelvir, the rollout of Paxlovid has been slow: doctors in the United States were dispensing only 40,000 or fewer prescriptions per week until mid-April. Since then, the number of prescriptions has risen to more than 160,000 a week, according to the latest figures from the Centers for Disease Control and Prevention.
That rise puts selective pressure on the virus, promoting mutations that help it survive in the presence of the drug. And because each infected person makes trillions of copies of SARS-CoV-2, the virus has plenty of opportunities to test different mutations as it replicates.
So far, those mutations don’t seem to have affected the effectiveness of Paxlovid. Nirmatrelvir prevents the major protease of SARS-CoV-2 (MPRO) of cutting a long precursor molecule made by the virus into shorter active proteins, an essential step in SARS-CoV-2 reproduction. In February, Pfizer researchers reported in: JBC Accelerated Communication that nirmatrelvir remained effective at arresting the activity of MPRO in multiple SARS-CoV-2 variants, including Alpha, Beta, Delta, Gamma, Lambda, and Omicron, as well as the original strain.
However, the recent studies suggest that the virus is on the cusp of developing resistance — a fate that befell many antiviral drugs. For example, two preprints posted to bioRxiv on June 7 show that SARS-coV-2 grown in the lab quickly gains the ability to prevent the attack of nirmatrelvir. Two research groups independently cultured the coronavirus with low levels of niramatrelvir, killing some of the virus, but not the entire virus. Such tests are designed to simulate what might happen in an infected person who does not take the entire regimen of the drug or an immunocompromised patient who has difficulty clearing the virus.
One such study, led by Dirk Jochmans, a virologist at KU Leuven in Belgium, found that after 12 rounds of nirmatrelvir treatment, SARS-CoV-2 accumulated three mutations – at positions 50, 166 and 167 in the sequence of amino acids that make up mPRO–which reduced the susceptibility of the virus to nirmatrelvir 20-fold, as determined by the dose of medicine needed to kill half of the virus in a sample. The other study, led by Judith Margarete Gottwein, an immunologist at the University of Copenhagen, also discovered possible resistance-conferring mutations at positions 50 and 166 in MPRO † When those mutations occurred together, the virus was 80 times less susceptible to nirmatrelvir. “This tells us which mutations to look for [in patients]Gottwein says.
Indeed, some of these mutations are already present in coronavirus-infected people, according to work by Adam Godzik, a bioinformatics expert at the University of California, Riverside. Godzik and his colleagues searched the GISAID database, a catalog of more than 10 million SARS-CoV-2 genomes sequenced from viruses isolated from infected individuals, looking for amino acid changes at positions in MPRO near where niramatrelvir binds. In a bioRxiv preprint posted May 30, they reported that mutations in amino acids 166 and 167 — two of the resistance mutations signaled by the Belgian group — were already present in viruses circulating in humans. Because these mutations occurred before the widespread use of Paxlovid, they likely occurred randomly, Godzik says. However, he adds that they reveal that the enzyme has some flexibility in these positions that could help the virus evade the drug.
And the list of possible resistance mutations continues to grow. In a paper posted yesterday on bioRxiv, Jun Wang, a medicinal chemist at Rutgers University, and colleagues report 66 common mutations to MPRO near the niramatrelvir binding site. Like Godzik’s team, they scanned the GISAID database to find altered versions of the protease, but then went a step further. Add the gene for each of these variants of MPRO until Escherichia coli bacteria, they provided stockpiles of the enzymes for additional testing: first, to determine whether each variant still performed the essential tasks of cutting viral proteins, and second, to determine whether the M mutationsPRO to resist niramatrelvir. Eleven of the 66 variants retained the function of the protease (the others deteriorated it), and five of the 11 were resistant to nirmatrelvir, requiring at least a 10-fold increase in the drug to kill half the virus in the sample. kill. One of those variants had a previously observed resistance mutation, at position 166, but the other four had new solutions at positions 144, 165, 172, and 192. The conclusion of all this work, Wang says, “It’s just a matter of time before we see resistance emerging.”
So why hasn’t it already happened? One possibility is that not enough people have taken Paxlovid yet to force the virus to mutate. Another explanation, Wang says, is that there are multiple mutations in M. may be necessaryPRO for the virus to bypass Paxlovid while remaining both fully functional and easily transferable. So far, adds Aditya Shah, an infectious disease specialist at the Mayo Clinic, studies show that in patients with a rebound of symptoms, which happens in only 2% or less of those taking the drug, the rebound is not due to appears to be due to resistance mutations. “It’s reassuring,” Shah says, but no evidence that the virus won’t make its way into the drug eventually.
Pfizer says its Paxlovid regimen can prevent resistance. Patients only take the drug for a short period of time and usually receive a dose “several times higher” than needed to prevent the virus from multiplying in cells, minimizing the chance of the virus mutating, says Kit Longley, a researcher. spokesperson for the company.
Giving patients multiple antivirals can prevent resistance by making it more difficult for the virus to work its way through several compounds at the same time, a strategy that has proven highly effective in treating other viruses, including HIV and hepatitis C. , says Ho. Two other SARS-CoV-2 antivirals are authorized in the United States, but they have drawbacks. The other oral drug, molnupiravir, has been shown to be significantly less effective than Paxlovid and has raised safety concerns because it induces random genetic mutations in the virus — which usually prevents it from replicating, but can also create dangerous new variants, some warn. scientists. And remdesivir, which interferes with the virus’s ability to copy its genome, is only allowed for hospitalized patients and must be given intravenously. A preprint posted yesterday on bioRxiv suggests that combining molnupiravir and nirmatrelvir is more effective at fighting SARS-CoV-2 infections than either of the antivirals given alone, at least in mice. But the strategy has yet to be widely embraced by doctors.
Meanwhile, pharmaceutical companies race to complete clinical trials of additional SARS-CoV-2 antivirals, some of which target MPRO at different locations. But they aren’t there yet. And numerous researchers, including representatives of the nonprofit Drugs for Neglected Diseases Initiative, have complained that Pfizer hasn’t made Paxlovid readily available for testing combination therapies. The company has said it plans to conduct those investigations itself, although some are skeptical.
Until more antiviral drugs become available, Paxlovid will essentially be left alone, raising fears it will lose its clout sooner or later. When pressed by a single antiviral drug, viruses usually find a way to bypass the drug, Gottwein says. “If it can, it will happen.” And at least according to the latest lab results, it can happen.